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Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities

In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior...

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Autores principales: Zheng, Yue, Wang, Huan, Yu, Zheng, Haroon, Fauzi, Hernández, Maria E., Chistoserdova, Ludmila
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589939/
https://www.ncbi.nlm.nih.gov/pubmed/33092280
http://dx.doi.org/10.3390/microorganisms8101614
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author Zheng, Yue
Wang, Huan
Yu, Zheng
Haroon, Fauzi
Hernández, Maria E.
Chistoserdova, Ludmila
author_facet Zheng, Yue
Wang, Huan
Yu, Zheng
Haroon, Fauzi
Hernández, Maria E.
Chistoserdova, Ludmila
author_sort Zheng, Yue
collection PubMed
description In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.
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spelling pubmed-75899392020-10-29 Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities Zheng, Yue Wang, Huan Yu, Zheng Haroon, Fauzi Hernández, Maria E. Chistoserdova, Ludmila Microorganisms Article In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae. MDPI 2020-10-20 /pmc/articles/PMC7589939/ /pubmed/33092280 http://dx.doi.org/10.3390/microorganisms8101614 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zheng, Yue
Wang, Huan
Yu, Zheng
Haroon, Fauzi
Hernández, Maria E.
Chistoserdova, Ludmila
Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title_full Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title_fullStr Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title_full_unstemmed Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title_short Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities
title_sort metagenomic insight into environmentally challenged methane-fed microbial communities
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589939/
https://www.ncbi.nlm.nih.gov/pubmed/33092280
http://dx.doi.org/10.3390/microorganisms8101614
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