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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem

BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities...

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Autores principales: Broman, Elias, Izabel-Shen, Dandan, Rodríguez-Gijón, Alejandro, Bonaglia, Stefano, Garcia, Sarahi L., Nascimento, Francisco J. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377124/
https://www.ncbi.nlm.nih.gov/pubmed/35965333
http://dx.doi.org/10.1186/s40168-022-01321-z
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author Broman, Elias
Izabel-Shen, Dandan
Rodríguez-Gijón, Alejandro
Bonaglia, Stefano
Garcia, Sarahi L.
Nascimento, Francisco J. A.
author_facet Broman, Elias
Izabel-Shen, Dandan
Rodríguez-Gijón, Alejandro
Bonaglia, Stefano
Garcia, Sarahi L.
Nascimento, Francisco J. A.
author_sort Broman, Elias
collection PubMed
description BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01321-z.
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spelling pubmed-93771242022-08-16 Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem Broman, Elias Izabel-Shen, Dandan Rodríguez-Gijón, Alejandro Bonaglia, Stefano Garcia, Sarahi L. Nascimento, Francisco J. A. Microbiome Research BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea. RESULTS: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments. CONCLUSIONS: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40168-022-01321-z. BioMed Central 2022-08-15 /pmc/articles/PMC9377124/ /pubmed/35965333 http://dx.doi.org/10.1186/s40168-022-01321-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Broman, Elias
Izabel-Shen, Dandan
Rodríguez-Gijón, Alejandro
Bonaglia, Stefano
Garcia, Sarahi L.
Nascimento, Francisco J. A.
Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title_full Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title_fullStr Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title_full_unstemmed Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title_short Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem
title_sort microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the baltic benthic ecosystem
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9377124/
https://www.ncbi.nlm.nih.gov/pubmed/35965333
http://dx.doi.org/10.1186/s40168-022-01321-z
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