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Complete genome sequence of Desulfurispirillum indicum strain S5T
Standards in Genomic Sciences volume 5, pages371–378(2011)
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.
Desulfurispirillum indicum type strain S5T (=DSM 22839T =ATCC BAA-1389T) was isolated from an estuarine sediment for its ability to grow on selenate . D. indicum belongs to the Chrysiogenetes, a deeply branching phylum that includes three other cultured species: Chrysiogenes arsenatis , Desulfurispirillum alkaliphilum , and Desulfurispira natronophila . The four microorganisms are all strict anaerobes and are capable of using a variety of terminal electron acceptors and a few short-chain 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.
D. indicum forms a deeply branching clade related to Chrysiogenes arsenatis, an arsenate respiring bacterium that cannot use selenate as electron acceptor, and Desulfurispira natronophila that only uses sulfur or arsenate as terminal electron acceptor (Table 1). Interestingly, its closest relative D. alkaliphilum, with a 16S rRNA gene identity of 99.8%, is not capable of either arsenate or selenate respiration. The phylogenetic position of D. indicum relative to its closest relatives is shown in Figure 1. This Gram-negative bacterium is spiral-shaped and accumulates electron-dense granules when grown in the presence of selenium (Figure 2).
Genome sequencing information
Genome project history
The genome of D. indicum strain S5 was selected for sequencing in 2007 by the DOE Joint Genome Institute as a part of the DOE JGI Community Sequencing Program. The Quality Draft (QD) assembly and annotation were completed on July 3, 2009, and presented for public access on December 31, 2009 in the ORNL database. The final complete genome was made available on September 14, 2010. Table 2 presents the project information and its association with MIGS version 2.0 compliance .
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 .
Genome sequencing and assembly
The draft genome of Desulfurispirillum indicum was generated at the DOE Joint Genome Institute (JGI) using a combination of Illumina  and 454 technologies . For this genome, we constructed and sequenced an Illumina GAii shotgun library which generated 16,867,720 reads totaling 607 Mbp, a 454 Titanium standard library which generated 234,340 reads and paired end 454 library with average insert sizes of 6, 18 and 23 Kbp which generated 475,179 reads totaling 291 Mbp of 454 data. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website . The initial draft assembly contained 117 contigs in 1 scaffold. The 454 Titanium standard data and the 454 paired end data were assembled together with Newbler, version 2.3. The Newbler consensus sequences were computationally shredded into 2 Kbp overlapping fake reads (shreds). Illumina sequencing data was assembled with Velvet, version 0.7.63 , and the consensus sequences were computationally shredded into 1.5 Kbp overlapping fake reads (shreds). We integrated the 454 Newbler consensus shreds, the Illumina Velvet consensus shreds and the read pairs in the 454 paired end library using parallel phrap, version SPS - 4.24 (High Performance Software, LLC). The software Consed [22–24] was used in the following finishing process: Illumina data was used to correct potential base errors and increase consensus quality using the software Polisher developed at JGI (Alla Lapidus, unpublished). Possible mis-assemblies were corrected using gapResolution (Cliff Han, unpublished), Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR (J-F Cheng, unpublished) primer walks. A total of 764 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. The total size of the genome is 2,928,377 bp and the final assembly is based on 220 Mbp of 454 draft data which provides an average 108 × coverage of the genome and 607 Mbp of Illumina draft data which provides an average 222 × coverage of the genome.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . 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. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE , RNAMMer , Rfam , TMHMM , and signalP .
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 protein-coding 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.
D. indicum strain S5 can use nitrate, nitrite, arsenate or selenate as the terminal electron acceptors for growth, while using the electron donors acetate, lactate or pyruvate [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 ( 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 , Desulfitobacterium hafniense , Sulfurospirillum barnesii  and Thauera selenatis [37,38]) . The genome of the selenite respirer Bacillus selenitireducens  has also been sequenced. Comparisons of the DMSO-like sequences from these genomes will help to generate testable hypotheses about functions and substrates of the various terminal reductases.
Narasingarao P, Häggblom MM. Identification of anaerobic selenate-respiring bacteria from aquatic sediments. Appl Environ Microbiol 2007; 73:3519–3527. PubMed doi:10.1128/AEM.02737-06
Macy JM, Nunan K, Hagen KD, Dixon DR, Harbour PJ, Cahill M, Sly LI. Chrysiogenes arsenatis gen. nov., sp. nov., a new arsenate-respiring bacterium isolated from gold mine wastewater. Int J Syst Bacteriol 1996; 46:1153–1157. PubMed doi:10.1099/00207713-46-4-1153
Sorokin DY, Foti M, Tindall BJ, Muyzer G. Desulfurispirillum alkaliphilum gen. nov. sp. nov., a novel obligately anaerobic sulfur- and dissimilatory nitrate-reducing bacterium from a full-scale sulfide-removing bioreactor. Extremophiles 2007; 11:363–370. PubMed doi:10.1007/s00792-006-0048-8
Sorokin DY, Muyzer G. Desulfurispira natronophila gen. nov. sp. nov.: an obligately anaerobic dissimilatory sulfur-reducing bacterium from soda lakes. Extremophiles 2010; 14:349–355. PubMed doi:10.1007/s00792-010-0314-7
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
List Editor. Validation List No. 85. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685–690. PubMed doi:10.1099/ijs.0.02358-0
Garrity GM, Holt JG. Phylum BV. Chrysiogenetes phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 421.
Garrity GM, Holt JG. Class I. Chrysiogenetes class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 421.
Garrity GM, Holt JG. Order I. Chrysiogenales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p.421.
Garrity GM, Holt JG. Family I. Chrysiogenaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 421.
List Editor. Validation List No. 131: List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2010; 60:1–2. doi:10.1099/ijs.0.021204-0
Rauschenbach I, Narasingarao P, Häggblom M. Desulfurispirillum indicum sp. nov., a selenate and selenite respiring bacterium isolated from an estuarine canal in southern India. Int J Syst Evol Microbiol 2011; 61:654–658. PubMed doi:10.1099/ijs.0.022392-0
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596–1599. PubMed doi:10.1093/molbev/msm092
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360
Fennell DE, Rhee SK, Ahn YB, Häggblom MM, Kerkhof LJ. Detection and characterization of a dehalogenating microorganism by terminal restriction fragment length polymorphism fingerprinting of 16S rRNA in a sulfidogenic, 2-bromophenol-utilizing enrichment. Appl Environ Microbiol 2004; 70:1169–1175. PubMed doi:10.1128/AEM.70.2.1169-1175.2004
Kerkhof L, Ward BB. Comparison of Nucleic Acid Hybridization and Fluorometry for Measurement of the Relationship between RNA/DNA Ratio and Growth Rate in a Marine Bacterium. Appl Environ Microbiol 1993; 59:1303–1309. PubMed
Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433–438. PubMed doi:10.1517/14622418.104.22.1683
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376–380. PubMed
The DOE Joint Genome Institute. http://www.jgi.doe.gov
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107
Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186–194. PubMed
Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175–185. PubMed
Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998; 8:195–202. PubMed
Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceedings of the 2006 international conference on bioinformatics and computational biology HR, Arabnia, H., Valafar, editor 2006. CSREA Press. p 141–146.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMed doi:10.1093/nar/25.5.955
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108. PubMed doi:10.1093/nar/gkm160
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003; 31:439–441. PubMed doi:10.1093/nar/gkg006
Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001; 305:567–580. PubMed doi:10.1006/jmbi.2000.4315
Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004; 340:783–795. PubMed doi:10.1016/j.jmb.2004.05.028
Rauschenbach I, Yee N, Häggblom MM, Bini E. Energy metabolism and multiple respiratory pathways revealed by genome sequencing of Desulfurispirillum indicum strain S5. Environ Microbiol 2011; 13:1611–1621. PubMed doi:10.1111/j.1462-2920.2011.02473.x
Knight V, Blakemore R. Reduction of diverse electron acceptors by Aeromonas hydrophila. Arch Microbiol 1998; 169:239–248. PubMed doi:10.1007/s002030050567
Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF. Isolation and characterization of a novel As(V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium. Appl Environ Microbiol 2001; 67:5568–5580. PubMed doi:10.1128/AEM.67.12.5568-5580.2001
Stolz JF, Ellis DJ, Blum JS, Ahmann D, Lovley DR, Oremland RS. Sulfurospirillum barnesii sp. nov. and Sulfurospirillum arsenophilum sp. nov., new members of the Sulfurospirillum clade of the epsilon Proteobacteria. Int J Syst Bacteriol 1999; 49:1177–1180. PubMed doi:10.1099/00207713-49-3-1177
Lowe EC, Bydder S, Hartshorne RS, Tape HL, Dridge EJ, Debieux CM, Paszkiewicz K, Singleton I, Lewis RJ, Santini JM, et al. Quinol-cytochrome c oxidoreductase and cytochrome c4 mediate electron transfer during selenate respiration in Thauera selenatis. J Biol Chem 2010; 285:18433–18442. PubMed doi:10.1074/jbc.M110.115873
Debieux CM, Dridge EJ, Mueller CM, Splatt P, Paszkiewicz K, Knight I, Florance H, Love J, Titball RW, Lewis RJ, et al. A bacterial process for selenium nanosphere assembly. Proc Natl Acad Sci USA 2011; 108:13480–13485. PubMed doi:10.1073/pnas.1105959108
Switzer Blum J, Burns Bindi A, Buzzelli J, Stolz JF, Oremland RS. Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.: two haloal-kaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Arch Microbiol 1998; 171:19–30. PubMed doi:10.1007/s002030050673
The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. This work was funded in part by NSF grant EAR 0843295.
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Bini, E., Rauschenbach, I., Narasingarao, P. et al. Complete genome sequence of Desulfurispirillum indicum strain S5T. Stand in Genomic Sci 5, 371–378 (2011). https://doi.org/10.4056/sigs.2425302
- Desulfurispirillum indicum S5