Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”

ABSTRACT The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits w...

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Autores principales:	Pamela Y. Camejo, Jorge Santo Domingo, Katherine D. McMahon, Daniel R. Noguera
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	“Ca. Nitrospira nitrosa” comammox NOB Nitrospira metagenomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/fa32f4af716548968af59121f5ce4077
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spelling	oai:doaj.org-article:fa32f4af716548968af59121f5ce40772021-12-02T18:15:43ZGenome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”10.1128/mSystems.00059-172379-5077https://doaj.org/article/fa32f4af716548968af59121f5ce40772017-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00059-17https://doaj.org/toc/2379-5077ABSTRACT The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as “Candidatus Nitrospira nitrosa,” and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in “Ca. Nitrospira nitrosa” mainly attributed to each strain’s niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of “Ca. Nitrospira nitrosa” and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus. IMPORTANCE Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches. Author Video: An author video summary of this article is available.Pamela Y. CamejoJorge Santo DomingoKatherine D. McMahonDaniel R. NogueraAmerican Society for Microbiologyarticle“Ca. Nitrospira nitrosa”comammoxNOBNitrospirametagenomicsMicrobiologyQR1-502ENmSystems, Vol 2, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	“Ca. Nitrospira nitrosa” comammox NOB Nitrospira metagenomics Microbiology QR1-502
spellingShingle	“Ca. Nitrospira nitrosa” comammox NOB Nitrospira metagenomics Microbiology QR1-502 Pamela Y. Camejo Jorge Santo Domingo Katherine D. McMahon Daniel R. Noguera Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
description	ABSTRACT The recently discovered comammox bacteria have the potential to completely oxidize ammonia to nitrate. These microorganisms are part of the Nitrospira genus and are present in a variety of environments, including biological nutrient removal (BNR) systems. However, the physiological traits within and between comammox and nitrite-oxidizing bacterium (NOB)-like Nitrospira species have not been analyzed in these ecosystems. In this study, we identified Nitrospira strains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under microaerobic conditions. We recovered metagenome-derived draft genomes from two Nitrospira strains: (i) Nitrospira sp. strain UW-LDO-01, a comammox-like organism classified as “Candidatus Nitrospira nitrosa,” and (ii) Nitrospira sp. strain UW-LDO-02, a nitrite-oxidizing strain belonging to the Nitrospira defluvii species. A comparative genomic analysis of these strains with other Nitrospira-like genomes identified genomic differences in “Ca. Nitrospira nitrosa” mainly attributed to each strain’s niche adaptation. Traits associated with energy metabolism also differentiate comammox from NOB-like genomes. We also identified several transcriptionally regulated adaptive traits, including stress tolerance, biofilm formation, and microaerobic metabolism, which might explain survival of Nitrospira under multiple environmental conditions. Overall, our analysis expanded our understanding of the genetic functional features of “Ca. Nitrospira nitrosa” and identified genomic traits that further illuminate the phylogenetic diversity and metabolic plasticity of the Nitrospira genus. IMPORTANCE Nitrospira-like bacteria are among the most diverse and widespread nitrifiers in natural ecosystems and the dominant nitrite oxidizers in wastewater treatment plants (WWTPs). The recent discovery of comammox-like Nitrospira strains, capable of complete oxidation of ammonia to nitrate, raises new questions about specific traits responsible for the functional versatility and adaptation of this genus to a variety of environments. The availability of new Nitrospira genome sequences from both nitrite-oxidizing and comammox bacteria offers a way to analyze traits in different Nitrospira functional groups. Our comparative genomics analysis provided new insights into the adaptation of Nitrospira strains to specific lifestyles and environmental niches. Author Video: An author video summary of this article is available.
format	article
author	Pamela Y. Camejo Jorge Santo Domingo Katherine D. McMahon Daniel R. Noguera
author_facet	Pamela Y. Camejo Jorge Santo Domingo Katherine D. McMahon Daniel R. Noguera
author_sort	Pamela Y. Camejo
title	Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
title_short	Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
title_full	Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
title_fullStr	Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
title_full_unstemmed	Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”
title_sort	genome-enabled insights into the ecophysiology of the comammox bacterium “<italic toggle="yes">candidatus</italic> nitrospira nitrosa”
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/fa32f4af716548968af59121f5ce4077
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Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “<italic toggle="yes">Candidatus</italic> Nitrospira nitrosa”

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