Complete genome sequence of Desulfurispirillum indicum strain S5T

Desulfurispirillum indicum strain S5T is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only includes three other cultured species. Strain S5T is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.


Introduction
Desulfurispirillum indicum type strain S5 T (=DSM 22839 T =ATCC BAA-1389 T ) was isolated from an estuarine sediment for its ability to grow on selenate [1]. D. indicum belongs to the Chrysiogenetes, a deeply branching phylum that includes three other cultured species: Chrysiogenes arsenatis [2], Desulfurispirillum alkaliphilum [3], and Desulfurispira natronophila [4]. The four microorganisms are all strict anaerobes and are capable of using a variety of terminal electron acceptors and a few shortchain fatty acids as electron donors and sources of carbon. Specifically, D. alkaliphilum can respire sulfur, fumarate, nitrate, nitrite and chromate, while C. arsenatis can grow using arsenate, nitrate and nitrite. Desulfurispira natronophila can grow under moderate haloalkaline conditions, respiring sulfur or arsenate. Thus, D. indicum is the only characterized Chrysiogenetes that is capable of dissimilatory reduction of both arsenate and selenate, in addition to nitrate and nitrite respiration. This feature makes it an ideal system to identify and elucidate the pathways for selenate and arsenate oxyanions respiration and their regulation. Here we summarize the features of D. indicum and present a description of its sequenced genome, which is the first sequenced genome of a member of the phylum Chrysiogenetes.

Genome sequencing information
Genome project history

Growth conditions and DNA isolation
D. indicum was grown in mineral salt medium at 28°C with 20 mM pyruvate as carbon source and 10 mM nitrate as electron acceptor, as previously described [12,16]. Genomic DNA was isolated from an 80-ml culture using a phenol-chloroform extraction protocol [17]. Standards in Genomic Sciences

Genome annotation
Genes were identified using Prodigal [26] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [27]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein.

Genome properties
The genome includes a single circular chromosome of 2,928,377 bp (56.1% GC content). In total, 2,668 genes were predicted, 2,619 of which are proteincoding genes. Of these, 2,137 protein coding genes were assigned to a putative function while those remaining were annotated as hypothetical proteins. 91 protein coding genes belong to 25 paralogous families in this genome corresponding to a gene content redundancy of 3.4%. The properties and the statistics of the genome are summarized in Table 3 and Table 4.   [12,33]. The inspection of the strain S5 genome has confirmed the physiological data, and furthermore has enabled the discovery of sequences encoding other DMSO-like terminal reductases, as well as enzymes for the oxidation of additional electron donors ( [33] and Fig.  3). The discovery of such sequences suggests that the respiratory capabilities of strain S5 are broader than expected, and allows us to formulate hypotheses on further substrates and TEAs to be tested. In particular, we are interested in the dissimilatory reduction of selenium and arsenic oxyanions. Although the reduction of selenium is an important mode of respiration, the genes responsible for this process remain largely uncharacterized and virtually nothing is known about their regulation, or their interactions with other respiratory pathways. Besides Desulfurispirillum indicum, the genomes of only four bacterial species capable of using selenate reduction for growth are currently available: Aeromonas hydrophila [34], Desulfitobacterium hafniense [35], Sulfurospirillum barnesii [36] and Thauera selenatis [37,38]) [12]. The genome of the selenite respirer Bacillus selenitireducens [39] has also been sequenced. Comparisons of the DMSOlike sequences from these genomes will help to generate testable hypotheses about functions and substrates of the various terminal reductases.