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A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments

Bryson, Samuel Joseph and Thurber, Andrew R. and Correa, Adrienne M. S. and Orphan, Victoria J. and Thurber, Rebecca Vega (2015) A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments. Environmental Microbiology, 17 (10). pp. 3708-3721. ISSN 1462-2912. https://resolver.caltech.edu/CaltechAUTHORS:20151112-154353069

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Abstract

Methane seep microbial communities perform a key ecosystem service by consuming the greenhouse gas methane prior to its release into the hydrosphere, minimizing the impact of marine methane sources on our climate. Although previous studies have examined the ecology and biochemistry of these communities, none has examined viral assemblages associated with these habitats. We employed virus particle purification, genome amplification, pyrosequencing and gene/genome reconstruction and annotation on two metagenomic libraries, one prepared for ssDNA and the other for all DNA, to identify the viral community in a methane seep. Similarity analysis of these libraries (raw and assembled) revealed a community dominated by phages, with a significant proportion of similarities to the Microviridae family of ssDNA phages. We define these viruses as the Eel River Basin Microviridae (ERBM). Assembly and comparison of 21 ERBM closed circular genomes identified five as members of a novel sister clade to the Microvirus genus of Enterobacteria phages. Comparisons among other metagenomes and these Microviridae major-capsid sequences indicated that this clade of phages is currently unique to the Eel River Basin sediments. Given this ERBM clade's relationship to the Microviridae genus Microvirus, we define this sister clade as the candidate genus Pequeñovirus.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1111/1462-2920.12758DOIArticle
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12758/abstractPublisherArticle
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.12758/suppinfoPublisherSupporting Information
ORCID:
AuthorORCID
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2014 Society for Applied Microbiology and John Wiley & Sons Ltd. Received 10 June, 2014; revised 15 December, 2014; accepted 15 December, 2014. The Gordon and Betty Moore Foundation (GBMF) provided funding to RVT for the generation of these metagenomes through the viral sequencing program. Funding also was provided by a National Science Foundation Grant #BIO-OCE 0825791 to VJO and #BIO-OCE 096037 to RVT, in addition to #OPP-1103428 that supported ART during the writing of this manuscript. Special thanks to Drs Jerome Payet and Jesse Zaneveld for helpful discussions of viral tree generation and analysis. The Oregon State University Center for Genome Research and Biocomputing (CGRB) provided computational infrastructure for genome assembly. The authors of this manuscript declare that they have no conflicts of interest in regard to the work presented here.
Funders:
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
NSFOCE-0825791
NSFOCE 096037
NSFOPP-1103428
Subject Keywords:Microbial population and community ecology
Issue or Number:10
Record Number:CaltechAUTHORS:20151112-154353069
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20151112-154353069
Official Citation:Bryson, S. J., Thurber, A. R., Correa, A. M. S., Orphan, V. J. and Vega Thurber, R. (2015), A novel sister clade to the enterobacteria microviruses (family Microviridae) identified in methane seep sediments. Environmental Microbiology, 17: 3708–3721. doi: 10.1111/1462-2920.12758
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:62084
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:18 Nov 2015 00:54
Last Modified:03 Oct 2019 09:15

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