Document Type
Article
Publication Date
2017
Keywords
Zetaproteobacteria, Bacterial genomics, Microbiology
Abstract
The Zetaproteobacteria are ubiquitous in marine environments, yet this class of Proteobacteria is only represented by a few closely-related cultured isolates. In high-iron environments, such as diffuse hydrothermal vents, the Zetaproteobacteria are important members of the community driving its structure. Biogeography of Zetaproteobacteria has shown two ubiquitous operational taxonomic units (OTUs), yet much is unknown about their genomic diversity. Genome-resolved metagenomics allows for the specific binning of microbial genomes based on genomic signatures present in composite metagenome assemblies. This resulted in the recovery of 93 genome bins, of which 34 were classified as Zetaproteobacteria. Form II ribulose 1,5-bisphosphate carboxylase genes were recovered from nearly all the Zetaproteobacteria genome bins. In addition, the Zetaproteobacteria genome bins contain genes for uptake and utilization of bioavailable nitrogen, detoxification of arsenic, and a terminal electron acceptor adapted for low oxygen concentration. Our results also support the hypothesis of a Cyc2-like protein as the site for iron oxidation, now detected across a majority of the Zetaproteobacteria genome bins. Whole genome comparisons showed a high genomic diversity across the Zetaproteobacteria OTUs and genome bins that were previously unidentified by SSU rRNA gene analysis. A single lineage of cosmopolitan Zetaproteobacteria (zOTU 2) was found to be monophyletic, based on cluster analysis of average nucleotide identity and average amino acid identity comparisons. From these data, we can begin to pinpoint genomic adaptations of the more ecologically ubiquitous Zetaproteobacteria, and further understand their environmental constraints and metabolic potential.
Publication Title
The ISME Journal
Volume
11
Issue
8
First Page
1900
Last Page
1914
DOI
10.1038/ismej.2017.40
Required Publisher's Statement
© The Author(s) 2017
Recommended Citation
Heather Fullerton, Kevin W. Hager, Sean M. McAllister, Craig L. Moyer. "Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i" The ISME Journal Vol 11 (2017) p. 1900-1914
Subjects - Topical (LCSH)
Metagenomics; Microbial mats--Hawaii; Microbial mats--Diversity; Hydrothermal vents--Hawaii; Iron bacteria
Supplementary information
Genre/Form
articles
Type
Text
Rights
Copying of this document in whole or in part is allowable only for scholarly purposes. It is understood, however, that any copying or publication of this document for commercial purposes, or for financial gain, shall not be allowed without the author’s written permission.
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.
Language
English
Format
application/pdf
Comments
Supplementary Information accompanies this paper on The ISME Journal website (http://www.nature.com/ismej)
Supplementary information is also available as additional files on this page.