Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Abstract

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

“…Methanogenesis is commonly associated with the biodegradation of crude oil in reservoirs [ 63 ] and is likely the main mechanism responsible for the formation of heavy oil in these ecosystems [ 64 ]. Methanogenic classes of the phylum Euryarchaeota have been repeatedly observed in oil reservoirs worldwide and considered part of their core microbiome [ 65 ].…”

“…The detection of the ack gene from Clostridiales in our samples suggests that they have the potential to generate and provide acetate to other taxa, e.g., Thermotogales and/or Methyloceanibacter . Members of Thermotogales have several times been detected in high-temperature oil reservoirs [ 65 ] and methanogenic enrichment cultures [ 66 , 67 , 70 , 72 ] and considered to be secondary fermenters during hydrocarbon degradation. Combined with the detection of several different methanogens in our samples, these suggest complex syntrophic interactions in Keri Lake sediments, probably involving more than two partners.…”

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

“…Although diversity and physiology of microorganisms inhabiting oil fields have been compiled and reviewed worldwide (Wentzel et al, 2013;Li et al, 2017;Sierra-Garcia et al, 2017), determining if the microorganisms recovered are indigenous to the subsurface environment and not from contamination sources is a thorny issue in petroleum microbiology. The reason is because several of the microbial community studies in petroleum reservoirs have analyzed produced waters and thus, there are some drawbacks to consider when interpreting petroleum microbiology.…”

Complete Genome Sequence of Marinobacterium aestuarii ST58-10 T , a Benzene-Degrading Bacterium Isolated from Estuarine Sediment

“…To date, 10 genomes of Marinobacterium species have been published in the NCBI genome database; however, the genome of only M. aestuarii ST58-10 T has been sequenced completely. Considering the unique benzene-degrading properties of this strain and its dominant composition in hydrocarbon-rich environments, such as oil reservoirs ( 3 , 4 ), we conducted genome sequencing to elucidate the physiological roles and metabolic potential of M. aestuarii ST58-10 T .…”