Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean
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...
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ftarchimer:oai:archimer.ifremer.fr:96098 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
topic |
Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome |
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Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome 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 |
description |
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 Fe-related metabolic ... |
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 |
Springer Science and Business Media LLC |
publishDate |
2023 |
url |
https://archimer.ifremer.fr/doc/00849/96098/104185.pdf https://archimer.ifremer.fr/doc/00849/96098/104186.pdf https://archimer.ifremer.fr/doc/00849/96098/104187.pdf https://archimer.ifremer.fr/doc/00849/96098/104188.pdf https://archimer.ifremer.fr/doc/00849/96098/104189.eps https://archimer.ifremer.fr/doc/00849/96098/104190.pdf https://archimer.ifremer.fr/doc/00849/96098/104191.pdf https://archimer.ifremer.fr/doc/00849/96098/104192.pdf https://archimer.ifremer.fr/doc/00849/96098/104193.pdf https://archimer.ifremer.fr/doc/00849/96098/104194.docx https://archimer.ifremer.fr/doc/00849/96098/104195.xlsx https://doi.org/10.1186/s40168-023-01600-3 https://archimer.ifremer.fr/doc/00849/96098/ |
geographic |
Southern Ocean |
geographic_facet |
Southern Ocean |
genre |
Southern Ocean |
genre_facet |
Southern Ocean |
op_source |
Microbiome (2049-2618) (Springer Science and Business Media LLC), 2023-08 , Vol. 11 , N. 1 , P. 187 (12p.) |
op_relation |
https://archimer.ifremer.fr/doc/00849/96098/104185.pdf https://archimer.ifremer.fr/doc/00849/96098/104186.pdf https://archimer.ifremer.fr/doc/00849/96098/104187.pdf https://archimer.ifremer.fr/doc/00849/96098/104188.pdf https://archimer.ifremer.fr/doc/00849/96098/104189.eps https://archimer.ifremer.fr/doc/00849/96098/104190.pdf https://archimer.ifremer.fr/doc/00849/96098/104191.pdf https://archimer.ifremer.fr/doc/00849/96098/104192.pdf https://archimer.ifremer.fr/doc/00849/96098/104193.pdf https://archimer.ifremer.fr/doc/00849/96098/104194.docx https://archimer.ifremer.fr/doc/00849/96098/104195.xlsx doi:10.1186/s40168-023-01600-3 https://archimer.ifremer.fr/doc/00849/96098/ |
op_rights |
info:eu-repo/semantics/openAccess restricted use |
op_doi |
https://doi.org/10.1186/s40168-023-01600-3 |
container_title |
Microbiome |
container_volume |
11 |
container_issue |
1 |
_version_ |
1786200377465503744 |
spelling |
ftarchimer:oai:archimer.ifremer.fr:96098 2023-12-24T10:25:02+01:00 Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean Debeljak, Pavla Bayer, Barbara Sun, Ying Herndl, Gerhard J. Obernosterer, Ingrid 2023-08 application/pdf https://archimer.ifremer.fr/doc/00849/96098/104185.pdf https://archimer.ifremer.fr/doc/00849/96098/104186.pdf https://archimer.ifremer.fr/doc/00849/96098/104187.pdf https://archimer.ifremer.fr/doc/00849/96098/104188.pdf https://archimer.ifremer.fr/doc/00849/96098/104189.eps https://archimer.ifremer.fr/doc/00849/96098/104190.pdf https://archimer.ifremer.fr/doc/00849/96098/104191.pdf https://archimer.ifremer.fr/doc/00849/96098/104192.pdf https://archimer.ifremer.fr/doc/00849/96098/104193.pdf https://archimer.ifremer.fr/doc/00849/96098/104194.docx https://archimer.ifremer.fr/doc/00849/96098/104195.xlsx https://doi.org/10.1186/s40168-023-01600-3 https://archimer.ifremer.fr/doc/00849/96098/ eng eng Springer Science and Business Media LLC https://archimer.ifremer.fr/doc/00849/96098/104185.pdf https://archimer.ifremer.fr/doc/00849/96098/104186.pdf https://archimer.ifremer.fr/doc/00849/96098/104187.pdf https://archimer.ifremer.fr/doc/00849/96098/104188.pdf https://archimer.ifremer.fr/doc/00849/96098/104189.eps https://archimer.ifremer.fr/doc/00849/96098/104190.pdf https://archimer.ifremer.fr/doc/00849/96098/104191.pdf https://archimer.ifremer.fr/doc/00849/96098/104192.pdf https://archimer.ifremer.fr/doc/00849/96098/104193.pdf https://archimer.ifremer.fr/doc/00849/96098/104194.docx https://archimer.ifremer.fr/doc/00849/96098/104195.xlsx doi:10.1186/s40168-023-01600-3 https://archimer.ifremer.fr/doc/00849/96098/ info:eu-repo/semantics/openAccess restricted use Microbiome (2049-2618) (Springer Science and Business Media LLC), 2023-08 , Vol. 11 , N. 1 , P. 187 (12p.) Prokaryotic membrane transporters Organic substrate utilization Iron uptake Metatranscriptomics Metaproteomics Metagenome-assembled genomes Southern Ocean Ocean microbiome text Article info:eu-repo/semantics/article 2023 ftarchimer https://doi.org/10.1186/s40168-023-01600-3 2023-11-28T23:51:15Z 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 Fe-related metabolic ... Article in Journal/Newspaper Southern Ocean Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Southern Ocean Microbiome 11 1 |