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Atencio B, Geisler E, Rubin-Blum M, Bar-Zeev E, Adar EM, Ram R, Ronen Z. Metabolic adaptations underpin high productivity rates in relict subsurface water. Sci Rep 2024; 14:18126. [PMID: 39103408 PMCID: PMC11300587 DOI: 10.1038/s41598-024-68868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024] Open
Abstract
Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel's Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L-1 d-1 (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin-Benson-Bassham cycle and the Wood-Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.
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Affiliation(s)
- Betzabe Atencio
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Eyal Geisler
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Maxim Rubin-Blum
- Department of Marine Biology, Israel Oceanographic and Limnological Research Institute, Haifa, Israel
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Edo Bar-Zeev
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Eilon M Adar
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Roi Ram
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
- Geological Survey of Israel, Jerusalem, Israel
- Institute of Environmental Physics, Heidelberg University, 69120, Heidelberg, Germany
| | - Zeev Ronen
- Department of Environmental Hydrology and Microbiology, Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel.
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Li Y, Chen J, Tang S, Xi Z. Microbial Communities Affected by Hydraulic Fracturing and Environmental Factors within an In Situ Coal Reservoir. Microorganisms 2023; 11:1657. [PMID: 37512830 PMCID: PMC10385777 DOI: 10.3390/microorganisms11071657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of coalbed methane bioengineering enables the conversion and utilization of carbon dioxide through microbial action and the carbon cycle. The environment of underground coal reservoirs is the result of a comprehensive effort by microorganisms. Some studies on reservoir microorganisms have progressed in laboratory conditions. However, it does not replicate the interaction between microorganisms and the environment on site. Hydraulic fracturing is an engineering technology to improve the natural permeability of tight reservoirs and is also a prerequisite for increasing biomethane production. In addition to expanding the pore and fracture systems of coal reservoirs, hydraulic fracturing also improves the living conditions of microbial communities in underground space. The characteristics of microbial communities in the reservoir after hydraulic fracturing are unclear. To this end, we applied the 16S rRNA sequencing technique to coalbed methane production water after hydraulic fracturing south of the Qinshui Basin to analyze the microbial response of the hydraulic fracturing process in the coal reservoir. The diversity of microbial communities associated with organic degradation was improved after hydraulic fracturing in the coal reservoir. The proportion of Actinobacteria in the reservoir water of the study area increased significantly, and the abundance of Aminicenantes and Planctomycetes increased, which do not exist in non-fracturing coalbed methane wells or exist at very low abundance. There are different types of methanogens in the study area, especially in fracturing wells. Ecological factors also determine the metabolic pathway of methanogens in coal seams. After hydraulic fracturing, the impact on the reservoir's microbial communities remains within months. Hydraulic fracturing can strengthen the carbon circulation process, thereby enhancing the block's methane and carbon dioxide circulation. The study provides a unique theoretical basis for microbially enhanced coalbed methane.
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Affiliation(s)
- Yang Li
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
- Key Laboratory of Petroleum Resources and Prospecting, China University of Petroleum, Beijing 102249, China
| | - Jian Chen
- School of Earth and Environment, Anhui University of Science and Technology, Huainan 232001, China
- The Key Laboratory of Universities in Anhui Province for Prevention of Mine Geological Disasters, Anhui University of Science and Technology, Huainan 232001, China
| | - Shuheng Tang
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
| | - Zhaodong Xi
- School of Energy Resource, China University of Geosciences, Beijing 100083, China
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Ministry of Education, Beijing 100083, China
- Key Laboratory of Strategy Evaluation for Shale Gas, Ministry of Land and Resources, Beijing 100083, China
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Munro-Ehrlich M, Nothaft DB, Fones EM, Matter JM, Templeton AS, Boyd ES. Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman. Front Microbiol 2023; 14:1138656. [PMID: 37125170 PMCID: PMC10130571 DOI: 10.3389/fmicb.2023.1138656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning >130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data.
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Affiliation(s)
- Mason Munro-Ehrlich
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Daniel B. Nothaft
- Department of Geosciences, University of Colorado, Boulder, Boulder, CO, United States
| | - Elizabeth M. Fones
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
| | - Juerg M. Matter
- School of Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | - Alexis S. Templeton
- Department of Geosciences, University of Colorado, Boulder, Boulder, CO, United States
| | - Eric S. Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
- *Correspondence: Eric S. Boyd,
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