Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs

Gittins, Daniel A.; Bhatnagar, Srijak; Hubert, Casey R.J.

doi:10.1128/msystems.00884-22

Cited by 4 publications

(1 citation statement)

References 72 publications

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“…Then, the abundance of Desulfobacterota declined steadily over time, while the abundance of Cloacimonadota increased, suggesting a potential competition between these two phyla. Desulfobacterota, Thermotogota, and Cloacimonadota have been identified as core phyla specifically in low-temperature oil reservoirs (Hidalgo et al, 2021;Gittins et al, 2023;Zhou et al, 2023). Core phyla are phyla that are prevalent and most prominent within various oil reservoirs around the world.…”

Section: Discussionmentioning

confidence: 99%

Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis

Beilig,

Pannekens,

Voskuhl

et al. 2024

Front. Microbiomes

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Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m−2 OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.

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Section: Discussionmentioning

confidence: 99%

Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis

Beilig,

Pannekens,

Voskuhl

et al. 2024

Front. Microbiomes

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Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation

Machado,

Dias,

Cayô

et al. 2024

Microbiol Spectr

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Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia ( Borkfalkiaceae , Lachnospiraceae , Monoglobaceae , and Oscillospiraceae families) and Bacilli ( Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia , Bacilli , UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health. IMPORTANCE Spores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia , Bacilli , and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.

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Anaerobic Oxidation of Oil by Microbial Communities of Bottom Sediments of a Natural Oil Seepage Site (Bolshaya Zelenovskaya, Middle Baikal)

Pavlova,

Bukin,

Izosimova

et al. 2024

Microbiology

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The microbial communities of bottom sediments of the Bolshaya Zelenovskaya oil seepage site (Lake Baikal) were investigated to assess their diversity and potential functional activity in the anaerobic degradation of oil. Microorganisms of the subsurface and deep sediment layers were grown in enrichment cultures supplemented with oil and various electron acceptors for 1 year at 10°C, and it was found that the concentrations of n-alkanes and polyaromatic hydrocarbons decreased by 1.2–2 and 2.2–2.8 times, respectively. Hydrocarbon conversion was accompanied by generation of hydrocarbon gases (methane and ethane). The microbial community of subsurface sediments had a higher bacterial diversity than the community of deep horizons and was composed of microorganisms specialized in degradation of a broad range of substrates, including oil hydrocarbons. The community of the deep sediment layer was dominated by Atribacterota, Caldisericota, and Bathyarchaeia (Thermoproteota), as well as members of the “rare biosphere”: Elusimicrobiota and Candidatus Hadarchaeota. Apparently, oil degradation in the bottom sediments of Lake Baikal is primarily mediated by members of the phyla Bacillota, Pseudomonadota, Chloroflexota, Actinomycetota, Desulfobacterota, Atribacterota, Halobacteriota, and Bathyarchaeia (Thermoproteota).

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Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs

Cited by 4 publications

References 72 publications

Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis

Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis

Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation

Anaerobic Oxidation of Oil by Microbial Communities of Bottom Sediments of a Natural Oil Seepage Site (Bolshaya Zelenovskaya, Middle Baikal)

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