Comparison of the active and resident community of a coastal microbial mat

Abstract Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potent...

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Autores principales:	Daniela Clara Cardoso, Anna Sandionigi, Mariana Silvia Cretoiu, Maurizio Casiraghi, Lucas Stal, Henk Bolhuis
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2665e11076b643c19ce44a7524c91cc6
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spelling	oai:doaj.org-article:2665e11076b643c19ce44a7524c91cc62021-12-02T15:05:43ZComparison of the active and resident community of a coastal microbial mat10.1038/s41598-017-03095-z2045-2322https://doaj.org/article/2665e11076b643c19ce44a7524c91cc62017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03095-zhttps://doaj.org/toc/2045-2322Abstract Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the “resident community” (DNA) with the “active community” (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.Daniela Clara CardosoAnna SandionigiMariana Silvia CretoiuMaurizio CasiraghiLucas StalHenk BolhuisNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daniela Clara Cardoso Anna Sandionigi Mariana Silvia Cretoiu Maurizio Casiraghi Lucas Stal Henk Bolhuis Comparison of the active and resident community of a coastal microbial mat
description	Abstract Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fraction. In addition, we aimed to establish an optimal and feasible sampling protocol that takes potential spatial and temporal heterogeneity into account. The coastal microbial mat investigated here was sampled randomly and at regular time points during one 24-h period. DNA and RNA was extracted and after conversion of the RNA fraction to cDNA, the V1-V3 and the V3-V4 regions of the 16S rRNA gene were targeted for high-throughput amplicon sequencing. We show that the community composition varies little in time and space whereas two amplified 16S regions gave significant different results. The largest differences were found when comparing the “resident community” (DNA) with the “active community” (cDNA/RNA); in the latter, Cyanobacteria dominated for almost 95% while they represented 60% of the resident fraction.
format	article
author	Daniela Clara Cardoso Anna Sandionigi Mariana Silvia Cretoiu Maurizio Casiraghi Lucas Stal Henk Bolhuis
author_facet	Daniela Clara Cardoso Anna Sandionigi Mariana Silvia Cretoiu Maurizio Casiraghi Lucas Stal Henk Bolhuis
author_sort	Daniela Clara Cardoso
title	Comparison of the active and resident community of a coastal microbial mat
title_short	Comparison of the active and resident community of a coastal microbial mat
title_full	Comparison of the active and resident community of a coastal microbial mat
title_fullStr	Comparison of the active and resident community of a coastal microbial mat
title_full_unstemmed	Comparison of the active and resident community of a coastal microbial mat
title_sort	comparison of the active and resident community of a coastal microbial mat
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2665e11076b643c19ce44a7524c91cc6
work_keys_str_mv	AT danielaclaracardoso comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat AT annasandionigi comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat AT marianasilviacretoiu comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat AT mauriziocasiraghi comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat AT lucasstal comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat AT henkbolhuis comparisonoftheactiveandresidentcommunityofacoastalmicrobialmat
_version_	1718388692549107712

Comparison of the active and resident community of a coastal microbial mat

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