Stoichiometric model and flux balance analysis for a mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum

Biotechnology Progress

Volumn 31, Issue 2, 2015, Pages 307-315

  Merino, M P ^a   Andrews, B A ^a   Asenjo, J A ^a  

^a UNIVERSITY OF CHILE   (Chile)

Author keywords

Archaea; Bioleaching; Ferroplasma acidiphilum; Flux balance analysis; Iron oxidizing bacteria; Leptospirillum ferrooxidans; Mixed culture; Stoichiometric model

Indexed keywords

BIOLEACHING; CELL PROLIFERATION; IRON; IRON ANALYSIS; METABOLISM; SULFUR COMPOUNDS;

ARCHAEA; FERROPLASMA ACIDIPHILUM; FLUX BALANCE ANALYSIS; IRON OXIDIZING BACTERIA; LEPTOSPIRILLUM FERROOXIDANS; MIXED CULTURES; STOICHIOMETRIC MODELS;

BACTERIA;

BACTERIA (MICROORGANISMS); FERROPLASMA ACIDIPHILUM; LEPTOSPIRILLUM FERRIPHILUM; LEPTOSPIRILLUM FERROOXIDANS;

IRON;

BACTERIUM; BIOLOGICAL MODEL; COCULTURE; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; METABOLISM; OXIDATION REDUCTION REACTION; PROCEDURES; THERMOPLASMATALES;

BACTERIA; COCULTURE TECHNIQUES; IRON; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; MODELS, BIOLOGICAL; OXIDATION-REDUCTION; THERMOPLASMALES;

EID: 84928183475     PISSN: 87567938     EISSN: 15206033     Source Type: Journal    
DOI: 10.1002/btpr.2028     Document Type: Article

References (39)

1. Schippers A, Sand W. 1999. Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur. Appl Environ Microbiol. 65:319-321.
2. Holmes DS, Bonnefoy V. 2007. Genetic and bioinformatics insights into iron and sulfur oxidation mechanisms of bioleaching organisms. In: Rawlings D, Johnson B, editors. Biomining. Berlin: Springer.
3. Baker BJ, Banfield JF. 2003. Microbial communities in acid mine drainage. FEMS Microbiol Ecol. 44:139-152.
4. Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC II, Shah M, Hettich RL, Banfield JF. 2005. Community proteomics of a natural microbial biofilm. Science. 308:1915-1920.
5. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 428:37-43.
6. Goltsman DS, Dasari M, Thomas BC, Shah MB, VerBerkmoes NC, Hettich RL, Banfield JF. 2013. New group in the Leptospirillum clade: cultivation-independent community genomics, proteomics and transcriptomics of the new species "Leptospirillum group IV UBA BS". Appl Environ Microbiol. 79:5384-5393.
7. Rawlings DE, Tributsch H, Hansford GS. 1999. Reasons why 'Leptospirillum'-like species rather than Thiobacillus ferrooxidans are the dominant iron-oxidizing bacteria in many commercial processes for the biooxidation of pyrite and related ores. Microbiology. 145 (Pt 1):5-13.
8. Mi S, Song J, Lin J, Che Y, Zheng H, Lin J. 2011. Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation. J Microbiol. 49:890-901.
9. Dopson M, Baker-Austin C, Hind A, Bowman JP, Bond PL. 2004. Characterization of Ferroplasma isolates and Ferroplasma acidarmanus sp. nov., extreme acidophiles from acid mine drainage and industrial bioleaching environments. Appl Environ Microbiol. 70:2079-2088.
10. Golyshina OV, Pivovarova TA, Karavaiko GI, Kondrateva TF, Moore ER, Abraham WR, Lunsdorf H, Timmis KN, Yakimov MM, Golyshin PN. 2000. Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiol. 50 (Pt 3):997-1006.
11. Golyshina OV, Timmis KN. 2005. Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments. Environ Microbiol. 7:1277-1288.
12. Pivovarova TA, Kondrat'eva TF, Batrakov SG, Esipov SE, Sheichenko VI, Bykova SA, Lysenko AM, Karavaiko GI. 2002. Phenotypic features of Ferroplasma acidiphilum strains Yt and Y-2. Mikrobiologiia. 71:809-818.
13. Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. 2013. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring bacteria. BMC Genomics. 14:485.
14. Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. 2006. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol. 72:1558-1568.
15. Geng J, Song HS, Yuan J, Ramkrishna D. 2012. On enhancing productivity of bioethanol with multiple species. Biotechnol Bioeng. 109:1508-1517.
16. Zomorrodi AR, Maranas CD. 2012. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol. 8:e1002363.
17. Hold C, Andrews BA, Asenjo JA. 2009. A stoichiometric model of Acidithiobacillus ferrooxidans ATCC 23270 for metabolic flux analysis. Biotechnol Bioeng. 102:1448-1459.
18. Merino MP, Andrews BA, Asenjo JA. 2010. Stoichiometric model and metabolic flux analysis for Leptospirillum ferrooxidans. Biotechnol Bioeng. 107:696-706.
19. Levican G, Ugalde JA, Ehrenfeld N, Maass A, Parada P. 2008. Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. BMC Genomics 9:581.
20. Barreto M, Jedlicki E, Holmes DS. 2005. Identification of a gene cluster for the formation of extracellular polysaccharide precursors in the chemolithoautotroph Acidithiobacillus ferrooxidans. Appl Environ Microbiol. 71:2902-2909.
21. Dopson M, Baker-Austin C, Bond PL. 2005. Analysis of differential protein expression during growth states of Ferroplasma strains and insights into electron transport for iron oxidation. Microbiology. 151(Pt 12):4127-4137.
22. Nemoto N, Shida Y, Shimada H, Oshima T, Yamagishi A. 2003. Characterization of the precursor of tetraether lipid biosynthesis in the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles. 7:235-243.
23. Batrakov SG, Pivovarova TA, Esipov SE, Sheichenko VI, Karavaiko GI. 2002. Beta-d-glucopyranosyl caldarchaetidylglycerol is the main lipid of the acidophilic, mesophilic, ferrous iron-oxidising archaeon Ferroplasma acidiphilum. Biochim Biophys Acta. 1581:29-35.
24. Nishihara M, Yamazaki T, Oshima T, Koga Y. 1999. sn-glycerol-1-phosphate-forming activities in Archaea: separation of archaeal phospholipid biosynthesis and glycerol catabolism by glycerophosphate enantiomers. J Bacteriol. 181:1330-1333.
25. Koga Y, Morii H. 2007. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev. 71:97-120.
26. Pe'er I, Felder CE, Man O, Silman I, Sussman JL, Beckmann JS. 2004. Proteomic signatures: amino acid and oligopeptide compositions differentiate among phyla. Proteins. 54:20-40.
27. Stephanopoulos GN, Aristidou AA, Nielsen J. 1998. Metabolic Engineering. London: Academic Press.
28. Ingraham JL, Maaloe O, Neidhardt FC. 1983. Growth of the bacterial cell. Sunderland: Sinnauer Associates.
29. Feist AM, Scholten JC, Palsson BO, Brockman FJ, Ideker T. 2006. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2:2006.0004.
30. Varma A, Palsson BO. 1993. Metabolic capabilities of Escherichia Coli. I. Synthesis of biosynthetic precursors and cofactors. J Theor Biol. 165:477-502.
31. Gahan CS, Sundkvist JE, Dopson M, Sandstrom A. 2010. Effect of chloride on ferrous iron oxidation by a Leptospirillum ferriphilum-dominated chemostat culture. Biotechnol Bioeng. 106:422-431.
32. Pardelha F, Alburquerque MG, Reis MA, Dias JM, Olivera R. 2012. Flux balance analysis of mixed microbial cultures: application to the production of polyhydroxyalkanoates from complex mixtures of volatile fatty acids. J Biotechnol. 162:336-345.
33. Llaneras F, Pico J. 2007. A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient. BMC Bioinformatics. 8:421.
34. Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV. 1999. Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res. 9:608-928.
35. Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman WB. 1997. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene. 197:GC11-GC26.
36. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC-Y, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PMK, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A. 98:7835-7840.
37. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, De Vos WM, Van Der Oost J. 2003. The unique features of glycolytic pathways in Archaea. Biochem J. 375:231-246.
38. Campbell BJ, Cary SC. 2004. Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents. Appl Environ Microbiol. 70:6282-6289.
39. Hugler M, Huber H, Stetter KO, Fuchs G. 2003. Autotrophic CO2 fixation pathways in archaea (Crenarchaeota). Arch Microbiol. 179:160-173.