Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following expe...

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Autores principales:	Frank J Stewart, Tage Dalsgaard, Curtis R Young, Bo Thamdrup, Niels Peter Revsbech, Osvaldo Ulloa, Don E Canfield, Edward F Delong
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/73f2e270b9014b35a280ba805f180f01
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spelling	oai:doaj.org-article:73f2e270b9014b35a280ba805f180f012021-11-18T07:18:29ZExperimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.1932-620310.1371/journal.pone.0037118https://doaj.org/article/73f2e270b9014b35a280ba805f180f012012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22615914/?tool=EBIhttps://doaj.org/toc/1932-6203Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.Frank J StewartTage DalsgaardCurtis R YoungBo ThamdrupNiels Peter RevsbechOsvaldo UlloaDon E CanfieldEdward F DelongPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 5, p e37118 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Frank J Stewart Tage Dalsgaard Curtis R Young Bo Thamdrup Niels Peter Revsbech Osvaldo Ulloa Don E Canfield Edward F Delong Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
description	Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.
format	article
author	Frank J Stewart Tage Dalsgaard Curtis R Young Bo Thamdrup Niels Peter Revsbech Osvaldo Ulloa Don E Canfield Edward F Delong
author_facet	Frank J Stewart Tage Dalsgaard Curtis R Young Bo Thamdrup Niels Peter Revsbech Osvaldo Ulloa Don E Canfield Edward F Delong
author_sort	Frank J Stewart
title	Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
title_short	Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
title_full	Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
title_fullStr	Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
title_full_unstemmed	Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.
title_sort	experimental incubations elicit profound changes in community transcription in omz bacterioplankton.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/73f2e270b9014b35a280ba805f180f01
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Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton.

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