Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System

ABSTRACT We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shot...

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Autores principales:	Ameet J. Pinto, Daniel N. Marcus, Umer Zeeshan Ijaz, Quyen Melina Bautista-de lose Santos, Gregory J. Dick, Lutgarde Raskin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Nitrospira comammox drinking water systems Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/80544678741648158bf5f3c176505289
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spelling	oai:doaj.org-article:80544678741648158bf5f3c1765052892021-11-15T15:21:39ZMetagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System10.1128/mSphere.00054-152379-5042https://doaj.org/article/80544678741648158bf5f3c1765052892016-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00054-15https://doaj.org/toc/2379-5042ABSTRACT We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems.Ameet J. PintoDaniel N. MarcusUmer Zeeshan IjazQuyen Melina Bautista-de lose SantosGregory J. DickLutgarde RaskinAmerican Society for MicrobiologyarticleNitrospiracomammoxdrinking water systemsMicrobiologyQR1-502ENmSphere, Vol 1, Iss 1 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Nitrospira comammox drinking water systems Microbiology QR1-502
spellingShingle	Nitrospira comammox drinking water systems Microbiology QR1-502 Ameet J. Pinto Daniel N. Marcus Umer Zeeshan Ijaz Quyen Melina Bautista-de lose Santos Gregory J. Dick Lutgarde Raskin Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
description	ABSTRACT We report metagenomic evidence for the presence of a Nitrospira-like organism with the metabolic potential to perform the complete oxidation of ammonia to nitrate (i.e., it is a complete ammonia oxidizer [comammox]) in a drinking water system. This metagenome bin was discovered through shotgun DNA sequencing of samples from biologically active filters at the drinking water treatment plant in Ann Arbor, MI. Ribosomal proteins, 16S rRNA, and nxrA gene analyses confirmed that this genome is related to Nitrospira-like nitrite-oxidizing bacteria. The presence of the full suite of ammonia oxidation genes, including ammonia monooxygenase and hydroxylamine dehydrogenase, on a single ungapped scaffold within this metagenome bin suggests the presence of recently discovered comammox potential. Evaluations based on coverage and k-mer frequency distribution, use of two different genome-binning approaches, and nucleic acid and protein similarity analyses support the presence of this scaffold within the Nitrospira metagenome bin. The amoA gene found in this metagenome bin is divergent from those of canonical ammonia and methane oxidizers and clusters closely with the unusual amoA gene of comammox Nitrospira. This finding suggests that previously reported imbalances in abundances of nitrite- and ammonia-oxidizing bacteria/archaea may likely be explained by the capacity of Nitrospira-like organisms to completely oxidize ammonia. This finding might have significant implications for our understanding of microbially mediated nitrogen transformations in engineered and natural systems. IMPORTANCE Nitrification plays an important role in regulating the concentrations of inorganic nitrogen species in a range of environments, from drinking water and wastewater treatment plants to the oceans. Until recently, aerobic nitrification was considered to be a two-step process involving ammonia-oxidizing bacteria or archaea and nitrite-oxidizing bacteria. This process requires close cooperation between these two functional guilds for complete conversion of ammonia to nitrate, without the accumulation of nitrite or other intermediates, such as nitrous oxide, a potent greenhouse gas. The discovery of a single organism with the potential to oxidize both ammonia and nitrite adds a new dimension to the current understanding of aerobic nitrification, while presenting opportunities to rethink nitrogen management in engineered systems.
format	article
author	Ameet J. Pinto Daniel N. Marcus Umer Zeeshan Ijaz Quyen Melina Bautista-de lose Santos Gregory J. Dick Lutgarde Raskin
author_facet	Ameet J. Pinto Daniel N. Marcus Umer Zeeshan Ijaz Quyen Melina Bautista-de lose Santos Gregory J. Dick Lutgarde Raskin
author_sort	Ameet J. Pinto
title	Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
title_short	Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
title_full	Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
title_fullStr	Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
title_full_unstemmed	Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System
title_sort	metagenomic evidence for the presence of comammox <italic toggle="yes">nitrospira</italic>-like bacteria in a drinking water system
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/80544678741648158bf5f3c176505289
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Metagenomic Evidence for the Presence of Comammox <italic toggle="yes">Nitrospira</italic>-Like Bacteria in a Drinking Water System

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