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Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly.

ABSTRACT: Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013). Although the dominant bacteria and the proportion of hydrogenotrophic and acetoclastic methanogens were different among oil metagenomes, compared with the metagenomes from other environments, all the oil metagenomes contained higher abundances of genes involved in methanogenic hydrocarbon degradation and stress response systems. In addition, a "shape-sorting" manner was proposed for the assembly of microbial communities in oil reservoirs, with the oil reservoir acting as a function sorter to select microbes with special functions from its endemic pool of microorganisms. At the functional level, we found that environmental metagenomes were generally clustered according to their isolation environments but not their geographical locations, suggesting selective processes to be involved in the assembly of microbial communities based on functional gene composition.

SUBMITTER: Nie Y

PROVIDER: S-EPMC4981601 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly.

Nie Yong Y Zhao Jie-Yu JY Tang Yue-Qin YQ Guo Peng P Yang Yunfeng Y Wu Xiao-Lei XL Zhao Fangqing F

Frontiers in microbiology 20160812

Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited i ...[more]

PMID: 27570522

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Project description:BackgroundThe expansion of offshore oil exploration increases the risk of marine species being exposed to oil pollution in currently pristine areas. The adverse effects of oil exposure through toxic properties of polycyclic aromatic hydrocarbons (PAHs) have been well studied in Atlantic cod (Gadus morhua). Nevertheless, the fate of conjugated metabolites in the intestinal tract and their effect on the diversity of intestinal microbial community in fish is less understood. Here, we investigated the intestinal microbial community composition of Atlantic cod after 28 days of exposure to crude oil (concentration range 0.0-0.1 mg/L).ResultsAnalysis of PAH metabolites in bile samples confirmed that uptake and biotransformation of oil compounds occurred as a result of the exposure. Various evidence for altered microbial communities was found in fish exposed to high (0.1 mg/L) and medium (0.05 mg/L) concentrations of oil when compared to fish exposed to low oil concentration (0.01 mg/L) or no oil (control). First, altered banding patterns were observed on denaturing gradient gel electrophoresis for samples pooled from each treatment group. Secondly, based on 16S rRNA sequences, higher levels of oil exposure were associated with a loss of overall diversity of the gut microbial communities. Furthermore, 8 operational taxonomic units (OTUs) were found to have significantly different relative abundances in samples from fishes exposed to high and medium oil concentrations when compared to samples from the control group and low oil concentration. Among these, only one OTU, a Deferribacterales, had increased relative abundance in samples from fish exposed to high oil concentration.ConclusionsThe results presented herein contribute to a better understanding of the effects of oil contamination on the gut microbial community changes in fish and highlight the importance of further studies into the area. Our findings suggest that increased relative abundance of bacteria belonging to the order Deferribacterales may be indicative of exposure to oil at concentrations higher than 0.05 mg/L.

Project description:Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

Project description:The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.

Dataset Information

Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly.

Publications

Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly.

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