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Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria

Speth, Daan R. and Lagkouvardos, Ilias and Wang, Yong and Qian, Pei-Yuan and Dutilh, Bas E. and Jetten, Mike S. M. (2017) Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria. Microbial Ecology, 74 (1). pp. 1-5. ISSN 0095-3628. https://resolver.caltech.edu/CaltechAUTHORS:20170117-083209355

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Abstract

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://dx.doi.org/10.1007/s00248-017-0929-7DOIArticle
https://link.springer.com/article/10.1007%2Fs00248-017-0929-7PublisherArticle
http://rdcu.be/tQgOPublisherFree ReadCube access
Additional Information:© 2017 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Received: 17 September 2016; Accepted: 01 January 2017; First online: 10 January 2017. Daan R. Speth was supported by BE-Basic FP 07.002.01. Bas E. Dutilh was supported by the Netherlands Organization for Scientific Research (NWO) Vidi grant 864.14.004. Mike S. M. Jetten was supported by the European Research Council advanced grants 232937 and 339880 and the NWO gravitation SIAM 024002002. Accession Numbers: The raw sequencing reads described in this paper has been deposited to Genbank/EBI/DDBJ under SRA accession number SRX1894129. The assembled, annotated draft genome has been deposited at DDBJ/ENA/GenBank under the accession MAYW00000000. The version described in this paper is version MAYW01000000. Compliance with Ethical Standards. The authors declare that they have no conflict of interest.
Funders:
Funding AgencyGrant Number
BE-BasicFP 07.002.01
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)864.14.004
European Research Council (ERC)232937
European Research Council (ERC)339880
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)SIAM 024002002
Subject Keywords:Scalindua; Anammox; Red Sea; Genome binning; Metagenomics; Salt adaptation
Issue or Number:1
Record Number:CaltechAUTHORS:20170117-083209355
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170117-083209355
Official Citation:Speth, D.R., Lagkouvardos, I., Wang, Y. et al. Microb Ecol (2017) 74: 1. doi:10.1007/s00248-017-0929-7
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:73513
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Jan 2017 23:40
Last Modified:03 Oct 2019 16:28

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