Microbial Ecology

, Volume 72, Issue 1, pp 175–184 | Cite as

Methanogen Population of an Oil Production Skimmer Pit and the Effects of Environmental Factors and Substrate Availability on Methanogenesis and Corrosion Rates

  • Okoro Chuma Conlette
  • Nwezza Elebe Emmanuel
  • Okpokwasili Gideon Chijoke
Environmental Microbiology


Assessment of microbial communities from an oil production skimmer pit using 16S rRNA gene sequencing technique revealed massive dominance of methanogenic archaea in both the skimmer pit water and sediment samples. The dominant genera of methanogens involved are mostly the acetotrophic Methanosaeta (36–83 %), and the hydrogenotrophic Methanococcus (49 %) indicating that methanogenesis is the dominant terminal metabolic process in the skimmer pit. Further studies showed that the methanogens had their optimal activity at pH 6–6.5, salinity of 100 mM, and temperature of 35–45 °C. When appropriate substrates are available and utilized by methanogens, methane production correlates with general corrosion rates (r = +0.927; p < 0.01), and under different conditions of pH, salinity and temperature, methane production showed significantly strong positive correlations (r = +0.824, +0.827, and +0.805; p < 0.01, respectively) with general corrosion rates. To the best of our knowledge, this research work was the first to assess microbial community composition of an oil production skimmer pit at Escravos facility in Nigeria.


Skimmer pit Acetotrophic methanosaeta Hydrogenotrophic methanococcus Methanogenesis Environmental conditions 



This work was supported by grants from the Nigerian Petroleum Technology Development Fund (PTDF). We acknowledge the earlier DNA analysis and pyrosequencing carried out with grants from Gerrit Voordouw, University of Calgary, Alberta Canada.

Supplementary material

248_2016_764_MOESM1_ESM.docx (59 kb)
ESM 1 (DOCX 58 kb)


  1. 1.
    Ban Q, Li J, Zhang L, Jha AK (2013) Phylogenic diversity of methanogenic archaea and the kinetics of methane production at slightly acidic conditions of an anaerobic sludge. Int J Agric Biol 15:347–351Google Scholar
  2. 2.
    Blake LI, Treit A, Qvreasl L, Head IM, Gray ND (2015) Response of methanogens in Arctic sediments to temperature and methanogenic substrate availability. PLoS One 10(6):eo129733CrossRefGoogle Scholar
  3. 3.
    Boopathy R (1991) Danels L (1991) Effect of pH on anaerobic mild steel corrosion by methanogenic bacteria. Appl Environ Microbiol 57:2104–2108PubMedPubMedCentralGoogle Scholar
  4. 4.
    Chae KJ, Jang A, Yim SK (2008) The effects of digestion temperature and temperature shock on the biogas yields from the mesophylic anaerobic digestion of swine manure. Bioresour Technol 99:1–6CrossRefPubMedGoogle Scholar
  5. 5.
    Daniels L, Belay N, Rajagopal BJ, Weiner PJ (1987) Bacterial methanogenesis and growth from CO2 with elemental iron as the sole source of electrons. Science 237:509–511CrossRefPubMedGoogle Scholar
  6. 6.
    Dhake RK, Waghmare CK, Alam S, Kambo DV, Sigh L (2003) Effects of propionate toxicity on methanogenesis of soil at psychrophilic temperature. Bioresour Technol 87:299–303CrossRefGoogle Scholar
  7. 7.
    Dolfing J, Larter SR, Head IM (2008) Thermodynamic constrains on methanogenic crude oil biodegradation. ISME J 2:442–452CrossRefPubMedGoogle Scholar
  8. 8.
    Eaton AD, Clesceri LS, Greenberg AE (1995) Standard methods for the examination of water and waste water, 19th edn. United Books Press, Batimore, p 1126Google Scholar
  9. 9.
    Fey A, Conrad R (2003) Effects of temperature on the rate limiting steps in the methanogenic degradation pathway in rice field soil. Soil Biol Biochem 35:1–8CrossRefGoogle Scholar
  10. 10.
    Fey A, Claus P, Conrad R (2004) Temporal change of 13C isotope signatures and methanogenic pathways in rice field soil incubated anoxically at different temperatures. Geochim Cosmochim 68:293–306CrossRefGoogle Scholar
  11. 11.
    Gao P, Huimei T, Li G, Sun H, Ma T (2015) Microbial diversity and abundance in the Xinjiang Luliang long-term water-flooding petroleum reservoir. Microbiology Open. John Wiley and Sons Ltd (Publishers). pp. 1–11Google Scholar
  12. 12.
    Gieg LM, Duncan KE, Suflita JM (2008) Bioenergy production via microbial conversion of residual oil to natural gas. Appl Environ Microbiol 74:3022–3029CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Gittel A, Sorenson KB, Skorhus TL, Ingvorsen K, Schramm A (2009) Prokaryotic community structure and sulphate reducer activity in water from high temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 77(22):7086–7096CrossRefGoogle Scholar
  14. 14.
    Glissmann K, Chin KJ, Casper P, Conrad R (2004) Methanogenic pathways and archaeal community structure in the sediment of eutrophic lake Dagow. Effects of temperature. Microbial Ecol 48:389–399CrossRefGoogle Scholar
  15. 15.
    Grabowski A, Nercessian O, Fayolle F, Blanchet D, Jeanthon C (2005) Microbial diversity in production waters of a low temperature biodegraded oil reservoir. FEMS Microbiol Ecol 54:427–445CrossRefPubMedGoogle Scholar
  16. 16.
    Head IM, Aitkem CM, Group PR (2010) Hydrocarbon degradation in petroleum reservoirs. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin, pp 3098–3107Google Scholar
  17. 17.
    Huson D, Richter D, Rausch C, Dezulian T, Franz M, Rupp R (2007) Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinf 8:460CrossRefGoogle Scholar
  18. 18.
    Jones DM, Head IM, Gray ND, Adams JJ, Rowan AK, Aitken CM (2008) Crude oil biodegradation via methanogenesis in subsurface petroleum reservoirs. Nature 451:176–180CrossRefPubMedGoogle Scholar
  19. 19.
    Kanso S (2003) Molecular studies of bacterial communities in the great Atesian Basin Aquifers. Ph.D. Thesis. Griffith University, Queensland Australia. 194ppGoogle Scholar
  20. 20.
    Larsen J, Ragmussen K, Pedersen H, Sorensen K, Lundgard T, Skovhus TL (2010) Consortia of MIC Bacteria and Archaea causing pitting corrosion in top side oil production facilities. Paper NACE 10252 presented at the NACE Corrosion Annual Conference and Exposition, San Antonio TX. March 14–18, 2010Google Scholar
  21. 21.
    Li H, Yang SZ, Mu BZ, Rong ZF, Zhang J (2007) Molecular phylogenetic diversity of a microbial community associated with high temperature petroleum reservoir at an offshore field. FEMS Microbiol Ecol 60:74–84CrossRefPubMedGoogle Scholar
  22. 22.
    Li D, Midgley DJ, Ross PS, Oytan Y, Abel GC, Vock H, Daud WA, Hendry P (2012) Microbial biodiversity of a Malaysian oil field and a systematic comparison with oil reservoir worldwide. Arch Microbiol 194:513–523CrossRefPubMedGoogle Scholar
  23. 23.
    Magot M (2005) Indigenous microbial communities in oil fields. In: Ollivier B, Magot M (eds) Petroleum Microbiology. ASM, Washington, pp 21–34CrossRefGoogle Scholar
  24. 24.
    Magot M, Ollivier B, Patel B (2000) Microbiology of petroleum reservoirs. Antonie Van Leeuwenhoek 77:103–116CrossRefPubMedGoogle Scholar
  25. 25.
    Mand J, Park HS, Jack TR, Voordouw G (2014) The role of acetogens in microbially influenced corrosion of steel. Front Microbiol 5:268CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Mand J, Park HS, Okoro C, Lomans BP, Smith S, Chiejina L, Voordouw G (2016) Microbial methane production associated with carbon steel corrosion in a Nigerian oil field. Front Microbiol 6:1538CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Margesin R, Schinner F (2001) Biodegradation and bioremediation of hydrocarbons in extreme environments. Appli Microbiol Biotechnol 56:650–663CrossRefGoogle Scholar
  28. 28.
    Mayumi D, Dolfing J, Sakata S, Maeda H, Miyagawa H, Ikarachi M (2013) C02 concentration dictates alternative methanogenic pathways in oil reservoirs. Nat Commun 4:1–6CrossRefGoogle Scholar
  29. 29.
    Mishra SR, Pattnaik P, Sethunathan N, Aahya TK (2003) Anion mediated salinity affecting methane production in a flooded alluvial soil. Geomicrobiol J 20:579–586CrossRefGoogle Scholar
  30. 30.
    Nozhevnikova AN, Nekrasova V, Ammann A, Zehider AJB, Wehrli B, Holliger C (2007) Influence of temperature and high acetate concentration on methanogenesis in lake sediment slurries. FEMS Microbiol Ecol 62:336–344CrossRefPubMedGoogle Scholar
  31. 31.
    Okoro C, Agrawal A, Callbeck C (2012) Simultaneous biosurfactant production and hydrocarbon biodegradation by the resident aerobic flora of an oil production skimmer pit at elevated temperature and saline conditions. Life Sci J 9(3):356–364Google Scholar
  32. 32.
    Okoro C, Smith S, Chiejina L, Lumactud R, An D, Park HS, Voordouw J, Lomans BP, Voordouw G (2014) Comparison of microbial communities involved in souring and corrosion in offshore and onshore oil production facilities in Nigeria. J Ind Microbiol Biotechnol 41:665–678CrossRefPubMedGoogle Scholar
  33. 33.
    Orphan VJ, Taylor LT, Hafenbradl D, Delong EF (2000) Culture dependent and culture independent characterization of microbial assemblages associated with high temperature petroleum reservoirs. Appl Environ Microbiol 66:700–711CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Park HS, Chatterjee I, Dong X, Wang SH, Sensen CW, Caffrey SM, Jack TR, Boivin J, Voordouw G (2011) Effect of sodium bisulfite injection on the microbial community composition in a brackish-water-transporting pipeline. Appl Environ Microbiol 7:6908–6917CrossRefGoogle Scholar
  35. 35.
    Pham DV, Hnatow LL, Zhang S, Fallon DR, Jackson SC, Tomb JF, DeLong EF, Keeler SJ (2009) Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods. Environ Microbiol 11(1):176–187CrossRefPubMedGoogle Scholar
  36. 36.
    Pruesse EC, Quast K, Knittel B, Fuchs W, Ludwig J, Peplies J, Glöckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35:7188–7196CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Ramos-Padrón E, Bordenave S, Lin S, Bhaskar IM, Dong X, Sensen CW, Fournier J, Voordouw G, Gieg LM (2011) Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond. Environ Sci Technolo 45:439–446CrossRefGoogle Scholar
  38. 38.
    Schloss PD, Westcott SL (2011) Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol 77:3219–3226CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Schloss PD, Westcott SL, Thomas R, Hall JR, Hartmann M, Hollister EB, Lesniewski RA (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Soh J, Dong X, Caffrey SM, Voordouw G, Sensen CW (2013) Phonenix 2. A locally installable large scale 16S rRNA gene sequence analysis pipeline with web interface. J Biotechnol 167:393–403CrossRefPubMedGoogle Scholar
  41. 41.
    Stevens SH, Ferry JG, Schoell M (2012) Methanogenic conversion of C02 into methane. A potential remediation technology for C02 storage sites. Prepared for US department of Energy. Office of Science, ChicagoGoogle Scholar
  42. 42.
    Suarez AS, Lopez AL, Sanchez AT, Yara P, Orfilia A, Terrados J, Arndo J (2011) Response of sulfate reducing bacteria to an artificial oil spill in a coastal marine sediment. Environ Microbiol. doi: 10.1111/j.1462-2920.2011.01451.x Google Scholar
  43. 43.
    Tabatabaei RA, Abdullah RN, Wright ADG, Shirai Y, Saraki K, Sulaiman A, Hasan MA (2010) Importance of methanogenic archaea populations in anaerobic waste water treatments. Proc Biochem 55:1214–1225CrossRefGoogle Scholar
  44. 44.
    Trüper HG, Schlegel HG (1964) Sulfur metabolism in Thiorhodanceae. Quantitative measurements in growing cells of Chromatium okehii. Antonie van Leewenhoek 30:225–238CrossRefGoogle Scholar
  45. 45.
    Uchiyama T, Ito K, Mori K, Tsurumaru H, Harayama S (2010) Iron-corroding methanogen isolated from a crude-oil storage tank. Appl Environ Microbiol 76(6):1783–1788CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Waldron PJ, Petsh ST, Matim AM, Nusslein K (2007) Salinity constraints of subsurface Archaeal diversity and methanogenesis on sedimentary rock rich in organic matter. Appl Environ Microbiol 73(13):4171–4179CrossRefPubMedPubMedCentralGoogle Scholar
  47. 47.
    Wang LY, Duan RY, Liu JF, Yang SZ, Gu JD, Mu BZ (2012) Molecular analysis of microbial community structures in water flooded petroleum reservoirs with different temperatures. Biogeosciences 9:4645–4659CrossRefGoogle Scholar
  48. 48.
    Ye R, Jin Q, Bohannan B, Keller JK, McAllister SA (2012) pH controls over anaerobic carbon mineralization, the efficiency of methane production and methanogenic pathways in Peatlands across an ambrotrophic-minerotrophic gradient. Soil Biol Biochem 54:36–47CrossRefGoogle Scholar
  49. 49.
    Youssef N, Elshahed MS, McLnerney MS (2009) Microbial process in oil fields; Culprits, Problems and Opportunities. In; Advances in applied microbiology. 66:141–251. Laskin, A. I, Sariaslani S and Gadd, G.M (eds.). ASM press (Pub.)Google Scholar
  50. 50.
    Yue JC, Clayton MK (2005) A similarity measure based on species proportions. Commun Stat Theory Methods 34:2123–2131CrossRefGoogle Scholar
  51. 51.
    Zhang T, Fang HHP, Ko BCB (2003) Methanogen population in a marine biofilm corrosive to mild steel. Appl Microbiol Biotechnol 63:101–106CrossRefPubMedGoogle Scholar
  52. 52.
    Zhu X, Lubeck J, Kilbane JJ (2003) Characterization of microbial communities in gas industrial pipelines. Appli Environ Microbiol 69(9):5354–5363CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Okoro Chuma Conlette
    • 1
  • Nwezza Elebe Emmanuel
    • 2
  • Okpokwasili Gideon Chijoke
    • 3
  1. 1.Department of Biology, Microbiology and BiotechnologyFederal UniversityIkwoNigeria
  2. 2.Department of Mathemetics/Computer science/Statistics/InformaticsFederal UniversityIkwoNigeria
  3. 3.Department of MicrobiologyUniversity of Port HarcourtPort HarcourtNigeria

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