Abundance and Diversity of Methanotrophs and Propanotrophs in Soils above Yangxin Oil Reservoir, China

References

• Baum MG, Bleschert K-H, Wagner M, Schmitt M. 1997. Application of surface prospecting methods in the Dutch North Sea. Petrol Geosci 3:171–181.
   Web of Science ®Google Scholar
• Bowman JP, Sly LI, Nichols PD, Hayward A. 1993. Revised taxonomy of the methanotrophs: description of Methylobacter gen. nov., emendation of Methylococcus, validation of Methylosinus and Methylocystis species, and a proposal that the family Methylococcaceae includes only the group I methanotrophs. Int J Syst Bacteriol 43:735–753.
   Google Scholar
• Brisbane PG, Ladd JN. 1965. The role of micro-organisms in petroleum exploration. Annu Rev Microbiol 19:351–364.
   Web of Science ®Google Scholar
• Chan BJ. 2011. PCR Primers for The Detection of Propane and Butane-Oxidizing Microorganisms. S.M. Dissertation, California Polytechnic State University, San Luis Obispo, CA.
   Google Scholar
• Chao A, Shen T-J. 2003. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ Ecol Stat 10:429–443.
   Web of Science ®Google Scholar
• Costello AM, Lidstrom ME. 1999. Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066–5074.
   PubMed Web of Science ®Google Scholar
• Dedysh SN, Knief C, Dunfield PF. 2005. Methylocella species are facultatively methanotrophic. J Bacteriol 187:4665–4670.
   PubMed Web of Science ®Google Scholar
• Dedysh SN, Liesack W, Khmelenina VN, Suzina NE, Trotsenko YA, Semrau JD, Bares AM, Panikov NS, Tiedje JM. 2000. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs. Int J Syst Evol Microbiol 50:955–969.
   PubMed Web of Science ®Google Scholar
• Deutzmann JS, Wörner S, Schink B. 2011. Activity and diversity of methanotrophic bacteria at methane seeps in eastern Lake Constance sediments. Appl Environ Microbiol 77:2573–2581.
   PubMed Web of Science ®Google Scholar
• Dumont MG, Murrell JC. 2005. Community-level analysis: Key genes of aerobic methane oxidation. Meth Enzymol 397:413–427.
   PubMed Web of Science ®Google Scholar
• Dunfield PF, Yuryev A, Senin P, Smirnova AV, Stott MB, Hou S, Ly B, Saw JH, Zhou Z, Ren Y. 2007. Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia. Nature 450:879–882.
   PubMed Web of Science ®Google Scholar
• Hakemian AS, Rosenzweig AC. 2007. The biochemistry of methane oxidation. Annu Rev Biochem 76:223–241.
   PubMed Web of Science ®Google Scholar
• Hanson RS, Hanson TE. 1996. Methanotrophic bacteria. Microbiol Rev 60:439–471.
   PubMedGoogle Scholar
• Håvelsrud OE, Haverkamp TH, Kristensen T, Jakobsen KS, Rike AG. 2011. A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments. BMC Microbiol 11:221.
   PubMed Web of Science ®Google Scholar
• He R, Wooller MJ, Pohlman JW, Quensen J, Tiedje JM, Leigh MB. 2012. Diversity of active aerobic methanotrophs along depth profiles of arctic and subarctic lake water column and sediments. ISME J 6:1937–1948.
   PubMed Web of Science ®Google Scholar
• Henckel T, Roslev P, Conrad R. 2000. Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil. Environ Microbiol 2:666–679.
   PubMed Web of Science ®Google Scholar
• Holmes AJ, Costello A, Lidstrom ME, Murrell JC. 1995. Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett 132:203–208.
   PubMed Web of Science ®Google Scholar
• Holmes AJ, Roslev P, McDonald IR, Iversen N, Henriksen K, Murrell JC. 1999. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Appl Environ Microbiol 65:3312–3318.
   PubMed Web of Science ®Google Scholar
• Horz H-P, Rich V, Avrahami S, Bohannan BJ. 2005. Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change. Appl Environ Microbiol 71:2642–2652.
   PubMed Web of Science ®Google Scholar
• Islam T, Jensen S, Reigstad LJ, Larsen Ø, Birkeland N-K. 2008. Methane oxidation at 55°C and pH 2 by a thermoacidophilic bacterium belonging to the Verrucomicrobia phylum. Proc Natl Acad Sci 105:300–304.
   PubMed Web of Science ®Google Scholar
• Kadnikov VV, Mardanov AV, Beletsky AV, Shubenkova OV, Pogodaeva TV, Zemskaya TI, Ravin NV, Skryabin KG. 2012. Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal. FEMS Microbiol Ecol 79:348–358.
   PubMed Web of Science ®Google Scholar
• Klusman RW, Saaed MA. 1996. Comparison of light hydrocarbon microseepage mechanisms in hydrocarbon migration and its nearsurface expression. AAPG Memoir 66:157–168.
   Google Scholar
• Kolb S, Knief C, Dunfield PF, Conrad R. 2005. Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ Microbiol 7:1150–1161.
   PubMed Web of Science ®Google Scholar
• Kolb S, Knief C, Stubner S, Conrad R. 2003. Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl Environ Microbiol 69:2423–2429.
   PubMed Web of Science ®Google Scholar
• Kotani T, Kawashima Y, Yurimoto H, Kato N, Sakai Y. 2006. Gene structure and regulation of alkane monooxygenases in propane-utilizing Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7. J Biosci Bioeng 102:184–192.
   PubMed Web of Science ®Google Scholar
• Kotani T, Yurimoto H, Kato N, Sakai Y. 2007. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J Bacteriol 189:886–893.
   PubMed Web of Science ®Google Scholar
• Kreader CA. 1996. Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl Environ Microbiol 62:1102–1106.
   PubMed Web of Science ®Google Scholar
• McCain WD 1990. The properties of petroleum fluids. Tulsa, OK: PennWell Books.
   Google Scholar
• Mogilewskii G. 1938. Microbiological investigations in connecting with gas surveying. Razvedka Nedr 8:59–68.
   Google Scholar
• Mohanty SR, Bodelier PL, Floris V, Conrad R. 2006. Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils. Appl Environ Microbiol 72:1346–1354.
   PubMed Web of Science ®Google Scholar
• Murrell JC, McDonald IR, Gilbert B. 2000. Regulation of expression of methane monooxygenases by copper ions. Trends Microbiol 8: 221–225.
   PubMed Web of Science ®Google Scholar
• Perry JJ. 1980. Propane utilization by microorganisms. Adv Appl Microbiol 26:89–115.
   Google Scholar
• Pol A, Heijmans K, Harhangi HR, Tedesco D, Jetten MS, den Camp HJO. 2007. Methanotrophy below pH 1 by a new Verrucomicrobia species. Nature 450:874–878.
   PubMed Web of Science ®Google Scholar
• Rasheed M, Kalpana M, Veena Prasanna M, Lakshmi M, Madhavi T, Tiwari DM, Patil D, Dayal A, Raju S. 2012. Geo-microbial and light gaseous hydrocarbon anomalies in the near surface soils of Deccan Syneclise Basin, India: Implications to hydrocarbon resource potential. J Petrol Sci Eng 84:33–41.
   Web of Science ®Google Scholar
• Rasheed M, Veena Prasanna M, Satish Kumar T, Patil D, Dayal A. 2008. Geo-microbial prospecting method for hydrocarbon exploration in Vengannapalli Village, Cuddapah Basin, India. Curr Sci 95:361–366.
   Web of Science ®Google Scholar
• Rasheed MA, Lakshmi M, Srinu D, Dayal AM. 2011. Bacteria as indicators for finding oil and gas reservoirs: A case study of the Bikaner-Nagaur Basin, Rajasthan, India. Petrol Sci 8:264–268.
   Web of Science ®Google Scholar
• Saunders DF, Burson KR, Thompson CK. 1999. Model for hydrocarbon microseepage and related near-surface alterations. AAPG Bull 83:170–185.
   Web of Science ®Google Scholar
• Schloss PD, Handelsman J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501–1506.
   PubMed Web of Science ®Google Scholar
• Sealy J. 1974. A geomicrobial method of prospecting for oil. Oil Gas J 8:142–146.
   Google Scholar
• Shennan JL. 2006. Utilisation of C2–C4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol 81:237–256.
   Web of Science ®Google Scholar
• Stolyar S, Costello AM, Peeples TL, Lidstrom ME. 1999. Role of multiple gene copies in particulate methane monooxygenase activity in the methane-oxidizing bacterium Methylococcus capsulatus bath. Microbiology 145:1235–1244.
   PubMed Web of Science ®Google Scholar
• Thrasher J, Fleet AJ, Hay SJ, Hovland M, Düppenbecker S. 1996. Understanding geology as the key to using seepage in exploration: the spectrum of seepage styles. AAPG Special Volumes: 223–241.
   Google Scholar
• Tucker J, Hitzman D. 1994. Detailed microbial surveys help to improve reservoir characterization. Oil Gas J 6:65–69.
   Google Scholar
• Vorobev AV, Baani M, Doronina NV, Brady AL, Liesack W, Dunfield PF, Dedysh SN. 2011. Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase. Int J Syst Evol Microbiol 61:2456–2463.
   PubMed Web of Science ®Google Scholar
• Wagner M, Wagner M, Piske J, Smit R. 2002. Case histories of microbial prospection for oil and gas, onshore and offshore in northwest Europe, in Surface exploration case histories: Applications of geochemistry, magnetics, and remote sensing, Schumacher D, LeSchack LA, eds., AAPG Studies in Geology No. 48 and SEG Geophysical References Series No. 11, p. 453–479.
   Google Scholar
• Wu XY, Xu XM, Wu CF, Fu SY, Deng MC, Feng L, Yuan JP, Wang JH. 2014. Responses of microbial communities to light-hydrocarbon microseepage and novel indicators for microbial prospecting of oil/gas in the Beihanzhuang Oilfield, Northern Jiangsu, China. Geomicrobiol J 31:697–707.
   Web of Science ®Google Scholar
• Xu KW, Tang YP, Ren C, Zhao KB, Wang WM, Sun YG. 2013. Activity, distribution, and abundance of methane-oxidizing bacteria in the near surface soils of onshore oil and gas fields. Appl Microbiol Biotechnol 97:7909–7918.
   PubMed Web of Science ®Google Scholar
• Zhang CY, He Z, Zhang S, Yin MY, Ning Z, Liu YC. 2014. Quantitative significance of functional genes of methanotrophs and propanotrophs in soil above oil and gas fields, China. J Petrol Sci Eng 120:170–176.
   Google Scholar
• Zhang F, She YH, Zheng Y, Zhou Z, Kong SQ, Hou DJ. 2010. Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China. Appl Microbiol Biotechnol 86:1183–1194.
   PubMed Web of Science ®Google Scholar