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

Abstract

Background: Microorganisms 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.

Results: Here, 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.

Conclusion: Our 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.

Keywords: Auxotrophy; Hydrocarbon degradation; Metagenomics and metatranscriptomics; Microbial community; Oil reservoir.

Fig. 1

Taxonomic analysis of metagenomes evaluated from unassembled reads by MetaPhlAn2 and Metaxa2 and from assembled 16S rRNA gene sequences. Bar graph is showing the percent abundance of the different members at order level, and only members with more than 0.1% abundance in either sample is showed here. Archaeal members are marked in gray. To get a better visualization, relative abundances of archaeal members are normalized to total number of archaeal members

Fig. 2

Metabolic reconstruction of a putative model for n-hexadecane degradation in Bin9 (Archaeoglobus) and Bin1 (Acinetobacter). Expression level of each gene is represented by bars, one bar equaling a FPKM value of 10. Genes whose FPKM value equal 0 are marked in red. a Proposed anaerobic degradation of n-alkane by Bin9. Orange arrows indicate pathways that are associated with acetogenesis; blue arrows represent pathways that are associated with complete oxidation of n-alkanes coupled to sulfate reduction. b Proposed aerobic n-alkane degradation by Bin1 based on genomic information

Fig. 3

DNA and cDNA mapping rate of GBs for sample W15. The GBs above the dashed line showed cDNA/DNA > 0.5

Fig. 4

Phylogenetic tree of high-quality GBs. Circles represent each genome. The completeness of genomes is shown as the radian, and similarities of amino acid sequences to reference genomes are indicated by color. Genome size and estimated contamination rate are provided inside each circle

Fig. 5

Specific amino acid auxotrophies and vitamin auxotrophies present in high-quality GBs. The auxotrophy of specific compound was confirmed if more than one gene was absent in the synthetic pathway, or overall transcriptional level of pathway was low compared to genomes with complete pathway in which only one gene was absent. Aerobic species are covered in gray. Amino acids are in depicted in blue and vitamins in brown. Amino acids have been ranked according to biosynthetic cost (arrow). A colored square denotes that a species can synthesize an amino acid. The intensity of each color (based on the scale) represents the relative expression of the synthesis pathways, with darker/more intense color indicating higher expression. Auxotrophies are marked by a red cross. A black line next to the box represents the presence of a transporter. A transport system is not required for vitamins B2 and B3