Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1, a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1 is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 proteincoding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1 was sequenced as part of the DOE Joint Genome Institute Community Science Program. Introduction Soda lakes are formed in inland arid areas where ground water, rich in CO2/bicarbonate, but poor in divalent cations (calcium and magnesium), accumulates in basins and evaporates. The resulting system has a stable high pH above 9 and up to 11, high soluble carbonate alkalinity reaching molar concentrations and moderate to extremely high salinity [1]. Despite these extreme characteristics, a rich microbial community is found to thrive in such lakes, driving highly active biogeochemical cycles. Thus far, knowledge on the dynamics of and the connections between these cycles is limited [2]. A better understanding of the biogeochemistry and the microbial species involved will lead to clearer insights into the ecology of soda lakes. Our research focuses on the species involved in the sulfur cycling in hypersaline soda lakes. To learn more about the community involved in the oxidizing part of the cycle, we have sequenced a large number of strains of the dominant cultivated haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Here we present the partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1. Organism information Classification and features T. thiocyanodenitrificans ARhD 1 is a Gram-negative bacterium belonging to the Gammaproteobacteria (Fig. 1). It is a motile rod with dimensions 0.4–0.6 × 1.5– 5 μm (Fig. 2). Basic information about the organism is summarized in Table 1. It is obligately chemolithoautotrophic and haloalkaliphilic. Energy is derived from the oxidation of a variety of inorganic sulfur compounds including sulfide, thiosulfate, thiocyanate, polysulfide, elemental sulfur and tetrathionate. It is facultatively anaerobic, capable of growth with nitrate or nitrite as electron acceptor when thiosulfate or thiocyanate serves as electron donor, although anaerobic growth with thiocyanate is extremely slow (0.006 h compared to 0.032 h in the presence of oxygen). At present, T. thiocyanodenitrificans is the only sulfur-oxidizing bacterium for which anaerobic growth with thiocyanate * Correspondence: [email protected] Microbial Systems Ecology, Department of Aquatic Microbiology, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands Full list of author information is available at the end of the article © 2015 Berben et al. Open Access 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Berben et al. Standards in Genomic Sciences (2015) 10:84 DOI 10.1186/s40793-015-0080-3