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Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion

BACKGROUND: The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial c...

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Autores principales: De Vrieze, Jo, Regueiro, Leticia, Props, Ruben, Vilchez-Vargas, Ramiro, Jáuregui, Ruy, Pieper, Dietmar H., Lema, Juan M., Carballa, Marta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103597/
https://www.ncbi.nlm.nih.gov/pubmed/27843490
http://dx.doi.org/10.1186/s13068-016-0652-5
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author De Vrieze, Jo
Regueiro, Leticia
Props, Ruben
Vilchez-Vargas, Ramiro
Jáuregui, Ruy
Pieper, Dietmar H.
Lema, Juan M.
Carballa, Marta
author_facet De Vrieze, Jo
Regueiro, Leticia
Props, Ruben
Vilchez-Vargas, Ramiro
Jáuregui, Ruy
Pieper, Dietmar H.
Lema, Juan M.
Carballa, Marta
author_sort De Vrieze, Jo
collection PubMed
description BACKGROUND: The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated. RESULTS: The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation. CONCLUSIONS: This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13068-016-0652-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-51035972016-11-14 Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion De Vrieze, Jo Regueiro, Leticia Props, Ruben Vilchez-Vargas, Ramiro Jáuregui, Ruy Pieper, Dietmar H. Lema, Juan M. Carballa, Marta Biotechnol Biofuels Research BACKGROUND: The microbial community in anaerobic digestion is mainly monitored by means of DNA-based methods. This may lead to incorrect interpretation of the community parameters, because microbial abundance does not necessarily reflect activity. In this research, the difference between microbial community response on DNA (total community) and RNA (active community) based on the 16S rRNA (gene) with respect to salt concentration and response time was evaluated. RESULTS: The application of higher NaCl concentrations resulted in a decrease in methane production. A stronger and faster response to salt concentration was observed on RNA level. This was reflected in terms of microbial community composition and organization, as richness, evenness, and overall diversity were differentially impacted. A higher divergence of community structure was observed on RNA level as well, indicating that total community composition depends on deterministic processes, while the active community is determined by stochastic processes. Methanosaeta was identified as the most abundant methanogen on DNA level, but its relative abundance decreased on RNA level, related to salt perturbation. CONCLUSIONS: This research demonstrated the need for RNA-based community screening to obtain reliable information on actual community parameters and to identify key species that determine process stability. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13068-016-0652-5) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-09 /pmc/articles/PMC5103597/ /pubmed/27843490 http://dx.doi.org/10.1186/s13068-016-0652-5 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
De Vrieze, Jo
Regueiro, Leticia
Props, Ruben
Vilchez-Vargas, Ramiro
Jáuregui, Ruy
Pieper, Dietmar H.
Lema, Juan M.
Carballa, Marta
Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title_full Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title_fullStr Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title_full_unstemmed Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title_short Presence does not imply activity: DNA and RNA patterns differ in response to salt perturbation in anaerobic digestion
title_sort presence does not imply activity: dna and rna patterns differ in response to salt perturbation in anaerobic digestion
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103597/
https://www.ncbi.nlm.nih.gov/pubmed/27843490
http://dx.doi.org/10.1186/s13068-016-0652-5
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