Dataset Information

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics.

ABSTRACT: To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.

SUBMITTER: Kadnikov VV

PROVIDER: S-EPMC7509429 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics.

Kadnikov Vitaly V VV Mardanov Andrey V AV Beletsky Alexey V AV Karnachuk Olga V OV Ravin Nikolai V NV

Frontiers in microbiology 20200903

To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic <i>Methanobacteriaceae;</i> acetoclastic and methylotrophi ...[more]

PMID: 33013807

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Project description:BackgroundSubsurface microorganisms contribute to important ecosystem services, yet little is known about how the composition of these communities is affected by small scale heterogeneity such as in preferential flow paths including biopores and fractures. This study aimed to provide a more complete characterization of microbial communities from preferential flow paths and matrix sediments of a clayey till to a depth of 400 cm by using 16S rRNA gene and fungal ITS2 amplicon sequencing of environmental DNA. Moreover, shotgun metagenomics was applied to samples from fractures located 150 cm below ground surface (bgs) to investigate the bacterial genomic adaptations resulting from fluctuating exposure to nutrients, oxygen and water.ResultsThe microbial communities changed significantly with depth. In addition, the bacterial/archaeal communities in preferential flow paths were significantly different from those in the adjacent matrix sediments, which was not the case for fungal communities. Preferential flow paths contained higher abundances of 16S rRNA and ITS gene copies than the corresponding matrix sediments and more aerobic bacterial taxa than adjacent matrix sediments at 75 and 150 cm bgs. These findings were linked to higher organic carbon and the connectivity of the flow paths to the topsoil as demonstrated by previous dye tracer experiments. Moreover, bacteria, which were differentially more abundant in the fractures than in the matrix sediment at 150 cm bgs, had higher abundances of carbohydrate active enzymes, and a greater potential for mixotrophic growth.ConclusionsOur results demonstrate that the preferential flow paths in the subsurface are unique niches that are closely connected to water flow and the fluctuating ground water table. Although no difference in fungal communities were observed between these two niches, hydraulically active flow paths contained a significantly higher abundance in fungal, archaeal and bacterial taxa. Metagenomic analysis suggests that bacteria in tectonic fractures have the genetic potential to respond to fluctuating oxygen levels and can degrade organic carbon, which should result in their increased participation in subsurface carbon cycling. This increased microbial abundance and activity needs to be considered in future research and modelling efforts of the soil subsurface.

Project description:The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles.

Project description:Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.

Project description:One of the most promising planetary bodies that might harbor extraterrestrial life is Mars, given the presence of liquid water in the deep subsurface. The upper crust of Mars is mainly composed of >3.7-billion-year-old basaltic lava where heat-driven fluid circulation is negligible. The analogous crustal environment to the Martian subsurface is found in the Earth's oceanic crust composed of basaltic lava. The basaltic crust tends to cool down for 10-20-million-years after formation. However, microbial life in old cold basaltic lava is largely unknown even in the Earth's oceanic crust, because the lack of vigorous circulation prevents sampling of pristine crustal fluid from boreholes. Alternatively, it is important to investigate deep microbial life using pristine drill cores obtained from basaltic lava. We investigated a basaltic rock core sample with mineral-filled fractures drilled during Integral Ocean Drilling Project Expedition 329 that targeted 104-million-year-old oceanic crust. Mineralogical characterizations of fracture-infilling minerals revealed that fractures/veins were filled with Mg-rich smectite called saponite and calcium carbonate. The organic carbon content from the saponite-rich clay fraction in the core sample was 23 times higher than that from the bulk counterpart, which appears to be sufficient to supply energy and carbon sources to saponite-hosted life. Furthermore, a newly developed method to detect microbial cells in a thin-section of the saponite-bearing fracture revealed the dense colonization of SYBR-Green-I stained microbial cells spatially associated with saponite. These results suggest that the presence of saponite in old cold basaltic crust is favorable for microbial life. In addition to carbonaceous chondrite, saponite is a common product of low-temperature reactions between water and mafic minerals on Earth and Mars. It is therefore expected that deep saponite-bearing fractures could host extant life and/or the past life on Mars.

Dataset Information

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics.

Publications

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics.

Similar Datasets

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