The diversity of hydrogen-producing microorganisms in a high temperature oil reservoir and its potential role in promoting the in situ bioprocess

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Jin-Feng Liu, Serge Maurice Mbadinga, Wen-Ji Ke, Ji-Dong Gu, Bo-Zhong Mu


Hydrogen-producing microorganisms are believed to play an important role in energy metabolism of micro-organisms in anaerobic environments and hence are one of the crucial factors for influencing the activity and develop-ment of these microorganisms. Consequently, they provide the biological foundation for the biotechnology such as MEOR (Microbial Enhanced Oil Recovery) and microbial fixation of CO2 and conversion of it into CH4 and etc. How-ever, knowledge on the community of hydrogen-producing microorganisms and their potential in subsurface formations are still limited. In this study, hydrogen-producing microorganisms in the production water from an oilfield as well as enrichment cultures were analyzed with clone library analysis of [FeFe]-hydrogenase encoding genes. The results show that [FeFe]-hydrogenase genes in production water are diverse and related to Bacteroidetes, Firmicutes, Spirochaetes and uncultured. Anaerobic incubations established within the oil reservoir production water and generating 202 mmol H2/mol glucose during 7-day incubation at 55°C indicate a high frequency of members of the Firmicutes. This study implies that hydrogen-producing microorganisms in oil reservoir may play a positive role in promoting the in situ bio-process via hydrogen production once common nutrients are available. These data are helpful for evaluating, developing, and utilizing hydrogen-producing microorganisms in oil reservoirs for biological fixation and conversion of CO2 into CH4 as well as MEOR.



microbial community;hydrogen-producing microorganisms; functional gene biomarker; enrichment culture; oil reservoir

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McInerney M J, Sieber J R and Gunsalus R P, 2009, Syntrophy in anaerobic global carbon cycles. Current Opinion in Biotechnology, vol.20(6): 623–632.

Schink B, 1997, Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews, vol.61(2): 262–280.

Boyd E S, Hamilton T L, Swanson K D, et al., 2014, [FeFe]-hydrogenase abundance and diversity along a vertical redox gradient in Great Salt Lake, USA. International Journal of Molecular Sciences, vol.15(12): 21947– 21966.

Thauer R K, Klein A R and Hartmann G C, 1996, Reactions with molecular hydrogen in microorganisms: evidence for a purely organic hydrogenation catalyst. Chemical Reviews, vol.96(7): 3031–3042.

Rudyk S N and Søgaard E G, 2010, How specific microbial communities benefit the oil industry: microbial-enhanced oil recovery (MEOR), in Whitby C and Skovhus T L (eds), Applied Microbiology and Molecular Biology in Oilfield Systems. Springer Netherlands, Milton Keynes UK, 179–187.

Sen R, 2008, Biotechnology in petroleum recovery: the microbial EOR. Progress in Energy and Combustion Science, vol.34(6): 714–724.

Grigoryan A A, Cornish S L, Buziak B, et al., 2008, Competitive oxidation of volatile fatty acids by sulfate- and nitrate-reducing bacteria from an oil field in Argentina. Applied and Environmental Microbiology, vol.74(14): 4324–4335.

Hubert C and Voordouw G, 2007, Oil field souring control by nitrate-reducing Sulfurospirillum spp. that out-compete sulfate-reducing bacteria for organic electron donors. Applied and Environmental Microbiology, vol.73(8): 2644–2652.

Liu J-F, Sun X-B, Yang G-C, et al., 2015, Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration. Frontiers in Microbiology, vol.6: 236.

Mayumi D, Dolfing J, Sakata S, et al., 2013, Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs. Nature Communications, vol.4: 1998.

Vignais P M and Billoud B, 2007, Occurrence, classification, and biological function of hydrogenases: an overview. Chemical Reviews, vol.107(10): 4206–4272.

Kim J Y H and Cha H J, 2013, Recent progress in hydrogenase and its biotechnological application for viable hydrogen technology. Korean Journal of Chemical Engineering, vol.30(1): 1–10.

Corr M J and Murphy J A, 2011, Evolution in the understanding of [Fe]-hydrogenase. Chemical Society Reviews, vol.40(5): 2279–2292.

Boyd E S, Spear J R and Peters J W, 2009, [FeFe] hydrogenase genetic diversity provides insight into molecular adaptation in a saline microbial mat community. Applied and Environmental Microbiology, vol.75(13): 4620–4623.

Fang H, Zhang T and Liu H, 2002, Microbial diversity of a mesophilic hydrogen-producing sludge. Applied Microbiology and Biotechnology, vol.58(1): 112–118.

Schmidt O, Drake H L and Horn M A, 2010, Hitherto unknown [Fe-Fe]-hydrogenase gene diversity in anaerobic and anoxic enrichments from a moderately acidic fen. Applied and Environmental Microbiology, vol.76(6): 2027–2031.

Xing D, Ren N and Rittmann B E, 2008, Genetic diversity of hydrogen-producing bacteria in an acidophilic ethanol-H-2-coproducing system, analyzed using the [Fe]-hydrogenase gene. Applied and Environmental Microbiology, vol.74(4): 1232–1239.

Boyd E S, Hamilton T L, Spear J R, et al., 2010, [FeFe]- hydrogenase in Yellowstone National Park: Evidence for dispersal limitation and phylogenetic niche conservatism. The ISME Journal, vol.4(12): 1485–1495.

Baba R, Kimura M, Asakawa S, et al., 2014, Analysis of [FeFe]-hydrogenase genes for the elucidation of a hydrogen-producing bacterial community in paddy field soil. FEMS Microbiology Letters, vol.350(2): 249–256.

Wang L-Y, Duan R-Y, Liu J-F, et al., 2012, Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures. Biogeosciences, vol.9(11): 4645–4659.

Guan J, Xia L-P, Wang L-Y, et al., 2013, Diversity and distribution of sulfate-reducing bacteria in four petroleum reservoirs detected by using 16S rRNA and dsrAB genes. International Biodeterioration and Biodegradation, vol.76: 58–66.

Huber T, Faulkner G and Hugenholtz P, 2004, Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics, vol.20(14): 2317– 2319.

Yu Y, Breitbart M, McNairnie P, et al., 2006, FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics, vol.7: 57.

Altschul S F, Madden T L, Schäffer A A, et al., 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, vol.25(17): 3389–3402.

Tamura K, Peterson D, Peterson N, et al., 2011, MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, vol.28(10): 2731–2739.

Saitou N and Nei M, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, vol.4(4): 406–425.

Wang L-Y, Gao C-X, Mbadinga S M, et al., 2011, Characterization of an alkane-degrading methanogenic enrichment culture from production water of an oil reservoir after 274 days of incubation. International Biodeterioration and Biodegradation, vol.65(3): 444–450.

Chen S and Dong X, 2005, Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater. International Journal of Systematic and Evoutionary Microbiology, vol.55(Pt 6): 2257–2261.

Grabowski A, Nercessian O, Fayolle F, et al., 2005, Microbial diversity in production waters of a low-tem-perature biodegraded oil reservoir. FEMS Microbiology Ecology, vol.54(3): 427–443.

Mohd Yasin N H, Rahman N A A, Man H C, et al., 2011, Microbial characterization of hydrogen-producing bacteria in fermented food waste at different pH values. Inter-national Journal of Hydrogen Energy, vol.36(16): 9571– 9580.

Lee J-H, Lee D-G, Park J-I, et al., 2010, Bio-hydrogen production from a marine brown algae and its bacterial diversity. Korean Journal of Chemical Engineering, vol.27(1): 187–192.

Hahnke S, Maus I, Wibberg D, et al., 2015, Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab- scale biogas reactor. Journal of Biotechnology, vol.193: 34–36.

Xu S-Y, He P-Q, Dewi S-Z, et al., 2013, Hydrogen-producing microflora and Fe-Fe hydrogenase diversities in seaweed bed associated with marine hot springs of Kalianda, Indonesia. Current Microbiology, vol.66(5): 499– 506.

Ley R E, Harris J K, Wilcox J, et al., 2006, Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Applied and Environmental Microbiology, vol.72(5): 3685–3695.

Ratti R P, Delforno T P, Sakamoto I K, et al., 2015, Thermophilic hydrogen production from sugarcane bagasse pretreated by steam explosion and alkaline delignification. International Journal of Hydrogen Energy, vol.40(19): 6296–6306.

Im W-T, Kim D-H, Kim K-H, et al., 2012, Bacterial community analyses by pyrosequencing in dark fermentative H2-producing reactor using organic wastes as a feedstock. International Journal of Hydrogen Energy, vol.37(10): 8330–8337.

Feng W-W, Liu J-F, Gu J-D, et al., 2011, Nitrate-reducing community in production water of three oil reservoirs and their responses to different carbon sources revealed by nitrate-reductase encoding gene (napA). International Biodeterioration and Biodegradation, vol.65(7): 1081– 1086.

Wang L-Y, Ke W-J, Sun X-B, et al., 2014, Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches. Applied Microbiology and Biotechnology, vol.98(9): 4209–4221.

Jayasinghearachchi H S and Lal B, 2011, Oceanotoga teriensis gen. nov., sp. nov., a thermophilic bacterium isolated from offshore oil-producing wells. International Journal of Systematic and Evolutionary Microbiology, vol.61(Pt 3): 554–560.

Miranda-Tello E, Fardeau M L, Thomas P, et al., 2004, Petrotoga mexicana sp. nov., a novel thermophilic, anaerobic and xylanolytic bacterium isolated from an oil- producing well in the Gulf of Mexico. International Journal of Systematic and Evolutionary Microbiology, vol54(Pt 1): 169–174.

Miranda-Tello E, Fardeai M-L, Joullan C, et al., 2007, Petrotoga halophila sp. nov., a thermophilic, moderately halophilic, fermentative bacterium isolated from an off-shore oil well in Congo. International Journal of Systematic and Evolutionary Microbiology, vol.57(Pt 1): 40– 44.

L'Haridon S, Miroshnichenko M L, Hippe H, et al., 2002, Petrotoga olearia sp. nov. and Petrotoga sibirica sp. nov., two thermophilic bacteria isolated from a continental petroleum reservoir in Western Siberia. International Jour-nal of Systematic and Evolutionary Microbiology, vol. 52(Pt 5): 1715–1722.

Lien T, Madsen M, Rainey F A, et al., 1998, Petrotoga mobilis sp. nov., from a North Sea oil production well. International Journal of Systematic and Evolutionary Microbiology, vol.48(Pt 3): 1007–1013.

Takahata Y, Nishijima M, Hoaki T, et al., 2001, Thermo-toga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan. International Journal of Systematic and Evolutionary Microbiology, vol.51(Pt 5): 1901–1909.

Ravot G, Magot M, Fardeau M-L, et al., 1995, Thermo-toga elfii sp. nov., a novel thermophilic bacterium from an African oil-producing well. International Journal of Systematic and Evolutionary Microbiology, vol.45(2): 308–314.

Fardeau M-L, Ollivier B, Patel B K C, et al., 1997, Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. International Journal of Systematic and Evolutionary Microbiology, vol. 47(4): 1013–1019.

Jayasinghearachchi H S, Sarma P M and Lal B, 2012, Biological hydrogen production by extremely thermophilic novel bacterium Thermoanaerobacter mathranii A3N isolated from oil producing well. International Jou-rnal of Hydrogen Energy, vol. 37(7): 5569–5578.

48. Fardeau M L, Magot M, Patel B K C, et al., 2000, Thermoanaerobacter subterraneus sp. nov., a novel thermophile isolated from oilfield water. International Journal of Systematic and Evolutionary Microbiology, vol. 50(Pt 6): 2141–2149.

Cayol J L, Ollivier B, Patel B K C, et al., 1995, Description of Thermoanaerobacter brockii subsp. lactiethylicus subsp. nov., isolated from a deep subsurface French oil well, a proposal to reclassify Thermoanaerobacter finniias Thermoanaerobacter brockii subsp. finnii comb. nov., and an emended description of Thermoanaerobacter b-rockii. International Journal of Systematic and Evolutionary Microbiology, vol.45(4): 783–789.

Magot M, Fardeau M-L, Arnauld O, et al., 1997, Spiro-chaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field. FEMS Microbiology Letters, vol.155(2): 185–191.

Maune M W and Tanner R S, 2012, Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum. International Journal of Systematic and Evolutionary Microbiology, vol.62(Pt 4): 832–838.

Greening C, Biswas A, Carere C R, et al., 2016, Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival. The ISME Journal, vol.10(3): 761–777.

Hawkes F R, Dinsdale R, Hawkes D L, et al., 2002, Sustainable fermentative hydrogen production: challenges for process optimisation. International Journal of Hydrogen Energy, vol.27(11–12): 1339–1347.

Levin D B, Pitt L and Love M, 2004, Biohydrogen production: Prospects and limitations to practical application. International Journal of Hydrogen Energy, vol.29(2): 173–185.

Taguchi F, Mizukami N, Saito-Taki T, et al., 1995, Hydrogen production from continuous fermentation of xylose during growth of Clostridium sp. strain No. 2. Canadian Journal of Microbiology, vol.41(6): 536–540.

Lin P-Y, Whang L-M, Wu Y-R, et al., 2007, Biological hydrogen production of the genus Clostridium: metabolic study and mathematical model simulation. International Journal of Hydrogen Energy, vol.32(12): 1728–1735.

Niimi T, Sugai Y, Sasaki K, et al., 2009, Canadian International Petroleum Conference 2009 and 60th Annual Technical Meeting of the Petroleum Society, Volume 1 of 2, June 16–18, 2009: Basic study on the microbial conversion of CO2 into CH4 in depleted oil reservoir by using hydrogen-producing bacteria and hydrogenotrophic methanogens. Society of Petroleum Engineers, Richardson, Texas, 997–998.

Sugai Y, Purwasena I A, Sasaki K, et al., 2012, Experimental studies on indigenous hydrocarbon-degrading and hydrogen-producing bacteria in an oilfield for microbial restoration of natural gas deposits with CO2 sequestration. Journal of Natural Gas Science and Engineering, vol.5: 31–41.

Huang L, Yu L, Luo Z, et al., 2014, A microbial enhanced oil recovery trial in Huabei Oilfield in China. Petroleum Science and Technology, vol.32(5): 584–592.

Bhupathiraju V K, McInerney M J and Knapp R M, 1993, Pretest studies for a microbially enhanced oil recovery field pilot in a hypersaline oil reservoir. Geomicrobiology Journal, vol.11(1): 19–34.

Zhang F, She Y-H, Li H-M, et al., 2012, Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour point oil reservoir. Applied Microbiology and Biotechnology, vol. 95(3): 811–821.

Arora P, Ranade D R and Dhakephalkar P K, 2014, Development of a microbial process for the recovery of petroleum oil from depleted reservoirs at 91–96 °C. Bioresource Technology, vol.165: 274–278.



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