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Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO 2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO 2 , yet there has been little consideration of the subsurface microbial impact on CO 2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO 2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO 2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H 2 generation. We expect that the bioavailability of H 2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO 2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO 2 storage sites and its potential impact.

Carbon capture and storage (CCS) is a key technology to mitigate the environmental impact of carbon dioxide (CO 2 ) emissions. An understanding of the potential trapping and storage mechanisms is required to provide confidence in safe and secure CO 2 geological sequestration 1,2 . Depleted hydrocarbon reservoirs have substantial CO 2 storage potential 1 , 3 , and numerous hydrocarbon reservoirs have undergone CO 2 injection as a means of enhanced oil recovery (CO 2 -EOR), providing an opportunity to evaluate the (bio)geochemical behaviour of injected carbon. Here we present noble gas, stable isotope, clumped isotope and gene-sequencing analyses from a CO 2 -EOR project in the Olla Field (Louisiana, USA). We show that microbial methanogenesis converted as much as 13-19% of the injected CO 2 to methane (CH 4 ) and up to an additional 74% of CO 2 was dissolved in the groundwater. We calculate an in situ microbial methanogenesis rate from within a natural system of 73-109 millimoles of CH 4 per cubic metre (standard temperature and pressure) per year for the Olla Field. Similar geochemical trends in both injected and natural CO 2 fields suggest that microbial methanogenesis may be an important subsurface sink of CO 2 globally. For CO 2 sequestration sites within the environmental window for microbial methanogenesis, conversion to CH 4 should be considered in site selection., (© 2021. The Author(s).)

Microorganisms living in deep-oil reservoirs face extreme conditions of elevated temperature and hydrostatic pressure. Within these microbial communities, members of the order Thermotogales are predominant. Among them, the genus Pseudothermotoga is widespread in oilfield-produced waters. The growth and cell phenotypes under hydrostatic pressures ranging from 0.1 to 50 MPa of two strains from the same species originating from subsurface, Pseudothermotoga elfii DSM9442 isolated from a deep African oil-producing well, and surface, P. elfii subsp. lettingae isolated from a thermophilic sulfate-reducing bioreactor, environments are reported for the first time. The data support evidence for the piezophilic nature of P. elfii DSM9442, with an optimal hydrostatic pressure for growth of 20 MPa and an upper limit of 40 MPa, and the piezotolerance of P. elfii subsp. lettingae with growth occurring up to 20 MPa only. Under the experimental conditions, both strains produce mostly acetate and propionate as volatile fatty acids with slight variations with respect to the hydrostatic pressure for P. elfii DSM9442. The data show that the metabolism of P. elfii DSM9442 is optimized when grown at 20 MPa, in agreement with its piezophilic nature. Both Pseudothermotoga strains form chained cells when the hydrostatic pressure increases, especially P. elfii DSM9442 for which 44% of cells is chained when grown at 40 MPa. The viability of the chained cells increases with the increase in the hydrostatic pressure, indicating that chain formation is a protective mechanism for P. elfii DSM9442., Competing Interests: ZS and AJ were employed by the ExxonMobil Research and Engineering Company. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest., (Copyright © 2020 Roumagnac, Pradel, Bartoli, Garel, Jones, Armougom, Fenouil, Tamburini, Ollivier, Summers and Dolla.)

Hot oil reservoirs harbor diverse microbial communities, with many of them inhabiting thermophilic or hyperthermophilic fermentative Thermotogae species. A new Thermotoga sp. strain TFO was isolated from an Californian offshore oil reservoir which is phylogenetically related to thermophilic species T. petrophila RKU-1 T and T. naphthophila RKU-10 T , isolated from the Kubiki oil reservoir in Japan. The average nucleotide identity and DNA-DNA hybridization measures provide evidence that the novel strain TFO is closely related to T. naphthophila RKU-10 T , T. petrophila RKU-1 T and can not be differentiated at the species level. In the light of these results, the reclassification of T. naphthophila RKU-10 and strain TFO as heterotypic synonyms of T. petrophila is proposed. A pangenomic survey of closely related species revealed 55 TFO strain-specific proteins, many of which being linked to glycosyltransferases and mobile genetic elements such as recombinases, transposases and prophage, which can contribute to genome evolution and plasticity, promoting bacterial diversification and adaptation to environmental changes. The discovery of a TFO-specific transport system dctPQM, encoding a tripartite ATP-independent periplasmic transporter (TRAP), has to be highlighted. The presence of this TRAP system assumes that it could assist in anaerobic n-alkane degradation by addition of fumarate dicarboxylic acid, suggesting a niche-specific gene pool which correlates with the oil reservoir that T. petrophila TFO inhabits. Finally, T. naphthophila RKU-10, T. petrophila RKU-1 T , T. petrophila TFO form a distinct phylogenetic lineage with different geographic origins, share the same type of ecological niche including the burial history of fields. Theses findings might support the indigenous character of this species in oil reservoirs., (Copyright © 2020. Published by Elsevier GmbH.)

Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico. These elevated salinity (149-181 ppt salinity, 4-5× salinity of seawater) reservoirs have limited taxonomic and functional microbial diversity dominated by methanogens, Halanaerobium and other Firmicutes lineages, and contained less abundant lineages such as Deltaproteobacteria. Metagenome assembled genomes (MAGs) were generated and analyzed from the various wells. Methanogen MAGs were closely related to Methanohalophilus euhalobius , a known methylotrophic methanogen from a high salinity oil environment. Based on metabolic reconstruction of genomes, the Halanaerobium perform glycine betaine fermentation, potentially produced by the methanogens. Industrial introduction of methanol to prevent methane hydrate formation to this environment is likely to be consumed by these methanogens. As such, this subsurface oil population may represent influences from industrial processes., (Copyright © 2020 Christman, León-Zayas, Summers and Biddle.)

We present here the draft genome sequence of a pyridine-degrading bacterium, Micrococcus luteus ATCC 49442, which was reclassified as Pseudarthrobacter sp. strain ATCC 49442 based on its draft genome sequence. Its genome length is 4.98 Mbp, with 64.81% GC content., (Copyright © 2020 Gupta et al.)

Here, we report the draft genome sequence of Arthrobacter sp. strain ATCC 49987, consisting of three contigs with a total length of 4.4 Mbp. Based on the genome sequence, we suggest reclassification of Arthrobacter sp. strain ATCC 49987 as Pseudarthrobacter sp. strain ATCC 49987., (Copyright © 2020 Gupta et al.)

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name U Petromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that U Petromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.

Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafloor hydrocarbon seeps have been demonstrated to significantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10-15 cm below seafloor) were collected from five natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chloroflexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fixation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. Although ANME-1 archaea and SRB are present in low relative abundances, genome bins from the reference sites are dominated by uncultured members of NC10 and anammox Scalindua, suggesting a prevalence of nitrogen transformations for energy in non-seep pelagic sediments. This study suggests that hydrocarbon seeps can greatly change the microbial community structure by stimulating nitrogen fixation, inherently shifting the nitrogen metabolism compared to those of the reference sediments.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation., (Copyright © 2019 Gupta et al.)

The phylum Thermotogae gathers thermophilic, hyperthermophic, mesophilic, and thermo-acidophilic anaerobic bacteria that are mostly originated from geothermally heated environments. The metabolic and phenotypic properties harbored by the Thermotogae species questions the evolutionary events driving the emergence of this early branch of the universal tree of life. Recent reshaping of the Thermotogae taxonomy has led to the description of a new genus, Pseudothermotoga, a sister group of the genus Thermotoga within the order Thermotogales. Comparative genomics of both Pseudothermotoga and Thermotoga spp., including 16S-rRNA-based phylogenetic, pan-genomic analysis as well as signature indel conservation, provided evidence that Thermotoga caldifontis and Thermotoga profunda species should be reclassified within the genus Pseudothermotoga and renamed as Pseudothermotoga caldifontis comb. nov. (type strain=AZM44c09 T ) and Pseudothermotoga profunda comb. nov. (type strain=AZM34c06 T ), respectively. In addition, based upon whole-genome relatedness indices and DNA-DNA Hybridization results, the reclassification of Pseudothermotoga lettingae and Pseudothermotoga subterranea as latter heterotypic synonyms of Pseudothermotoga elfii is proposed. Finally, potential genetic elements resulting from the distinct evolutionary story of the Thermotoga and Pseudothermotoga clades are discussed., (Copyright © 2018 The Authors. Published by Elsevier GmbH.. All rights reserved.)

Reaching a depth of 713 m below the surface, the Soudan Underground Iron Mine (Soudan, MN, USA) transects a massive Archaean (2.7 Ga) banded iron formation, providing a remarkably accessible window into the terrestrial deep biosphere. Despite organic carbon limitation, metal-reducing microbial communities are present in potentially ancient anoxic brines continuously emanating from exploratory boreholes on Level 27. Using graphite electrodes deposited in situ as bait, we electrochemically enriched and isolated a novel halophilic iron-reducing Deltaproteobacterium, 'Desulfuromonas soudanensis' strain WTL, from an acetate-fed three-electrode bioreactor poised at +0.24 V (vs. standard hydrogen electrode). Cyclic voltammetry revealed that 'D. soudanensis' releases electrons at redox potentials approximately 100 mV more positive than the model freshwater surface isolate Geobacter sulfurreducens, suggesting that its extracellular respiration is tuned for higher potential electron acceptors. 'D. soudanensis' contains a 3,958,620-bp circular genome, assembled to completion using single-molecule real-time (SMRT) sequencing reads, which encodes a complete TCA cycle, 38 putative multiheme c-type cytochromes, one of which contains 69 heme-binding motifs, and a LuxI/LuxR quorum sensing cassette that produces an unidentified N-acyl homoserine lactone. Another cytochrome is predicted to lie within a putative prophage, suggesting that horizontal gene transfer plays a role in respiratory flexibility among metal reducers. Isolation of 'D. soudanensis' underscores the utility of electrode-based approaches for enriching rare metal reducers from a wide range of habitats.