DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

ABSTRACT Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed bio...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Arda Gülay, S. Jane Fowler, Karolina Tatari, Bo Thamdrup, Hans-Jørgen Albrechtsen, Waleed Abu Al-Soud, Søren J. Sørensen, Barth F. Smets
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	nitrification comammox Nitrospira DNA SIP RNA SIP Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c4a99d20ee4a4f6cba3c1bce8486a56f
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c4a99d20ee4a4f6cba3c1bce8486a56f
record_format	dspace
spelling	oai:doaj.org-article:c4a99d20ee4a4f6cba3c1bce8486a56f2021-11-15T15:54:47ZDNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters10.1128/mBio.01870-192150-7511https://doaj.org/article/c4a99d20ee4a4f6cba3c1bce8486a56f2019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01870-19https://doaj.org/toc/2150-7511ABSTRACT Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira. Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4+ or NO2− in the presence of 13C-HCO3− (labeled) or 12C-HCO3− (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3− uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome. IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3− uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.Arda GülayS. Jane FowlerKarolina TatariBo ThamdrupHans-Jørgen AlbrechtsenWaleed Abu Al-SoudSøren J. SørensenBarth F. SmetsAmerican Society for MicrobiologyarticlenitrificationcomammoxNitrospiraDNA SIPRNA SIPMicrobiologyQR1-502ENmBio, Vol 10, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	nitrification comammox Nitrospira DNA SIP RNA SIP Microbiology QR1-502
spellingShingle	nitrification comammox Nitrospira DNA SIP RNA SIP Microbiology QR1-502 Arda Gülay S. Jane Fowler Karolina Tatari Bo Thamdrup Hans-Jørgen Albrechtsen Waleed Abu Al-Soud Søren J. Sørensen Barth F. Smets DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
description	ABSTRACT Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira. Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4+ or NO2− in the presence of 13C-HCO3− (labeled) or 12C-HCO3− (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3− uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome. IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3− uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.
format	article
author	Arda Gülay S. Jane Fowler Karolina Tatari Bo Thamdrup Hans-Jørgen Albrechtsen Waleed Abu Al-Soud Søren J. Sørensen Barth F. Smets
author_facet	Arda Gülay S. Jane Fowler Karolina Tatari Bo Thamdrup Hans-Jørgen Albrechtsen Waleed Abu Al-Soud Søren J. Sørensen Barth F. Smets
author_sort	Arda Gülay
title	DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
title_short	DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
title_full	DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
title_fullStr	DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
title_full_unstemmed	DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters
title_sort	dna- and rna-sip reveal <italic toggle="yes">nitrospira</italic> spp. as key drivers of nitrification in groundwater-fed biofilters
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/c4a99d20ee4a4f6cba3c1bce8486a56f
work_keys_str_mv	AT ardagulay dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT sjanefowler dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT karolinatatari dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT bothamdrup dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT hansjørgenalbrechtsen dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT waleedabualsoud dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT sørenjsørensen dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters AT barthfsmets dnaandrnasiprevealitalictoggleyesnitrospiraitalicsppaskeydriversofnitrificationingroundwaterfedbiofilters
_version_	1718427242404511744

DNA- and RNA-SIP Reveal <italic toggle="yes">Nitrospira</italic> spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

Ejemplares similares