Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation
- 690 Downloads
Successful bioremediation of oil pollution is based on a comprehensive understanding of the in situ physicochemical conditions and indigenous microbial communities as well as the interaction between microorganisms and geochemical variables. Nineteen oil-contaminated soil samples and five uncontaminated controls were taken from six major oilfields across different geoclimatic regions in China to investigate the spatial distribution of the microbial ecosystem. Microbial community analysis revealed remarkable variation in microbial diversity between oil-contaminated soils taken from different oilfields. Canonical correspondence analysis (CCA) further demonstrated that a suite of in situ geochemical parameters, including soil moisture and sulfate concentrations, were among the factors that influenced the overall microbial community structure and composition. Phylogenetic analysis indicated that the vast majority of sequences were related to the genera Arthrobacter, Dietzia, Pseudomonas, Rhodococcus, and Marinobacter, many of which contain known oil-degrading or oil-emulsifying species. Remarkably, a number of archaeal genera including Halalkalicoccus, Natronomonas, Haloterrigena, and Natrinema were found in relatively high abundance in some of the oil-contaminated soil samples, indicating that these Euryarchaeota may play an important ecological role in some oil-contaminated soils. This study offers a direct and reliable reference of the diversity of the microbial community in various oil-contaminated soils and may influence strategies for in situ bioremediation of oil pollution.
KeywordsMicrobial community analysis Illumina sequencing Oil-degrading bacteria Oil-emulsifying bacteria Crude oil bioremediation
We thank Dr. Ying Huang for her help and suggestions on the statistical analysis. We thank Dr. Amanda Luther for thoughtful reviews of the manuscript and discussion of the topics therein.
This study was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB06020200), the National Natural Science Foundation of China (Grant No. 41376077 and No. 41406067), the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant No. SIDSSE-QN-201303), and the Open Fund of Key Laboratory of Marine Spill Oil Identification and Damage Assessment Technology (Grant No. 201307).
Conflict of interest
Weimin Sun declares that he has no conflict of interest. Jiwei Li declares that he has no conflict of interest. Lei Jiang declares that he has no conflict of interest. Zhilei Sun declares that he has no conflict of interest. Meiyan Fu declares that she has no conflict of interest. Xiaotong Peng declares that he has no conflict of interest.
This article does not contain any studies with human participants performed by any of the authors.
- An D, Brown D, Chatterjee I, Dong X, Ramos-Padron E, Wilson S, Bordenave S, Caffrey SM, Gieg LM, Sensen CW (2013) Microbial community and potential functional gene diversity involved in anaerobic hydrocarbon degradation and methanogenesis in an oil sands tailings pond 1. Genome 56(10):612–618CrossRefPubMedGoogle Scholar
- Atlas R (1993) Bacteria and bioremediation of marine oil spills. Oceanus;(United States) 36(2)Google Scholar
- Atlas RM, Bartha R (1992) Hydrocarbon biodegradation and oil spill bioremediation Advances in microbial ecology. Springer, pp 287-338Google Scholar
- Bowman JP, McCammon SA, Brown MV, Nichols DS, McMeekin TA (1997) Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl Environ Microb 63(8):3068–3078Google Scholar
- Fowler SJ, Gutierrez‐Zamora ML, Manefield M, Gieg LM (2014) Identification of toluene degraders in a methanogenic enrichment culture. FEMS Microbiol EcolGoogle Scholar
- Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill. Appl Environ Microb 77(22):7962–7974CrossRefGoogle Scholar
- Kunapuli U, Jahn MK, Lueders T, Geyer R, Heipieper HJ, Meckenstock RU (2010) Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons. Int J Syst Evol Micr 60(3):686–695CrossRefGoogle Scholar
- Lenchi N, İnceoğlu Ö, Kebbouche-Gana S, Gana ML, Llirós M, Servais P, García-Armisen T (2013) Diversity of microbial communities in production and injection waters of algerian oilfields revealed by 16S rRNA gene amplicon 454 pyrosequencing. PLoS One 8(6), e66588PubMedCentralCrossRefPubMedGoogle Scholar
- MacNaughton SJ, Stephen JR, Venosa AD, Davis GA, Chang Y-J, White DC (1999) Microbial population changes during bioremediation of an experimental oil spill. Appl Environ Microb 65(8):3566–3574Google Scholar
- Nilsen RK, Torsvik T (1996) Methanococcus thermolithotrophicus isolated from North Sea oil field reservoir Water. Appl Environ Microb 62(2):728–731Google Scholar
- Pinhassi J, Zweifel UL, Hagstroëm A (1997) Dominant marine bacterioplankton species found among colony-forming bacteria. Appl Environ Microb 63(9):3359–3366Google Scholar
- Plakunov V, Zhurina M, Belyaev S (2008) Resistance of the oil-oxidizing microorganism Dietzia sp. to hyperosmotic shock in reconstituted biofilms. Microbiology 77(5):515–522Google Scholar
- Puškárová A, Bučková M, Chovanová K, Harichová J, Karelová E, Godočíková J, Polek B, Ferianc P, Pangallo D (2013) Diversity and PAH growth abilities of bacterial strains isolated from a contaminated soil in Slovakia. Biologia 68(4):587–591Google Scholar
- Rosenberg E, Zuckerberg A, Rubinovitz C, Gutnick D (1979) Emulsifier of Arthrobacter RAG-1: isolation and emulsifying properties. Appl Environ Microb 37(3):402–408Google Scholar
- Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microb 75(23):7537–7541CrossRefGoogle Scholar
- Song H, Wang X, Bartha R (1990) Bioremediation potential of terrestrial fuel spills. Appl Environ Microb 56(3):652–656Google Scholar
- Swannell R, Lee K, McDonagh M (1996) Field evaluations of marine oil spill bioremediation. Microbiol R 60(2):342–365Google Scholar
- von der Weid I, Marques JM, Cunha CD, Lippi RK, Dos Santos SC, Rosado AS, Lins U, Seldin L (2007) Identification and biodegradation potential of a novel strain of Dietzia cinnamea isolated from a petroleum-contaminated tropical soil. Adv Appl Microbiol 30(4):331–339Google Scholar
- Wang X, Chi C, Nie Y, Tang Y, Tan Y, Wu G, Wu X (2011a) Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain. Bioresource Technol 102(17):7755–7761Google Scholar