In-depth characterization of denitrifier communities across different soil ecosystems in the tundra
International audience Abstract Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N 2 O). However, the microorganisms involved in the cycling of N 2 O in this system remain largely unch...
Published in: | Environmental Microbiome |
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Main Authors: | , , , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2022
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Online Access: | https://cea.hal.science/cea-04425162 https://doi.org/10.1186/s40793-022-00424-2 |
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ftunivaixmarseil:oai:HAL:cea-04425162v1 |
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Aix-Marseille Université: HAL |
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English |
topic |
[SDV]Life Sciences [q-bio] [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] |
spellingShingle |
[SDV]Life Sciences [q-bio] [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] Pessi, Igor Viitamäki, Sirja Virkkala, Anna-Maria Eronen-Rasimus, Eeva Delmont, Tom Marushchak, Maija Luoto, Miska Hultman, Jenni In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
topic_facet |
[SDV]Life Sciences [q-bio] [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] |
description |
International audience Abstract Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N 2 O). However, the microorganisms involved in the cycling of N 2 O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N 2 O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N 2 O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N 2 O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella . Fens, which had in general net-zero N 2 O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N 2 O fluxes, our results suggest that the observed spatial patterns of N 2 O fluxes in the tundra are related to differences in the composition of denitrifier communities. |
author2 |
Finnish Environment Institute (SYKE) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Helsingin yliopisto = Helsingfors universitet = University of Helsinki Natural Resources Institute Finland (LUKE) |
format |
Article in Journal/Newspaper |
author |
Pessi, Igor Viitamäki, Sirja Virkkala, Anna-Maria Eronen-Rasimus, Eeva Delmont, Tom Marushchak, Maija Luoto, Miska Hultman, Jenni |
author_facet |
Pessi, Igor Viitamäki, Sirja Virkkala, Anna-Maria Eronen-Rasimus, Eeva Delmont, Tom Marushchak, Maija Luoto, Miska Hultman, Jenni |
author_sort |
Pessi, Igor |
title |
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
title_short |
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
title_full |
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
title_fullStr |
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
title_full_unstemmed |
In-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
title_sort |
in-depth characterization of denitrifier communities across different soil ecosystems in the tundra |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://cea.hal.science/cea-04425162 https://doi.org/10.1186/s40793-022-00424-2 |
genre |
Northern Finland Tundra |
genre_facet |
Northern Finland Tundra |
op_source |
ISSN: 2524-6372 EISSN: 2524-6372 Environmental Microbiome https://cea.hal.science/cea-04425162 Environmental Microbiome, 2022, 17 (1), pp.30. ⟨10.1186/s40793-022-00424-2⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s40793-022-00424-2 cea-04425162 https://cea.hal.science/cea-04425162 doi:10.1186/s40793-022-00424-2 |
op_doi |
https://doi.org/10.1186/s40793-022-00424-2 |
container_title |
Environmental Microbiome |
container_volume |
17 |
container_issue |
1 |
_version_ |
1799486064223584256 |
spelling |
ftunivaixmarseil:oai:HAL:cea-04425162v1 2024-05-19T07:45:56+00:00 In-depth characterization of denitrifier communities across different soil ecosystems in the tundra Pessi, Igor Viitamäki, Sirja Virkkala, Anna-Maria Eronen-Rasimus, Eeva Delmont, Tom Marushchak, Maija Luoto, Miska Hultman, Jenni Finnish Environment Institute (SYKE) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Helsingin yliopisto = Helsingfors universitet = University of Helsinki Natural Resources Institute Finland (LUKE) 2022-06-11 https://cea.hal.science/cea-04425162 https://doi.org/10.1186/s40793-022-00424-2 en eng HAL CCSD BioMedCentral info:eu-repo/semantics/altIdentifier/doi/10.1186/s40793-022-00424-2 cea-04425162 https://cea.hal.science/cea-04425162 doi:10.1186/s40793-022-00424-2 ISSN: 2524-6372 EISSN: 2524-6372 Environmental Microbiome https://cea.hal.science/cea-04425162 Environmental Microbiome, 2022, 17 (1), pp.30. ⟨10.1186/s40793-022-00424-2⟩ [SDV]Life Sciences [q-bio] [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] info:eu-repo/semantics/article Journal articles 2022 ftunivaixmarseil https://doi.org/10.1186/s40793-022-00424-2 2024-04-25T00:36:03Z International audience Abstract Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N 2 O). However, the microorganisms involved in the cycling of N 2 O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N 2 O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N 2 O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N 2 O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella . Fens, which had in general net-zero N 2 O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N 2 O fluxes, our results suggest that the observed spatial patterns of N 2 O fluxes in the tundra are related to differences in the composition of denitrifier communities. Article in Journal/Newspaper Northern Finland Tundra Aix-Marseille Université: HAL Environmental Microbiome 17 1 |