Datasets:

abhi26
/

research-papers-gpt-neox

text stringlengths 35 171k
It also highlights that the interaction among several disciplines, such as environ- mental/chemical engineering, biotechnology, mineralogy, chemistry and microbial ecology lays the foundation for a new type of approach for solving problems through efﬁcient recovery solutions. 5. Conclusions This study evaluated the biological and chemical possibilities regarding the extraction of metals from crystalline diopside-bearing slag and its amorphous counterpart. The ele- ments bound in sulﬁdes, intermetallic compounds and glass were extracted much easier than those contained in diopside. The leaching sequence delineated here can be stated as follows: sulﬁdes (sphalerite > chalcopyrite) > intermetallic phases > glass > diopside. Citric acid was found to improve extraction rates as compared to A. thiooxidans -mediated leaching. If the use of a bacterially-mediated method is intended, it is evident that either lower pulp density or extension of bioleaching time has to be considered. Slags eventually revealed a potential for Zn recovery, whereas recovery of Cu and Pb from this material is rather unsuitable. The use of the proposed methods for this material at an industrial scale would be economically unproﬁtable. The original material after treatment was partially depleted in metals, but it was not possible to remove Pb completely from this waste that disqualiﬁes its potential for use in construction or agriculture sectors. This study provides impor- tant insight into the dissolution of diopside bearing and glassy slags and is relevant to development of suitable treatment of slags to mitigate their environmental ﬁngerprint. Supplementary Materials: The following are available online at [URL] 63X/11/3/262/s1, Figure S1: Two weeks long leaching of elements from diopside-bearing slag as a function of pulp density, Figure S2: Two weeks long leaching of elements from glassy slag as a function of pulp density. Author Contributions: Conceptualization, A. P. ; Funding acquisition, A. P. ; Investigation, B. M. , M. N. , A. P. ; Methodology, M. N. , B. M. , A. P. ; Data curation: A. P. , B. M. ; Visualization, B. M. , A. P. ; Writing—original draft, A. P. ; Writing—review and editing, B. M. All authors have read and agreed to the published version of the manuscript. Funding: This work was ﬁnancially supported by the National Science Centre (NCN) in Poland in the frame of the SONATA program under grant agreement UMO-2018/31/D/ST10/00738 to A. P. Acknowledgments: The authors thank Jakub Kierczak (Uniwersytet Wrocławski) for his valuable advice given on this work. The authors would also like to gratefully acknowledge time devoted by Editors and Reviewers in evaluating this work as well as their valuable comments and remarks. Conﬂicts of Interest: The authors declare no conﬂict of interest. Minerals 2021 ,11, 262 17 of 19 References 1. Radetzki, M. Seven thousand years in the service of humanity-the history of copper, the red metal. Resour. Policy 2009 ,34, 176–184. [Cross Ref] 2. Bellemans, I. ; De Wilde, E. ; Moelans, N. ; V erbeken, K. Metal losses in pyrometallurgical operations—A review. Adv. Colloid Interface Sci. 2018 ,255, 47–63. [Cross Ref] [Pub Med] 3. Ettler, V. Soil contamination near non-ferrous metal smelters: A review. Appl. Geochem. 2016 ,64, 56–74. [Cross Ref] 4. Tyszka, R. ; Pietranik, A. ; Kierczak, J. ; Ettler, V. ; Mihaljevic, M. ; Weber, J. Anthropogenic and lithogenic sources of lead in Lower Silesia (Southwest Poland): An isotope study of soils, basement rocks and anthropogenic materials. Appl. Geochem. 2012 , 27, 1089–1100. [Cross Ref] 5. Tyszka, R. ; Pietranik, A. ; Kierczak, J. ; Zieli ´ nski, G. ; Darling, J. Cadmium distribution in Pb-Zn slags from Upper Silesia, Poland: Implications for cadmium mobility from slag phases to the environment. J. Geochem. Explor. 2018 ,186, 215–224. [Cross Ref] 6. Piatak, N. M. ; Seal, R. R. Mineralogy and environmental geochemistry of historical iron slag, Hopewell Furnace National Historic Site, Pennsylvania, USA. Appl. Geochem. 2012 ,27, 623–643. [Cross Ref] 7. Ettler, V. ; Legendre, O. ; Bodenan, F. ; Touray, J. -C. Primary Phases and Natural Weathering of Old Lead Zinc Pyrometallurgical Slag from Pribram, Czech Republic. Can. Mineral. 2001 ,39, 873–888. [Cross Ref] 8. Parsons, M. B. ; Bird, D. K. ; Einaudi, M. T. ; Alpers, C. N. Geochemical and mineralogical controls on trace element release from the Penn Mine base-metal slag dump, California. Appl. Geochem. 2001 ,16, 1567–1593. [Cross Ref] 9. Piatak, N. M. ; Seal, R. R. Mineralogy and the release of trace elements from slag from the Hegeler Zinc smelter, Illinois (USA). Appl. Geochemistry 2010 ,25, 302–320. [Cross Ref] 10. Kierczak, J. ; Pietranik, A. Mineralogy and composition of historical Cu slags from the rudawy janowickie mountains, Southwestern Poland. Can. Mineral. 2011 ,49, 1281–1296. [Cross Ref] 11. Tyszka, R. ; Kierczak, J. ; Pietranik, A. ; Ettler, V. ; Mihaljeviˇ c, M. Extensive weathering of zinc smelting slag in a heap in Upper Silesia (Poland): Potential environmental risks posed by mechanical disturbance of slag deposits. Appl. Geochem. 2014 ,40, 70–81. [Cross Ref] 12. Lottermoser, B. G. Mobilization of heavy metals from historical smelting slag dumps, north Queensland, Australia. Mineral. Mag. 2002 ,66, 475–490. [Cross Ref] 13. Ettler, V. ; Johan, Z. ; Kˇ r íbek, B. ; Šebek, O. ; Mihaljeviˇ c, M. Mineralogy and environmental stability of slags from the Tsumeb smelter, Namibia. Appl. Geochem. 2009 ,24, 1–15. [Cross Ref] 14. Fomchenko, N. ; Uvarova, T. ; Muravyov, M. Effect of mineral composition of sulﬁdic polymetallic concentrates on non-ferrous metals bioleaching. Miner. Eng. 2019 ,138, 1–6. [Cross Ref] 15. Kaksonen, A. H. ; Lavonen, L. ; Kuusenaho, M. ; Kolli, A. ; Närhi, H. ; Vestola, E. ; Puhakka, J. A. ; Tuovinen, O. H. Bioleaching and recovery of metals from ﬁnal slag waste of the copper smelting industry. Miner. Eng. 2011 ,24, 1113–1121. [Cross Ref] 16. Liu, R. ; Mao, Z. ; Liu, W. ; Wang, Y. ; Cheng, H. ; Zhou, H. ; Zhao, K. Selective removal of cobalt and copper from Fe (III)-enriched high-pressure acid leach residue using the hybrid bioleaching technique. J. Hazard. Mater. 2020 , 121462. [Cross Ref] [Pub Med] 17. Muravyov, M. I. ; Fomchenko, N. V. ; Usoltsev, A. V. ; Vasilyev, E. A. ; Kondrat’Eva, T. F. Leaching of copper and zinc from copper converter slag ﬂotation tailings using H 2SO4and biologically generated Fe 2(SO 4)3. Hydrometallurgy 2012 ,119, 40–46. [Cross Ref] 18. Warchulski, R. ; Gaw˛ eda, A. ; K ˛ adziołka-Gaweł, M. ; Szopa, K. Composition and element mobilization in pyrometallurgical slags from the Orzeł Biały smelting plant in the Bytom–Piekary ´Sl ˛ askie area, Poland. Mineral. Mag. 2015 ,79, 459–483. [Cross Ref] 19. Kupczak, K. ; Warchulski, R. ; Dulski, M
[URL] 22. Hallberg ZF, Wang XC, Wright TA, Nan B, Ad O, Yeo J, Hammond MC (2016) Hybrid promiscuous (Hypr) GGDEF enzymes produce cyclic AMP-GMP (3', 3'-c GAMP). Proc Natl Acad Sci U S A 113(7):1790-1795. [URL] 23. Nelson JW, Breaker RR (2017) The lost language of the RNA World. Sci Signal 10(483). [URL] 24. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN,Link KH, Breaker RR (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321 (5887):411-413. [URL] 25. Kellenberger CA, Wilson SC, Hickey SF, Gonzalez TL, Su Y, Hallberg ZF, Brewer TF, Iavarone AT, Carlson HK, Hsieh YF,Hammond MC (2015) GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP. Proc Natl Acad Sci U S A 112(17):5383-5388. [URL] 26. Kellenberger CA, Wilson SC, Sales-Lee J, Hammond MC (2013) RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP. J Am Chem Soc 135(13):4906-4909. [URL] 27. Nelson JW, Sudarsan N,Phillips GE, Stav S,Lunse CE,Mc Cown PJ,Breaker RR (2015) Control of bacterial exoelectrogenesis by c-AMP-GMP. Proc Natl Acad Sci U S A 112 (17):5389-5394. [URL] 28. Li F, Cimdins A, Rohde M, Jansch L, Kaever V, Nimtz M, Romling U (2019) Dnc V synthesizes cyclic GMP-AMP and regulates biofilm formation and motility in Escherichia coli ECOR31. m Bio 10(2):e02492-e02418 29. Burroughs AM, Zhang D, Schaffer DE, Iyer LM, Aravind L (2015) Comparative genomic analyses reveal a vast, novel network of nucleotide-centric systems in biological conflicts, immunity and signaling. Nucleic Acids Res 43(22):10633-10654. [URL] gkv1267 30. Whiteley AT, Eaglesham JB, de Oliveira Mann CC, Morehouse BR, Lowey B, Nieminen EA, Danilchanka O, King DS,Lee ASY, Mekalanos JJ, Kranzusch PJ (2019) Bacterial c GAS-like enzymes synthesize diverse nucleotide signals. Nature 566(7743), 259-263. doi:[URL] 10. 1038/s41586-019-0953-5 31. Margolis SR, Wilson SC, Vance RE (2017) Evolutionary origins of c GAS-STING signaling. Trends Immunol 38(10):733-743. [URL] 32. Bose D (2017) c GAS/STING pathway in cancer: Jekyll and Hyde story of cancer immune response. Int J Mol Sci 18(11). [URL] 33. Chen Q, Sun L, Chen ZJ (2016) Regulation and function of the c GAS-STING pathway of cytosolic DNA sensing. Nat Immunol 17(10):1142-1149. [URL] 34. Tan X, Sun L, Chen J, Chen ZJ (2018) Detection of microbial infections through innate immune sensing of nucleic acids. Annu Rev Microbiol 72:447-478. [URL] micro-102215-095605 35. Gao D, Wu J, Wu YT, Du F, Aroh C,Yan N, Sun L, Chen ZJ (2013) Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science 341 (6148):903-906. [URL] 36. West AP, Khoury-Hanold W, Staron M, Tal MC, Pineda CM, Lang SM, Bestwick M, Duguay BA,Raimundo N, Mac Duff DA, Kaech SM, Smiley JR, Means RE, Iwasaki A, Shadel GS (2015) Mitochondrial DNA stress primes the antiviral innate immune response. Nature 520 (7548):553-557. [URL] 35Microbial Cyclic GMP-AMP Signaling Pathways 623 37. Zhang X, Shi H, Wu J, Zhang X, Sun L, Chen C, Chen ZJ (2013) Cyclic GMP-AMP containing mixed phosphodiester linkages is an endogenous high-affinity ligand for STING. Mol Cell 51 (2):226-235. [URL] 38. Woodward JJ, Iavarone AT, Portnoy DA (2010) c-di-AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response. Science 328(5986):1703-1705. [URL] 39. Burdette DL, Monroe KM, Sotelo-Troha K, Iwig JS, Eckert B, Hyodo M, Hayakawa Y, Vance RE (2012) STING is a direct innate immune sensor of cyclic di-GMP. Nature 478 (7370):515-518. [URL] 40. Gao P, Ascano M, Zillinger T, Wang W, Dai P, Serganov AA, Gaffney BL, Shuman S, Jones RA, Deng L, Hartmann G, Barchet W, Tuschl T, Patel DJ (2013) Structure-function analysis of STING activation by c[G(2',5')p A(3',5')p] and targeting by antiviral DMXAA. Cell 154 (4):748-762. [URL] 41. Mc Farland AP, Luo S, Ahmed-Qadri F, Zuck M, Thayer EF, Goo YA, Hybiske K, Tong L, Woodward JJ (2017) Sensing of bacterial cyclic dinucleotides by the oxidoreductase RECON promotes NF-kappa B activation and shapes a proinflammatory antibacterial state. Immunity 46 (3):433-445. [URL] 42. Kranzusch PJ, Wilson SC, Lee AS,Berger JM, Doudna JA,Vance RE (2015) Ancient origin of c GAS-STING reveals mechanism of universal 2',3' c GAMP signaling. Mol Cell 59 (6):891-903. [URL] 43. Mc Farland AP, Burke TP, Carletti AA, Glover RC,Tabakh H, Welch MD,Woodward JJ (2018) RECON-dependent inflammation in hepatocytes enhances Listeria monocytogenes cell- to-cell spread. MBio 9(3). [URL] 44. Ryjenkov DA, Simm R, Romling U, Gomelsky M (2006) The Pil Z domain is a receptor for the second messenger c-di-GMP: the Pil Z domain protein Ycg R controls motility in enterobacteria. J Biol Chem 281(41):30310-30314. [URL] 45. Amikam D, Galperin MY (2006) Pil Z domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22(1):3-6. [URL] 46. Jones CJ, Utada A, Davis KR, Thongsomboon W, Zamorano Sanchez D, Banakar V, Cegelski L, Wong GC, Yildiz FH (2015) C-di-GMP regulates motile to sessile transition by modulating Msh A Pili biogenesis and near-surface motility behavior in Vibrio cholerae. PLo S Pathog 11(10):e1005068. [URL] 47. Almblad H, Harrison JJ, Rybtke M, Groizeleau J, Givskov M, Parsek MR, Tolker-Nielsen T (2015) The cyclic AMP-Vfr signaling pathway in Pseudomonas aeruginosa is inhibited by cyclic di-GMP. J Bacteriol 197(13):2190-2200. [URL] 48. Chen ZH, Singh R, Cole C, Lawal HM, Schilde C, Febrer M, Barton GJ, Schaap P (2017) Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proc Natl Acad Sci U S A 114(3):516-521. [URL] 1073/pnas. 1608393114 49. da Costa Vasconcelos FN, Maciel NK, Favaro DC, de Oliveira LC, Barbosa AS, Salinas RK, de Souza RF, Farah CS, Guzzo CR (2017) Structural and enzymatic characterization of a c AMP-dependent diguanylate cyclase from pathogenic Leptospira species. J Mol Biol 429 (15):2337-2352. [URL] 50. Luo Y, Zhao K, Baker AE, Kuchma SL, Coggan KA, Wolfgang MC, Wong GC, O'Toole GA (2015) A hierarchical cascade of second messengers regulates Pseudomonas aeruginosa sur- face behaviors. MBio 6(1)
Journal of Environmental Management 250 (2019) 109502 Contents lists available at Science Direct Maviranmental Journal of Environmental Management ELSEVIER journal homepage: www. elsevier. com/locate/jenvman Research article Ni and Cu recovery by bioleaching from the printed circuit boards of mobile phones in non-conventional medium Check for Mahdokht Arshadi, Sheida Nili, Soheila Yaghmaei* Chemical and Petroleum Engineering Deparment, Sharif University of Technology,Tehran, Iran ARTICLEINFO ABSTRACT Keywords: There is a substantial volume of mobile phone waste every year. Due to the disadvantages of traditional methods, Bioleaching it is necessary to look for biological processes that are more eco-friendly and economical to recover metals from Mobile phone PCBs e-waste. Fungi provide large amounts of organic acids and dissolve metals but using sucrose in the medium is not Penicilum simplicissimum economical. In this paper, the main objective is to find a suitable alternative carbon substrate instead of sucrose Non-conventional medium for fungi bioleaching of Ni and Cu in printed circuit boards (PCBs) of mobile phones using Penicillium simpli- Metal recovery cissimum. Four kinds of carbon sources (including sucrose, cheese whey, sugar, and sugar cane molasses) were selected. Also, p H and number of spores in inoculum were optimized by response surface methodology (RSM) for all carbon sources. The results showed the simultaneous maximum recovery of Cu and Ni is not possible. For Cu recovery, sugar is the best economical and simplistic medium instead of sucrose. Maximum recovery of Cu (90%) gained at the p H of 7, 3. 3 × 107 spores, and in sugar. The amount of Ni recovery (89%) was highest in molasses, at the p H of 2, and 10° spores. The results proved non-conventional carbon sources improve bioleaching effi- ciency and the possibility of industrialization. 1. Introduction enough efficient and environmental friendly in every situation (Vera et al. , 2013). Physical and chemical technologies consume high energy, Waste of electronic and electric instruments (e-waste) has the they are expensive, and some of the chemicals produced agents influ- highest rate of growth in the world; the bulk part of the residues pro- ence the environment negatively (Veit et al. , 2006). duces in developing countries. E-waste contains dangerous and precious Biotechnological leaching processes which are more eco-friendly, metals simultaneously like As, Pb, Cu, Ni, Au, Ag, Pd, Pt, etc. (Islam and economical, and doesn't require specialized labors than other chemical Huda, 2019; Marra et al. , 2018). Recent researches show that the methods have been used to recover valuable metals from e-waste amounts of mobile phone wastes grow exponentially. It is reported that (Faraji et al. , 2018; Marra et al. , 2018). there are more than 4. 57 billion users of the mobile phone around the In the bioleaching process, organic or inorganic acids produced by world since 2017 (Bauer et al. , 2019) and the average life expectancy of microorganisms (including bacteria or fungi) solute metals (Auerbach mobile phone reduced from 2. 9 years in 2011 to 2. 21 years in 2018 (Liu et al. , 2019). Compared to bacteria, fungi can tolerate toxic materials et al. , 2019). In the latest reports, estimated that at the end of 2015, more; they have a shorter lag phase and faster leaching rate. Fungal more than 7 billion mobile phones used worldwide. Around 10 million bioleaching has four main mechanisms: (1) acidolysis (the principal kilograms of them are discarded yearly. The e-waste contains about mechanism) in which by producing the organic acids, metals dissolve in 50% of plastics and different metals like gold, silver, copper, nickel, and mentioned acids; (2) complexolysis where the metals make complexes iron. The concentration of Au and Ag within PCBs is more than ten with produced organic or amino acids; (3) redoxolysis in which organic times rather than natural ores (Arshadi et al. , 2018b). acids reduce the metals; and (4) bioaccumulation in which the myce- Most of the used metals in mobile phone wastes can be reused and lium acts as a sink for the metal ions (Faraji et al. , 2018; Mirazimi et al. , recycled using different physical, chemical, and biological methods. Old 2015). By the formation of metal complexes, the toxicity of metal re- manual divesting techniques like mechanical treatment (such as duces. Aspergillus and Penicillum are the most used heterotrophic fungi crushing and jigging), hydrometallurgical, and pyrometallurgical in recovering of heavy and worth metals from solid wastes because they methods have been used to recover e-waste. These methods result in a can provide large amounts of organic acids (citrate, gluconate, and high recovery of valuable metals (Ren et al. , 2014). But they are not oxalate) (Faraji et al. , 2018). * Corresponding author. E-mail address: [EMAIL] (S. Yaghmaei). [URL] Received 28 May 2019; Received in revised form 15 August 2019; Accepted 31 August 2019 0301-4797/ 2019 Published by Elsevier Ltd. M. Arshadi, et al. Journal of Environmental Management 250 (2019) 109502 Bioleaching methods divide into three categories including (1) one- medium is an important strategy to make production economically vi- step bioleaching, in which fungus is inoculated to the medium with able (Salari et al. , 2019). solid waste, (2) two-step bioleaching, in which the solid waste adds to Molasses is a cheap carbon source and a food industry by-product in the medium when the fungus is in its logarithmic growth phase, (3) the proces of sugar beet or cane production (Sun et al. , 2019). The spent-medium bioleaching, in which the fungus is in the stationary composition of molasses varies depending on the quality of the raw phase; the highest level of organic acids in the medium provide and product. Considering the high sucrose content of the molasses, it would then the solid phase is added to the biomass (Mirazimi et al. , 2015). seem to be a natural alternative to synthetic media for P. simplicissium Choosing an effective method depends on the type of substrate and also growth and metabolite production (Gojgic-Cvijovic et al. , 2019). Sun the selected microorganism (Amiri et al. , 2011). Several physical, et al. (2019) showed the economical production of some metabolites chemical, and biological variables affect the bioleaching process (such using molasses (Sun et al. , 2019). Cheese whey is the byproduct of the as carbon and nitrogen source, oxygen supply, p H, temperature, in- cheese production with high biochemical oxygen demand. Cheese whey oculation content, and etc. ). These parameters have to be optimized to contains about 55% of nutrients in the original milk supports the me- reach the maximum amount of recovery. p H is one of the main para- tabolite production in microbial fermentation (Salari et al. , 2019). meters in the bioleaching process (Muddanna and Baral, 2019). Some Sugar has a similar composition to sucrose; it is not pure and contains researchers attend to fungal bioleaching of metals from solid waste galactose too. utilized Aspergillus niger and P. simplicissimum as the most effective It is noteworthy that the application of fungal bioleaching in solid microbes. In a first reported attempt, Brandl et al. (2001) used these waste is limited; there are a lot of gaps in this field. In our knowledge, fungi to recover metals from e-waste. The microbial growth was in- too limited research was found to study bioleaching of e-waste using P. hibited in a higher pulp density of 10 g/l. During the six weeks of the simplicissimum. Especially using sucrose in the medium is not econom- adaptation phase, fungi grew at a concentration of 1oo/l. Both fungi ical. Finding an appropriate substitution instead of sucrose is one of the mobilized Cu and Sn by 65%, Al, Zn, Pb, and Ni more than 95% from e- essential aims of industrializing this biological method (Gojgic-Cvijovic waste (Brandl et al. , 2001). et al. , 2019). Xia et al. (2018) aimed to study the feasibility of recovery of metals In this research, extraction of Ni and Cu from mobile phone wastes from e-waste by mixed fungal cultures in the stirred tank reactors. At using P. simplicissimum fungi was investigated. The aim of this study the first step, the fungi adopted to 80 g/l of the e-waste sample. At the was to find the optimized conditions for growing P. simplicissimum end of the bioleaching process, community structure analysis proved fungus in industrial medium (including sugar cane molasses, cheese that A. niger (28%) and Purpureocillium lilacinum (72%) were the two whey, and sugar) before the medium scale in the laboratory (bio- dominated fungal species. About 56% of Cu, 20% of Pb, 15. 7% of Al, leaching in bioreactors) and comparison to the principal medium of P. 49% of Zn, and 8% of Sn were recovered (Xia et al
was less when compared to lower p H values (Fig. 2a). Metal recovery from LIB during the bioleaching process generally In contrast, the redox potential decreases as the pulp density happens by acid dissolution, but the presence of an oxidizing agent increases. In the first two days of bioleaching, a sharp reduction in such as H2O2 or Fe3+ ions will reduce the acid intake (Meshram Eh occurred at higher pulp densities above 20 g/L. After two days, et al. , 2015; Niu et al. , 2014). the redox potential increased continuously, because of the bio- The protons (H+) attack the oxygen atom of Li Co O2, followed by leaching process as well as the oxidation of Fe2+ ions into Fe3+ hydrolysis due to protonated oxygen atoms that detach the metals during bacterial growth at low pulp densities (Fig. 2b). At high pulp from battery powder. When the Fe. + ions are oxidized by densities 40, 70, and 100 g/L of LIB powder, however, the Eh A. ferrooxidans to Fe3+ ions to gain the energy, the formation of increased slightly or remained constant after two days, confirming biogenic ferrous ions reduces the insoluble Co3+ ions into soluble that the bacteria were less active and no more bioleaching Co2+. This reaction happened via “the oxidative attack of Fe+3 ion happened. During the bioleaching process, the metal dissolution of on the reductive dissolution of Co+3" (Mishra et al. , 2008). The LIBs goes through a different oxidation-reduction process, which dissolution of cobalt and lithium also occurs during the bioleaching alters due to the variation in leaching solution compositions. Redox process is related to their sulfate formation (Xin et al. , 2009). potential is one of the crucial and controlling factors in bioleaching However, the formation of sulfate intermediates of cobalt and by the ferric sulfate oxidation process (Cordoba et al. , 2008; lithium initiated by the sulfur metabolism of A. ferrooxidan sup- Sandstrom et al. , 2005; Klauber, 2008; Li et al. , 2013). The redox ports the dissolution of metals in the leaching solution (Eqn. (7) - couple Fe3+ /Fe2+ will show the oxidation/reduction potential (ORP) (13)) (Xin et al. , 2009; Weijin et al. , 2019). of the bioleaching systems, in which high ORP indicates a high concentration of Fe3+ ions in the medium. 2Fe2+ + 1/2O2 + 2H+ → 2Fe3+ + H20 (7) The changes in ferric ion concentration during the bioleaching process is an important parameter that shows the biological ac- 4Li Co O2 + 12H+ → 4Li+ + 4Co2+ + 6H20 + O2 (8) tivity of A. ferrooxidans. In the first three days of bioleaching, the ferric ion concentration dropped sharply for pulp densities from Fe2+ + Li Co O2 + 4H+ → Fe3+ + Co2+ + Li+ + 2H20 (9) 5 g/L to 100 g/L due to the attack of ferric ions in the culture me- dium on the metals of the LIB powder; therefore, there is a decline Li2O + 2H+ → 2Li++ H20 (10) in the ferric ions during the leaching process. After three days, the Fe3+ ions in the medium were constant for the remaining days for Fe2+ + Co3+ → Fe3+ + Co2+ (Co O) (11) pulp densities 5 g/L to 20 g/L, which indicates to be the bacteria is still active (Fig. 2c). This result indicates the bacteria could tolerate Co O + 2H+ → Co2++ H20 (12) the pulp density up to 20 g/L. For high pulp densities above 20 g/L, the Fe3+ concentration reached below 0. 5 g/L within one day. It can 2Fe SO4 + 2Li Co O2 + 4H2SO4 → be understood that the presence of the bacteria at high pulp den- Fe2(SO4)3 + 2Co SO4 + Li2SO4 + 4H20 (13) sities 40 g/L to 100 g/L did not have any activity because they could not tolerate the metal toxicity that has been leached out into the The goal of LIB bioleaching is the process optimization by solution. Jarosite formation during the A. ferrooxidans growth also increasing the pulp density to get higher metals recovery. Maxi- utilizes the Fe3+ ions for the complex (Daoud and Karamanev, mizing the metal recovery would be more cost-effective when 2006). working with high pulp densities because the reactor volume needed for bacterial culture production (bio-lixiviants) were 3. 3. 1. Metalextractionfrom LIBs smaller when compared with low pulp densities. In addition to During the bioleaching process, cobalt and lithium reactor cost, the growth nutrient and other convenience costs S JJ. Roy, S. Madhavi and B. Cao Journalof Cleaner Production280(2021）124242 Table 1 Leaching effciency of Cobalt and Lithium from LIB with pulp density 100 g/L after bioleaching with A. ferrooxidans by three cycles of replenishing bacterial culture produced by modified 9K media with different concentration of Fe SO4 compared with the control (modified 9k media with different conc. of Fe SO4). Pulp density of LIB powder Bacteria/Media Fe SO4 1st 2nd 3rd Total In Modified leaching leaching leaching %Leaching 9K Media 24 h% 24 h% 24 h% 72 h 100 g/L Acidithiobacillusferooxidans 45 g/L Co: 22. 76 ± 0. 19 10. 32 ± 0. 19 7. 53 ± 0. 13 40. 61 Li: 19. 33 ±0. 06 13. 94 ± 0. 02 9. 65 ± 0. 02 42. 92 Control (media) 45 g/L Co: 17. 22 ± 0. 28 8. 09 ± 0. 37 3. 82± 0. 02 29. 13 Li: 16. 39 ±0. 06 10. 01 ±0. 17 7. 50 ± 0. 01 33. 90 100 g/L Acidithiobacillusferooxidans 90 g/L Co: 35. 75 ± 0. 42 14. 53 ± 0. 23 4. 32 ± 0. 04 54. 59 Li: 29. 11 ± 0. 11 17. 56 ± 0. 10 7. 94 ± 0. 01 54. 61 Control (media) 90 g/L Co: 16. 68 ±0. 19 8. 99 ± 0. 32 3. 58 ± 0. 16 29. 25 Li: 15. 23 ±0. 09 9. 24 ± 0. 23 7. 88± 0. 07 32. 35 100g/L Acidithiobacillusferrooxidans 150 g/L Co: 45. 24 ± 0. 31 33. 06 ± 0. 40 15. 72 ± 0. 04 94. 02 Li: 28. 48 ± 0. 40 21. 70 ± 0. 04 10. 12 ± 0. 01 60. 30 Control (media) 150 g/L Co: 16. 06 ± 0. 06 8. 73 ± 0. 04 6. 85 ± 0. 02 31. 64 Li: 13. 88 ±0. 02 7. 15 ± 0. 01 5. 29 ± 0. 01 26. 32 Table 2 Leaching efficiency of Cobalt and Lithium compared with H2SO4 and Fe3+ concentration, when a different dosage of Fe SO4 used in the modified 9K media for A. ferooxidans growth. Pulp density of LIB Fe SO4 in Modified Fe3+ Conc. (g/L) H2SO4 Conc. (M) Total % Total % powder 9K Media Cobalt Leaching Lithium Leaching 3 cycles of Replenishing 3 cycles of Replenishing 100 g/L 45 g/L 14. 96 ± 1. 39 0. 17 ± 0. 01 44. 51 42. 92 100 g/L 90 g/L 25. 46 ± 1. 97 0. 30 ± 0. 02 54. 59 54. 61 100 g/L 150 g/L 36. 86 ± 2. 10 0. 52 ± 0. 01 94. 02 60. 30 p 1200 1200 L G L-Li Co O2 1000 1000 L G G-Graphite 800 800 600 600 400 400 200 200 15 25 36 46 56 66 76 15 25 36 46 56 66 76 2Theta 2Theta C d 1200 1200 1000 1000 800 800 600 600 400 200 200 15 25 36 46 56 66 76 15 25 36 46 56 66 76 2Theta 2 Theta Fig. 4. XRD analysis of original LIB powder of particle size <100 μm before and after bioleaching with different A. ferrooxidans culture media with different H2SO4 and Fe3- concentrations. a) LIB powder b) Modified 9K media (45 g Fe SO4) c) Modified 9K media(90 g Fe SO4) d) Modified 9K media( 150 g Fe SO4). would be lower at high pulp densities with higher leaching eff- 3. 3. 2. Replenishing of bacterial culture ciency (Thompson et al. , 2017)
describe, these efforts can be organized into a three- tiered hierarchy of modeling goals (Figure 1c): 1) Sequence-to-function goals, which seek to understand Sequence-to-function models for ML-driven relationships between nucleic acid (NA) sequences of design of genetic parts individual genetic parts and their effect on circuit The most fundamental level of functional encoding for a behavior; 2) Composition-to-function goals, which focus genetic element (e. g. , a promoter) is its NA sequence,. on learning how combinations of genetic parts work which determines both its physiochemical properties Current Opinion in Biomedical Engineering 2024, 31:100553 www. sciencedirect. com Machine Learning to Accelerate Synthetic Biology Rai et al. 5. and interactions with other molecular species (e. g. , More recent studies have focused on using ML to binding to a TF). Decoupling the contributions that explore NA sequence design for genetic elements features of an NA sequence make to these properties is explicitly intended for synthetic circuit construction [63-65] (Figure 2b). In one notable study, data from a challenging for biophysical models [39] and has moti- vated application of ML to create predictive sequence-. library of ~10' RNA toe-hold switches were used to to-function mappings for different categories of genetic train an MLP model to predict fold-change expression elements. These efforts were predicated on the wide- between repressed and activated switch configurations. spread availability of next-generation sequencing significantly outperforming regression-based models (NGS) technology, primarily the Illumina platform [40], that rely on biophysical parameterization [66]. In another piece, expression measurements from >105 which has emerged in the past two decades as a primary workhorse for generating large-scale datasets for funda- bacterial RBSs were measured and used to train a CNN- Res Net model to predict expression with high accuracy mental regulatory processes including transcription [41-43], translation [44,45], epigenetic regulation [46], [67]. The use of a DNA recombinase-mediated activity and chromatin accessibility [47,48] (Figure 2a). Seminal assay enabled time series measurements across their li- work applying ML models to these datasets has pro- brary and led to less noisy data and greater model ac- vided deep insight into relationships between NA curacy. In more recent work, activity measurements of a sequence and evolved regulatory grammar [49-52] and, 280k-member library of 75 bp human 5' UTRs were used to train a CNN to predict effects on tuning critically, demonstrated an important ML scaling prin- transgene reporter expression in human cells [68]. A ciple: parallel increases in NGS training dataset size and ML model complexity can yield higher predictive follow-up to this work expanded the model's capabil- power. Examples highlighting this principle include Sei, ities, training on ~200k shorter length sequences (25 and 50 bp) to learn cell type-specific expression [69]. a large deep NN trained on >22,000 Ch IP datasets across >1,300 cell types [53]. Sei accurately classifies enhancer sequences and predicts the effects of muta- A number of reports have appeared over the last year tions on cell type-specific expression activity. More describing the use of data from both native and syn- recently, Avsec and colleagues developed Enformer. thetic sequences to train models of varied size, featu- [54], a transformer LM trained on >7,000 genomic and rization, and accuracy (Figure 2c). One standout is the Ch IP datasets that is capable of integrating features recently reported Evo (Figure 2c, bottom), a versatile across long (>100 kb) length scales (e. g. , long-range regulatory model trained on >20 million prokaryotic genomes that can make functional predictions for a chromatin effects and DNA accessibility. range of tasks across DNA, RNA, and protein expression landscapes [70]. Like Enformer, Evo was developed as While these studies demonstrate that highly predictive. an early-generation foundation model: a large model (in excess of 10' parameters) trained across diverse datasets models can be trained on native genomic sequence diversity, the development of massively parallel re- using significant computational power. Foundation porter assays (MPRAs)-an approach enabled by ad- models can be appropriated as community resources to vances in low-cost DNA synthesis-has facilitated use. achieve a variety of goals, potentially including assisting gene circuit design, as we discuss below. of non-native sequence libraries to train models that predict activity for elements ranging from promoters The studies described in this section demonstrate the [55,56] and enhancers [57,58], to UTRs and introns feasibility of using HT biological data to train highly [59,60] (Figure 2b). In one notable study, data from a predictive sequence-to-function ML models for. ~30M-member library of 80 bp enhancer sequences different genetic part categories, and offer a new strat- tested in yeast were used to train a transformer model to predict promoter activity [61]. The model predicted egy for generating registries of systematically tuned how enhancer mutations can "evolve" new, program- functional variants for each category-an activity that has med expression activities. Following a similar approach been historically carried out using random mutagenesis to decipher TF regulatory grammar in mammalian cells, and selection approaches. Importantly, they also reveal Sahu and colleagues measured diverse (>10) syn- key technical and logistical considerations for devising thetic enhancer libraries (50-170 bp in length) and ML-based projects. First, NA composition and overall used the data to train logistic regression and CNN library diversity should align with the prediction task. Probing underdetermined design spaces may require models, revealing that TFs regulate promoters in an. additive manner with weak motif grammar, consistent large, diverse libraries that prioritize coverage, while with a billboard model of gene regulation [57]. Taken elements containing well-characterized sequence together, these studies have demonstrated the ability motifs can permit more targeted diversification. Model of ML models to explore non-native sequence choice and feature selection are closely coupled with these considerations. While model classes that use bio- design space to not only program artificial regulatory physically consistent feature selection can offer mech- activity, but to gain insight into native regulatory function [62]. anistic explanations of circuit behavior [55,62], higher www. sciencedirect. com Current Opinion in Biomedical Engineering 2024, 31:100553 6 v SI: Synthetic Signaling and Engineering Cell Therapy Figure 2 MODELS TRAINED ON PUBLICDATASETS Training Feature Genetic element/ Model Training Prediction goal Accuracy Ref. data source diversity class selection part category Chip. TF inding one hetd genomic sequence predict chromatin profiles and No S a tses ents. I Zhou 2015 coding sequence variant in human cells Dnase HS sequence enehetd predict chro (Re Cet) AUPRC Avsec 2021 loci regulated by pluripotency factors sequence lict tissue-specific chromatin profile Chi P: TF binding AUROC = CNN tissue specific mutationsd 2 x10 57 hrom. serarks encodec NGS datasets (1D conv) Zhou 2018 one hot predict cell type-specific expression Chi P: TF binding, CNN 2. 1 10 NGS AUROC Dnase HS >1,300 cell typ dil. conv. ) 5. 3 X 10 human, Chi P: TF binding promoters, enhancers gene expression activity across AUROC= gen. sequence segments 1. 6 X 102 mo Transforme encodec 0. 7-0. 9 Avsec2021 ATACseq, DNAse HS >10cell types organisms and cell types Chen2022 Avsec2021 Transformer CNN INPUTS OUTPUTS INPUTS OUTPUTS ACTO human >T binding, Thbindinaies senomis genomic sequences nouse acccessiblity activity one-hot fully ne-hot self layer's a tenion encode layers b MODELS TRAINED ON MPRA DATASETS predicomotersequence 2. 2 x10 bacterial promoters energyfro =0. 80 (60-120 bp) ene hed 9. 1 X 10 MLP riboswitches flow-seq =0. 43 (148 bp) TF binding 1 X 10 predict expression from non-linear = 0. 92 flow-seq pronobers eerneeees from sequence in yeas 1X10 ssion activity from predict expres yeast promoters 1 x 1ers (1DCov) ereedee promoter sequences flow-seq yeast promoters CNN =0. 79 Kotopka2020 240-320 bp) in yeas sequence cell type-specific CRE predict transcript. activity in different 7. 8 X 10 CNN =0. 5 Gosai 2023 RNA-seq cell types from enhancer CREs encoded enhancer (2D Conv) 0. 65 in human cells (200 bp) DNA recorde 2. 7 X 10 sionactivity enceded bacterial RBS =0. 93 Hollerer 2020 RBSvariants (Res Net) ine. coli sequence expressior (18 bp) 2. 8 X 10 ene det (2D Conv) human 5UTRs UTRs = 0. 93 Sample 2019 profiling by NGS 50 bp) NND encoded (2D Conv) 60 = 0. 62 sequence predict expression activity from logistic TF binding humanenha AUPRC = STARR-seq and GREs ~9X10 Sahu2022 , one ho (50-500 bp) ed sec one hot oredict expression activity (3 ) = 0
067 d−1, 1. 24 and 0. 61 , respectively. Figure 9 shows the fitted curves on the experimental data of the conversion X(U) vs time. Also, Fig. 9 shows that the model with [ Fe3+]0. 61 has better fitting than the model with (Fe3+/Fe2+)0. 5, proving direct relation between uranium column bioleaching and [Fe3+]. Fig. 9 Experimental data under optimum conditions and kinetic model of uranium bioleaching in column with F(C)=[Fe3+]0. 61 and (Fe3+/Fe2+)0. 5 Based on the previous investigation, the kinetics equation of uranium bioleaching in column with R2=0. 99 can be written in the following form: 3 0. 61 4. 17( ) 1 (1 0. 016 [Fe ] )t X t t   (12) H. ZARE TA V AKOLI, et al/Trans. Nonferrous Met. Soc. China 27(2017) 2691 −2703 2702 4 Conclusions The column bioleaching of uranium ore by indigenous strain of Acidithiobacillus ferrooxidans was carried out to investigate the optimum condition for enhancing uranium recovery. The four significant parameters (initial ferrous ion concentration, p H, aeration rate and inoculation percent) were selected for further optimization by applying Plackett −Burman design. Afterwards, these four factors were optimized via CCD as, [Fe2+]initial =2. 89 g/L, aeration rate 420 m L/min, p H 1. 45 and inoculation percent (v/v) 6%. The confirmation experiment approved the highest extraction of uranium under optimal conditions as 90. 27%. ANOV A results showed that the most effective factor for uranium recovery was initial ferrous ion concentration and the less effective factor was inoculation percent. A couple of statistically significant interactions are derived between [Fe2+]initial and inoculation percent as well as aeration rate and inoculation percent. The analysis of the uranium ore bioleaching residue under different conditions confirmed the formation of K-jarosite on the surface of minerals. By using optimal conditions uranium bioleaching recovery increased at column and jarosite precipitation was minimized. The kinetic model for uranium column bioleaching is expressed as ()Xt 3 0. 61 4. 171 (1 0. 016 [Fe ] ) ,t t which is consistent with experimental results. Acknowledgments The authors thank the Tarbiat Modares University & Nuclear Science and Technology Research Institute for their financial support. References [1] GILLIGAN R, NIKOLOSKI A N. The extraction of uranium from brannerite —A literature revie w [J]. Minerals Engineering, 2015, 71: 34−48. [2] GHORBANI Y , BECKER M, MAINZA A N, FRANZIDIS J P , PETERSEN J. Large particle effects in chemical/biochemical heap leach processes a review [J]. Minerals Engineering, 2011, 24: 1172 −1184. [3] GHORBANI Y , BECKER M, PETERSEN J, MAINZA A N, FRANZIDIS J P. Investigation of the effect of mineralogy as rate-limiting factors in large particle leaching [J]. Minerals Engineering, 2013, 52: 38− 51. [4] TUOVINEN O H, HSU C J. Effect of p H, iron concentration, and pulp density on the solubilisation of uranium from ore material in chemical and microbiological acid leach solutions: Regression equation and confidence band analysis [J]. Hydrometallurgy, 1984, 12: 141 −149. [5] ABHILASH, PANDEY B D. Role of ferric ions in bioleaching of uranium from low tenor Indian ore [J]. Canadian Metallurgical Quaterly, 2011, 50(2): 102 −112. [6] FOWLER T A, HOLMES P R, CRUNDWELL F K. On the kinetics and mechanism of the dissolution of pyrite in the presence of Thiobacillus ferrooxidans [J]. Hydrometallurgy, 2001, 59: 257 −270. [7] HO E M, QUAN C H. Iron(II) oxidation by SO 2/O2 for use in uranium leaching [J]. Hydrometallurgy, 2007, 85: 183 −192. [8] AHONEN L, TUOVINEN O H. Bacterial leaching of complex sulfide ore samples in bench-scale column reactors [J]. Hydrometallurgy, 1995, 37: 1− 21. [9] ACEVEDO F. Present and future of bioleaching in developing countries [J]. Electronic Journal of Biotechnology, 2002, 5(2): 52−56. [10] MALIK A, DASTIDAR M G, ROYCHOUDHURY P K. Factors limiting bacterial iron oxidation in biodesulphurization system [J]. International Journal of Mineral Processing, 2004, 73: 34 −42. [11] DREISINGER D. Copper leaching from primary sulfides: Options for biological and chemical extraction of copper [J]. Hydrometallurgy, 2006, 83: 10 −21. [12] PRADHAN K C, NATHSARMA K, SRINIV ASA R, SUKLA L B, MISHRA B K. Heap bioleaching of chalcopyrite: A review [J]. Minerals Engineering, 2008, 21: 355 −362. [13] MELLADO M E, CISTERNAS L A, GÁLVEZ E D. An analytical model approach to heap leaching [J]. Hydrometallurgy, 2009, 95: 33−42. [14] GUAY R, SILVER M, TORMA A E. Ferrous iron oxidation and uranium extraction by Thiobacillus ferrooxidans [J]. Biotechnology and Bioengineering, 1977, 19: 727 −740. [15] JUNIOR O G. Bacterial leaching of uranium ore from Figueira-PR, Brazil, at laboratory and pilot scale [J]. FEMS Microbiology Reviews, 1993, 11: 237 −242. [16] MUNOZ J A, BLASQUEZ M L, BALLESTER A, GONZALEZ F. A study of the bioleaching of a Spanish uranium ore. Part III: column experiments [J]. Hydrometallurgy, 1995, 38: 79 −97. [17] QIU G Z, LI Q, YU R, SUN Z H, LIU Y , CHE M, YIN H, YANG Z H, YI L L, XU L, SUN L, LIU X. Column bioleaching of uranium embedded in granite porphyry by a mesophilic acidophilus consortium [J]. Bioresource Technology, 2011, 102: 4697 −4702. [18] ABHILASH, MEHTA K D, KUMAR V , PANDEY B D, TAMRAKAR P K. Column bioleaching of a low grade silicate ore of uranium [J]. Mineral Processing and Extractive Metallurgy Review, 2010, 31: 224 −235. [19] ABHILASH, PANDEY B D, SINGH A K. Comparative performance of uranium bioleaching from low grade Indian apatite rock in column and bioreactor [J]. Energy Procedia, 2013, 39: 20 −32. [20] ZARE TA V AKOLI H, ABDOLLAHY M, AHMADI S J, KHODADADI DARBAN A. The effect of particle size, irrigation rate and aeration rate on column bioleaching of uranium ore [J]. Russian Journal of Non-Ferrous Metals, 2017, 58(3): 188 −199. [21] KARAMANEV D G, NIKOLOV L N, MAMATARKOV A V. Rapid simultaneous quantitative determination of ferric and ferrous ions in drainage waters and similar solutions [J]. Minerals Engineering, 2002, 15: 341 −346. [22] MONTGOMERY D C. Design and analysis of experiments [M]. New York: John Wiley and Sons, 2008. [23] ARSHADI M, MOUSA VI S M. Multi-objective optimization of heavy metals bioleaching from discarded mobile phone PCBs: Simultaneous Cu and Ni recovery using Acidithiobacillus ferrooxidans [J]. Separation and Purification Technology, 2015, 147: 210−219. [24] BOUFFARD S C. Understanding the heap biooxidation of sulfidic refractory gold ores [D]. Vancouver: University of British Columbia, 2003. [25] FINKELESTEIN N P, NEEDED C R S, NICOL M J. An electrochemical model for the leaching of uranium dioxide [C]// National Institute for Metallurgy. Johannesburg (South Africa): IAEA, 1972. H. ZARE TA V AKOLI, et al/Trans. Nonferrous Met. Soc. China 27(2017) 2691 −2703 2703 [26] BURKIN A R. Chemical hydrometallurgy: Theory and principles [M]. London: Imperial College Press, 2001
Experimental data (left) is represented as blue dots with error bars and the fitted model is represented as the yellow trace. Residuals of the fit (right) is also shown. S33 Curve-fitting Residuals P1-BA(5) (metal) 0. 0 Polymer excluded volume model 10-1 10-1 Q(A-1) Q(A-1) P6-HA (metal) 0. 3 0. 2 0. 1- 0. 0 10 -0. 2 Polymer excluded 10 -0. 3 volume model -0. 4 - 10-1 10-1 Q(A-1) Q(A-1) P5-c HA (metal) 0. 6 0. 4 0. 2 0. 0- -0. 2 -0. 4 Polymer excluded -0. 8 - volume model -1. 0 10-1 10-1 Q(A-1) Q(A-1) P8-LA (metal) Polymer excluded volume model 10- Q(A-1) Q(A-1) Figure S48. Fitting of the polymer excluded volume model to small-angle scattering (SAXS) profiles of polymer dissolved to 2. 5 mg/m L in buffer (40 m M MES, 100 m M KCl, p H 6) with 0. 1 [Eu3+]/[AA]. Experimental data (left) is represented as blue dots with error bars and the fitted model is represented as the yellow trace. Residuals of the fit (right)is alsoshown. S34 Block 1 Block 2 Block3 b1 Target DP (NIPAM) 49 0 49 Target DP (n BA) 0 15 0 Target DP (t BA) 38 NIPAM added (mmol) 3. 857 o 2. 151 n BA added (mmol) 0 0. 766 0 t BA added (mmol) 0 1. 940 0 CTA added (μmol) 78. 7 Macro CTAadded(umol)a 51. 1 43. 9 AIBN added (umol) 3. 9 2. 6 2. 2 (macro)CTA / AIBN 20 20 20 1,4-dioxane added (m L) 1. 930 1. 022 1. 485 Total volume (m L) 1. 930 1. 416 1. 485 Table S4. Synthesis of b1 block copolymer. quantity calculated using Mn calculated from 'H NMR of block copolymer intermediate and the mass of macro(CTA) used in the extension reaction. b2 Block 1 Block2 Block3 Target DP (NIPAM) 24 50 24 Target DP (n BA) 1 8 Target DP (t BA) 19 19 NIPAM added (mmol) 1. 889 3. 666 1. 484 n BA added (mmol) 0. 551 0 0. 495 t BA added (mmol) 1. 496 0 1. 175 CTA added (μmol) 78. 7 Macro CTAadded(mmol)a 73. 3 61. 8 AIBN added (umol) 3. 9 3. 7 3. 1 (macro)CTA/ AIBN 20 20 20 1,4-dioxane added(m L) 1. 670 1. 921 1. 937 Total volume (m L) 1. 970 1. 921 2. 18 Table S5. Synthesis of b2 block copolymer. a quantity calculated using Mn calculated from 1H NMR of block copolymer intermediate and the mass of macro(CTA) used in the extension reaction. b1 b2 Block 1 NIPAM (DP) 45. 7 21. 3 n BA(DP) 0 5. 8 t BA (DP) 0 15. 3 % conversion (NIPAM) 95. 8 94. 8 % conversion (n BA) 0 93. 4 % conversion (t BA) 92. 1 Block 2 NIPAM (DP) 0 42. 6 10. 1 n BA (DP) 0 t BA (DP) 25. 8 0 % conversion (NIPAM) 0 92. 0 % conversion (n BA) 92. 1 % conversion (t BA) 92. 2 Block 3 NIPAM (DP) 37. 2 20. 9 n BA (DP) 0. 1 6. 7 t BA (DP) 0. 2 15. 4 % conversion (NIPAM) 89. 3 90. 6 % conversion (n BA) 100 92. 3 % conversion (t BA) 100 90. 2 Table S6. Summary of 'H NMR data for block copolymer synthesis. Monomer DP were calculated by subtracting the monomer alkene of a post-polymerization crude sample from a pre-polymerization sample; NIPAM (5. 51 ppm) n BA (5. 87 ppm), t BA (6. 05 ppm). S35 Mn Mw D B1 5550 5870 1. 06 B2 10290 11150 1. 08 B3-postcapping 14490 16410 1. 13 Table S7. summary of organic phase SEC data for the synthesis of block copolymer b1. Molecular weights are calculated relative to PEG calibration standards (1,100,000-238 Da). Mn Mw D B1 5750 6100 1. 06 B2 10460 11230 1. 07 14850 16740 B3-postcapping 1. 13 Table S8. summary of organic phase SEC data for the synthesis of block copolymer b2. Molecular weights are calculated relative to PEG calibration standards (1,100,000-238 Da). OC NC dioxane H2)11CH g b,c acetone water 47. 7 3. 0 0 8. 5 8. 07. 57. 06. 56. 0 8 (ppm) Figure S49. Pre-polymerization 'H NMR for the first block of b1. Integrations are set relative to the methyl group, i. (600 MHz, acetone-d6). S36 dioxane acetone CH2)11CH water g,h b,c 2. 0 3. 0 0 7. 5 7. 0 6. 5 6. 0 5. 5 5. 0 4. 5 4. 0 3. 5 1. 5 1. 0 0. 5 8 (ppm) Figure S50. Post-polymerization H NMR for the first block of b1. Integrations are set relative to the methyl group, j. (600 MHz, acetone-d6). b,c f,g dioxane acetone (CH2)11CH3 b,c,f,g d,i,n,o,p water 10. 9 28. 0 3. 0 4. 0 8（ppm Figure S51. Pre-polymerization 'H NMR for the second block of b1. Integrations are set relative to the methyl group, q. (600 MHz, acetone-d6). S37 dioxane acetone d. i. n. o. b,c,f,g 0. 9 2. 2 3. 0 8. 5 8. 0 7. 5 7. 0 6. 0 5. 5 5. 0 4. 5 4. 0 3. 5 3. 02. 52. 01. 5 1. 00. 5 Figure S52. Post-polymerization 'H NMR for the second block of b1. Integrations are set relative to the methyl group, q. (600 MHz, acetone-d6). b，c h,i 1,m dioxane acetone b,c,h,i,l,m NC (CH2)11CH3 water 6. 3 16. 6 22. 4. 0 8. 0 7. 5 7. 0 6. 5 6. 0 5. 0 4. 0 3. 5 3. 0 2. 5 1. 0 0. 5 8（ppm） Figure S53. Pre-polymerization 'H NMR for the first block of b2. Integrations are set relative to the methyl group, s. (600 MHz, acetone-do). S38 h， dioxane acetone j,o,q,r,s (CH2)11CH water b,c,h,i,l,m Ik a d 0. 4 1. 3 1. 2 0 8. 5 7. 5 7. 0 6. 5 6. 0 5. 5 5. 0 4. 5 4. 0 3. 5 2. 0 1. 5 1. 00. 5 6 (ppm) Figure S54. Post-polymerization 'H NMR for the first block of b2. Integrations are set relative to the methyl group, t. (600 MHz, acetone-do). b,c (CH2)11CH3 dioxane acetone b,c e,g h,j,k,l,m water 46. 3. 0 8. 0 7. 5 7. 0 6. 0 5. 5 5. 0 4. 5 4. 0 3. 02. 52. 0 1. 0 0. 5 8 (ppm) Figure S55. Pre-polymerization 'H NMR for the second block of b2. Integrations are set relative to the methyl group, n. (600 MHz, acetone-d6). S39 dioxane acetone (CH2)11CH3 h,j,k,l,m b,c e,g water 3. 0 8. 5 7. 0 6. 5 6. 0 5. 5 4. 5 4. 0 3. 0 2. 5 2. 0 1. 5 05 Figure S56. Post-polymerization 'H NMR for the second block of b2. Integrations are set relative to the methyl group, n. (600 MHz, acetone-d6). NC HO DMSO m,n,f 26. 1 69. 4 93. 7 12512011. 511. 010. 510. 09. 59. 08
These deﬁned or partially deﬁned microbial communities are exposed to various growth conditions and contaminants to promote tolerance to more extreme conditions that may be encountered in some mineral processes or contaminated sites, with the ultimate goal of enhancing biomining and bioremediation efﬁciency. A summary of natural and deﬁned mixed microbial consortia used for enhanced biomining and remediation purposes are outlined in Table 2. Genes 2018 ,9, 116 16 of 28 Table 2. Examples of enhanced biomining consortia and their design purposes Microbial community members Natural/Deﬁned Design Purpose Reference Leptospirillum sp. (MT6), Acidimicrobium ferrooxidans, Acidithiobacillus caldus, Alicylobacillus sp. (Y004), Sulfobacillus spp. , Ferroplasma sp. (MT17)Deﬁned Reduced jarosite production during chalcopyrite leaching with sulfuric acid produced by sulfur oxidation. [204] A. ferrooxidans and Acidophilium acidophilum Deﬁned Heterotrophic removal of inhibiting organic compounds produced during microbial growth. [206] Leptospirillum MT6 and A. caldus and the heterotroph Ferroplasma sp. MT17 Deﬁned Increased acid production. [205] A. ferrooxidans ATCC 23270, A. thiooxidans DSM 622, L. ferrooxidans DSM 2391, L. ferriphilum DSM 14647 and A. caldus S2Deﬁned Improved attachment to mineral surfaces. Leptospirillum attachment promoted the secondary attachment if A. caldus on the surface of pyrite. [207] Two strains A. ferrooxidans isolated from the coal mine. Natural isolates Increased growth and improved leaching rates. [209] A. thiooxidans A01, A. ferrooxidans (CMS), L. ferriphilum (YSK), A. caldus (S1), Acidiphilium spp. (DX1-1), F. thermophilum (L1), S. thermosulﬁdooxidans (ST)Deﬁned Increased growth and improved leaching rates by the introduction of a non-indigenous species to the consortium constructed from indigenous isolates. [210] A. ferrooxidans ATCC 23270, A. thiooxidans (mesophilic) A. caldus ,L. ferriphilum (moderately thermophilic)Deﬁned Improved leach yields by promoting growth of moderate thermophiles. [208] Uncharacterised environmental salt tolerant, iron and sulfur oxidising enrichment cultures mixed with various mesophilic, moderately thermophilic and thermophilic pure cultures obtained from culture collections. Mix of natural consortia and deﬁned cultures Improve salt tolerance with naturally occurring microbes enriched from salty and acidic environments. [12] Genes 2018 ,9, 116 17 of 28 Systems biology can be used to systematically understand diverse physiological processes of cells and their interactions and to optimally design synthetic microbial consortia for any given process [ 211]. Engineering cell-to-cell interactions and communications is at the heart of engineering synthetic communities and optimising biomining of mineral ores [ 212]. Exopolymeric substances (EPS) play a key role in in biofilm formation [ 213], and for biomining microbes, the biofilm allows for direct attachment of cells to the mineral surface and the formation of a microenvironment that favours leaching [ 214]. Several studies have shown that biofilm formation in biomining environments is crucial for interspecies communication [ 215] and vice versa [ 21,216,217]. However, further characterisation of the interactions and communication between species within a biomining microbial consortium is required to facilitate engineering new and exciting microbial consortia with novel and industrially relevant functionality. In addition to engineering the genomes and the interactions and communication between species within a microbial consortium, it is possible to engineer the environment to compliment ﬁne tuning for community composition, activity, and function [ 197,218]. An example of this was demonstrated by Li et al. , [ 219], whereby bioﬁlm formation was enhanced by modifying one or multiple growth variables to promote the initial attachment of Sulfobacillus thermosulﬁdooxidans and continuous bioﬁlm development on pyrite. Similar methodologies could be undertaken to ﬁne tune the growth and activity of engineered microbial communities for biomining processes. Research has been limited to the transformation of pure cultures, including species within the genera Acidithiobacillus and Sulfolobus [ 51,61]. Generally speaking, the efﬁciency of transformation for these extremophiles is very low, and further work dedicated to developing methods for the generation of stable transformants, and improving transformation efﬁciency is required. Brune and Bayer [198] and Rawlings and Johnson [ 220] both stated that while it could be possible to improve efﬁciency and yields of bioleaching and biooxidation using engineered microbial consortia, factors such as competition with native microbes, stability of transformed species and engineered communities, process sterility, process conditions, and other regulatory requirements would determine the practicability at industrial-scale. It is likely that maintaining and controlling engineered microbial communities within a non-ideal and non-controlled environment, such as a bioleaching heap or open vat reactor, would be difﬁcult, and the ability to characterise and engineer all complex interactions would be close to impossible. However, as more work is undertaken to fully elucidate the complete microbial diversity in these unique environments and their interactions, the rational design for microbial consortia engineering and overall efﬁciency of biomining and other associated processes of remediation and waste management could possibly be improved. 3. Conclusion Synthetic and computational biology have the potential to improve the traits of naturally existing microorganisms so they can be productively implemented in biomining and other industrial processes. For acidophiles, the development of genetic tools has lagged behind the developments for other microbes. The delay has not been due to a lack of interest in these microorganisms, but rather a reﬂection of the difﬁculties in establishing such a system. In combination with the comprehensive genome-enabled stoichiometric modelling studies, it should be feasible to design genetically engineered microorganisms with higher bioleaching activity, leading to an overall increase in the efﬁciency of biomining processes. Nevertheless, likewise with the other ﬁelds, the applications of GMOs in mining industries would be signiﬁcantly enhanced by the support of regulatory agencies in developing a safe implementation of the technology. Acknowledgments: Funding received from CSIRO Synthetic Biology Future Science Platform and CSIRO Land and Water is gratefully acknowledged. The authors thank Dr Ka Yu Cheng and Dr Carol Hartley from CSIRO for reviewing the manuscript. Author Contributions: Y. G. wrote a large part of the manuscript; N. J. B. , H. K. , V. S. , R. P. C. and A. H. K. contributed to various sections of the manuscript. Conﬂicts of Interest: The authors declare no conﬂict of interest. Genes 2018 ,9, 116 18 of 28 References 1. Kaksonen, A. H. ; Boxall, N. J. ; Usher, K. M. ; Ucar, D. ; Sahinkaya, E. Biosolubilisation of metals and metalloids. In Sustainable heavy metal remediation ; Rene, E. R. , Sahinkaya, E. , Lewis, A. , Lens, P. N. L. , Eds. ; Springer International Publishing: Cham, Switzerland, 2017; Volume 1, pp. 233–283. 2. Kaksonen, A. H. ; Mudunuru, B. M. ; Hackl, R. The role of microorganisms in gold processing and recovery– A review. Hydrometallurgy 2014 ,142, 70–83. [Cross Ref] 3. Coker, J. A. Extremophiles and biotechnology: Current uses and prospects. F1000Research 2016 ,5. [Cross Ref] [Pub Med] 4. Kaksonen, A. H. ; Sarkijarvi, S. ; Peuraniemi, E. ; Junnikkala, S. ; Puhakka, J. A. ; Tuovinen, O. H. Metal biorecovery in acid solutions from a copper smelter slag. Hydrometallurgy 2017 ,168, 135–140. [Cross Ref] 5. Bryan, C. G. ; Watkin, E. L. ; Mc Credden, T. J. ; Wong, Z. R. ; Harrison, S. T. L. ; Kaksonen, A. H. The use of pyrite as a source of lixiviant in the bioleaching of electronic waste. Hydrometallurgy 2015 ,152, 33–43. [Cross Ref] 6. Kaksonen, A. H. ; Boxall, N. ; Bohu, T. ; Usher, K. ; Morris, C. ; Wong, P. ; Cheng, K. Recent advances in biomining and microbial characterisation. Sol. St. Phen. 2017 ,262, 33–37. [Cross Ref] 7. Kaksonen, A. H. ; Morris, C. ; Hilario, F. ; Rea, S. M. ; Li, J. ; Usher, K. M. ; Wylie, J. ; Ginige, M. P
This phenomenon was attributed to the increase of arsenic concentration in the pregnant leaching solution (PLA), which subsequently became inhibitory to the strain. Similarly, Park and Cho [ 49] leached valuable metals from mine waste by column experiments at room temperature. They satisfactorily leached Cu and iron from the ore. Also, the synergy between bioleaching and electrochemical processes has been proven to be successful to recover metals from mine tailings. Lee et al. [ 50] revealed that the removal speed of an integrated process of biological leaching and electrokinetics was around 2. 5 times faster than that obtained in independent processes. Similarly, Park et al. [ 51] obtained Cu recoveries of approximately 98% after applying electrowinning to the PLA obtained by biological means which is signiﬁcantly higher than the 78% obtained by acid leaching. Minerals 2016 ,6, 128 7 of 21 The research within bioleaching of mine tailings demonstrated that this technology is an actual alternative to traditional methods, such as cyanide leaching, to recover metals from mine tailings and mitigate implicit environmental issues. Our research shows that the studies are mainly focused on determining the optimum operating conditions for the process in ﬂask and column experiments. The importance and inﬂuence of bacterial shape and adaptation in the process were also underlined by the scholars who presented their ﬁndings in Korean journals. Table 2. Bioleaching research of mine tailings according to the parameters studied and recoveries achieved as well as microorganisms used in the studies. The articles appear in chronological order. Author(s) Microorganism(s) Parameters p H Particle Size Time (Day) Leaching (%) [50] Ind. bacteriaa Bioleaching/electrokinetics 10–12 2000m 29 As: 64. 5 [44] A. thiooxidans Mineral source 2. 0 177m 20 - [42] Ind. bacteriaa Bacterial attachment 3. 5 841m 20 - [49] Ind. bacteriaa Leaching feasibility 4. 2 +2000 m 22 - [40] Ind. bacteriaa Attachment 3. 5 841m 50 - [41] Ind. bacteriaa Attachment 3. 5 841m 80 - [45] Ind. bacteriaa Bacterial adaptation 2. 82 1 mm 42 - [47] A. ferrooxidans Surface pretreatment 1. 5 10–10 mm 20 Cu: 72 [51] A. ferrooxidans Bioleaching/electrokinetics 2 4 cm 13 Cu: 76 [48]A. thiooxidans and A. ferrooxidans Removal rates in long-term experiments. 1. 8 +4000 m 450 As: 70 [46] Ind. bacteriaa Effect of bacterial adaptation 2. 6 and 2. 8 2380m 43 Cu: 92. 79 a Indigenous bacteria. 4. 3. Bioleaching of Electronic Waste Discarded cell phones, appliances, and printed circuit boards constitute the majority of e-wastes that may contain precious metals (Cu and Au), heavy metals (Pb, Sb and Hg), and other compounds (polybrominated diphenyl ethers and polychlorinated biphenyls) [ 52,53]. The constant growing demand for precious metals to satisfy industrial and population growth-related necessities has added to the strengthening and implementation of environmental policies, such as extended product responsibility, thereby highlighting the importance of treating e-waste. Bioleaching is gaining ground as an effective pathway for metal recovery from this source. Nevertheless, its application in this ﬁeld still requires further research, especially to determine optimum operational conditions and to ﬁnd a feasible process that may combine other technologies. The aim of this section is to address the work to date in the bioleaching of e-waste from electronic wastes found in Korean journals. Table 3 presents the relevant highlights of the research produced on the bioleaching of electronic waste. Table 3. Bioleaching research of electronic waste according to the parameters studied and recoveries achieved as well as microorganisms used in the studies. The articles appear in chronological order. Author(s) Microorganism(s) Parameters p H Particle Size Time (Day) Leaching (%) [54] T. ferrooxidans Solid concentration 2. 0 149m 7Cu and Co: 90; Al, Zn, and Ni: 40 [55] A. niger Chemical vs. biological leaching5. 5–6. 0500m 72Cu and Co: 95; Al, Zn and Pb: 15–35 [56] A. niger Bioleaching and solvent extraction combination2. 5500m - Cu: 99. 9 Several scholars reported their ﬁndings in metal recovery from electronic scrap by microbiological means. In ﬂask experiments, Ahn et al. [ 54] used T. ferrooxidans to leach heavy metals from e-waste and they focused on determining the optimum pulp density for the process. They achieved a 90% leaching efﬁciency of Cu and Co and a 40% efﬁciency of Al, Zn, and Ni at 10% of the solid concentration. However, the precipitation into lead (II) sulfate (Pb SO 4) and stannous oxide reduced Pb and tin (Sn) leaching, respectively. As a reference, the scholars compared these results with those obtained from the Minerals 2016 ,6, 128 8 of 21 bioleaching of metal powders containing the target metals; bioleaching of electronic scrap presented higher efﬁciencies. The use of fungi to recover minerals from electronic waste was also reported in the Korean Journal Database. The impact of reaction time and concentration of organic acids on the leaching efﬁciency by A. niger was emphasized by Ahn et al. [ 55]; the researchers obtained 95% leaching efﬁciency of Cu and Co at an electronic scrap concentration of 50 g/L. Using the same fungal species, Ahn et al. [ 56] conducted a combined process of bioleaching, solvent extraction (with LIX84), and electrowinning to recover Cu and Sn from a solution of electronic scrap. They reported a 99% recovery leaching rate that was directly proportional to the concentration of LIX84, considering 20% ( v/v) of LIX84 as the concentration limit. The results obtained using microorganisms to recover metals from e-waste are encouraging. Unfortunately, the currently scarce amount of literature from Korean journals makes it difﬁcult to determine the trends and future directions. Similar to the research approach used to treat other materials, the ﬁndings presented in Korean journals were related to the determination of basic operating conditions. Nonetheless, this area, due to its relevance from an environmental and economic perspective, has high potential and an intensive cooperation between academia and industry have to meet to exploit the opportunities. 4. 4. Bioleaching of Ores and Metal Concentrates Metal recovery from ores and concentrates constitute the main application of bioleaching worldwide. The proof of this fact is reﬂected in the 33 commissioned plants worldwide since 1986 (17 heap leaching and 16 stirred tank reactors) [ 57]. The main constraints that the bioleaching of mineral ores and concentrates face are mainly related to the long extraction times, the necessity to further process the generated by-products, and the metal toxicity to the biomining microorganisms. This section addresses the relevant ﬁndings to process these materials published in Korean journals. Table 4 summarizes the research conducted in this area. Table 4. Bioleaching research of mineral ores and metal concentrates research according to the parameters studied and recoveries achieved as well as microorganisms used in the studies. The articles appear in chronological order. Author(s) Microorganism(s) Parameters p H Particle Size Time (Day) Leaching (%) [58] T. ferrooxidans Particle size, pulp density, and Fe concentration2. 0 210–250 m 18 Cu: 78 [59] - Review - - - - [60] A. ferrooxidans Energy source, initial p H, pulp density, and temperature1. 0–2. 574m 30 Cu: 80 [61] A. ferrooxidans Thermal pretreatment 1. 5 - 33Ni: 59. 18 Co: 65. 09 [62] - Review - - - - [63] A. ferrooxidans Feasibility assessment 1. 5 1–9. 5 mm 100 Co: 10 [64] Ind. bacteriaa Chemical vs. biological leaching 4. 0 841m 10 - [65] Ind. bacteriaa Initial p H and temperature 4. 0, 7. 0, 9. 0 74m 19 - [66] Ind. bacteriaa Pulp density 4. 4 841m 84 - [67] - Review - - - - [68] Ind. bacteriaa Bacterial attachment 4. 20 74m 45 - [69]L. ferriphilum, Acidithiobacillus caldus Bacterial attachment 2. 0 149m - - [70] Ind. Bacteriaa Feasibility 3. 2 - 28 - [71] - Review - - - - [72] Ind. bacteriaa Temperature 2. 43 841m 16 - [73] A. ferrooxidans Feasibility assessment 1. 75 - 10 - [74] A. niger Strain variations 3. 5 - 23 Cu: 98 [75] A. niger Manganese supplement 6. 8 74m 27 Ni: 38. 6 [76] A
monteilii was also reported to be unable to use the following carbon sources: N-acetylglucosamine, esculin, m-aminobenzoate, p-aminobenzoate, 3-aminobutyrate, amygdalin, D-arabitol, L-arabitol, arbutin, L-cysteine, dulcitol, ethylamine, L-fucose,β-gentiobiose, glucosamine, glycogen, isophthalate, 5-ketogluconate, D-lyxose, L-lyxose, melezitose, melibiose, L-methionine, α-methylglucoside, α-methyl- D-mannoside, α-methyl-xyloside, raffinose, L-sorbose, terephthalate, raffinose, tagatose, D-tryptophan, D-turanose, xylitol, and L-xylose. c P. rhodesiae was also found to use acetylglucosamine and D-arabitol, and was unable to grow on esculin, 2-aminobenzoate, 3-aminobenzoate, 4-aminobenzoate, 3-aminobutyrate, amygdalin, L-arabitol, arbutin, L-cysteine, dulcitol, ethylamine, L-fucose, gentio- biose, glucosamine, glycogen, norvaline, raffinose, salicin, sorbose, D-tagatose, terephthalate, D-turanose, urea, xylitol, and L-xylose. d Positive for P. veronii ; results on other substrates not reported. e P. monteilii not tested. f No information on P. veronii. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc. , in association with Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria 47 TABLE 7. Characteristics differentiating Pseudomonas aeruginosa, P. balearica, P. stutzeri ,a n d P. putidaa Characteristics P. aeruginosa P. balearica P. putida P. stutzeri Type of colony : Smooth + + Wrinkled + + Number of flagella 1 1 >1 1 Hydrolysis of : Gelatin + − − − Starch − + − + Utilization of : Maltose − + d + Xylose − + d − γ-Aminobutyrate − − d d Malate d + − + Suberate d − − d Mannitol + − − d Ethylene glycol − − − + Denitrification + + − + Growth at : 42∘C + + − d 46∘C − + − d Growth in media with 8. 5% Na Cl − + − − Fatty acid content (%): C17:0 cyclo0. 8 4. 71 >5 0. 28–1. 72 C19:0 cyclo1. 2 3. 8 Traces 0. 32-1. 45 Mol% G +C of the DNA 67 64. 1–64. 4 60. 7–62. 5 60. 9–64. 9 a For symbols see standard definitions. Data from Bennasar et al. (1996) and Stanier et al. (1966). in Table 8. Details of its fatty acid composition are known (Stead, 1992). The organism causes drippy gill of mushrooms, and one of the main differences with another mushroom pathogen, P. tolaasii , is in the utilization of benzoate. Catechol is oxidized to a black pigment diffusing into the medium, a character also present in P. agarici. The species was tentatively assigned to RNA group I by Byng et al. (1980), and this position was fur-ther confirmed by r RNA–DNA hybridization (De Vos et al. ,1985) and by r DNA sequencing (Moore et al. , 1996). The mol %G+Co ft h e D N Ai s : 58. 8–61. 1 ( T m). Type strain : ATCC 25941, DSM 11810, LMG 2289. Gen Bank accession number (16S r RNA ): Z76652. Pseudomonas alcaligenes Monias 1928, 332AL. al. ca. li’ge. nes. M. L. adj. alcaligenes alkali-producing. Characteristics useful to differentiate the species from other Pseudomonas species are given in Tables 9 and 10. For further descriptive information see Ralston-Barrett et al. (1976) and Stanier et al. (1966). The nutritional spectrum isvery narrow, resembling that of highly mutated fluorescent organisms. The gelatinase reaction is negative. The type strain was isolated from swimming pool water (Hugh and Ikari, 1964). The mol %G+Co ft h e D N Ai s :6 4 – 6 8( B d ). This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc. , in association with Bergey’s Manual Trust. 48 Bergey’s Manual of Systematics of Archaea and Bacteria TABLE 8. Characters distinguishing some fluorescent Pseudomonas species associated with mushroom culturea Characteristics P. agarici P. cichorii P. fluorescens biovar II P. tolaasii Levan formation from sucrose − − + − Arginine dihydrolase − − + + Denitrification − − + − Gelatin hydrolysis − − + + Egg yolk reaction − + − + Growth at the expense of : Trehalose − − + d 2-Ketogluconate − − + d meso-Inositol − + + + L-Valine d − + + β-Alanine + − + + L-Arabinose − + + d Sucrose − + + − Sorbitol − − + + Adonitol − − d d Ethanol − − + d meso-Tartrate − + − + Nicotinate − − − + Staining of mushroom caps d + Pitting of mushroom caps − + a For symbols see standard definitions. Data from Fahy (1981) and Stanier et al. (1966). Type strain : Stanier 142, ATCC 14909, LMG 1224NCIB 9945, NCTC 10367. Gen Bank accession number (16S r RNA ): Z76653. Pseudomonas amygdali Psallidas and Panagopoulos 1975, 105AL. a. myg’da. li. L. n. amygdalum almond; L. gen. n. amygdali of the almond. The following description is taken from Psallidas and Panagopoulos (1975). Rods, 0. 7 ×1. 7μm or much longer (filaments can be 10–15 times the length of normal cells). Motile by means of one to six polar flagella. No PHB accumulated. Grows better in potato-dextrose medium than in nutrient agar. Growth range, 3–32∘C. No growth below p H 5. No fluorescent pig- ment produced. Acid is formed from D-ribose, L-arabinose, glucose, mannose, galactose, fructose, sucrose, mannitol, and sorbitol. No utilization of xylose, L-rhamnose, L-sorbose,cellobiose, lactose, maltose, melibiose, trehalose, raffinose, inulin, esculin, amygdalin, arbutin, salicin, dulcitol, ery- thritol, glycerol, inositol, dextrin and α-methyl- D-glucoside. Malate, citrate, succinate, and fumarate are utilized. Glu-conate is slowly assimilated. Acetate, propionate, oxalate, maleate, malonate, tartrate, lactate, sulfanilic acid, picrate, hippurate, and benzoate are not utilized. Among the nat- ural amino acids, serine, aspartate, glutamate, arginine, asparagine, proline, and histidine are utilized. Not usedas carbon and/or nitrogen sources are glycine, β-alanine, leucine, isoleucine, valine, lysine, ornithine, tyrosine, pheny- lalanine, tryptophan, cystine, cysteine, methionine, and creatine. Some isolates are urease positive. Tween 80 and trib- utyrin are rapidly hydrolyzed. Lechithinase and arginine dihydrolase negative. Gelatin, casein, esculin, arbutin, and starch are not hydrolyzed. Nitrates are not reduced. Rotting of potato slices does not occur, but the organism is positive in the hypersensitivity test on tobacco leaves. Further details. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc. , in association with Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria 49 TABLE 9. General characteristics of some nonfluorescent Pseudomonas speciesa Characteristics P. alcaligenes P. corrugata P. luteola P. mendocina P. oryzihabitans P. pseudoalcaligenes P. stutzeri Cell diameter, μm 0. 5 0. 8 0. 7–0. 8 0. 8 0. 7–0. 8 0. 7–0. 8 Cell length, μm 2. 0–3
Anaerobic degradation of indolic compounds by sulfate-reducing enrichment cul-tures, and description of Desulfobacterium indolicum gen. nov. , sp. nov. Arch. Microbiol. 146: 170–176. Bale, S. J. , K. Goodman, P. A. Rochelle, J. R. Marchesi, J. C. Fry, A. J. Weightman and R. J. Parkes. 1997. Desulfovibrio profun- dussp. nov. , a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int. J. Syst. Bacteriol. 47: 515–521. Beijerinck, M. W. 1895. Über Spirillum desulfuricans als Ursache von Sulfatreduktion. Zentralbl. Bakteriol. Par-asitenkd. Infektionskr. Hyg. Abt. I Orig. 1:1 – 9 ;4 9 – 5 9 ; 104–114. Biebl, H. and N. Pfennig. 1977. Growth of sulfate-reducing bacteria with sulfur as electron acceptor. Arch. Microbiol. 112: 115–117. Brauman, A. , J. F. Köenig, J. Dutreix and J. L. Garcia. 1990. Characterization of two sulfate-reducing bacteria from the gut of the soil-feeding termite, Cubitermes speciosus. Antonie Leeuwenhoek 58: 271–275. Campbell, L. L. , M. A. Kasprzycki and J. R. Postgate. 1966. Desulfovibrio africanus sp. n. , a new dissimilatory sulfate-reducing bacterium. J. Bacteriol. 92: 1122–1127. Caumette, P. , Y. Cohen and R. Matheron. 1991a. Isolation and characterization of Desulfovibrio halophilus sp. nov. , isolated from Solar Lake (Sinai). Syst. Appl. Microbiol. 14: 33–38. Caumette, P. , Y. Cohen and R. Matheron. 1991b. In Valida- tion of the publication of new names and new combina-tions previously effectively published outside the IJSB. List No. 37. Int. J. Syst. Bacteriol. 41: 331. Chase, A. R. , J. W. Miller and J. B. Jones. 1984. Leaf spot and blight of Asplenium nidus caused by Pseudomonas gladioli. Plant Dis. 68: 344–347. Cooper, D. M. , D. L. Swanson, S. M. Barns and C. J. Gebhart. 1997. Comparison of the 16S ribosomal DNA sequencesfrom the interacellular agents of proliferative enteritisin a hamster, deer, and ostrich with the sequence of a porcine isolate of Lawsonia intracellularis. Int. J. Syst. Bacteriol. 47: 635–639. Cord-Ruwisch, R. , B. Ollivier and J. L. Garcia. 1986. Fructose degradation by Desulfovibrio sp. in pure cul- ture and in coculture with Methanospirillum hungatei. Curr. Microbiol. 13: 285–289. Devereux, R. , S. H. He, C. L. Doyle, S. Orkland, D. A. Stahl, J. Le Gall and W. B. Whitman. 1990. Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. J. Bacteriol. 172: 3609–3619. Dilling, W. and H. Cypionka. 1990. Aerobic respiration in sulfate-reducing bacteria. FEMS Microbiol. Lett. 71: 123–127. Dreyfus, B. , J. L. Garcia and M. Gillis. 1988. Characteriza- tion of Azorhizobium caulinodans gen. nov. , sp. nov. , astem-nodulating nitrogen-fixing bacterium isolated from Sesbania rostrata. Int. J. Syst. Bacteriol. 38: 89–98. Dunn, B. E. , H. Cohen and M. J. Blaser. 1997. Helicobacter pylori. Clin. Microbiol. Rev. 10: 720–741. Eaglesome, M. D. , M. I. Sampath and M. M. Garcia. 1995. A detection assay for Campylobacter fetus in bovine semen by restriction analysis of PCR amplified DNA. Vet. Res. Commun. 19: 253–263. Esnault, G. , P. Caumette and J. L. Garcia. 1988a. Char- acterization of Desulfovibrio giganteus sp. nov. , asulfate-reducing bacterium isolated from a brackishcoastal lagoon. Syst. Appl. Microbiol. 10: 147–151. Esnault, G. , P. Caumette and J. L. Garcia. 1988b. In Valida- tion of the publication of new names and new combina-tions previously effectively published outside the IJSB. List No. 26. Int. J. Syst. Bacteriol. 38: 328–329. Feio, M. J. , I. B. Beech, M. Carepo, J. M. Lopes, C. W. S. Cheung, R. Franco, J. Guezennec, J. R. Smith, J. I. Mitchell, J. J. G. Moura and A. R. Lino. 1998. Isolation and charac-terization of a novel sulphate-reducing bacterium of the Desulfovibrio genus. Anaerobe 4: 117–130. Feio, M. J. , I. B. Beech, M. Carepo, J. M. Lopes, C. W. S. Che- ung, R. Franco, J. Guezennec, J. R. Smith, J. I. Mitchell,J. J. G. Moura and A. R. Lino. 2000. In Validation of the publication of new names and new combinations previ- ously effectively published outside the IJSB. List No. 75. Int. J. Syst. Evol. Microbiol. 50: 1415–1417. This article is © 2005 Bergey’s Manual Trust. Published by John Wiley & Sons, Inc. , in association with Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria 15 Foley, J. E. , J. V. Solnick, J. M. Lapointe, S. S. Jang and N. C. Pedersen. 1998. Identification of a novel enteric Heli- cobacter species in a kitten with severe diarrhea. J. Clin. Microbiol. 36: 908–912. Folkerts, M. , U. Ney, H. Kneifel, E. Stackebrandt, E. G. Witte, H. Förstel, S. M. Schoberth and H. Sahm. 1989a. Desul- fovibrio furfuralis sp. nov. , a furfural degrading strictly anaerobic bacterium. Syst. Appl. Microbiol. 11: 161–169. Folkerts, M. , U. Ney, H. Kneifel, E. Stackebrandt, E. G. Witte, H. Förstel, S. Schoberth and H. Sahm. 1989b. In Valida- tion of the publication of new names and new combina-tions previously effectively published outside the IJSB. List No. 31. Int. J. Syst. Bacteriol. 39: 495–497. Fröhlich, J. , H. Sass, H. D. Babenzien, T. Kuhnigk, A. Varma, S. Saxena, C. Nalepa, P. Pfeiffer and H. König. 1999a. Isolation of Desulfovibrio intestinalis sp. nov. from the hindgut of the lower termite Mastotermes darwiniensis. Can. J. Microbiol. 45: 145–152. Fröhlich, J. , H. Sass, H. D. Babenzien, T. Kuhnigk, A. Varma, S. Saxena, C. Nalepa, P. Pfeiffer and H. König. 1999b. In Validation of the publication of new names and newcombinations previously effectively published outside the IJSB. List No. 71. Int. J. Syst. Bacteriol. 49: 1325–1326. Gallus, C. , N. Gorny, W. Ludwig and B. Schink. 1997. Anaer- obic degradation of alpha-resorcylate by a nitrate-reducingbacterium, Thauera aromatica strain AR-1. Syst. Appl. Microbiol. 20: 540–544. Gebhart, C
Unfortunately, the ﬂight experiment did not result in usable data due to a technical failure. Another example is the PBR@LSR project. In this project, a PBR inoculated with Chlorella vulgaris was brought to the ISS in 2019. The proposed experiment time was 6 months, but the experiment had to be terminated after a few weeks due to technical issues(Keppler et al. , 2018). Table 4 shows a selection of space ﬂight experiments using photosynthetic unicellular organisms in illuminated test chambers (PBRs) that have been in space over the last 30 years. Since not all of the experiments in space have been successful, not all space experiments were published so that only experiments published in peer reviewed papers that could be used as references are shown. DISCUSSION In this section, we highlight the diﬀerent challenges in context of PBR for space applications in order to give an overview of Frontiers in Microbiology \| www. frontiersin. org 8 June 2021 \| Volume 12 \| Article 699525 fmicb-12-699525 June 29, 2021 Time: 15:9 # 9 Fahrion et al. Photobioreactors in Space FIGURE 1 \| (A) Nostoc sp. /Euglena gracilis container of the ﬁrst space ﬂight experiment associated with MELi SSA (Dubertret et al. , 1987), courtesy of ESA. (B)Limnospira indica hardware from the Art EMISS-B experiment (Poughon et al. , 2020, original source: QINETIQ). knowledge gaps and problems that already occurred or might arise in the future of BLSS research. Safety and Reliability – Robustness, Resilience, and Redundancy The safety and reliability of a life support system is of utmost importance. In order to avert fatal incidents, several back- up facilities and control mechanisms have to be installed and the system has to be monitored consistently. All possible scenarios have to be calculated and evaluated beforehand to avoid failure, because failure can be fatal for the crew (Bartsev et al. , 1996). For example, a failure in O 2production has to be intercepted by an emergency system before a drop in the O 2concentration of the cabin occurs. A high degree of redundancy has to be achieved. Physicochemical emergency back-up systems, plant compartments and diﬀerent PBRs could be put in parallel that can be uncoupled from each other. And not all bioreactors need to be operated in long duration continuous production, but a regime of alternating batches or operation and downtime of bioreactors could be implemented, if shown to be advantageous for operation, harvesting or maintenance. In addition, reliable mathematical models for the bioreactors are essential to keep all processes predictable (Vernerey et al. , 2001). This is a highly strategic point when the recycling eﬃciencies of diﬀerent elements and compounds are coupled and intertwined as it is the case for BLSS, such as MELi SSA. In this case, the action on an operational variable has distributed consequences at several points of the recycling system, calling for an intelligent control strategy based on knowledge models taking into account the dynamic exchanges between the diﬀerent parts of the recycling system. The other important point for life support systems for space is that the buﬀer tanks generally have a minimal capacity entailing an online control strategy. The criteria for reliability, availability, maintainability and supportability (RAMS) engineering have to be applied in the BLSS research. Gas Exchange and O 2/CO 2Balance Between Consumer and Producer As mentioned, on average, one human needs 0. 82 kg of O 2 and produces1. 04 kg of CO 2per day. Depending on the activity level, the ratio of exhaled CO 2to consumed O 2, i. e. , the respiratory coeﬃcient, can vary (Anderson et al. , 2018). On the other hand, the O 2production of algae and cyanobacteria can be characterized by a photosynthetic coeﬃcient, describing the ratio of produced moles of O 2per consumed moles of CO 2. This ratio is dependent on the organism (and its biochemical composition) and the nutrient substrate (e. g. , the nitrogen source). The stoichiometric eqs. 3, 4 [simpliﬁed from Cornet et al. (1998)] show this dependence for Limnospira indica on the examples ammonium (NH 3) and nitrate (NO 3or here: HNO 3) as nitrogen sources. Solving the stoichiometric equations reveals that the photosynthetic coeﬃcient for ammonium is 1. 0 and for nitrate1. 4. CO 2C0:528H2OC0:173NH 3Cnhn. CH 1:575O0:459N0:173 C1:034O2 (3) CO 2C0:701H2OC0:173HNO 3Cnhn. CH 1:575O0:459N0:173 C1:381O2 (4) Importantly, it must be outlined that photosynthetic growth stoichiometry has no degree of freedom when the composition of nitrogen source (or its degree of reduction) is ﬁxed so that the photosynthetic coeﬃcient is only depending and linked to the culture conditions. The number of photons required to ﬁx 1 mol of carbon is depending on the culture conditions. Away from photo inhibition conditions, a typical value is n= 20 mol photons per mol of carbon ﬁxed (Cornet and Dussap, 2009; Poulet et al. , 2020). In order to avoid an imbalance in gas composition, a system has to be developed to combine the respiratory quotient of the crew members and the photosynthetic coeﬃcient of the Frontiers in Microbiology \| www. frontiersin. org 9 June 2021 \| Volume 12 \| Article 699525 fmicb-12-699525 June 29, 2021 Time: 15:9 # 10 Fahrion et al. Photobioreactors in Space microalgae. In some experiments, successes were achieved (see section “Photosynthetic Microorganisms as Catalysers for Air Revitalization in Space”). However, gas exchange in space is much more complex, due to the lower or lack of gravity. There is still very little information about the gas, water and solute transport in microgravity in living organisms. Moreover, microgravity conditions strongly modify the environment of the chemical and biochemical processes, e. g. , implying lack of sedimentation and impaired gas and liquid phase separation. Consequently, transport is limited to diﬀusion causing an increase of boundary layer thickness and therefore a signiﬁcant decrease of mass and heat transfer coeﬃcients. This can cause problems with pumping and the mineral availability for the cultures and has to be elucidated more thoroughly (Klaus et al. , 1997). In situ Resource Utilization and Light as an Energy Source Another challenge is the complete closure of a BLSS. So far, no loop has an eﬃciency of 100%, which means that all tested life support systems still rely on external addition of diﬀerent substances like carbonate or trace elements, etc. For example, the 105 days long Lunar Palace 1 experiment (plants, insects, and three crew members) reached a full oxygen and water recycling but only 20. 5% nitrogen recovery from urine and 55% of the food was regenerated. In this approach, physico-chemical and biological processes were combined (Fu et al. , 2016). Some substances are either diﬃcult to ﬁnd in the space environment or it is very costly and time consuming to convert them into a usable form. Therefore, space habitats for humans have to be fully functional under the speciﬁc conditions and have to rely on the materials available around and only a small amount of material brought from Earth. For example, lunar regolith, mars soil and CO 2in the Martian atmosphere are promising substances to be used forin situ resource utilization (ISRU) (Montague et al. , 2012; Muscatello and Santiago-Maldonado, 2012). The usage of photoautotrophic organisms helps to overcome parts of the material problems because their main energy source is light. But so far, only experiments using artiﬁcial light (e. g. , halogen lamps or LEDs) have been ﬂown ( Table 4 ) which means that the naturally available solar energy is not used directly so far. One of the main reasons is that the natural light intensities and spectral energy distributions available in space are not compatible with the needs of the photosynthetic organisms. The intensity of sun light depends on the distance from the sun and the irradiation spectrum in deep space consists of a diﬀerent wavelength composition than the irradiation we experience on ground due to absorption of light in the Earth’s atmosphere (Cockell and Horneck, 2001). Besides that, the ISS, Moon and Mars surface are eclipsed for 50% of the time and the day and night cycles, e. g. , on the moon are very diﬀerent from Earth. For example, one lunar night is as long as 18 Earth days (Alvarado et al. , 2021; Xie et al. , submitted)1. Also, the intensity 1Xie, G. , Zhang, Y. , Y ang, J. , Yu, D. , Ren, M. , Qiu, D. , et al. (submitted). Adaptation to real 1/6 g Moon Gravity Contributes To Plant Development And Expeditious Acclimation To Super-Freezing. Chongqing, Research Square. doi: 10
A systematic approach in collecting the information is desirable to reduce the time or extraneous data requirements. In any flowsheet design and synthesis case, it is always recommended to start creating the flowsheet at a high level and gradually build the individual unit operations at the process level. This gives a preliminary screening of missing information and identifies the level of details required for each important process investigation. A block diagram is the most preferred method in showing the overall system configuration and material and energy flows. The block diagram for an integrated gasification system is shown in Figure 14. 6. The operating conditions (e. g. , temperature and pressure) of the gasification process, gas cleaning and conditioning and synthesis reaction are needed to solve the mass and energy balances of the integrated gasification flowsheet, as shownin the block diagram in Figure 14. 6. This information can normally be found in literature, technology provider websites,existing technology reports, etc. Mass balances include the flow and composition of feed, gas product, conditioned syngas and product streams. Energy balances include the heat released or consumed within the reactors and separators as well as the heat exchange processes involved between processes. The next step is detailed process modeling. This can be done using mathematical modeling if detailed reaction equations can be specified. Alternatively, the simulation modeling method can be adopted. Simulation packages such as Aspen Plus, Aspen HYSYS and PRO/II are among the widely used process simulation softwares in industry. They contain well-established unit operation models, thermodynamic property packages, chemical component databases and calculation algorithms that allow process modeling to be carried out efficiently and the generation of reliable results. Nevertheless, it should be remembered that validation of results ought to be performed no matter which modeling method (mathematicalor simulation) is adopted. Gasification Gas Cleaning and Conditioning Conditioned Syngas Synthesis Reaction Feed(Bio-oil) Product(Methanol) Gas Product Figure 14. 6 Block diagram showing the integrated gasiﬁcation system. 488 Bioreﬁneries and Chemical Processes The following general procedures can be adopted for simulation modeling of a process: Step 1. Set up a flowsheet environment comprising the following: r Pick the chemical components involved in the whole plant from the component database. r Choose a suitable thermodynamic property package. Step 2. Build the flowsheet starting from the main unit operation blocks: r Select a suitable unit operation model for the process to be modeled. Consider the simplest form of the model from a choice of readily available models. If the results are not satisfactory, then a more rigorous model is to be adopted, including a user-defined model. r Obtain the operating parameters of the processes to be modeled from the literature. r Perform simulation. r Validate the simulation results against the literature results. Step 3. Create the models for other auxiliary equipment and connect the streams between the processes: r The auxiliary facility includes devices for increasing or decreasing temperature and pressure, mixer or splitter as well as flash separators for vapor–liquid separation. Depending on the modeler’s preference, Steps 2 and 3 can also be carried out simultaneously by modeling the unit operation blocks in sequential order. This is sometimes more efficient because the intermediate streams between processes can be simulated and used for the later processes. Otherwise, an initial guess has to be made for the feed streams to the main unit operation. An example using ASPEN Plus simulation modeling is shown for the bio-oil integrated gasification system for the production of methanol. Refer to the Online Resourcematerialinthe Companion Website:Chapter14 for the operating conditions of the processes and their modeling, design and integration using Aspen Plus. 14. 5. 2 Sensitivity Analysis 14. 5. 2. 1 Sensitivity Analysison Gasification Process Gasification is the core process of the system. Its operating condition affects the operation, cost, product yields and purities of the downstream processes. For example, if a lower pressure is used in the gasifier, while the downstream process demands a higher pressure, then compression of syngas is needed, thus leading to a higher operating cost. On theother hand, a high pressure gasifer differs from the atmospheric or slightly higher pressure gasifier in terms of material of construction, lining and thickness of the reactor wall. If undesirable components are present in syngas due to an unoptimized operating condition, it would need more downstream cleaning or otherwise it might affect the product yieldfrom the synthesis reactions. Cautious choice of operating parameters of the gasifier is vital, since operating conditions decide the performance of the entire system. The operating parameters that can be manipulated in the gasifier to produce favorable syngas quality are as follows: r Pressurer Temperaturer Oxygen flow rate or oxygen-to-feed ratior Steam flow rate or steam-to-feed ratio Steam is normally added as the gasifying medium. Generally, moist biomass has enough moisture to atomize biomass to ease the primary pyrolysis or devolatilization reactions in the gasifier. Since bio-oil is in liquid form and has a significant amount of water, steam is not needed in this case. Bio-Oil Reﬁning I 489 Sensitivity analysis should be performed for the variation of the above-mentioned operating parameters. There should be a systematic way to move towards optimal operating conditions. This would give an idea on the range of the correct conditions to generate syngas with the desired quality. There are three main criteria to inspect when carrying out sensitivity analysis for the gasifier: r The H2/CO molar ratior By-product formation such as CH4r No NOxor SOxformation by retaining an oxygen lean environment. Oxygen input should just be adequate to convert all carbon present in the biomass into carbon monoxide. Only consider the net oxygen requirement by subtracting theoxygen content in the biomass and associated moisture. (a)Pressureof Gasifier Pressure has a negligible impact on the syngas composition. This is primarily due to equimolar stoichiometric gasificationreactions and the pressure has less effect in changing the equilibrium composition, according to Le Chatelier’s principle. Although the effect of pressure on the syngas composition is negligible, the downstream operation ought to be taken into account while considering the operating pressure of the gasifier. For example, methanol synthesis operates at high pressure (e. g. 100 bar). Therefore, the pressure of the gasifier is elevated to reduce the compression power. There alsoexists a trade-off between the cost of operating the gasifier at high pressure and the cost of compression of syngas before the synthesis reaction. For CHP generation, the recommended biomass gasifier pressure is 30–50 bar. (b)Temperatureof Gasifier A higher temperature in the gasifier is preferred due to the following reasons: r Higher mole fraction of CO and H2r Lower mole fraction CO2and CH4 This is shown in Figure 14. 7(a). H2and CO are the main constituents of the methanol synthesis reaction; hence higher amounts of these components are desirable. However, the amount of H2decreases beyond 1000◦C. The decline of the H2component also suggests that the heating value of the syngas is lowered. Lower power is obtained if syngas is utilized for power generation. This can still be improved by placing a water gas shift reaction to increase the proportion of H2. On the other hand, the H2/CO molar ratio of the syngas should be monitored so that the syngas can be fed to the downstream process without undergoing rigorous conditioning (i. e. , water gas shift). The H2/CO molar ratio is lowered sharply between temperatures of 500◦C and 700◦C, and the effect is less significant beyond 700◦C. This is shown in Figure 14. 7(b). CO2and CH4are undesirable products from gasification. CO2has a dilution effect on the heating value of syngas and cost is incurred for removing CO2. The CO2content in the syngas at the temperature beyond 1000◦C is acceptable. A relatively higher proportion of CH4is helpful if the syngas is used to generate power, but is undesirable for synthesis reactions such as methanol and FT liquids. For CHP generation, a gasifier temperature of 950◦C is recommended. (c)Variationofoxygen-to-feedratio The oxygen input to gasification reaction needs to be properly controlled. This is because excess oxygen input causes more CO2rather than CO formation, that is, the combustion reaction dominates the partial oxidation reaction. This is evident from Figure 14. 8(a), which shows that increasing the O2/feed molar ratio leads to undesirable effects such as an increase in CO2and a decrease in CO and H2formation. Also, a higher H2/CO molar ratio in syngas can be attained at a lower O2/feed molar ratio, shown in Figure 14. 8(b). Hence, less theoretical oxygen is to be maintained in the gasifier. The following are the heuristics for gasification process operations: r Pressure – select a pressure by considering the operating conditions of the downstream processes. r Temperature – use a temperature close to 1000◦C. r Oxygen-to-feed molar ratio – use a lower oxygen-to-feed molar ratio, that is, around 0. 5. 490 Bioreﬁneries and Chemical Processes (a) 0. 45 0. 40 0. 350. 350. 250. 200. 150. 100. 05 0. 00 0 500 1000 1500 2000H CO2 H2O CH4COComponents’ Mole Fraction Temperature (°C) 0. 000. 501. 001. 502. 002. 503. 003. 504. 004. 50 1600 1400 1200 1000 800 600 (b)400H2/CO Molar Ratio Temperature (°C) Figure 14
1371/journal. pcbi. 1000312. Tshilombo, A. F. , 2006. Mechanism and kinetics of chalcopyrite passivation and depassivation during ferric and microbial leaching. Ph D thesis. University of British Columbia, Canada. Tuovinen, O. H. , Bhatti, T. M. , 1999. Microbiological leaching of uranium ores. Miner. Metall. Process. 16 (4), 51 –60. Van Niekerk, J. , 2019. Personal communication. Unlocking value from refractory gold projects using the Outotec BIOX process. Oral presentation at Journée Scientifique en bio hydrométallurgie. Vald’Or, Québec, Canada, 26 September 2019. Vardanyan, N. , Sevoyan, G. , Navasardyan, T. , Vardanyan, A. , 2018. Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium. Environ. Technol. 40(26), 3467-3472. Vera, M. , Schippers, A. , Sand, W. 2013. , Progress in bioleaching: fundamentals and mechanisms of bacterial metal sulfide oxidation – part A. Appl. Microbiol. Biotechnol. 97(17), 7529 -7541. Vickers, C. , Small, I. , 2018. The synthetic biology revolution is now – here’s what that means. The Conversation. September 5, 2018. [URL] -synthetic -biology -revolution -is-now-heres -what -that-means -102399. Vuorenmaa, E. A. , Mä kinen, J. , Korhonen, T. , Neitola, R. , Kaksonen, A. H. , 2017. Pilot -scale bioleaching of metals from pyritic ashes. Solid State Phenom , 262, 147-150. Wang, H. , Liu, X. , Liu, S. , Yu, Y. , Lin, Jianqun, Lin, Jianqiang, Pang, X. , Zhao, J. , 2012. Development of a markerless gene replacement system for Acidithiobacillus ferrooxidans and construction of a pfk B Mutant. Appl. Environ. Microbiol. 78(6), 1826 -1835. doi:10. 1128/AEM. 07230 -11. Wang, J. T. , Hong, Y. W. , Lin, Z. C. , Zhu, C. L. , Da, J. , Chen, G. H. , Jiang, F. , 2019. A novel biological sulfur reduction process for mercury -contaminated wastewater treatment. Water Res. 160, 288 -295. Watling, H. R. , 2006. The bioleaching of sulphide minerals with emphasis on copper sulphides – A review. Hydrometallurgy 84, 81 -108. Wei, X. , Liu, D. , Huang, W. , Huang, W. and Lei, Z. , 2020. Simultaneously enhanced Cu bioleaching from E -wastes and recover ed Cu ions by direct current electric field in a bioelectrical reactor. Bioresource Technol. 298, 122566. Wu, X. , Zhao, F. , Rahunen, N. , Varcoe, J. R. , Avignone -Rossa, C. , Thumser, A. E. , Slade, R. C. T. , 2011 A role for microbial palladium nanoparticles in e xtracellular electron transfer. Angew. Chem. Int. Ed. 50, 427 -430. Xia, J. L. , Song, J. -J. , Liu, H. -C. , Nie, Z. -Y. , Shen, L. , Yuan, P. , Ma, C -Y. , Zheng, L. , Zhao, Y. -D. , 2018. Study on catalytic mechanism of silver ions in bioleaching of chalcopyrite by SR -XRD and XANES. Hydrometallurgy 180, 26 -35. Yan, S. , Cheng, K. Y. , Morris, C. , Douglas, G. , Ginige, M. P. , Zheng, G. , Zhou, L. , Kaksonen, A. H. , 2020. Sequential hydrotalcite precipitation and biological sulfate reduction for acid mine Journal Pre-proof Journal Pre-proof 40 drainage treatment. Chemosphere. 252, 126570. Yelloji Rao, M. K. , Natarajan, K. A. , 1989. Electrochemical effects of mineral -mineral interactions on the flotation of chalcopyrite and sphalerite. Int. J. Miner. Process. 27(3), 279 -293. Yu, Y. , Liu, X. , Wang, H. , Li, X. , Lin, J. , 2014. Construction and characterization of tet H overexpression and knockout strains of Acidithiobacillus ferrooxidans. J. Bacteriol. 196(12), 2255-2264. doi:10. 1128/JB. 01472 -13. Yu, Z. , Han, H. , Feng, P. , Zhao, S. , Zhou, T. , Kakade, A. , Kulshrestha, S. , Majeed, S. , Li, X. , 2020. Recent advances in the recovery of metals from waste through biological processes. Bi o- resour. Technol. 297, 122416. doi:10. 1016/j. biortech. 2019. 122416. Yuehua, H. , Guanzhou, Q. , Jun, W. and Dianzuo, W. , 2002. The effect of silver -bearing catalysts on bioleaching of chalcopyrite. Hydrometallurgy 64(2), 81 -88. Yunker, S. B. , Radovich, J. M. , 1986. Enhancement of growth and ferrous iron oxidation rates of T. Ferrooxidans by electrochemical reduction of ferric iron. Biotechnol, Bioeng, 28(12), 1867-1875. Zea, L. , Mc Lean, R. J. C. , Rook, T. A. , Angle, G. , Carter, D. L. , Delegard, A. , Denvir, A. , Ge r- lach, R. , Gorti, S. , Mc Ilwaine, D. , Nur, M. , Peyton, B. , Stewart, P. , Sturman, P. , Velez Justin i- ano, Y. A. , Potential biofilm control strategies for extended spaceflight missions (in review) Zhang, R. , Hedrich, S. , Ostertag -Henning, C. , Schippers, A. , 2018 a Effect of elevated pressure on ferric iron reduction coupled to sulfur oxidation by biomining microorganisms. Hydrometa l- lurgy 178, 215 -223. Zhang, Y. P. , Zhang, L. , Li, L. H. , Chen, G. H. , Jiang, F. , 2018b. A novel elemental sulfur reduction and sulfide oxidation integrated process for wastewater treatment and sulfur recycling. Chemical Eng. J. 342, 438 -445. Zhang, L. , Zhang, Z. F. , Sun, R. R. , Liang, S. , Chen, G. H. , Jiang, F. , 2018c. Self -accelerating su l- fur re -duction via polysulfide to realize a high -rate sulfidogenic reactor for wastewater treatment. Water Res. 130, 161 -167. Zhao, H. B. , Wang, J. , Tao, L. , Cao, P. , Yang, C. , Qing, W. , Qiu, G. , 2017. Roles of oxidants and reductants in bio leaching system of chalcopyrite at normal atmospheric pressure and 45 degrees C. Int. J. Miner. Process. 162, 81 -91. Journal Pre-proof Journal Pre-proof 41 Highlights  Deep subsurface and space biomining are gaining increasing interest  Biomining is being expanded to alternative lixiviants and commodities  Low-grade feed utilisation often requires integrated processes and impurity r e- moval  Waste mining and industrial ecology can help to maximise the use of resources  The capabilities of biomining microbes are being expanded through synthetic biology Journal Pre-proof Journal Pre-proof
Within Lan TERN’s dynamicrange,wecalculated EC50 valuesfor Lan TERNtobe976n Mforlanthanumand4. 71 μMforytterbium,withnomeasurableresponsetocalcium (Supplemental Table1),copper(II), cobalt(II),iron(II), magnesium, ormanganese(Supplemental Figure9). Thisis Figure1. Rational engineering of EFhandmotifsconverts GCa MP intoalanthanide sensor. (A)Sequencesof EFhands1,2,3,and4of GCa MP,Lan M-GCa MP, and Lan TERN. Aminoacidsidenticalto GCa MParegreen;aminoacidsderivedfrom Mex-Lan Mandnotfoundin GCa MPareblue;interveninglinkers(nottoscale)aredepictedaslines. Redstarsindicateaminoacidsidechainsshownasredsticksin(B). (B) Overlaidmodelsofmetal-bound Lan M-GCa MP (blue)and Lan TERN(green). Prolinesat EFhandposition2andputativelanthanide-binding aspartatesat EFhandposition9areshownasredsticks. (C)Fluorescence measurements of500n MLan M-GCa MP (see Figure1A,middleand Figure1B,blue)inthepresenceofvaryingcalcium,lanthanum,andytterbiumconcentrations. Pointsanderrorbarsrepresentthemeanand standarddeviationofthreetechnicalreplicatesfromthesameproteinpurification andworkingdilution. Graphsoftwoadditionalprotein purifications canbefoundin Supplemental Figure3. (D)Fluorescence measurements of500n MLan TERN(see Figure1A,bottom,and Figure 1B,green)invaryinglanthanum,ytterbium,andcalciumconcentrations. Pointsanderrorbarsrepresentthemeanandstandarddeviationofthree technicalreplicatesfromthesameproteinpurificationandworkingdilution. Graphsoftwoadditionalproteinpurifications canbefoundin Supplemental Figure4. ACSSynthetic Biology pubs. acs. org/synthbio Technical Note [URL] ACSSynth. Biol. 2024,13,958−962959 animprovement ofgreaterthan2ordersofmagnitudeover Lan M-GCa MP. Lan TERN’s lanthanide-dependent increasein fluorescence versusbaselinealsoincreasedover Lan M- GCa MP’s(e. g. ,>10-foldchangevs∼3. 5-foldchangein responsetolanthanum) (Figure1d). Wealsomeasuredthe apparent Kdof Lan TERNfor La3+usingchelator-buffered titrations12andcalculatedittobe40−60p M,whichisinline withotherworkonproteinscontaining Lan MEFhands (Supplemental Figure11). 3,7 Importantly, our Lan TERNdesignalsoswitchesthe functionof GCa MP. Wefoundthat Lan TERNdoesnot respondtocalcium,asitsresponsetolanthanideswasnearly identicalinthepresenceofcalciumconcentrations ashighas 500μM(Supplemental Figure10). Toconfirmtheimportance oftheprolineresidueinthesecondpositionofeach engineered EFhand,wecreateda Lan TERNvariantwhere thesecondpositionprolinewasback-mutated tothecognate aminoacidfoundinwild-typecalmodulin. Asexpected,these mutationsreducedthesensor’sresponsetolanthanides by approximately 10-foldandrestoreditsresponsetocalcium (Supplemental Figure2). Finally,wecharacterized Lan TERN’s responseto10 lanthanides thatspantheatomicweightofthisclass. Lan TERNrespondstoalllanthanidestested:weobserveda 14-foldorgreaterlanthanide-dependent fluorescence increase versusbaseline(Figure2). Thesensorexhibitedbinding preferences similarto Mex-Lan M, generallyresponding at lowerconcentrations ofthelighterlanthanides(Figure2B). 3,4 Thedifferencein EC50valuesforthelightestandheaviest lanthanidestesteddifferedbyapproximately 4-fold. However, Lan TERN’s EC50valuesareontheorderoftheconcentration ofthesensor,meaningthat Lan TERN’s actualaffinityforthe lanthanidesislikelymuchhigher. ■DISCUSSION Inthisstudy,wereporttheconstruction of Lan TERN,a lanthanide-responsive fluorescent protein. Werationallyengineered EFhandmotifstobuildafluorescentprotein sensorwithswitchedspecificityforlanthanidesversuscalcium. Thiscapabilityopensnewavenuesforthecreationof improvedlanthanide-binding proteins. Lan TERNcouldbe usedasasensingtoolindirectedevolutionstudiestoidentify mutationsin EFhandsthatincreasetheselectivityandaffinity forspecificlanthanides. Forexample,improvedvariantsof Lan TERNcouldbefoundusingyeastsurfacedisplayand fluorescence-activated cellsorting,whichisnotpossibleusing luminescence sensorsbasedonterbium. Theseimproved binderscouldbeusedinsyntheticbiologicalapproachesfor separatinglanthanides. Alternatively, Lan TERNcouldalsobeusedtodevelop engineered calmodulin domainsforbiosensing systems. Lan TERN’s M13andengineeredcalmodulindomainscould besplitandusedaslanthanide-dependent heterodimeric binders. Eachofthesedomainscouldthenbeattachedto components ofadimerization-based cellcontrolsystem. Such systemscouldthenutilizethelanthanide-dependent dimeriza- tionof M13and Lan TERNcalmodulintocreatealanthanide- dependentresponseforcellularfunctionssuchastran- scription13,14orphosphorylation15ortocreateluminescence- basedsensors. 16Thesesystems,especiallywhencombined withcalmodulins fromimprovedandmorespecific Lan TERN variants,wouldenablethecreationoforganismsthatrespond tothepresenceoflanthanidesandassistintheextractionand separationoflanthanides. ■METHODS Detailedprotocolsforallmethodsusedinthisreportaregiven inthe Supporting Information. Annotatedsequencesforall constructsusedarelistedinthe SIzipfile. AT7bacterial expressionconstructfor Lan TERNisavailableon Addgene (Addgene ID214061). ■ASSOCIATED CONTENT +sıSupporting Information The Supporting Information isavailablefreeofchargeat [URL] Supplemental methodsandprotocolsforexperiments andanalysisperformedinthisreport;La,Yb,and Ca dose−response of Lan M-GCa MP variantswithdifferent Lan Mhandordering(Supplemental Figure1);La,Yb, and Cadose−response of Lan TERN withback mutationsinthesecondpositionofeach EFhand (Supplemental Figure2);La,Yb,and Cadose−response of Lan M-GCa MP, includingallthreeindependent proteinpurifications (Supplemental Figure3);La,Yb, and Cadose−response of Lan TERN,includingallthree independent proteinpurifications (Supplemental Figure 4);La,Yb,and Cadose−response of Lan M-GCa MP variantswithdifferent Lan Mhandorderings,including allthreeindependent proteinpurifications (Supplemen- tal Figure5);La,Yb,and Cadose−response of Lan TERNshowingnonmonotonic dynamicsoutsideof Lnmax(Supplemental Figure6);La,Yb,and Cadose− responseof Lan TERNwithbackmutationsinthe secondpositionofeach EFhand,includingallthree independent proteinpurifications (Supplemental Figure 7);dose−response of Lan M-GCa MP to10lanthanides, includingallthreeindependent proteinpurifications (Supplemental Figure8);Lan TERN responseto Figure 2. Lan TERN responds toalltestedlanthanides. (A) Fluorescence measurements of500n MLan TERNinthepresenceof varyingconcentrations oflanthanideslistedinorderofatomicmass. Pointsanderrorbarsrepresentthemeanandstandarddeviationof threetechnicalreplicatesfromthesameproteinpurification and workingdilution. Linesrepresentalinearinterpolation between points. Graphsoftwoadditionalproteinpurifications canbefoundin Supplemental Figure8. (B)Tableofcalculated EC50valuesof Lan TERNinresponsetolanthanides. Lanthanides areshowninorder ofatomicnumber(Z). Valuesrepresentthemean ±standard deviationsofthreeindependent proteinpurifications of Lan TERN. Valuesfortheindividualproteinpurifications canbefoundin Supplemental Table1. ACSSynthetic Biology pubs. acs. org/synthbio Technical Note [URL] ACSSynth. Biol
The concentration of polysaccharide in EPS of at- there are only a few free metal ions, such as Fe3+, Fe2+, and tached cells in various growth phases decreases with the in- Cu2+ on the ore surface due to EPS bound action. It was re- crease in p H value as the following order: p H 1. 0 > 1. 5 > 2. 0 ported that Fe2 can shift from EPS phase into solution phase, > 2. 5, which is positively related to the solution acidity. but it is difficult for Fe3+ to shift from EPS phase into solu- However, there is an obvious difference, the amount of tion phase due to its hydroxylation and EPS complex action. polysaccharide in EPS of free cells in the leaching solution At the same time, small molecule H ions can move freely is closely related to the total concentration of solution in the in the EPS biofilm layer. The result is in agreement with Ref. logarithmic phase, whereas, the concentration of polysac- [19]. Zeng et al. [17] reported that the EPS concentration charide in EPS of the attached cells on ore is only related to gradually increased with the bioleaching time and reached a the p H value of the bioleaching solution in the logarithmic stable value toward the end. This was because the solution phase. It indicates that the attached cells on the ore surface p H value decreased gradually with the bioleaching time and are moderately affected by the concentration of soluble reached a stable value toward the end in this study. 18 35 (a) (b) 16 Logarithmic phaseof cells growth Adaptive phase of cells growth 25 10 20 15 10 1. 0 1. 5 2. 5 1. 0 1. 5 2. 0 2. 5 p Hvalues p Hvalues (d) 12 Deathphaseofcellsgrowth Stationary phaseof cells growth 1. 0 1. 5 2. 0 2. 5 1. 0 1. 5 2. 0 2. 5 p Hvalues p H values Fig. 3. Variation of extracellular polysaccharide content extracted from attached microorganisms with p H values: (a) adaptive phase; (b) logarithmic phase; (c) stationary phase; (d) death phase. 4. Conclusions increase in p H values, but is not related to the total concen- tration of soluble metal ions in the solution due to the EPS (1) The influence of p H values on extracellular polysac- bound action in the biofilm on the chalcopyrite surface. charides secreted by free cells in the bioleaching solution is closely related to three factors: the solution p H value, the Acknowledgements total concentration of soluble metal ions, and the ability of growth and metabolism. The optimal bacterial growth con- This work was financially supported by the National Ba- ditions are less suitable for EPS production. sic Research Priorities Programof China(No. (2) The polysaccharide concentration in EPS by attached 2010CB630903) and the National Nature Science Founda- cells is higher than that by free cells, and decreases with the tion of China (No. 31200382). 316 Int. J. Miner. Metall. Mater. , Vol. 21, No. 4, Apr. 2014 References Soc. China, 21(2011), No. 7, p. 1634. [11] C. Pogliani and E. Donati, The role of exopolymers in the bioleaching of a non-ferrous metal sulphide, J. Ind. Microbiol. [1] H. R. Watling, The bioleaching of sulphide minerals with Biotechnol. , 22(1999), p. 88. emphasis on copper sulphides: a review, Hydrometallurgy, 84(2006), No. 1-2, p. 81. [12] T. Gehrke, R. Hallmann, and W. Sand, Importance of [2] N. Pradhan, K. C. Nathsaram, K. Srinivasa Rao, L. B. Sukla, exopolymers from Thiobacillus ferrooxidans and Lepto- and B. K. Mishra, Heap bioleaching of chalcopyrite: a review, spirillum ferrooxidans for bioleaching. [in] Biohydrometal- Miner. Eng. , 21(2008), No. 5, p. 355. lurgical Processing, C. A. Jerez, T. Vargas, H. Toledo, and J. V. Wiertz, eds. , University of Chile, Santiago, 1(1995), p. 2. [3] C. Klauber, A critical review of the surface chemistry of acidic ferric sulphate dissolution of chalcopyrite with regards [13] T. Gehrke, J. Telegdi, D. Thierry, and W. Sand, Importance to hindered dissolution, Int. J. Miner. Process. , 86(2008), No. of extracellular polymeric substances from Thiobacillus fer- 1-4, p. 1. rooxidans for bioleaching, Appl. Environ. Microbiol. , [4] J. Vilcaez, R. Yamada, and C. Inoue, Effect of p H reduction 64(1998), No. 7, p. 2743. [14] K. Kinzler, T. Gehrke, J. Telegdi, and W. Sand, Bioleaching: and ferric ion addition on the leaching of chalcopyrite at thermophilic temperatures, Hydrometallurgy, 96(2009), No. a result of interfacial processes caused by extracellular poly- 1-2, p. 62. meric substances (EPS), Hydrometallurgy, 71(2003), No. 1-2, N. Hiroyoshi, H. Kitagawa, and M. Tsunekawa, Effect of so- p. 83. [5] [15] R. L. Yu, J. Liu, A. Chen, D. L. Zhong, Q. Li, W. Q. Qin, G. Z. lution composition on the optimum redox potential for chal- Qiu, and G. H. Gu, Interaction mechanism of Cu2+, Fe3+ ions copyrite leaching in sulfuric acid solutions, Hydrometallurgy, 91(2008), No. 1-4, p. 144. and extracellular polymeric substances during bioleaching chalcopyrite by Acidithiobacillus ferrooxidans ATCC2370, [6] IY. G. Wang, L. J. Su, L. J. Zhang, W. M. Zeng, J. Z. Wu, L. L. Trans. Nonferrous Met. Soc. China, 23(2013), p. 231. Wan, G. Z. Qiu, X. H. Chen, and H. B. Zhou, Bioleaching of chalcopyrite by defined mixed moderately thermophilic con- [16] R. L. Yu, Y. Ou, J. X. Tan, F. D. Wu, J. Sun, L. Miao, and D. L. Zhong, Effect of EPS on adhesion of Acidithiobacillus fer- sortium including a marine acidophilic halotolerant bacterium, Bioresour. Technol. , 121(2012), p. 348. rooxidans on chalcopyrite and pyrite mineral surfaces, Trans. [7] J. A. Brierley, Acidophilic thermophilic archaebacteria: po- Nonferrous Met. Soc. China, 21(2011), No. 2, p. 407. [17] W. M. Zeng, G. Z. Qiu, H. B. Zhou, X. D. Liu, M. Chen, W. L. tential application for metals recovery, FEMS Microbiol. Lett. , Chao, C. G. Zhang, and J. H. Peng, Characterization of ex- 75(1990), No. 2-3, p. 287. [8]E. Gomez, A. Ballester, M. L. Blazquez, and F. Gonzalez, tracellular polymeric substances extracted during the bioleaching of chalcopyrite concentrate, Hydrometallurgy, Silver-catalysed bioleaching of a chalcopyrite concentrate with mixed cultures of moderately thermophilic microorgan- 100(2010), No. 3-4, p. 177. isms, Hydrometallurgy, 51(1999), No. 1, p. 37. [18] Y. D. Karkhanis, J. Y. Zeltner, J. J. Jackson, and D. J. Carlo, A new and improved microassay to determine 2-keto-3-de- [9] W. Sand and T. Gehrke, Extracellular polymeric substances mediate bioleaching/biocorrosion via interfacial processes oxyoctonate in lipopolysaccharide of gram-negative bacteria, involving iron (Il) ions and acidophilic bacteria, Res. Micro- Anal. Biochem. , 85(1978), No. 2, p. 595. [19] R. L. Yu, J. X. Tan, G. L. Gu, Y. H. Hu, and G. Z. Qiu, Mecha- biol. , 157(2006), No. 1, p. 49. [10] R. L. Yu, D. L. Zhong, L. Miao, F
C Results after 1 week at 80 °C. High conversion is mediate. B, C Percentage of different species formed during the Click Zip process achieved even for the slower-reacting Ln" ions (≥85% from Sm" to Lu" and Y"), as a function of the metal and time. Conditions: 0. 5 m M Ph L' and 1. 0 m M Ln" salt with low amounts of side-products (red bar). The efficacy of Click Zip is low for (including " and Sc I) in 50 m M aq. MOPS/Na OH buffer (p H 7. 0) at 80 °C (except metal ions that are too large (La to Nd") or too small (Sc"), yet the corresponding for column L, where no metal was added). Analysis: HPLC with UV detection at Ph{Ln} can still be isolated (except for very labile Ph(Sc). The reaction without = 280 nm (further details in Supplementary Fig. 3). Starting purity of Ph L prior to any Ln" (column L) provides a mixture of products. Identified side-products the experiment is labelled as CONTROL (details about Ph L' stability in Supple- include Ph L-MOPS adduct (see Supplementary Fig. 4), Ca" chelate Ph Ca, and mentary Fig. 4). Identified species are colour-coded as shown in the legend, with all empty cages (1,4-cz-Ph L and 1,5-cz-Ph L'). Source data available in Supplemen- other detected species jointly shown in red. B Results after1h at 80 °C. The efficacy tary Data 2. Nature Communications \|(2024)15:9836 2 Article [URL] best described as a metal-templated Huisgen cycloaddition. Practically yields under specific optimized conditions, confirmed by X-ray analy speaking, the Click Zip process runs as one-pot reaction in fully aqu- sis (Supplementary Fig. 10). These results indicate that complexation eous solution under heating (80 °C). of a size-matched metal ion (here Na') or a specific degree of proto- nation (intramolecular hydrogen bonds) have similar templating Note on abbreviated notation effects towards 1,5-triazole formation, while the absence of metal For brevity, the following notation will be used throughout the text for templating may provide the other isomer. specific chemical species (see Supplementary Fig. 2): I (open che- Direct complexation of Ln" ions with 1,5-cz-Ph L' was unsuccess- lator); RL (L derivatized with R); [M(RL')] (open chelate of metal M ful, with no Ph{Ln} product detectable after heating to 80 °℃ for 1 week with RL'); 1,4-cz-RL' and 1,5-cz-RL' (empty cages with 1,4- and 1,5- or 6 months (Supplementary Figs. 11 and 12). Instead, formation of triazole bridge, respectively); 1,4-cz-[M(RL')] and 1,5-cz-[M(RL')] Ph{Ca} was observed, detected previously in trace amounts in reac- (Click Zip chelates with 1,4- and 1,5-triazole bridge, respectively). Unless tions with Ln" ions (Fig. 1) and synthesis of empty cages (Supple- important for isomer distinction, the most discused 1,5-cz-[M(RL)] is mentary Fig. 9), likely due to Ca" ions leaching from the glassware. This further abbreviated to R(M}. is in stark contrast to the 1,4-cz-Ph L' isomer, which provided 1,4-cz- [Ln(Ph L')] chelates by direct complexation of Ln" ions under the same Metal ion role and preferences conditions, though with mediocre yields. Lanthanide chelates of both Several observations point towards a templating rather than catalytic types thus could be accessed via different strategies (Supplemen- role of the Ln" ion in the Click Zip reaction. Firstly, the Click Zip rates tary Fig. 13). and yields strongly depend on ionic radius, increasing from La'to Lu (Fig. 1B-C, numerical values for all plots are available in Supplementary Kinetic inertness Data 2), with '" flling between Dy and Ho", confirming this trend. The kinetic inertness of the chelates was tested by acid-assisted Secondly, using excess metal expediates the complexation, but the dechelation under pseudo-first-order conditions with excess HCl, unchelated metal does not promote intermolecular triazole cross- quantitatively monitored by LC-MS and expressed as half-lives. linking. Thirdly, the purity, yield, and reaction rate of Click Zip are Chelates of a DOTA derivative [Ln(NO2Bn DOTA)], amenable to LC- remarkably independent of concentration (5 μM-50 m M), with devia- MS detection, served as a reference34. Four increasingly demanding tions notable only at the extreme limits (Supplementary Fig. 5). conditions from 0. 1 M HCI at 25 °C to 6. 0 M HCl at 80 °C were used to Overall, these results indicate that the chelated metal ion exerts cover a broad range of half-lives. This revealed an increase in inert- indirect steric effects through coordination of the pyridines rather ness across the series of Ph{Ln} chelates, spanning 10 orders of than participating directly in the azide-alkyne cycloaddition. It is worth magnitude from La to Lu (Fig. 2A). Starting from Sm, Ph{Ln} sur- noting that, for lanthanides from the end of the series, the efficacy and passed inertness of the DOTA system, steadily improving up to Lu purity of the Click Zip reaction is easily amenable to upscaling (Sup- (Supplementary Figs. 14-18). Ph{Lu} showed very high resistance to plementary Fig. 6). dechelation even under the harshest conditions (Fig. 2B). With an estimated half-life of 3 years in 6. 0 M HCl at 80 °C, this system 1,4-/1,5-Triazole selectivity exhibits greater inertness than other lanthanide chelates previously The surprising regioselectivity of Click Zip towards 1,5-triazole pro- reported as highly inert27-29. In contrast, the isomeric 1,4-cz ducts regardless of the Ln" choice and ligand derivatizations (Sup- [Ln(Ph L')] chelates were much less kinetically inert, approximately 2 plementary Fig. 3) prompted investigation with computational orders of magnitude worse than the DOTA system. Inertness of chemistry methods. The largest La", smallest Lu", and selected non- selected Ph{Ln} chelates (Ln = Eu, Ho, Lu) was also tested under lanthanides (Ca", Li', Na', K) were compared in terms of the calculated transmetallation conditions with Zn" and Cu" ions (Supplementary Gibbs free energies of their open intermediate [M(L')] and bridged 1,5- Fig. 19). No reaction with Zn" and only a few percent of Cu chelate cz-[M(L')] and 1,4-cz-[M(L')] products. For all these metals there was a were observed after 1 week at 80 °C with 10-fold excess of these clear thermodynamic drive to both products, as expected for Huisgen metals, further confirming high inertness of the chelates even cycloaddition. The 1,5-isomer was favoured in all cases, except for the towards this mechanism of dechelation. large La" and K' ions (Supplementary Figs. 7 and 8). However, experi- mental results proved that even La" provided exclusively the 1,5-iso- Solid-state structures, isostructurality, isomerism mer (Fig. 1). This discrepancy was explained by considering the The striking differences in properties between the 1,5-triazole- and 1,4- reaction mechanism and kinetics. The transition state leading to the triazole-bridged chelates are best understood from their solid-state 1,5-triazole product was significantly lower in energy and therefore structures (Fig. 3). In the case of Ph{Lu}, the 1,5-triazole is part of an 18- kinetically preferred in both La" and Lu", in agreement with the membered ring, where all five donor N-atoms (three from cyclen, two experimental results. The reason seems to be partial de-coordination from pyridines) can coordinate tightly to the Lu" ion. On the other of the pyridines required for both transition states, which is more hand, the 1,4-triazole in 1,4-cz-[Lu(Ph L')] chelate increases the size of pronounced and energetically demanding for the 1,4-isomer (Supple- this ring to 19 atoms, bringing steric strain and chain conformations mentary Figs. 7 and 8, Supplementary Data 3). The peculiar case of that disfavour simultaneous coordination of both pyridines. This alkaline metals will be discussed next. mismatch explains why the 1,4-cz-[Ln(Ph L')] chelates are not pro- duced via the Click Zip reaction and are much less inert
/ Chemical Geology 217 (2005) 147-169 Table 7 concentration investigated in this study, a single Estimates of n obtained from the chloride dependence of the straight line was sufficient to fit the data (except for solubility data Nd at 150 C, where the data show significant scatter), Ln PO4 T (C) n implying a relatively constant value of n. Because the La PO4 23 0. 350. 08 ionic strength was not held constant as chloride 50 0. 830. 21 concentration was varied, the values of n given in Nd PO4 23 0. 240. 02 Table 7 include the non-specific effects of ionic 50 0. 630. 09 strength (i. e. , activity coefficients) in addition to the 150 2. 21. 9 23 Sm PO4 0. 480. 25 formation of chloride complexes. In the case of 50 0. 380. 31 reaction (3), increased ionic strength should favor YPO4 23 0. 410. 25 increased solubility from activity coefficient effects 50 0. 630. 26 alone. Thus, the values of n given in Table 7 overestimate the degree of complexation of the REE by chloride. calculated errors on the n values represent the standard error of the slope given by regression. Nevertheless, taking all these issues into account, analysis, and do not include errors resulting from the values of n for all the REE at 23 C indicate that the variation in ionic strength. In general, the value of the predominant species for all the REE investigated is the uncomplexed ion Ln3+, with a possible small n will not be constant as a function of chloride contribution from the first chloride complex Ln C12+. concentration if stepwise complexation occurs; it should increase with chloride concentration as the The fact that n appears to be constant (i. e. , a straight number of chloride ions bound to the Ln3+ ion. line fits the data well) suggests that the contribution of Ln Cl2+ is indeed very minor, and that the apparent increases. However, over the range of chloride teapparel T = 23C T=23C n = 0. 240. 02 n =0. 350. 08 Iog m H,PO4 Iog m H,PO4 5 4 -5 -6 I + PNw f l + c"u 6o\| / b) a) 8 -1. 0 -0. 5 0. 0 0. 5 1. 0 -1. 5 -0. 5 0. 0 0. 5 1. 0 -1. 5 -1. 0 Iog mc I log mc I 3 6 T = 23C T = 23C log m H,PO4 n =0. 480. 25 n = 0. 410. 25 f'Od`Hu 60I +^u f 4 -8 O -5 msm + Ic O 9 O O O -6 60 60\| -10 d) c) 11 -1. 5 -1. 0 -0. 5 0. 5 1. 0 -1. 5 -1. 0 -0. 5 0. 5 1. 0 0. 0 0. 0 log mc I Iog mc I Fig. 5. Representative plots of (logm1n+logmh,po. ) vs. logmci at 23 C for: (a) La; (b) Nd; (c) Sm; and (d) Y. These plots yield estimates of the value of n in Eq. (15) 163 Z. S. Cetiner et al. / Chemical Geology 217 (2005) 147-169 increase in solubility with chloride concentration at 23 by chloride in our experiments is relatively small. especially as the chloride concentration decreases. C may be a result of activity coefficient effects alone At 50 C, the values of n tend to increase, but they We carried out one final set of calculations to remain less than 1. 0. This possibly indicates an investigate the effect of chloride complexation on the increased proportion of Ln Cl2+, consistent with the. solubility of REE phosphates over the range of expected increase in stability of the chloride com- temperatures investigated in this work. Using the. plexes with increasing temperature. Nevertheless, the values of Ks3 for Nd PO4 at infinite dilution deter- Ln3+ ion still probably represents a significant. mined in this study, the stability constants determined proportion of the REE, especially at the lower. by Gammons et al. (1996) for Nd(IIl)-chloride chloride concentrations. The value of n for Nd at complexes, the Helgeson b equation for activity corrections, and the p H, total chloride, and H,PO4 150 C is significantly larger than at the lower. temperatures, but the uncertainty of this estimate is concentrations of our experiments, we calculated a quite large. Moreover, the data are not well fit by a theoretical concentration of Nd in each of our simple straight line when plotted as (logmin+. experimental solutions assuming equilibrium with log mh,po. ) vs. logmecr. There may be a problem. Nd PO4. These values are compared with the actual measured values in Table 8. It should be noted that with the measured phosphate concentrations for the ernr rrnne nnee ar ernnanne ee aae ee rrennnnner very similar results are obtained if the Nd(III) stability two orders of magnitude, whereas the Nd concen- constants of Migdisov and Williams-Jones (2002) are trations range over less than one order of magnitude used. This similarity is expected because the two sets of stability constants are in very good agreement. over the range of chloride concentrations investigated. At 25 C and 50 C, the calculated and measured Moreover, the Nd concentrations increase systemati- concentrations of Nd agree satisfactorily, given the cally with increasing chloride concentration, but the Cally una PDNIIOSI ee Satlslactonny, givenl the possible sources of error, even at the higher total. phosphate concentrations vary non-systematically (Table 3). It appears as although the phosphate chloride concentrations. The maximum deviation is a factor of three, with the measured values generally, concentrations for the 0. 1- and 1. 0-m experiments may be too high. The value of n depends on the but not always, greater than the calculated values. It is phosphate concentration as implied by Eq. (15), so also clear from these calculations that, at 25 C and 50 C, chloride complexes represent less (and in most any errors in the determination of phosphate concen-. tration would contribute to errors in the estimation of cases much less) than 50% of the total REE n. The results of Gammons et al. (1996) suggest that concentration. The abovementioned possible error in total measured phosphate concentration may account the average value of n between 0. 1 and 1. 0 mol kg chloride should be between 0 and 1. 0 at 150 C. Thus, for the much poorer agreement between calculated even at 150 C, the degree of complexation of Nd3+ and measured Nd concentrations at 150 C. A Table 8 Comparison of calculated and measured solubilities of Nd PO4(s) Temperature M Na C1 p Hm m Nd3+ m Nd Cl m Nd MH,PO9 m Nd Cl2+ m Nd measured calculated calculated calculated calculated 25 0. 1 1. 05 6. 98E-04 2. 42E-04 8. 11E-06 2. 50E-04 4. 05E04 8. 65E-04 0. 5 1. 05 3. 22E-05 3. 34E-04 3. 66E-04 4. 95E04 5. 05E-04 8. 61E-04 4. 36E-04 1 1. 05 6. 92E05 5. 37E04 5 1. 15 1. 07E-03 5. 00E-04 3. 62E04 8. 62E-04 6. 07E04 50 0. 1 1. 05 2. 17E-04 1. 24E-04 5. 56E06 1. 29E-04 2. 18E-04 1. 05 4. 13E-04 1 1. 49E-04 3. 09E05 1. 79E-04 3. 47E-04 8. 53E-04 5 1. 15 1. 02E-04 2. 09E-04 1. 07E04 6. 16E-04 150 0. 1 1. 05 1. 27E-05 2. 23E06 9. 03E-07 1. 74E-08 3. 15E-06 9. 96E07 7. 05E-07 0. 5 1. 05 4. 53E-06 1. 21E-05 1. 22E-05 2. 49E-05 2. 04E-06 1. 05 1. 89E-08 3. 37E-07 1 6. 05E-04 1. 24E-07 1. 95E-07 6. 28E-06 See text for details. 164 Z. S. Cetiner et al. / Chemical Geology 217 (2005) 147-169 potential problem with the measured total phosphate chloride concentration on the solubility of Nd phosphate at temperatures up to 300 C, using concentration is also indicated by the fact that, whereas the measured Nd concentration increases currently available thermodynamic data. In the previous paragraphs of this section, we have steadily with increasing chloride concentration, the provided a number of lines of evidence to suggest calculated Nd concentration increases from 0. 1 to 0. 5 that, at the temperatures and chloride concentrations m chloride, but then drops to a much lower value at 1. 0 m chloride
6H,O Method/Apparatus/Procedure: at all temperatures; its density was determined to be Isothermal method with analysis of the saturated solutions was used. The components were equilibrated in glass containers with continuous stirring 2. 491 g cm-3 and molar volume 149. 8 cm. mol-1 at an un- in a cryostat for 10-12 d. Weighed samples of the saturated solutions. specified temperature. were withdrawn with a syringe and analyzed for Tb content by titration with EDTA solution. The reported solubility values are mean results of Auxiliary Information. repeated measurements. Method/Apparatus/Procedure: Source and Purity of Materials: Isothermal method with chemical analysis of the equilibrium phases was Tb Cl, - 6H,O was prepared by dissolution of the corresponding oxide used. The components were equilibrated for 3-10 d in a thermostat with (99. 9+% pure) in HCl solution (of special purity). The product was twice continuous agitation of the mixtures. At low temperatures, equilibrium recrystallized from HCl solution and then from water. It was air dried at was reached within 6-8 d. Content of Tb in the separated phases was 30 C and analyzed for Tb and Cl contents. determined by titration with EDTA solution using xylenol orange indicator. The determinations were repeated five to ten times. Densities of. Estimated Error: indicator. The determinations were repeated five to ten times. Densities of Estimated Error: the solutions as well as of the solid hexahydrate were determined with a Solubility: precision of 2%. pycnometer. The hexahydrate density was measured by means of Temperature: precision of 0. 5 K. anhydrous toluene. Source and Purity of Materials: Original Measurements: Components: Tb Cl-6HO was prepared by dissolution of the corresponding oxide 36N. P. Sokolova, Zh. Neorg. (1) Terbium chloride; Tb Cl3; (99. 9+% pure) in HCl solution (of special purity). The reaction product [10042-88-3] Khim. 28, 782 (1983). was twice recrystallized from HCl solution and then from water. The (2) Water; H,O; [7732-18-5] crystals were dried in air at 30 C. The salt composition was checked: Tb by complexometric titration and Cl by the method of Volhard. Water Variables: Prepared by: content was found by difference. Composition: 0-68 mass % T. Mioduski and C. Guminski Tb Cl3 Estimated Error: Solubility: nothing specified. Temperature: precision of 0. 1 and 1 K at 0 C. Experimental Values Density: precision of 0. 003 g cm-3. Melting temperatures of Tb Cl,-HO mixtures as read from a figure and recalculated to molalities and mole fractions by the compilers Components: Original Measurements: 19A. V. Nikolaev, A. A. Sorokina, (1) Terbium chloride; Tb Cl3; 100w1 t/C Equilibrium solid phase m x1 N. P. Sokolova, G. S. [10042-88-3] H,O(s) (2) Water; H,O; [7732-18-5] Kotlyar-Shapirov, and L. I. 0. 0110 14. 2 0. 62 9- Bagryantseva, Izv. Sibir. Otd. 25. 3 1. 28 -16 0. 0225 H,O(s) Akad. Nauk SSSR, Ser. Khim. 34. 3 0. 0343 -31 H,O(s) 1. 97 Nauk (1), 46 (1978). 42. 5 0. 0479 2. 79 -48 H,O(s) +Tb Cl; 15HO 45. 5 3. 15 0. 0537 28 Tb Cl 15H,O+Tb Cl9H,O Variables: Prepared by: 47 3. 34 0. 0568 -20 Tb Cl, 9H,O+Tb Cl, -6H,O Temperature: 258-268 K T. Mioduski and C. Guminski 0. 0580 47. 6 3. 42 -11 Tb Clz -6HO Because eutectic thermal arrests were observed also in the field between Tb Cl 15H,O phase diagram and Tb Cl,. 9H,O, it is possible that an extra transformation of Tb Cl: 15H,O occurs at a temperature similar to the eutectic temperature. J. Phys. Chem. Ref. Data, Vol. 38, No. 4, 2009 s at: [URL] and permissions Downloaded 11 Sep MIODUSKI. GUMINSKI. AND ZENG 956 Auxiliary Information Composition of saturated solutions in the ternary Tb Clz-C,H,NO HCl-H,O system at 25 and 50 C Method/Apparatus/Procedure: Differential thermal analysis between -120 C and room temperature was ma t/C ma Equilibrium solid phaseb 100w1 100w2 performed. According to the earlier paper,109 the samples were prepared in 38. 0 4. 77 32. 0 10. 9 B+C sealed glass ampoules. The heating rate was 0. 2-0. 5 K min-'. The heating 37. 5 4. 22 29. 0 8. 88 c curves were recorded with a chromel/copel thermocouple. 39. 0 3. 68 21. 0 5. 38 c Source and Purity of Materials:d 43. 0 3. 60 12. 0 2. 73 c As in Ref. 109, Tb Cl-6HO was prepared by dissolution of the 50. 5 3. 85 0 0 c corresponding oxide (99. 9% pure) in excess of HCl solution. The product was twice recrystallized from HCl solution (very pure) and finally from amolalities calculated by the compilers water. b A=C,H,NO HCl; B=Tb Cl, 3C,H,NO 3HCl-5H,O; C=Tb Cl6H,O Estimated Error: The compound B was found to be congruently soluble. Its Solubility: nothing specified; reading-out procedure of +0. 5 mass %. Temperature: nothing specified; reading-out procedure of 0. 5 K. solubility was determined to be 83. 3 and 86. 1 mass % at 25 and 50 C, respectively. The melting points of the com- pounds A, B, and C were found to be 70, 60, and 155 C, 3. 3. Tb Cl3-Organic Compound-H,O Systems respectively. Auxiliary Information Original Measurements: Components: 65E. F. Zhuravlev, R. K. (1) Terbium chloride; Tb Cl3; Method/Apparatus/Procedure: Gaifutdinova, and Kh. G. [10042-88-3] The method of isothermal sections of the phase diagram with (2) Ethanolamine hydrochloride;. Zainullina, Zh. Neorg. Khim. 26 refractometric analysis of the solutions was used. Known amounts of the 2-aminoethanol 1651 (1981). components were equilibrated until refractive indices of the liquid phases hydrochloride; C,H,NO HCl; were constant. Compositions of the saturated solutions and the [2002-24-6] corresponding solid phases were found from inflection points on plots of (3) Water; H,O; [7732-18-5] the refractive index versus composition. The refractive indices were measured in a thermostated refractometer. Composition of the double salt Variables: Prepared by: B was confirmed by chemical analysis for contents of N, Cl, C, H, and Tb T. Mioduski and C. Guminski. Composition of mixtures (Tb by the oxalate method and by complexometric titration). Thermal Temperature: 298 and 323 K analysis of the compounds was carried out with the use of a Kurnakov. pyrometer. Experimental Values Source and Purity of Materials:. Composition of saturated solutions in the ternary Tb Cl, 6H,O was prepared by dissolution of the corresponding oxide. Tb Clz-C,H,NO HCl-H,O system at 25 and 50 C (chemically pure) in HCl solution (chemically pure). Analysis of the crystal product for Cl content confirmed the formula of the hexahydrate. ma 100w 100w2 Equilibrium solid phaseb m2a t/C C,H,NO-HCl was prepared by neutralization of the amine with HCl solution. The resulting solution was evaporated and the crystals. 30. 0 25 0 0 74. 5 A recrystallized. 0. 68 70. 5 28. 9 4. 5 A Estimated Error: 29. 0 66. 5 A 10. 0 1. 60 Solubility: nothing specified. 14. 5 2. 48 63. 5 29. 6 A Temperature: precision in thermal analysis of 5 K. 22. 0 4. 61 60. 0 34. 2 A+B 23. 0 58. 0 4. 56 31. 3 B 27. 0 4. 07 48. 0 19. 7 B 28. 0 46. 0 22. 5 B 5. 03 Components: Original Measurements: 31E. F. Zhuravlev, R. K. 31. 0 4. 17 41. 0 15. 0 B (1) Terbium chloride; Tb Cl3; Gaifutdinova, D
, 1999. Modeling of Diffusion in a Micro -Cracked Composite Laminate Using Approximate Solutions. Journal of Composite Materials 33, 872 -905. Ilankoon, I. M. S. K. , Neethling, S. J. , 2016. Liquid spread mechanisms in packed beds and heaps. The separation of length and time scales due to particle porosity. Miner als Engineering 86, 130 -139. Bailey, A. D. , Hansford, G. S. , 1993. Factors affecting bio ‐oxidation of sulfide minerals at high concentrations of solids: A review. Biotechnology and Bioengineering 42, 1164 -1174. Journal Pre-proof Journal Pre-proof Wong, J. W. C. , Xiang, L. , Chan, L. C. , 2002. p H Requirement for the Bioleaching of Heavy Metals from Anaerobically Digested Wastewater Sludge. Water, Air, and Soil Pollution 138, 25 -35. Yin, W. Z. , Tang, Y. , Ma, Y. Q. , Zuo, W. R. , Yao, J. , 2017. Comparison of sample properties and leaching characteristics of gold ore from jaw crusher and HPGR. Minerals Engineering 111, 140 -147. Journal Pre-proof Journal Pre-proof Highlights  Ore particles of the same size fraction but with different number of micro -cracks were prepared.  The influence of micro -cracks on the activities of bacteria was investigated.  An improve d approach to extract copper from low -grade copper ores by bioleaching was reported. Journal Pre-proof Journal Pre-proof
Coupling between IX, in which the oxygen level is brought back to light transfer and growth kinetics. Biotechnol. Bioeng. 40, non limiting conditions (40%). In this case, com- 817-825. partment II recovers complete nitrification per- Cornet, J. F. , Dussap, C. G. , Cluzel, P. , Dubertet, G. , 1992b. A structured model for simulation of cultures of the cyano- formance, and nitrite concentration decreases at bacterium Spirulina platensis in photobioreactors: II. Iden- the outlet of compartment IVa, following precisely tification of kinetic parameters under light and mineral the wash-out curve. limitations. Biotechnol. Bioeng. 40, 826N-834N. 330 F. Godia et al. I Journal of Biotechnology 99(2002） 319-330 Cornet, J. F. , Dussap, C. G. , Gros, J. B. , 1998. Kinetics and spectives. Proceedings of the 30th International Conference energetics of photosynthetic micro-organisms in photobio- on Environmental Systems, Toulouse, France. reactors. Adv. Biochem. Eng. /Biotechnol. 59, 153-224. Mergeay, M. , Verstraete, W. , Dubertret, G. , Lefort-tran, M. , Eckart, P. , 1994. Life Support and Biospheric. Herbert Utz Chipaux, C. , Binot, R. , 1988. MELISSA. A microorganisms Publisher, Munchen, Germany. based model for CELSS development. Proceedings of the Fulget, N. , Poughon, L. , Richalet, J. , Lasseur, C. h. , 1999. 3rd symposium on space thermal control and life support MELISSA: global control strategy of the artificial ecosys- systems. Noordwijk, The Netherlands. tem by using first principles models of the compartments. Nogueira, R. , Lazarova, V. , Manem, J. , Melo, L. F. , 1998. Adv. Space Res. 24, 397-405. Influence of dissolved oxygen on the nitrification kinetics in Gustavino, S. R. , Fadden, C. D. , Davenport, R. J. , 1994. Con- a circulating bed biofilm reactor. Bioprocess Eng. 19, 441- cepts for advanced waste water processing systems. Pro- 449. Tamponet, C. , Savage, C. , Amblard, P. , Laserre, J. C. , Per- ceedings of the 24th International Conference on sonne, J. C. , Germain, J. C. , 1999. Water recovery in space. Environmental Systems, Friedrichshafen, Germany. Society of Automotive Engineering Technical paper 941500. ESA Bul1. 97,56-60. Tamponnet, C. , Savage, C. , 1994. Closed ecological systems. J. Hendrikus, J. , Laambroek, H. J. , Gerards, S. , 1993. Competi- Biol. Educ. 28, 167-173. tion for limiting amounts of oxygen between Nitrosomonas Vernerey, A. , Albiol, J. , Lasseur, C. , Godia, F. , 2001. Scale-up europaea and Nitrobacter winogradsky grown in mixed and design of a pilot-plant photobioreactor for the con- cultures. Microbiology 159, 453-459. tinuous culture of Spirulina platensis. Biotechnol. Progr. 17, Joo, S. -H. , Kim, D. -J. , Yoo, I. -K. , Park, K. , Cha, G. -C. , 2000. 431-438. Partial nitrification in an upflow biological aerated filter by Vrati, S. , 1984. Single cell protein production by photosynthetic O2 limitation. Biotechnol. Lett. 22, 937-940. bacteria grown on the clarified effluents of a biogas plant. Lasseur, C. , Dixon, M. , Dubertret, G. , Dussap, G. , Godia, F. , Appl. Microbiol. Biotechnol. 19, 199-202. Gros, J. B. , Mergeay, M. , Richalet, J. , Verstraete, W. , 2000. Wijffels, R. H. , Tramper, J. , 1995. Nitrification by immobilized MELISSA: 10 years of research, results, status and per- cells. Enzyme Microb. Technol. 17, 482-492
a thiol-molecule/Cd²+ ratio of 2 at 100 μM or higher external Cd Cl, concentrations, physiological p H should suffice for complete the thiol-molecules/cadmiumacumulated ratio is <2, metal ion inactivation. However, at neutral p H indicating insufficient Cd2+ binding by thiol-mol- the Cd-2PC2 is also formed (approximately 30% ecules; since this is not accompanied by marked of total metal complexes), in which three cell toxicity, it is expected that other chelating (Fig. 6. 1c) or four thiol groups (Fig. 6. 1d) coordi- molecules and mechanisms are involved in Cd2+ nate the metal ion; at p H higher than 7 this last neutralization. complex prevails, and hence the thiol-molecule/ The cadmium accumulation in E. gracilis is cadmium ratio could also be 4 for reaching com- 33 times higher than in the green microalgae plete metal ion inactivation. Chlamydomonasacidophila and Chlamydomonas On the other hand, the intracellular zinc content reinhardtii (Garcia-Garcia et al. 2012; Mendoza- reaches a maximum of approximately 240- Cozatl et al. 2002, 2006a; Nishikawa et al. 2006; 320 nmol/10’ cells in E. gracilis cultured with Santiago-Martinez et al. 2015). This ability makes 300-1000 μM Zn Cl, for at least ten cell genera- E. gracilis a Cd-hyperaccumulator microorganism tions (i. e. , two subcultures); higher external Zn Cl2 because its cadmium accumulation capacity concentrations do not lead to greater intracellular (1. 1-4. 4 mg or 9. 5-39 μmoles/g DW (Garcia- zinc levels. At 300-400 μM Zn Cl2, the thiol-mole- Garcia et al. 2012; Mendoza-C6zatl et al. 2002. cule/zincacumulaed ratio is 0. 2, clearly indicating 2006a; Santiago-Martinez et al. 2015)) exceeds insufficient formation of thiol-molecules for han- the respective standard reference for cadmium in dling Zn. + stress. However, these elevated intra- Cd-hyperaccumulator plants (0. 1 mg/g DW) cellular zinc levels do not affect cell functions (Ali et al. 2013; Bhargava et al. 2012). (Sanchez-Thomas et al. 2016). E. gracilis can also It is worth recalling that for binding and full be considered as a Zn-hyperaccumulator microor- inactivation of Cd. +, four interacting electronega- ganism because its zinc accumulation capacity tive groups are required (Belcastro et al. 2009). reaches 2. 2-3 mg (34. 7-46. 1 μmoles) zinc/g DW At physiological GSH concentrations and p H, (Sanchez-Thomas et al. 2016), which is close to Cd2+ spontaneously, rapidly and predominantly the standard reference concentration for Zn. + in forms Cd-bis-glutathionate (GS-Cd-GS or Zn-hyperaccumulator plants (3. 0 mg zinc/g DW; Cd-GS2; Fig. 6. 1a), in which a tetrahedral coordi- Ali et al. 2013). Fig. 6. 1 Molecular interactions of GSH and phytoche- bond between Cys2 and Gly and the carboxylate group latin 2 (PC2) with Cd2+. (a) The predominant complex from Gly. (c) In the presence of higher amounts of PC2, formed between GSH and Cd’+ is constituted by two GSH Cd2+ is bound by the two thiol groups from Cys, and Cys2 molecules and one Cd. + ion. The two thiol groups and two and the carboxylate group of Gly of one PC2 molecule, water molecules establish the interaction with the divalent and one thiol group of a second PC2. (d) Another stable metal ion (Delalande et al. 2010). (b) At equimolar con- structure is the interaction of Cd2+ with the four thiol centrations, and neutral p H, Cd2+ is bound by two thiol groups of two PC2 molecules at p H > 7. Structures were groups from Cysi and Cys2, which upon binding release depicted using the physicochemical analysis described by their hydrogens as H+, and by two oxygens from the peptide Dorcak and Krezel (2003) Biochemistry and Physiology of Heavy Metal Resistance and Accumulation in Euglena 99 A NH3 Glu1 Cys1 Glu2 Cys2 Gly COO D NH3 Co O- 100 R. Moreno-Sanchez et al. In summary, the ability of E. gracilis to accu- glycine metabolism (Mendoza-Cozatl et al. mulate heavy metals depends at least partially on 2005). The sulfur assimilation pathway synthe- the formation of complexes with Cys, GSH, and sizes Cys, which is a precursor for methionine, phytochelatins in a thiol-molecule/metal ratio of GSH and protein syntheses (Koprivova and at least 2; and their subsequent compartmental- Kopriva 2014; Zheng et al. 2015). Plasma mem- ized into chloroplasts (Mendoza-Cozatl et al. brane sulfate transporters catalyze the first reac- 2006b) and probably mitochondria (Avilés et al. tion in the sulfur assimilation pathway. 2003), as E. gracilis lacks typical plant-like vacu- oles (Rocchetta et al. 2006; Sittenfeld et al. 2002; Sulfate transporters. The plasma membrane sulfate Sommer and Blum 1965). The stoichiometry for transporters are classified by their substrate affin- heavy metal complexation with sulfide is one, ity as high affinity sulfate transporters with Km resulting in the formation of insoluble salts (Cd S values for sulfate <100 μM, and low affinity sulfate and Zn S solubilities in water are 0. 13 andt transporters with Km values >100 μM (Garcia- 0. 6 mg/100 m L, respectively). Sulfide can also be Garcia et al. 2016; Mendoza-Cozatl et al. 2005). synthesized by E. gracilis (see Sect. 6. 3. 2. 2). The plasma membrane sulfate transporter activi- Therefore, these features place E. gracilis as one ties are perturbed by ionophores in E. gracilis, C. of the best candidates to be applied in the biore-reinhardti and Chlorella ellipsoidea (Garcia- mediation of water bodies polluted with Cd. + and Garcia et al. 2012; Matsuda and Colman 1995; Zn2+. When the thiol-molecule/metal ratio cannot Yildiz et al. 1994), because the uptake reaction is reach a value of 2 (i. e. , at high heavy metal con- an electrogenic process (co-transport of 3 H+ and centrations), E. gracilis may still exhibit signifi- 1 sulfate molecule; Fig. 6. 2) in which the H+ cant cell growth. Thus, other intracellular gradient is generated by a plasma membrane H+- mechanisms of metal inactivation and accumula- ATPase activity. Oxidative phosphorylation tion most likely become involved such as the seems the main contributor to ATP supply for transcriptional and biochemical activation of the sulfate uptake in C. reinhardti, C. ellipsoidea, E. polyphosphates (Poly P) and organic acid biosyn- gracilis and Rhodella maculata; while the photo- theses (see Sects. 6. 3. 3 and 6. 3. 4). synthesis inhibitor 3-(3,4-dichlorophenyl)-1,1- dimethylurea partially disrupts the sulfate uptake 6. 3. 2. 2 Sulfur Assimilation Pathway in E. gracilis and R. maculata (Garcia-Garcia The backbone of the phytochelatins metabolism et al. 2012; Matsuda and Colman 1995; Millard (Fig. 6. 2) comprises the sulfur assimilation path- and Evans 1982; Yildiz et al. 1994). way (SAP; from extracellular sulfate to Cys), The plasma membrane sulfate transport has GSH biosynthesis, phytochelatins biosynthesis been considered a control step of Cys synthesis and Cd-phytochelatin complexes formation, because the transporter activities are significantly transport and storage into vacuoles in plants and lower than those of all other enzymes of the sul- yeasts, and into chloroplasts and mitochondria in fur assimilation pathway, and GSH and phyto- E. gracilis as this protist does not have typical chelatins syntheses (Table 6. 3); thus, several vacuoles but it has minivacuoles (Rocchetta et al. groups have focused on studying their regulation 2006; Sittenfeld et al. 2002; Sommer and Blum mechanisms. For instance, under sulfate defi- 1965). Because phytochelatins metabolism con-( ciency, the high-affinity plasma membrane sul- sumes ATP and NADPH (eight high-energy fate transporters increase their activity in the bonds and eight NADPH molecules are used to green microalgae C. reinhardti (Yildiz et al. synthesize one PC2 molecule from sulfate, gluta- 1994) and C
2013;41:D636-47. 35 [31] Meyer BH, Zolghadr B, Peyfoon E, Pabst M, Panico M, Morris HR, et al. [43] Yarzabal A, Brasseur G, Ratouchniak J, Lund K, Lemesle-Meunier D, 76 36 Sulfoquinovose synthase - an important enzyme in the N-glycosylation De Moss JA, et al. The high-molecular-weight cytochrome c Cyc2 of 77 37 pathway of Sulfolobus acidocaldarius. Mol Microbiol 2011;82:1150-63. Acidithiobacillus ferrooxidans is an outer membrane protein. J Bacteriol 78 38 [32] Okibe N, Gericke M, Hallberg KB, Johnson DB. Enumeration and 2002;184:313-7. 79 39 characterization of acidophilic microorganisms isolated from a pilot 80 40 81 41 82 Please cite this article in press as: Talla E, et al. , Insights into the pathways of iron- and sulphur-oxidation, and biofilm formation from the chemolithotrophic acidophile Acidithiobacillus ferrivorans CF27, Research in Microbiology (2014), [URL]
Garbometer: A methodology for comprehensive evaluation of municipal solid waste management systems. Proceedings of ISWA World Congress 2013, 7-11 October, Vienna, Austria. Vienna: International Solid Waste Association (ISWA). Polaz, C. N. M. & B. A. N. Teixeira (2009). Indicadores de sustentabilidade para a gestão municipal de resíduos sólidos urbanos: Um estudo para São Carlos [Indicators of sustainability for municipal solid waste management: Case study of the city of São Carlos]. In Portuguese. Engenharia Sanitaria e Ambiental, 14(3), 411-420. Regions4Recycling (2014). Regions for Recycling: R4R Toolkit and Methodology. [URL] eu/R4R_toolkit/R4R_methodology Romualdo J. C. (2014). Development and testing of an indicator set to benchmark the performance of a national hazardous waste management system (MSc thesis). Imperial College London. Ronconi, M. (2001). The Development of Waste Indicators at European Union Level: Some Recent Eurostat Experiences. Working paper 29 to a joint ECE/ Eurostat Work Session on Methodological Issues in Waste Statistics. Statistical Commission and Econonmic Commission for Europe (ECE), Commission of the European Communities, Conference of European Statisticians and Eurostat. [URL] SWEEPNet (2014). Challenges and Opportunities for Solid Waste Management in the Mashreq and Maghreb Region. Sweepnet - The Regional Solid Waste Exchange of Information and Expertise network in Mashreq and Maghreb countries. [URL] UNSD (United Nations Statistics Division). (2013). Framework for the Development of Environment Statistics 2013. [URL] Wilson, D. C. , L. Rodic, M. J. Cowing et al. (2015). ‘Wasteaware’ benchmark indicators for integrated sustainable waste management in cities. Waste Management, 35 (1), 329-343. doi:10. 1016/j. wasman. 2014. 10. 006 Wilts, H. (2012). National waste prevention programs: Indicators on progress and barriers. Waste Management & Research, 30((9) Supplement), 29-35. Zaman, A. U. & S. Lehmann (2013). The zero waste index: A performance measurement tool for waste management systems in a ‘zero waste city’. Journal of Cleaner Production, 50, 123-132. Materials flow analysis Baccini, P. & P. H. Brunner (2012). Metabolism of the Anthroposhere - Analysis, Evaluation, Design. 2nd Edition. Cambridge, Massachusetts, U. S. : The MIT Press. Bringezu, S. (1997). Material flow indicators. In Moldan, B. and S. Billharz (Eds. ) Sustainability indicators. New York: John Wiley & Sons Ltd. , 168-176. Cleveland, C. J. & M. Ruth (1998). Indicators of Dematerialization and the Materials Intensity of Use. ” Journal of Industrial Ecology 2(3), 15-50. Hinterberger, F. , E. Luks & F. Schmidt-Bleek (1997). Material flows vs. “natural capital”: What makes an economy sustainable. Ecological Economics (23), 1-14. Loppolo, G. , R. Heijungs, S. Cucurachi et al. (2014). Urban Metabolism: Many Open Questions for Future Answers. In Salomone, R. & G. Saija (Eds. ) Pathways to Environmental Sustainability, Springer, 23-32. Pincetl, S. , P. Bunje & T. Holmes (2012). An expanded urban metabolism method: Toward a systems approach for assessing urban energy processes and causes. Landscape and Urban Planning, 193-202. Schmidt-Bleek, F. (1994). Revolution in resource productivity for a sustainable economy - a new research agenda. Fresenius Environmental Bulletin (2): 245-490. UNEP and CSIRO (2011). Resource Efficiency: Economics and Outlook for Asia and the Pacific. [URL] unep. org/publications/pmtdocuments//pdf/Resource_Efficiency_EOAP_web. pdf. UNEP and CSIRO (2013). Recent Trends in Material Flows and Resource Productivity in Asia and the Pacific. [URL] Global Waste Management Outlook West, J. , H. Schandl & S. Heyenga (2013). Resource Efficiency: Economics and Outlook for China. UNEP , CSIRO and IPM. ISBN 13:9789280733181. [URL] Chinese_2013. pdf Topic sheets Waste prevention Brook Lyndhurst for DEFRA (2009). WR1204 Household Waste Prevention Evidence Review: L1m1 – Executive Report. A report for Defra’s Waste and Resources Evidence Programme. Cox, J. , S. Giorgi, V. Sharp et al. (2010). Household waste prevention - A review of evidence, Waste Management and Research, 28(3): 193-219. EEA (European Environment Agency). (2013b). Waste prevention in Europe - the status in 2013, EEA Report No 9/2014. [URL] Sabogal, N. (2013). Cartagena Declaration on the Prevention, Minimization and Recovery of Hazardous Wastes and Other Wastes, Proceedings of the Eighth International Conference on Waste Management and Technology, Towards Ecological Civilization, Shanghai, China, October 23-25, 2013. UK, DEFRA (UK Department for Environment, Food & Rural Affairs). (2012). Business Waste Prevention Evidence Review – WR1403. [URL] Wilson, D. C. , D. Parker, J. Cox et al. (2012). Business waste prevention: A review of the evidence, Waste Management and Research, 30(9 SUPPL. 1): 17-28. Wilts, H. , G. Dehoust, D. Jepsen et al. (2013). Eco-innovations for waste prevention – Best practices, drivers and barriers. Science of the Total Environment, 461-462: 823-829. Sustainable consumption and production Clement, S. (Ed. ). (2007). The Procura+ Manual. A Guide to Cost-Effective Sustainable Public Procurement. 2nd edition. ICLEI – Local Governments for Sustainability. [URL] European Commission (EC). (2011b). Proposal for a Directive of the European Parliament and of the Council on Public Procurement, COM(2011) 896 Final, Brussels, 2011. [URL] Georghiou, L. , J. Edler, E. Uyarra et al. (2013). Policy instruments for public procurement of innovation: Choice, design and assessment, Technological Forecasting and Social Change. [URL] Lorek, S. & D. Fuchs (2013). Strong sustainable consumption governance – Precondition for a degrowth path. Journal of Cleaner Production 38: 36-43 Mc Donough, W. & M. Braungart (2002). Cradle to Cradle: Remaking the Way We Make Things. North Point Press, New York, U. S. Mc Donough, W. & M. Braungart (2013). The Upcycle: Beyond Sustainability – Designing for Abundance. North Point Press, New York, U. S. Tukker, A. , S. Emmert, M. Charter et al. (2008). Fostering change to sustainable consumption and production: An evidence based view, Journal of Cleaner Production 16(11): 1218-1225. UNEP (2009b). Design for sustainability: Step-by-step approach. [URL] Various other interesting publications on design for sustainability can be found at : [URL] UNEP (2012d). Global Outlook on Sustainable Consumption and Production Policies. Taking action together. [URL] Various other useful UNEP publications on this topic can be found at [URL] UNEP/Wuppertal Institute Collaborating Centre on SCP , with the Stockholm Environment Institute (2010). What public policy framework is required to encourage sustainable consumption business strategies. Annex A: Further resources[URL] Consumption_Policy_Instruments. pdf USEPA (U. S. Environmental Protection Agency). (n. d. ). The Revised (Draft) Guidelines for Product Environmental Performance Standards and Ecolabels for Voluntary Use in Federal Procurement. [URL] Small Island Developing States (SIDS) ADB (2014) Solid Waste Management in the Pacific – Financial Arrangements [URL] default/files/publication/42656/solid-waste-management-financial-arrangements. pdf and [URL] environment. gov. ki/. page_id=37 Secretariat of the Pacific Regional Environment Programme (SPREP). Regional Strategies on Hazardous waste and solid waste, Case studies. [URL] SIDS Accelerated Modalities of Action (S. A. M. O. A. ) Pathway [URL] Stock, P. (2014). Island Innovations – UNDP and GEF: Leveraging the Environment for the Sustainable Development of Small Island Developing States. UNDP. [URL] UNDP_WS_Island Innovations_UNDP_GEF_Leveraging_the_Env. pdf UNEP (2012f)
The solution was filtered after To prove the feasibility of the cycle, several experi- the bioleaching process was accomplished. Cu2+ in the ments were designed. 100 m L of adjusted 9K medium leachate was separated by displacement of iron power. was oxidized by bacteria first. And then, the supernatant Finally, the solution was diluted to the concentration was used to leaching 15 g/L PCBs. After the leaching pro- of 15 g/L Fe2+ for the bacterial oxidation again. Totally, cess was accomplished, the solution was filtered. Then, 100 g/L of PCBs were disposed with nine times of cycles. Cu2+ in the solution was separated by displacement of The tactic was as follows: the addition of PCBs was 15 g/L Wu et al. Bioresour. Bioprocess. (2018) 5:10 Page5of 13 at the first 4 cycles and 10 g/L at the next 4 cycles, and to the consumption of ferric iron in bacteria-free cul- 0 g/L PCBs at the last cycle for completely reaction. Sam- tural supernatant. In addition, the consumption of Fe3+ ples were collected to analyze p H, Eh, and the concentra- is shown in Fig. 2d. After 2 h, the content of ferric iron tions of Fe2+, Fe3+, and Cu2+. in the solution had been reduced to a low level under the condition of 15 g/L PCBs. Therefore, the residual copper Analytical methods in the PCBs could not be dissolved quickly. The p H and redox potential was measured by a p H meter To verify that the oxidation of Fe3+ was the predomi- and Eh meter (Mettler model FE20). The concentration of nant mechanism of the copper extraction from PCBs by ferrous iron was determined by titration with potassium bacteria-free cultural supernatant, ferric sulfate solution, dichromate in the presence of the indicator N-phenylan- bacteria-free cultural supernatant, pure water, and pure thranilic acid. Copper ion concentration was determined media were used to leach 15 g/L PCBs, and the result by atomic absorption spectrometer (Analytic Jena AG, is shown in Fig. 3. There was a little copper extracted Germany). The concentration of Fe3+ was determined by by pure water and pure medium in the initial p H of 1. 2, the titration of EDTA at p H 2 in the presence of sulpho- which indicated that in this process, the role of acid salicylic acid as an indicator. All experiments were done leaching was not significant. However, the copper recov- in orbital shaker incubators. ery of bacteria-free cultural supernatant and ferric sulfate solution was similar and much higher than that of pure Results and discussion water and pure medium which confirmed that the copper Copper extraction from PCBs using bacteria-free cultural in PCBs was dissolved by the oxidation of Fe3+. The result supernatant indicated that the indirect non-contact mechanism was A microbial consortium which Leptospirillum ferriphi- the predominant mechanism in bioleaching of copper lum and Sulfobacillus thermosulfidooxidans were the from PCBs. It was also demonstrated that there was no predominant organisms was used to produce the super- need for bacteria to contact with PCBs for the extraction natant. The microbial consortium had been adapted in of copper. In addition, the role of bacteria in bioleaching metal-contained medium for several years. In addition, of PCBs was most likely to regenerate Fe3+ as oxidant. the metal tolerance of the species in the literature and Jadhav and Hocheng (2013) investigated silver extraction the microbial consortium used in this paper are shown in from spent silver oxide-zinc button cell battery using Table 2. It was indicated that the mixed culture used in Acidithiobacillus ferrooxidans, and considered indirect this study had stronger metal tolerance. non-contact leaching was the predominant mechanism Figure 2 shows the leaching results of copper from for metal solubilization. Kim et al. (2005) demonstrated PCBs by bacteria-free cultural supernatant. As shown indirect non-contact leaching performed better than in Fig. 2a, the addition of PCBs would cause the rise of direct leaching in bioleaching of cadmium and nickel p H. It indicated that the PCBs was alkaline, and the result from synthetic sediments. was consistent with Yang et al. (2009) and Arshadi and Mousavi (2014). Figure 2c demonstrates that the leach- The toxic effect of PCBs on bacterial oxidation activity ing reactions mainly occurred at the first 2 h. In addi- It had been confirmed in the “Copper extraction from tion, almost 100% copper was dissolved by bacteria-free PCBs using bacteria-free cultural supernatant" sec- cultural supernatant when adding 5 g/L PCBs. The result tion that the chemical-leaching process (Eq. 2) could be indicated that the copper in the PCBs was released due directly achieved by bacteria-free cultural supernatant. to chemical oxidation by ferric ion. During the chemi- However, the bacteria were required to participate in the cal oxidation process, Fe3+ (strong oxidizing agent) was biooxidation of Fe2+ to Fe3+ (Eq. 1). To obtain the opti- constantly converted to Fe2+, and it was confirmed by mum oxidation rate of bacteria (without PCBs), growth Fig. 2b. In addition, with the amount of PCBs increasing. conditions of the mixed bacteria used in the experiment the recovery of copper gradually decreased. It was related were optimized (data not show). Finally, the optimum Table 2 Range of metal tolerance of different kinds of bacteria Reference Bacteria The maximum metal concentration whereby metabolic activity still occurs Tian et al. (2007) L. ferriphilum Ni2+(30-40 m M), Zn2+(20-30 m M), Co2+ (5-10 m M), Cu2+ (< 5 m M) and Cd2+ (< 5 m M) Dopson et al. (2003) S. thermosulfidooxidans 6 m M Cu2+,43 m M Zn2+,and 5 m M Ni2- Hallmann et al. (1992) L. ferrooxidans AI3+ (278 m M), Co2+ (17. 0 m M), Cu2+ (391 m M), Mn2+ (546 m M), Ni2+ (127 m M),and Zn2+ (461 m M) Current work Microbial consortium AI3+ (1049 m M), Zn2+ (1046 m M), Ni2+ (681 m M) and Cu2+ (781 m M) Wu et al. Bioresour. Bioprocess. (2018) 5:10 Page 6 of 13 a b 1. 9 5g/LPCB 5g/LPCB 10g/L PCB 1. 8 10g/LPCB 15g/L PCB 15g/L PCB 1. 7 10 1. 6- 1. 5- 1. 4 1. 3- 1. 2 1. 1 0. 0 0. 5 1. 0 1. 5 2. 0 2. 5 3. 0 3. 5 0. 0 0. 5 1. 0 1. 5 2. 0 2. 5 3. 0 4. 0 Time(h) Time(h) d C +—5g/LPCB 100- —10g/LPCB 15g/LPCB 80 (%) 60 40 5g/LPCB 20 10g/LPCB 15g/LPCB 0. 0 0. 5 1. 0 1. 5 2. 0 2. 5 3. 0 3. 5 4. 0 4. 5 0. 0 2. 0 2. 5 3. 0 3. 5 4. 0 Time(h) Time(h) Fig. 2 Time period evaluation of p H (a), Fe2+ ( concentration(b), concentration (d) in leaching of copper from PCBs by bacteria-free cultural supernatant biooxidation rate was obtained at the initial p H of 0. 9, the that the oxidation of ferrous ions by bacteria was an acid- temperature of 32 °C and the initial Fe2+ concentration consuming process. When the amount of the PCBs was of 15 g/L. As shown in Fig. 4c, the complete biooxidation increased, more ferric ions were required to be produced of 15 g/L Fe2+ required 24 h in 0 g/L PCBs, and the rates by bacteria to leaching copper from PCBs. Therefore, of consumption of Fe2+ were 0. 5833 g/L h. However, as more acid was consumed. (2) The PCBs was alkaline in shown in Fig. 2c, it only took 2 h for the bacteria-free nature. As the amount of PCBs increased, more acid was cultural supernatant (15 g/L Fe3+) to leach copper from needed to neutralize the allkaline substance in PCBs. The 15 g/L PCBs. In addition, the formation rate of Fe2+ was optimum growth p H of the mixed culture was between 6. 69 g/L h. This meant that the rate of Eq. (2) was 11. 47 0. 9 and 2. 0, so the experimental conditions (p H 1-2) did times faster than that of Eq. (1). This demonstrated that not exced the optimum range of bacterial growth. The the biooxidation of Fe2+ was the rate-determining step in change of Eh is shown in Fig. 4b. Ballor et al
org/10. 1016/j. jmb. 2106. 06056. cep. 2021. 108474. Li, L. , Cai, D. , Wang, C. , Han, J. , Ren, W. ,Zheng, J. , Wang, Z. , Tan, T. , 2015. Continuus Moghadami, F. , Fooladi, J. , Hosseini, R. , 2019. Introducing a thermotolerant L-lactic acid production from defatted rice bran hydrolysate using corn Stover Gluconobacterjaponicus strain,potentiallyuseful forcoenzyme Q10production. Folia bagasse immobilized carrier. RSC Adv. 5, 18511-18517. https:/doi. org/10. 1039/ Microbiol. (Praha). 64, 471-479. https:/doi. org/10. 1007/s12223-018-0666-4. c4ra04641b. Moghadami, F. , Hosseini, R. , Fooladi, J. , Kalantari, M. , 2021. Optimization of coenzyme Li, D. , Liu, L. , Qin, Z. , Yu, S. , Zhou, J. , 2022. Combined evolutionary and metabolic q10 production by Gluconobacter jqponicus fm10 using response surface engineering improve 2-keto-L-gulonic acid production in Gluconobacter oxydans methodology. J. Appl. Biotechnol. Rep. 8, 172-179. [URL] WSH-004. Bioresour. Technol. 354, 127107. [URL] jabr. 2021. 130940. biortech. 2022. 127107. Nakamura, K. , Nagaki, K, Matsutani, M. , Adachi, O. , Kataoka, N. , Ano, Y. , Liu, L. ,Zeng, W. , Du, G. , Chen, J. , Zhou, J. , 2019. Identification of NAD-dpendent Theeragool, G. , Matsushita, K, Yakushi, T. , 2021. Relocation of dehydroquinate xylitol dehydrogenase from Gluconobacter oxydans WSH-003. ACS Omega 4, dehydratase to the periplasmic space improves dehydroshikimate production with 15074-15080. [URL] Gluconobacter oxydans strain NBRC3244. Appl. Microbiol. Biotechnol. 105, Liu, D. , Hu, Z. C. , Ke, X. , Zheng, Y. G. , 2020a. Breeding of Gluconobacter oxydans with high 5883-5894. [URL] PQQ-dependent D-sorbitol dehydrogenase for improvement of 6-(N-hydroxyethyl)- Nguyen, T. M, Goto, M. , Noda, S. , Matsutani, M. , Hodoya, Y, Kataoka, N. , Adachi, O. , amino-6-deoxy-α-L-sorbofuranose production. Biochem. Eng. J. 161, 107642. Matsushita,K. ,akushi,T. ,20a. he5Ketofructose reuctase of Gluconobacte. [URL] Strain CHM43 is a novel class in the shikimate dehydrogenase family. J. Bacteriol. Liu, D. , Ke, X. , Hu, Z. C. , Zheng, Y. G. , 2020b. Combinational expression of D-sorbitol 203 [URL] dehydrogenase and pyrroloquinoline quinone increases 6-(N-hydroxyethyl)-amino- Nguyen, T. M. , Naoki, K. , Kataoka, N. , Matsutani, M. , Ano, Y. , Adachi, O. , Matsushita, K. , 6-deoxy-α-L-sorbofuranose production by Gluconobacter oxydans through cofactor Yakushi, T. , 2021b. Characterization of a cryptic, pyrroloquinoline quinone- manipulation. Enzym. Microb. Technol. 141, 109670. [URL] dependent dehydrogenase of Gluconobacter sp. strain CHM43. Biosci. Biotechnol. enzmictec. 2020. 109670. Biochem. 85, 998-1004. [URL] 24 M. Ripoll et al. Biotechnology Advances 65 (2023) 108127 Noman, A. E. , Al-Barha, N. S. , Sharaf, A. A. M. , Al-Maqtari, Q. A. , Mohedein, A. , Enzymes and Cells. Humana Press Inc. , Totowa, NJ, pp. 333-343. [URL] Mohammed, H. H. H. , Chen, F. , 2020. A novel strain of acetic acid bacteria 10. 1007/978-1-59745-053-9_29. Gluconobacter oxydans FBFS97 involved in riboflavin production. Sci. Rep. 10, 1-17. Schmitz, A. M. , Pian, B. , Medin, S. , Reid, M. C. , Wu, M. , Gazel, E. , Barstow, B. , 2021. https:/doi. 0rg/10. 1038/s41598-020-70404-4. Generation of a Gluconobacter oxydans knockout collection for improved extraction Ordonez, J. L, Canete-Rodriguez, A. M. , Calljon, R. M. , Santos-Duenas, M. I. , Troncoso, A. of rare earth elements. Nat. Commun. 12, 1-11. https:/doi. org/10. 1038/s41467- M. , Garcia-Garcia, I. , Garcia-Parrilla, M. C. , 2017. Effect of Gluconic acid submerged 021-27047-4. fermentation of strawberry Puree on amino acids and biogenic amines profile. Schweikert, S. , Kranz, A. , Yakushi, T. , Filipchyk, A. , Polen, T, Etterich, H. , Bringer, S. , J. Food Process. Preserv. 41, e12787 https:/doi. org/10. 1111/jfpp. 12787. Bott, M. , 2021. FNR-type regulator Gox R of the obligatorily aerobic acetic acid Pal, P. , Kumar, R. , Nayak, J. , Banerje, S. , 2017. Fermentative production of gluconic bacterium Gluconobacter oxydans affects expressionof genes involved in respiration acid in membrane-integrated hybrid reactor system: analysis of process and redox metabolism. Appl. Environ. Microbiol. 87, 1-20. [URL] intensification. Chem. Eng. Process. Process Intensif. 122, 258-268. https:/doi. org/ 10. 1128/AEM. 00195-21. 10. 1016/j. cep. 2017. 10. 016. Sethuramiah, A. , Kumar, R. , 2016. Statistics and experimental design in perspective. In: Pal, P. , Kumar, R. , Banerjee, S. , 2019. Purification and concentration of gluconic acid Modeling of Chemical Wear. Elsevier, pp. 129-159. [URL] from an integrated fermentation and membrane process using response surface 0-12-804533-6. 00006-8. optimized conditions. Front. Chem. Sci. Eng. 13, 152-163. https:/doi. org/10. 1007/ Shen, Y. , Zhou, X. , Xu, Y. , 2020. Enhancement of Gluconobacter oxydans resistance to s11705-018-1721-z. lignocelulosic-derived inhibitors in Xylonic acid production by overexpressing Park, Y. M. , Choi, E. S. , Rhee, S. -K. K. , 1994. Effect of toluene-permeabilization on Thioredoxin. Appl. Biochem. Biotechnol. 191, 1072-1083. [URL] oxidation of D-sorbitol to L-sorbose by Gluconobacter suboxydans cellsimmobilized in s12010-020-03253-6. calcium alginate. Biotechnol. Lett. 16, 345-348. htps:/doi. org/10. 1007/ Shiraishi, F. , Kawakami, K. , Kono, S. , Tamura, A. , Tsuruta, S. , Kusunoki, K, 1989. BF00245048. Characterization of production of free gluconic acid by Gluconobacter suboxydans Peters, B. , Junker, A. , Brauer, K. , Mihlthaler, B. , Kostner, D. , Mientus, M. , Liebl, W. , adsorbed on ceramic honeycomb monolith. Biotechnol. Bioeng. 33, 1413-1418. Ehrenreich, A. , 2013
Mechanical Activation of Waste Phosphors 96 Five grams of the waste phosphors was mixed with se ven zirconia balls (diameter-15 mm) and fed 97 into a zirconia pot (inner volume-45 m L, inner diam eter-40 mm) for activation using a planetary 98 MANUSCRIPT ACCEPTED ACCEPTED MANUSCRIPT5 ball-mill (Fritsch P-7, Germany) under ambient atmo sphere. During activation, an interval of 15 99 minutes was set after each milling run of 15 min, t o avoid the accumulation of generated heat. 100 Activated samples were under acid leaching within 1 2 h after MA. 101 2. 3. Acid Leaching 102 Acid leaching of inactivated/activated waste phosph ors was conducted at the temperature of 60°C for 103 15 min by magnetic stirring. The liquid/solid ratio was 60 m L/g with the lixiviant volume of 40 m L. 104 The lixiviant of 6 mol/L hydrochloric acid (HCl) so lution was used for the leaching process. After 105 leaching, the liquid-solid separation was carried o ut by vacuum filtration using a cellulose acetate 106 membrane (0. 45 µm). Quantitative analysis of REEs in solution was c onducted by Inductively Coupled 107 Plasma-Atomic Emission Spectroscopy (ICP-AES: IRIS Intrepid II XSP, Thermo Fisher), and ICP-MS 108 (X Series 2, Thermo Fisher) was also used when it wa s needed. 109 3. Results and discussion 110 3. 1. REEs Leaching Enhancement and Morphology chang es of waste phosphors 111 According to Figure 1, for raw waste phosphors samples, the aver age leaching rates of Ce, La and 112 Tb were only 0. 48%, 0. 67%, and 0. 33%, respectively. However, they were significantly elevated after 113 the MA. At the range of 200-600 rpm, the average le aching rate of Tb increased rapidly from 15. 4% to 114 89. 4% with the increase of milling bowls rotational speed (from now on referred to rotational speed - 115 RS). Then, a slight enhancement of about 3. 0% was a lso achieved when the RS increased further from 116 600 rpm to 800 rpm. Similarly, the leaching rate of Ce and La increased from 15. 4% and 14. 9% at 200 117 rpm to 93. 7% and 91. 4% at 600 rpm, respectively. Th en, there was a reduction of around 2% and an 118 increase of around 5% obtained in leaching rate of Ce and La when the RS increased to 800 rpm. 119 Leaching rates of Eu and Y fluctuated at all the ra nge of RS. The average leaching rate ranged 120 MANUSCRIPT ACCEPTED ACCEPTED MANUSCRIPT6 between 81. 1% and 93. 1% for Eu, and between 84. 6% a nd 94. 6% for Y, and no significant relationship 121 could be observed between these leaching rates and RS. 122 123 Figure 1 Changes in leaching rate of REEs, as well as median diameter (D 50 ) and specific surface area 124 (SSA) of waste phosphors activated at different RS (activation time 60 min). Part of leaching rates of 125 Tb, Eu, and Y (200–800 rpm) was adapted from (Tan e t al. , 2016). 126 Activation time could also positively affect the le aching rates of REEs when waste phosphors were 127 activated at the RS of 600 rpm (Fig. 2). Leaching ra tes of all the REEs were significantly improved 128 when the activation time increased from 15 to 60 mi n. The most significant enhancement was obtained 129 for Ce, which increased from 61. 9% to 93. 7%; simila r improvement was achieved for leaching rate of 130 La and Tb as well, from 61. 5% to 91. 4%, and from 59. 8% to 89. 4%. Meanwhile, the leaching rate of 131 Eu increased from 82. 0% to 90. 4%, and for Y from 87. 9% to 94. 4%. Increasing the activation time 132 from 60 to 240 min, however, increased the leaching rates for these five REEs by no more than 3%. 133 This innovative approach showed promising leaching rates for Eu and Y, around 95%, higher than 134 those obtained under optimization conditions in stu dies using only a hydrometallurgical 135 method. (Binnemans et al. , 2013; Tan et al. , 2015; W u et al. , 2014b) These rates were also close to the 136 highest rates of 94. 6% and 99. 1% for Y and Eu, resp ectively, achieved in a study conducted by Liu et 137 al. (2014) using an alkali sintering method. Further more, an enhancement of around 10% was obtained 138 for the leaching rate of Tb in this study when comp ared with it obtained by Liu et al. (2014) and 139 conventional methods. (Wu et al. , 2014b) 140 141 Figure 2 Changes in leaching rate of REEs, as well as D 50 and SSA of waste phosphors activated in 142 different activation time (RS-600 rpm). 143 It is well known that increases in the SSA of parti cles and reduction of particle size can accelerate 144 the leaching process and improve leaching rate. How ever, according to Fig. 1 and 2, changes in SSA 145 MANUSCRIPT ACCEPTED ACCEPTED MANUSCRIPT7 and D 50 of waste phosphors showed different, even contrary , trends compared with the changes in REE 146 leaching rates when the MA conditions changed (part icle size distribution of inactivated and activated 147 waste phosphors are presented in the Supplementary Material Fig. S1 and S2). With an increase in RS, 148 the SSA of waste phosphors enlarged gradually from 0. 14 m 2/g of inactivated sample at first, then 149 suffered a rapid decrease after peaking at the RS o f 400 rpm. SSA values were 3. 31 and 1. 82 m 2/g at 150 the RS of 400 and 600 rpm, respectively, while the D 50 values were 3. 13 and 7. 20 µm, respectively. 151 Similar changes were observed when the activation t ime changed (morphology changes are presented 152 in Fig. S3). The adhesion from Van der Waals forces and chemical forces (Opoczky, 1977; Wiewióra et 153 al. , 1993) could explain the aggregation and agglom eration phenomena at high RS and long activation 154 time. Therefore, the increase in SSA and the reduct ion in particle size of waste phosphors due to the 155 MA process cannot be inferred as the main reason fo r the significant changes in REE leaching rates. 156 Chemical characteristics and crystal structures of phosphors compounds appeared to be altered via MA 157 process, what made the leaching of REEs much easier. 158 3. 2. Analysis of Physicochemical Changes in Activat ed Waste Phosphors, and Exploration of the 159 Activation Mechanism 160 According to X-ray diffraction (XRD) patterns prese nted in Fig. 3, the intensity of characteristic 161 diffraction peaks (the position can be found in Fig. S4) decreased with an increase in the activation 162 degree: specifically, increases in RS and activatio n time, and some of the peaks even disappeared 163 during the activation processes. For example, the d iffraction peak of the highest intensity in the 164 inactivated sample decreased to about 32% after act ivating for 60 min under the condition of 600 rpm 165 (detail information in Fig. S5). Meanwhile, the ful l width at half-maximum (FWHM) of peaks also 166 broadened with simultaneous increases in RS and act ivation time. These results indicate that the 167 MANUSCRIPT ACCEPTED ACCEPTED MANUSCRIPT8 crystallite size of waste phosphors compounds decre ased, the crystal structure of waste phosphors 168 compounds was destroyed and transformed to a disord ered state due to the external mechanical force 169 caused by impact, friction, and shear during activa tion(Baláž, 2008). 170 171 Figure 3 Changes of XRD patterns in waste phosphors under different activation conditions: (a) RS 172 (activation time-60 min); (b) activation time (RS-6 00 rpm). 173 Most of the phosphorus (P) in phosphors presents in the green phosphor (La PO 4: Ce, Tb), and the Ce 174 and Tb are doped in the crystal structure of La PO 4 instead of La. The La PO 4 is used for the analysis of 175 P 2p X-ray photoelectron spectroscopy (XPS) spectra because the P 2p spectra of Tb PO 4 and Ce PO 4 176 are almost overlapped by it, since the molar quanti ties of Tb and Ce are much less than La. 177 178 Figure 4 XPS spectra of inactivated and activated ( 600 rpm, 60min) waste phosphors: (a) P 2p; (b) La 179 3d; (c) Tb 3d; (d) Y 3d 180 According to Fig. 4(a), related content of La x PO y increased after MA, from approximately 20% of 181 the raw sample to 27%. The generation of La x PO y through La PO 4 decomposition was accompanied by 182 the generation of La 2O3 (Eq. 1) (Ivanova et al. , 1996). Meanwhile, the bin ding energy of P 2p showed a 183 reduction of 1
, 2008; Illmer and PVK without Mn for Fe 62±98 14±2 68±45 Schinner, 1995; Rodriguez and Fraga, 1999; Souchie et al. , 2006). AMS 166 ± 25 9±4 102± 78 Also, REE-phosphates are known to have particularly low NBRIP 8±4 5±1 5±0 solubilities in water, on the order of 10-13 M (10-i g/L) (Firsching 343 Brisson et al. : Bioleaching of Rare Earth Elements from Monazite Biotechnology and Bioengineering and Brune, 1991), whereas the solubility of Ca3(PO4)2 is (Hassanien et al. , 2013), while Shin et al. reported leaching 3. 9 × 10-6 M (0. 0012 g/L) (Haynes, 2015). effciencies of only 0. 1% for bioleaching of monazite ore (Shin et al. , With AMS medium and both versions of PVK medium, glucose was 2015). Differences in ores, bioleaching organisms, experimental completely or almost completely consumed (final concentration conditions, and measurement methodologies may have contributed ≤0. 6 g/L) (Supplementary Fig. Sla). In contrast, with NBRIP medium, to the varying results. glucose concentrations were only reduced to 6. 3 ± 0. 1, 7. 4 ± 0. 1, and Given the relatively low leaching efficiency of monazite 7. 1 ± 0. 0 g/L for A. niger, ML3-1, and WE3-F respectively. Growth on bioleaching in this study, further optimization is necessary to NBRIP medium also resulted in smaller reductions in p H than growth achieve an economically viable process. There are several potential on other media (Supplementary Fig. S2a). avenues for improving overall leaching efficiency. The results of the In the study by Nautiyal introducing NBRIP medium, several growth conditions comparisons suggest some important factors. In versions of the medium were compared with several modifications addition to lacking several trace minerals, NBRIP medium also had of Pikovskaya medium, including the yeast extract free version used the lowest concentration of (NH4)2SO4 of all media tested (0. 1 g/L), in this study (PVK) (Nautiyal, 1999). They showed significantly while AMS had the highest (0. 66 g/L), suggesting that nitrogen enhanced solubilization of Ca;(PO4)bya variety of bacterial strains concentration may be an important factor. Increasing the leaching (five Pseudomonas and three Bacillus strains) with NBRIP medium. time may also be effective. Over 6 days of bioleaching, REE However, the poor performance of NBRIP medium in this study concentrations did not appear to have entirely leveled off (Fig. 2), with fungi indicates that despite its widespread use in phosphate and a longer leaching time may increase REE yield. Other process solubilization studies, NBRIP medium is not well suited for some designs beyond leaching in a single batch should also be considered PSMs and/or solubilization of some phosphate minerals. to further increase yield. The same monazite could be leached Among the five carbon sources tested, there was no clear over- several times with fresh medium and organisms to extract more performer (Fig. 2b). For ML3-1 and WE3-F, REE solubilization REEs, or a continuous fow process could be applied in which the profiles were similar for all carbon sources tested. REE monazite is retained via settling while the leachate is continuously solubilization performance for A. niger was much more variable recovered. Other potentially important factors not considered here between replicates with the same carbon source. In contrast to the include monazite grain size, aeration, and temperature. variability in REE solubilization, p H and carbon source consumption profiles were similar for A. niger for all carbon Proportional Release of REEs and Thorium During sources tested, as they also were for the other two isolates Bioleaching (Supplementary Fig. S1b and S2b). For the glucose concentrations tested (5, 10, and 100 g/L), higher Proportions of REEs and Th in monazite and in bioleaching glucose concentrations did not correspond to improved REE supernatant are shown in Fig. 3. The monazite sand used in this solubilization for ML3-1 and WE3-F (Fig. 2c). For A. niger, the study is dominated by Ce, La, Nd, and Pr, and the bioleaching performance was again quite variable, and although the average supernatant refected this composition (Fig. 3a). Release of Th REE concentration was highest for 100 g/L glucose, this difference during bioleaching was low in proportion to REEs. For standard was not statistically significant. The p H reduction was comparable growth conditions (AMS medium, 10 g/L glucose), averages for all glucose concentrations tested (Supplementary Fig. S2c). for released Th were 0. 026±0. 046, 0. 0003±0. 0001， and Interestingly, for the lowest glucose concentration (5g/L), 0. 0028 ±0. 0039 mole Th per mole REEs for A. niger, ML3-1, the glucose was consumed by the fourth day (Supplementary and WE3-F respectively (nine replicates each). In comparison, the Fig. S1), but REE concentrations continued to rise through the end monazite contained 0. 11 ± 0. 02 mole Th per mole REEs (seven of the experiment. For the highest glucose concentration replicates),indicting preferential release of REEs over Th relative to (100 g/L), glucose levels remained above 10g/L for the entire the amounts present in the monazite ore. experiment. These data indicate that glucose availability was not the In comparison, Th release in conventional monazite processing limiting factor for bioleaching under the conditions tested. varies. In the commonly used Na OH treatment process, the majority In a 2013 study, Qu and Lian examined bioleaching of REEs from of Th is leached along with REEs and must be separated in red mud, a byproduct of bauxite ore processing for alumina downstream processing (Gupta and Krishnamurthy, 1992; Peelman production, by Penicilum tricolor RM-10 (Qu and Lian, 2013). They et al. , 2014). The Ca Cl2/Ca CO3 process leaves most Th in the reported total REE concentrations in the leachate of 20 to 60 mg/L, residual, although this process also has less favorable REE yields compared to 60 to 120 mg/L for monazite bioleaching by ML3-1 and and requires much higher temperatures (Merritt, 1990; Peelman WE3-F in this study. These concentrations corresponded to leaching et al. , 2014). Th release during the sulfuric acid process depends on efficiencies of 20%-40%, compared to 3%-5% found in this study. the specific leaching conditions (Gupta and Krishnamurthy, 1992; Note that the red mud efficiency numbers are higher even though the Peelman et al. , 2014). overall concentrations are lower due to the lower starting concentrations of REEs in the red mud. Given the differences in Organic Acid Production During Bioleaching the ores (red mud vs. monazite) and experimental time scales (50 days vs. 6 days), it is not surprising that leaching efficiencies differ. Organic acid production was observed for all organisms, with each Two recent studies addressing monazite bioleaching reported organism producing a different set of acids. For a given organism, widely ranging leaching effciencies. Hassanien et al. reported organic acid production was variable, and not all acids were efficiencies of up to 75% for bioleaching of monazite concentrate detected in all biological replicates. Table III lists the maximum 344 Biotechnology and Bioenginering, Vol. 113, No. 2, February, 2016 production of higher concentrations of oxalic acid corresponded with lower concentrations of REEs, which is consistent with the Proportion of REEs and Th in Monazite known low solubility of REE-oxalates (Gadd, 1999). and in Bioleaching Supernatant ML3-1 produced primarily itaconic and succinic acids and WE3- other REEs F produced acetic, gluconic, and succinic acids. As noted above, Pr La Th ML3-1 showed high sequence similarity to A. terreus, some strains of which have been used industrially to produce itaconic acid (Magnuson and Lasure, 2004). A. niger and WE3-F also produced some compounds that generated large peaks in the HPLC UV 0. 1 absorbance chromatogram, but could not be identified based on the availablestandards. Other PSMstudieshave alsoobserved 3三E additional compounds presumed to be other organic acids Y potentially involved in phosphate solubilizing activity (Chen 40 uo. et al. , 2006). Abiotic Leaching With Hydrochloric Acid and Organic Acids For all abiotic leaching experiments, leaching was performed for 48 h. Preliminary experiments indicated that this was sufficient 0. 0 time to reach equilibrium REE concentrations. Leaching with inorganic HCl solutions representing a range of 105 acidities (p H 1. 8-3. 7) indicated an approximately linear (r² = 0. 96) A A a. b. inverse correlation between p H (final p H after leaching) and REE Figure 3

End of preview. Expand in Data Studio

abhi26/research-papers-gpt-neox

This dataset contains processed research papers optimized for GPT-NeoX-20B training.
The text has been cleaned, chunked to 2048 tokens, and formatted for causal language modeling.

Dataset Details

Total Samples: 9993
Unique Papers: 1017
Average Tokens per Sample: 1965.4
Token Range: 10 - 91659
Max Token Limit: 2048
Source Subdirectories: 1

Dataset Structure

Each sample contains:

text: The processed research paper text or chunk
Additional metadata available in some splits

Usage

from datasets import load_dataset

# Load the dataset
dataset = load_dataset("abhi26/research-papers-gpt-neox")

# Preview a sample
print(dataset['train'][0]['text'][:200])

Training Configuration

This dataset was created for training GPT-NeoX-20B with:

Maximum sequence length: 2048 tokens
Smart chunking to preserve semantic boundaries
Research paper specific cleaning and preprocessing

Citation

If you use this dataset, please cite the original research papers and acknowledge the preprocessing pipeline.

Downloads last month: 88

Size of downloaded dataset files:

42.3 MB

Size of the auto-converted Parquet files:

42.3 MB

Number of rows:

9,993