Metabolic capability and in situ activity of microorganisms in an oil reservoir

Abstract

BackgroundMicroorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy.ResultsHere, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery.ConclusionOur data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.Electronic supplementary materialThe online version of this article (10.1186/s40168-017-0392-1) contains supplementary material, which is available to authorized users.

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

“…However, these results must be interpreted with caution as the co‐culture contains yeast extract, which contains amino acids. Some recent studies also identify coordinated cross‐feeding between organisms (Hubalek et al ., ; Liu et al ., ; Zengler and Zaramela, ), suggesting nutrient exchange may be a prevalent and critical interaction for syntrophy.…”

The social network of microorganisms — how auxotrophies shape complex communities

“…Although auxotrophies and the role of amino acid and vitamin exchange have been identified recently in several microbial communities 5,6,31,32,61 , the dynamics of these complex interaction networks have only been revealed in simple co-culture experiments. However, interactions between multiple species can change over time according to nutrient availability and proteome allocation 4 .…”

“…Until recently, interactions have been viewed as successional activities of various members, each providing the energy source for the next member. However, on the basis of recent studies, a new picture has emerged, which emphasizes interdependencies and convoluted networks of microorganisms that are not limited to the exchange of electron donors for growth 2 but include the exchange of amino acids 2–6 , vitamins 7–9 and other cofactors 10,11 (FIG. 1).…”

Genomic and Transcriptomic Evidence Supports Methane Metabolism in Archaeoglobi

“…Furthermore, the assembly of the contig in "Ca. Methanomixophus hydrogenotrophicum" Bin16 was checked by PCR amplifications using DNA of W2 and W9 production water samples from the Jiangsu oil reservoir (18), and the amplicon sequences matched 99% to 100% to the partial mtrH gene and multiple genes located downstream in the contig ). The emergence of colocated genes homologous to distinct microorganisms could be a result of HGT or, as suggested, a remnant character of the LCA before gene losses.…”