Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean
International audience Background Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe unde...
Published in: | Microbiome |
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Main Authors: | , , , , |
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Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2023
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Online Access: | https://hal.sorbonne-universite.fr/hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032/document https://hal.sorbonne-universite.fr/hal-04198032/file/s40168-023-01600-3%20%282%29.pdf https://doi.org/10.1186/s40168-023-01600-3 |
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ftanrparis:oai:HAL:hal-04198032v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Portail HAL-ANR (Agence Nationale de la Recherche) |
op_collection_id |
ftanrparis |
language |
English |
topic |
Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome [SDE]Environmental Sciences |
spellingShingle |
Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome [SDE]Environmental Sciences Debeljak, Pavla Bayer, Barbara Sun, Ying Herndl, Gerhard, J Obernosterer, Ingrid Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
topic_facet |
Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome [SDE]Environmental Sciences |
description |
International audience Background Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. Results Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. Conclusion The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C-and ... |
author2 |
Sup'Biotech Universität Wien = University of Vienna Observatoire océanologique de Banyuls (OOB) Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) BGI Qingdao Partenaires INRAE Royal Netherlands Institute for Sea Research (NIOZ) ANR-17-CE01-0013,MOBYDICK,Biodiversité des Ecosystèmes Marins et Dynamique du Carbone dans le secteur de Kerguelen : approche intégrée(2017) |
format |
Article in Journal/Newspaper |
author |
Debeljak, Pavla Bayer, Barbara Sun, Ying Herndl, Gerhard, J Obernosterer, Ingrid |
author_facet |
Debeljak, Pavla Bayer, Barbara Sun, Ying Herndl, Gerhard, J Obernosterer, Ingrid |
author_sort |
Debeljak, Pavla |
title |
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
title_short |
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
title_full |
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
title_fullStr |
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
title_full_unstemmed |
Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean |
title_sort |
seasonal patterns in microbial carbon and iron transporter expression in the southern ocean |
publisher |
HAL CCSD |
publishDate |
2023 |
url |
https://hal.sorbonne-universite.fr/hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032/document https://hal.sorbonne-universite.fr/hal-04198032/file/s40168-023-01600-3%20%282%29.pdf https://doi.org/10.1186/s40168-023-01600-3 |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_source |
EISSN: 2049-2618 Microbiome https://hal.sorbonne-universite.fr/hal-04198032 Microbiome, 2023, 11 (1), pp.187. ⟨10.1186/s40168-023-01600-3⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/s40168-023-01600-3 hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032/document https://hal.sorbonne-universite.fr/hal-04198032/file/s40168-023-01600-3%20%282%29.pdf doi:10.1186/s40168-023-01600-3 |
op_rights |
http://hal.archives-ouvertes.fr/licences/etalab/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s40168-023-01600-3 |
container_title |
Microbiome |
container_volume |
11 |
container_issue |
1 |
_version_ |
1810481067331682304 |
spelling |
ftanrparis:oai:HAL:hal-04198032v1 2024-09-15T18:37:01+00:00 Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean Debeljak, Pavla Bayer, Barbara Sun, Ying Herndl, Gerhard, J Obernosterer, Ingrid Sup'Biotech Universität Wien = University of Vienna Observatoire océanologique de Banyuls (OOB) Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS) BGI Qingdao Partenaires INRAE Royal Netherlands Institute for Sea Research (NIOZ) ANR-17-CE01-0013,MOBYDICK,Biodiversité des Ecosystèmes Marins et Dynamique du Carbone dans le secteur de Kerguelen : approche intégrée(2017) 2023-08-19 https://hal.sorbonne-universite.fr/hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032/document https://hal.sorbonne-universite.fr/hal-04198032/file/s40168-023-01600-3%20%282%29.pdf https://doi.org/10.1186/s40168-023-01600-3 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s40168-023-01600-3 hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032 https://hal.sorbonne-universite.fr/hal-04198032/document https://hal.sorbonne-universite.fr/hal-04198032/file/s40168-023-01600-3%20%282%29.pdf doi:10.1186/s40168-023-01600-3 http://hal.archives-ouvertes.fr/licences/etalab/ info:eu-repo/semantics/OpenAccess EISSN: 2049-2618 Microbiome https://hal.sorbonne-universite.fr/hal-04198032 Microbiome, 2023, 11 (1), pp.187. ⟨10.1186/s40168-023-01600-3⟩ Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome [SDE]Environmental Sciences info:eu-repo/semantics/article Journal articles 2023 ftanrparis https://doi.org/10.1186/s40168-023-01600-3 2024-07-12T10:49:00Z International audience Background Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer. Results Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae. Conclusion The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C-and ... Article in Journal/Newspaper Southern Ocean Portail HAL-ANR (Agence Nationale de la Recherche) Microbiome 11 1 |