Cargando…

Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism

Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly–based metatranscriptomics to a...

Descripción completa

Detalles Bibliográficos
Autores principales: Sato, Yuya, Hori, Tomoyuki, Koike, Hideaki, Navarro, Ronald R., Ogata, Atsushi, Habe, Hiroshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513846/
https://www.ncbi.nlm.nih.gov/pubmed/31098412
http://dx.doi.org/10.1038/s42003-019-0418-2
_version_ 1783417774635220992
author Sato, Yuya
Hori, Tomoyuki
Koike, Hideaki
Navarro, Ronald R.
Ogata, Atsushi
Habe, Hiroshi
author_facet Sato, Yuya
Hori, Tomoyuki
Koike, Hideaki
Navarro, Ronald R.
Ogata, Atsushi
Habe, Hiroshi
author_sort Sato, Yuya
collection PubMed
description Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly–based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers—small minorities with relative abundances of <0.25%—governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome.
format Online
Article
Text
id pubmed-6513846
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-65138462019-05-16 Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism Sato, Yuya Hori, Tomoyuki Koike, Hideaki Navarro, Ronald R. Ogata, Atsushi Habe, Hiroshi Commun Biol Article Although metagenomics researches have illuminated microbial diversity in numerous biospheres, understanding individual microbial functions is yet difficult due to the complexity of ecosystems. To address this issue, we applied a metagenome-independent, de novo assembly–based metatranscriptomics to a complex microbiome, activated sludge, which has been used for wastewater treatment for over a century. Even though two bioreactors were operated under the same conditions, their performances differed from each other with unknown causes. Metatranscriptome profiles in high- and low-performance reactors demonstrated that denitrifiers contributed to the anaerobic degradation of heavy oil; however, no marked difference in the gene expression was found. Instead, gene expression-based nitrification activities that fueled the denitrifiers by providing the respiratory substrate were notably high in the high-performance reactor only. Nitrifiers—small minorities with relative abundances of <0.25%—governed the heavy-oil degradation performances of the reactors, unveiling an unexpected linkage of carbon- and nitrogen-metabolisms of the complex microbiome. Nature Publishing Group UK 2019-05-13 /pmc/articles/PMC6513846/ /pubmed/31098412 http://dx.doi.org/10.1038/s42003-019-0418-2 Text en © The Author(s) 2019 Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Sato, Yuya
Hori, Tomoyuki
Koike, Hideaki
Navarro, Ronald R.
Ogata, Atsushi
Habe, Hiroshi
Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title_full Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title_fullStr Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title_full_unstemmed Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title_short Transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
title_sort transcriptome analysis of activated sludge microbiomes reveals an unexpected role of minority nitrifiers in carbon metabolism
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513846/
https://www.ncbi.nlm.nih.gov/pubmed/31098412
http://dx.doi.org/10.1038/s42003-019-0418-2
work_keys_str_mv AT satoyuya transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism
AT horitomoyuki transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism
AT koikehideaki transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism
AT navarroronaldr transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism
AT ogataatsushi transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism
AT habehiroshi transcriptomeanalysisofactivatedsludgemicrobiomesrevealsanunexpectedroleofminoritynitrifiersincarbonmetabolism