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Title: Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Abstract

The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high-quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome-assembled genomes were compared with other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clades A and B respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I-V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clades A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated.

Authors:
 [1];  [1];  [2];  [1];  [1];  [1];  [2]; ORCiD logo [1]
  1. Department of MicrobiologyRadboud University Heyendaalseweg 135, 6525 AJ Nijmegen the Netherlands
  2. Earth and Planetary Sciences DepartmentUniversity of California, 2151 Berkeley Way Berkley CA 94720 USA
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1569086
Alternate Identifier(s):
OSTI ID: 1569087; OSTI ID: 1572063
Grant/Contract Number:  
AC02‐05CH11231; DE‐AC02‐05CH11231; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Name: Environmental Microbiology Journal Volume: 21 Journal Issue: 10; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United Kingdom
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Poghosyan, Lianna, Koch, Hanna, Lavy, Adi, Frank, Jeroen, Kessel, Maartje A. H. J., Jetten, Mike S. M., Banfield, Jillian F., and Lücker, Sebastian. Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. United Kingdom: N. p., 2019. Web. doi:10.1111/1462-2920.14691.
Poghosyan, Lianna, Koch, Hanna, Lavy, Adi, Frank, Jeroen, Kessel, Maartje A. H. J., Jetten, Mike S. M., Banfield, Jillian F., & Lücker, Sebastian. Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. United Kingdom. doi:10.1111/1462-2920.14691.
Poghosyan, Lianna, Koch, Hanna, Lavy, Adi, Frank, Jeroen, Kessel, Maartje A. H. J., Jetten, Mike S. M., Banfield, Jillian F., and Lücker, Sebastian. Mon . "Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface". United Kingdom. doi:10.1111/1462-2920.14691.
@article{osti_1569086,
title = {Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface},
author = {Poghosyan, Lianna and Koch, Hanna and Lavy, Adi and Frank, Jeroen and Kessel, Maartje A. H. J. and Jetten, Mike S. M. and Banfield, Jillian F. and Lücker, Sebastian},
abstractNote = {The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high-quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome-assembled genomes were compared with other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clades A and B respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I-V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clades A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated.},
doi = {10.1111/1462-2920.14691},
journal = {Environmental Microbiology},
number = 10,
volume = 21,
place = {United Kingdom},
year = {2019},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/1462-2920.14691

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Cited by: 8 works
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