Metagenomic evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System

Pinto, A. J., Marcus, D. N., Ijaz, U. Z. , Bautista-de lose Santos, Q. M., Dick, G. J. and Raskin, L. (2015) Metagenomic evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System. mSphere, 1(1), e00054-15. (doi:10.1128/mSphere.00054-15)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Pinto, Dr Ameet and Ijaz, Dr Umer Zeeshan
Authors: Pinto, A. J., Marcus, D. N., Ijaz, U. Z., Bautista-de lose Santos, Q. M., Dick, G. J., and Raskin, L.
College/School:College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:mSphere
Publisher:American Society for Microbiology
ISSN:2379-5042
ISSN (Online):2379-5042
Copyright Holders:Copyright © 2015 Pinto et al.
First Published:First published in mSphere 1(1):e00054-15
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
665801Healthy drinking waterAmeet PintoEngineering & Physical Sciences Research Council (EPSRC)EP/M016811/1ENG - ENGINEERING INFRASTRUCTURE & ENVIR