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Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO(3)(–) to N(2). This process may be performed entirely by complete denitrifiers capable of all four enzymatic st...

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Autores principales: Zhang, Irene H., Sun, Xin, Jayakumar, Amal, Fortin, Samantha G., Ward, Bess B., Babbin, Andrew R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10359470/
https://www.ncbi.nlm.nih.gov/pubmed/37474642
http://dx.doi.org/10.1038/s43705-023-00284-y
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author Zhang, Irene H.
Sun, Xin
Jayakumar, Amal
Fortin, Samantha G.
Ward, Bess B.
Babbin, Andrew R.
author_facet Zhang, Irene H.
Sun, Xin
Jayakumar, Amal
Fortin, Samantha G.
Ward, Bess B.
Babbin, Andrew R.
author_sort Zhang, Irene H.
collection PubMed
description Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO(3)(–) to N(2). This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N(2)O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.
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spelling pubmed-103594702023-07-22 Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones Zhang, Irene H. Sun, Xin Jayakumar, Amal Fortin, Samantha G. Ward, Bess B. Babbin, Andrew R. ISME Commun Article Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO(3)(–) to N(2). This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N(2)O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment. Nature Publishing Group UK 2023-07-20 /pmc/articles/PMC10359470/ /pubmed/37474642 http://dx.doi.org/10.1038/s43705-023-00284-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Irene H.
Sun, Xin
Jayakumar, Amal
Fortin, Samantha G.
Ward, Bess B.
Babbin, Andrew R.
Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title_full Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title_fullStr Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title_full_unstemmed Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title_short Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
title_sort partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10359470/
https://www.ncbi.nlm.nih.gov/pubmed/37474642
http://dx.doi.org/10.1038/s43705-023-00284-y
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