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Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments

INTRODUCTION: Long-term stability of underground CO(2) storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO(2) makes the Eger Rift in the Czech Republic a natural analogue to un...

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Autores principales: Jia, Zeyu, Lipus, Daniel, Burckhardt, Oliver, Bussert, Robert, Sondermann, Megan, Bartholomäus, Alexander, Wagner, Dirk, Kallmeyer, Jens
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246774/
https://www.ncbi.nlm.nih.gov/pubmed/37293225
http://dx.doi.org/10.3389/fmicb.2023.1105259
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author Jia, Zeyu
Lipus, Daniel
Burckhardt, Oliver
Bussert, Robert
Sondermann, Megan
Bartholomäus, Alexander
Wagner, Dirk
Kallmeyer, Jens
author_facet Jia, Zeyu
Lipus, Daniel
Burckhardt, Oliver
Bussert, Robert
Sondermann, Megan
Bartholomäus, Alexander
Wagner, Dirk
Kallmeyer, Jens
author_sort Jia, Zeyu
collection PubMed
description INTRODUCTION: Long-term stability of underground CO(2) storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO(2) makes the Eger Rift in the Czech Republic a natural analogue to underground CO(2) storage. The Eger Rift is a seismically active region and H(2) is produced abiotically during earthquakes, providing energy to indigenous microbial communities. METHODS: To investigate the response of a microbial ecosystem to high levels of CO(2) and H(2), we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H(2)/CO(2) headspace to simulate a seismically active period with elevated H(2). RESULTS AND DISCUSSION: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50–60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H(2) and CO(2), specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO(2) driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO(2) and H(2)-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO(2) concentrations, similar to those found in CCS sites.
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spelling pubmed-102467742023-06-08 Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments Jia, Zeyu Lipus, Daniel Burckhardt, Oliver Bussert, Robert Sondermann, Megan Bartholomäus, Alexander Wagner, Dirk Kallmeyer, Jens Front Microbiol Microbiology INTRODUCTION: Long-term stability of underground CO(2) storage is partially affected by microbial activity but our knowledge of these effects is limited, mainly due to a lack of sites. A consistently high flux of mantle-derived CO(2) makes the Eger Rift in the Czech Republic a natural analogue to underground CO(2) storage. The Eger Rift is a seismically active region and H(2) is produced abiotically during earthquakes, providing energy to indigenous microbial communities. METHODS: To investigate the response of a microbial ecosystem to high levels of CO(2) and H(2), we enriched microorganisms from samples from a 239.5 m long drill core from the Eger Rift. Microbial abundance, diversity and community structure were assessed using qPCR and 16S rRNA gene sequencing. Enrichment cultures were set up with minimal mineral media and H(2)/CO(2) headspace to simulate a seismically active period with elevated H(2). RESULTS AND DISCUSSION: Methane headspace concentrations in the enrichments indicated that active methanogens were almost exclusively restricted to enrichment cultures from Miocene lacustrine deposits (50–60 m), for which we observed the most significant growth. Taxonomic assessment showed microbial communities in these enrichments to be less diverse than those with little or no growth. Active enrichments were especially abundant in methanogens of the taxa Methanobacterium and Methanosphaerula. Concurrent to the emergence of methanogenic archaea, we also observed sulfate reducers with the metabolic ability to utilize H(2) and CO(2), specifically the genus Desulfosporosinus, which were able to outcompete methanogens in several enrichments. Low microbial abundance and a diverse non-CO(2) driven microbial community, similar to that in drill core samples, also reflect the inactivity in these cultures. Significant growth of sulfate reducing and methanogenic microbial taxa, which make up only a small fraction of the total microbial community, emphasize the need to account for rare biosphere taxa when assessing the metabolic potential of microbial subsurface populations. The observation that CO(2) and H(2)-utilizing microorganisms could only be enriched from a narrow depth interval suggests that factors such as sediment heterogeneity may also be important. This study provides new insight on subsurface microbes under the influence of high CO(2) concentrations, similar to those found in CCS sites. Frontiers Media S.A. 2023-05-24 /pmc/articles/PMC10246774/ /pubmed/37293225 http://dx.doi.org/10.3389/fmicb.2023.1105259 Text en Copyright © 2023 Jia, Lipus, Burckhardt, Bussert, Sondermann, Bartholomäus, Wagner and Kallmeyer. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Jia, Zeyu
Lipus, Daniel
Burckhardt, Oliver
Bussert, Robert
Sondermann, Megan
Bartholomäus, Alexander
Wagner, Dirk
Kallmeyer, Jens
Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title_full Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title_fullStr Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title_full_unstemmed Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title_short Enrichment of rare methanogenic Archaea shows their important ecological role in natural high-CO(2) terrestrial subsurface environments
title_sort enrichment of rare methanogenic archaea shows their important ecological role in natural high-co(2) terrestrial subsurface environments
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246774/
https://www.ncbi.nlm.nih.gov/pubmed/37293225
http://dx.doi.org/10.3389/fmicb.2023.1105259
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