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.

Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert

“…Fifteen months post rain, the community comprises an entirely new set of organisms but its functional potential recovered to a pre-rain state, suggesting that the community taxonomic structure entered an alternative equilibrium state during the recovery period [4, 11]. The functional consistency of a community, disconnected from taxonomic variance, has previously been documented in a variety of microbiomes and stems from functional redundancy of closely related taxa [6, 7, 52, 53]. In particular, isolated microbiomes such as miniature aquatic ecosystems found in bromeliad rosettes (similarly isolated as the halite nodules) appear to converge on identical functional landscapes through mechanisms such as stoichiometric balancing between metabolic pathways, despite great inter-community taxonomic diversity [54, 55].…”

CANT-HYD: A curated database of phylogeny-derived Hidden Markov Models for annotation of marker genes involved in hydrocarbon degradation

“…Metagenomes representing diverse environments such as petroleum reservoirs (36)(37)(38)(39), oil spill experimental microcosms (40,41), marine systems (42)(43)(44)(45), host-associated microbiomes (46)(47)(48) and other environments (49,50), were downloaded either as unassembled raw data from the NCBI SRA or as predicted gene sequences from the JGI Genome Portal (Supplementary Table ST4). Raw reads from unassembled metagenomes were filtered using BBDuk (sourceforge.net/projects/bbmap/) for a minimum quality of 15 and a minimum read length of 150bp.…”

Microbiome Assessment of Global Oil Reservoirs Reveals Site-Specific Hydrocarbon Degradation Functional Profiles

“…Seventeen datasets derived from publicly available shotgun metagenomes associated to oil fields were downloaded and used in this study. These data correspond to 17 samples distributed in six studies [1][2][3]6,11,12]. Metagenome data from oil reservoirs with different recovery management and temperatures located in different regions were included in order to investigate the influence of geographic location, temperature and anthropogenic interventions on functional and taxonomic profiles of the indigenous microbial communities through the recovery of petroleum-associated Metagenome Assembled Genomes (MAGs).…”