Distribution of <i>Acetothermia</i>-dominated microbial communities in alkaline hot springs of Baikal Rift Zone.

Zaitseva, S. V.; Lavrentieva, E. V.; Radnagurueva, A. A.; Батурина, О. А.; Kabilov, Мarsel R.; Бархутова, Д. Д.

doi:10.7287/peerj.preprints.3492v1

Cited by 5 publications

(5 citation statements)

References 2 publications

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“…For example, sequences assigned to the class Acetothermiia closely match with DNA sequences previously found in hydrothermal sediments (GenBank: FM868292). Members of this class were previously detected in anaerobic digesters, hot springs, and other deep biosphere studies ( Takami et al, 2012 ; Jungbluth et al, 2017 ; Zaitseva et al, 2017 ; Hao et al, 2018 ; Korzhenkov et al, 2018 ). Sequences assigned to the genus BRH-c8a from the family Desulfallas-Sporotomaculum match closely with sequences retrieved from deep groundwater (LC179584) and group with the genus Desulfotomaculum that can be found in deep subsurface environments ( Sousa et al, 2018 ; Watanabe et al, 2018 ).…”

Section: Discussionmentioning

confidence: 81%

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

et al. 2021

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The island of Surtsey was formed in 1963–1967 on the offshore Icelandic volcanic rift zone. It offers a unique opportunity to study the subsurface biosphere in newly formed oceanic crust and an associated hydrothermal-seawater system, whose maximum temperature is currently above 120°C at about 100m below surface. Here, we present new insights into the diversity, distribution, and abundance of microorganisms in the subsurface of the island, 50years after its creation. Samples, including basaltic tuff drill cores and associated fluids acquired at successive depths as well as surface fumes from fumaroles, were collected during expedition 5059 of the International Continental Scientific Drilling Program specifically designed to collect microbiological samples. Results of this microbial survey are investigated with 16S rRNA gene amplicon sequencing and scanning electron microscopy. To distinguish endemic microbial taxa of subsurface rocks from potential contaminants present in the drilling fluid, we use both methodological and computational strategies. Our 16S rRNA gene analysis results expose diverse and distinct microbial communities in the drill cores and the borehole fluid samples, which harbor thermophiles in high abundance. Whereas some taxonomic lineages detected across these habitats remain uncharacterized (e.g., Acetothermiia, Ammonifexales), our results highlight potential residents of the subsurface that could be identified at lower taxonomic rank such as Thermaerobacter, BRH-c8a (Desulfallas-Sporotomaculum), Thioalkalimicrobium, and Sulfurospirillum. Microscopy images reveal possible biotic structures attached to the basaltic substrate. Finally, microbial colonization of the newly formed basaltic crust and the metabolic potential are discussed on the basis of the data.

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Section: Discussionmentioning

confidence: 81%

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

et al. 2021

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“…While this phylum was not existent at atmospheric pressure (0.3%), its relative representativeness rose to 27.8% at high pressure. This lineage has been described in several oligotrophic thermal environments, such as hot springs, deep-sea sediments or deep aquifers ( Takami et al, 2012 ; Badhai et al, 2015 ; Kadnikov et al, 2017 ; Zaitseva et al, 2017 ; Varliero et al, 2019 ). Although it is not possible to determine how incubation at 90bar could have favored the growth of these microorganisms, it is obvious that this condition favored its activity and is a parameter that must be considered to isolate bacteria of this candidate group.…”

Section: Discussionmentioning

confidence: 99%

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

et al. 2021

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Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L−1 and a phosphate content of 0.02mg.L−1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria (“Candidatus Acetothermia”) with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.

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“…There are a number of possibilities for the observed decrease in KB-1 relative abundance, including that the KB-1 strains in this environment do not metabolize amino acids or that they perhaps were outcompeted by other microbes following the perturbation. Acetothermia and KB-1 organisms detected in other studies have revealed that the clade is capable of thriving in a range of organic matter concentrations, but if the KB-1 organisms in Inyo-BLM 1 are indeed heterotrophic (as are all the physiologically described representatives of this clade), our results imply that they are likely better adapted to in situ organic levels than to the excess provided during our amendment (Nigro et al, 2016;Zaitseva et al, 2017;Hao et al, 2018).…”

Section: Organic Nutrient Amendmentmentioning

confidence: 50%

“…To our knowledge, this dolomitic aquifer is the first time organisms from Candidate Division KB-1 have been found in abundance in a terrestrial, low-salinity system. KB-1 is now classified as a subgroup of phylum Acetothermia (formerly OP1), which has been detected in anaerobic digesters as well as hot springs and other deep biosphere studies (Takami et al, 2012;Zaitseva et al, 2017;Hao et al, 2018), although the recovered diversity of related organisms in our system fall within the more narrowly defined KB-1 clade (sometimes referred to as class Acetothermiia) and we have therefore retained that name here. The only sequenced and published genome for Candidate Division KB-1, recovered from the Red Sea, points to a central metabolism based on glycine betaine degradation, a common N-containing organic osmolyte in hypersaline environments but less likely to be found in abundance in non-marine environments (Nigro et al, 2016).…”

Section: Organic Nutrient Amendmentmentioning

confidence: 99%

Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

et al. 2020

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The microbial ecology of the deep biosphere is difficult to characterize, owing in part to sampling challenges and poorly understood response mechanisms to environmental change. Pre-drilled wells, including oil wells or boreholes, offer convenient access, but sampling is frequently limited to the water alone, which may provide only a partial view of the native diversity. Mineral heterogeneity demonstrably affects colonization by deep biosphere microorganisms, but the connections between the mineral-associated and planktonic communities remain unclear. To understand the substrate effects on microbial colonization and the community response to changes in organic carbon, we conducted an 18-month series of in situ experiments in a warm (57°C), anoxic, fractured carbonate aquifer at 752 m depth using replicate open, screened cartridges containing different solid substrates, with a proteinaceous organic matter perturbation halfway through this series. Samples from these cartridges were analyzed microscopically and by Illumina (iTag) 16S rRNA gene libraries to characterize changes in mineralogy and the diversity of the colonizing microbial community. The substrate-attached and planktonic communities were significantly different in our data, with some taxa (e.g., Candidate Division KB-1) rare or undetectable in the first fraction and abundant in the other. The substrate-attached community composition also varied significantly with mineralogy, such as with two Rhodocyclaceae OTUs, one of which was abundant on carbonate minerals and the other on silicic substrates. Secondary sulfide mineral formation, including iron sulfide framboids, was observed on two sets of incubated carbonates. Notably, microorganisms were attached to the framboids, which were correlated with abundant Sulfurovum and Desulfotomaculum sp. sequences in our analysis. Upon organic matter perturbation, mineral-associated microbial diversity differences were temporarily masked by the dominance of putative heterotrophic taxa in all samples, including OTUs identified as Caulobacter, Methyloversatilis, and Pseudomonas. Subsequent experimental deployments included a methanogen-dominated stage (Methanobacteriales and Methanomicrobiales) 6 months after the perturbation and a return to an assemblage similar to the pre-perturbation community after 9 months. Substrate-associated community differences were again significant within these subsequent phases, however, demonstrating the value of in situ time course experiments to capture a fraction of the microbial assemblage that is frequently difficult to observe in pre-drilled wells.

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Distribution of Acetothermia-dominated microbial communities in alkaline hot springs of Baikal Rift Zone.

Cited by 5 publications

References 2 publications

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

Microbial Diversity Under the Influence of Natural Gas Storage in a Deep Aquifer

Patterns of in situ Mineral Colonization by Microorganisms in a ~60°C Deep Continental Subsurface Aquifer

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