Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
ABSTRACT The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influen...
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American Society for Microbiology
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ftdoajarticles:oai:doaj.org/article:c65b0a4b481c4614b34088a88b3487fc 2023-05-15T16:13:07+02:00 Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere Margarita Lopez-Fernandez Domenico Simone Xiaofen Wu Lucile Soler Emelie Nilsson Karin Holmfeldt Henrik Lantz Stefan Bertilsson Mark Dopson 2018-12-01T00:00:00Z https://doi.org/10.1128/mBio.01792-18 https://doaj.org/article/c65b0a4b481c4614b34088a88b3487fc EN eng American Society for Microbiology https://journals.asm.org/doi/10.1128/mBio.01792-18 https://doaj.org/toc/2150-7511 doi:10.1128/mBio.01792-18 2150-7511 https://doaj.org/article/c65b0a4b481c4614b34088a88b3487fc mBio, Vol 9, Iss 6 (2018) metatranscriptomes mRNA rRNA deep biosphere groundwaters Microbiology QR1-502 article 2018 ftdoajarticles https://doi.org/10.1128/mBio.01792-18 2022-12-31T04:20:47Z ABSTRACT The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as “modern marine,” and an “old saline” groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available. IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence ... Article in Journal/Newspaper Fennoscandian Directory of Open Access Journals: DOAJ Articles mBio 9 6 |
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ftdoajarticles |
language |
English |
topic |
metatranscriptomes mRNA rRNA deep biosphere groundwaters Microbiology QR1-502 |
spellingShingle |
metatranscriptomes mRNA rRNA deep biosphere groundwaters Microbiology QR1-502 Margarita Lopez-Fernandez Domenico Simone Xiaofen Wu Lucile Soler Emelie Nilsson Karin Holmfeldt Henrik Lantz Stefan Bertilsson Mark Dopson Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
topic_facet |
metatranscriptomes mRNA rRNA deep biosphere groundwaters Microbiology QR1-502 |
description |
ABSTRACT The continental subsurface is suggested to contain a significant part of the earth’s total biomass. However, due to the difficulty of sampling, the deep subsurface is still one of the least understood ecosystems. Therefore, microorganisms inhabiting this environment might profoundly influence the global nutrient and energy cycles. In this study, in situ fixed RNA transcripts from two deep continental groundwaters from the Äspö Hard Rock Laboratory (a Baltic Sea-influenced water with a residence time of <20 years, defined as “modern marine,” and an “old saline” groundwater with a residence time of thousands of years) were subjected to metatranscriptome sequencing. Although small subunit (SSU) rRNA gene and mRNA transcripts aligned to all three domains of life, supporting activity within these community subsets, the data also suggested that the groundwaters were dominated by bacteria. Many of the SSU rRNA transcripts grouped within newly described candidate phyla or could not be mapped to known branches on the tree of life, suggesting that a large portion of the active biota in the deep biosphere remains unexplored. Despite the extremely oligotrophic conditions, mRNA transcripts revealed a diverse range of metabolic strategies that were carried out by multiple taxa in the modern marine water that is fed by organic carbon from the surface. In contrast, the carbon dioxide- and hydrogen-fed old saline water with a residence time of thousands of years predominantly showed the potential to carry out translation. This suggested these cells were active, but waiting until an energy source episodically becomes available. IMPORTANCE A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence ... |
format |
Article in Journal/Newspaper |
author |
Margarita Lopez-Fernandez Domenico Simone Xiaofen Wu Lucile Soler Emelie Nilsson Karin Holmfeldt Henrik Lantz Stefan Bertilsson Mark Dopson |
author_facet |
Margarita Lopez-Fernandez Domenico Simone Xiaofen Wu Lucile Soler Emelie Nilsson Karin Holmfeldt Henrik Lantz Stefan Bertilsson Mark Dopson |
author_sort |
Margarita Lopez-Fernandez |
title |
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
title_short |
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
title_full |
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
title_fullStr |
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
title_full_unstemmed |
Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere |
title_sort |
metatranscriptomes reveal that all three domains of life are active but are dominated by bacteria in the fennoscandian crystalline granitic continental deep biosphere |
publisher |
American Society for Microbiology |
publishDate |
2018 |
url |
https://doi.org/10.1128/mBio.01792-18 https://doaj.org/article/c65b0a4b481c4614b34088a88b3487fc |
genre |
Fennoscandian |
genre_facet |
Fennoscandian |
op_source |
mBio, Vol 9, Iss 6 (2018) |
op_relation |
https://journals.asm.org/doi/10.1128/mBio.01792-18 https://doaj.org/toc/2150-7511 doi:10.1128/mBio.01792-18 2150-7511 https://doaj.org/article/c65b0a4b481c4614b34088a88b3487fc |
op_doi |
https://doi.org/10.1128/mBio.01792-18 |
container_title |
mBio |
container_volume |
9 |
container_issue |
6 |
_version_ |
1765998729349824512 |