- Open Access
Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)
Standards in Genomic Sciencesvolume 2, pages149–157 (2010)
Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain 5175T (= DSM 6946 = ATCC 51133 = LMG 8192) is the type strain of the species Sulfurospirillum deleyianum, which is the type species of the genus Sulfurospirillum. The genus Sulfurospirillum was originally proposed by Schumacher et al. in 1992 . The generic name Sulfurospirillum derives from the chemical element ‘sulfur’ and ‘spira’ from Latin meaning coil, a coiled bacterium that reduces sulfur . The species is named after J. De Ley, a Belgian microbiologist who significantly contributed to bacterial systematics based on genetic relationships . Altogether, the genus Sulfurospirillum contains seven species . Strain 5175T was isolated from anoxic mud of a forest pond near Heinigen, Braunschweig area, Germany . It is unclear if further isolates of the species exist. Here, we present a summary classification and a set of features for S. deleyianum 5175T, together with the description of the complete genomic sequencing and annotation.
Classification and features
There were several uncultured clone sequences known in INSDC databases with at least 98% sequence identity to the 16S rRNA gene sequence (Y13671) of strain S. deleyianum 5175T. These were obtained from lake material in Dongping, China (FJ612333), deep subsurface groundwater in Japan (AB237694), and from the mangrove ecosystem of the Danshui River Estuary of Northern Taiwan (DQ234237) . No significant matches were reported with metagenomic samples at the NCBI BLAST server (November 2009).
Figure 1 shows the phylogenetic neighborhood of S. deleyianum 5175T in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome of S. deleyianum 5175T differ from each other by no more than one nucleotide, and differ by no more than one nucleotide from the previously published 16S rRNA sequence (Y13671).
The cells of strain 5175T are curved spiral rods of approximately 0.3–0.5 µm width and 1.0–3.0 µm length , with polar flagellation (Table 1 and Figure 2). Colonies are yellow-colored as a result of a flexirubin-type pigment . The cells contain cytochrome b and c . Strain 5175T is unable to rapidly decompose H2O2 (i.e. is catalase negative), does not need special growth factors (vitamins or amino acids), and is positive for oxidase . Strain 5175T grows anoxically with hydrogen, formate, fumarate, and pyruvate, but not lactate, as electron donor; acetate and hydrogen carbonate as carbon source and one of the following electron acceptors: nitrate, nitrite (which is reduced to ammonia), sulfite, thiosulfate, elemental sulfur (reduced to sulfide), dimethyl sulfoxide (reduced to dimethyl sulfide), fumarate, malate and aspartate (reduced to succinate) [1,18]. Sulfate is not reduced. Fumarate and malate can be fermented . Strain 5175T is able to grow microaerobically at 1–4% oxygen, but not at 21% oxygen . The substrates utilized for microaerobic growth are succinate, fumarate, malate, aspartate, pyruvate, oxoglutarate, and oxaloacetate . There is no oxidation of glycerol or acetate . An assimilatory sulfate reduction is lacking, and a source of reduced sulfur, e.g. sulfide  or L-cysteine, is required for growth . Further characteristics of the sulfur respiration of strain 5175T have been studied in detail [4,20].
Observations of ferric iron-reducing bacteria indicated that ferrihydrite was reduced to ferrous iron minerals via sulfur cycling with sulfide as the reductant. Ferric iron reduction via sulfur cycling was investigated in more detail with strain 5175T, which can utilize sulfur or thiosulfate as an electron acceptor . In the presence of cysteine (0.5 or 2 mM) as the sole sulfur source, no (microbial) reduction of ferrihydrite or ferric citrate was observed, indicating that S. deleyianum is unable to use ferric iron as an immediate electron acceptor . Interestingly, with thiosulfate at low concentration (0.05 mM), growth with ferrihydrite (6 mM) was possible, and sulfur was cycled up to 60 times .
An interesting syntrophism between strain 5175T and Chlorobium limicola 9330 has been reported . The substrate formate is not metabolized by Chlorobium, and the limiting amount of sulfur is alternately reduced by strain 5175T and oxidized by Chlorobium .
With respect to utilization of nitrate as terminal electron acceptor (dissimilatory nitrate reduction)  the dissimilatory hexaheme c nitrite has been studied in more detail. These include both structural and functional aspects [23–26].
Also, strain 5175T is able to use alternative electron acceptors. Strain 5175T is able to reduce the quinone moiety of anthraquinone-2,6-disulfonate (AQDS) and also to oxidize reduced anthrahydroquinone-2,6,-disulfonate (AH2QDS) as well . Additionally, oxidized metals may be used as terminal electron acceptors, such as arsenate [As(V)] and manganese [Mn(IV)], but not selenate [Se(VI)] or ferric iron [Fe(III)] .
The predominant menaquinone is MK-6 (88%), with small amounts of thermoplasmaquinone with six isoprene units (TPQ-6; 10%) and MK-5 (2%) . The polar-lipid fatty acid composition is 16:1ω7c (52.0%), 16:0 (29.2%), 18:1ω7c (17.2%), 15:0 (1.1%), and iso16:1 (0.6%) .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project . The genome project is deposited in the Genomes OnLine Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
S. deleyianum 5175T, DSM 6946, was grown anaerobically in DSM medium 541  at 28°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol with modification st/L for cell lysis as described in Wu et al. .
Genome sequencing and assembly
The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at http://www.jgi.doe.gov/. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 2,525 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the phrap assembler. Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones . Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. A total of 471 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 34.42× coverage of the genome. The final assembly contains 23,491 Sanger and 296,611 pyrosequence reads.
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. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform .
The genome consists of a 2,306,351 bp long chromosome with a 39.0% GC content (Table 3 and Figure 3). Of the 2,343 genes predicted, 2,291 were protein coding genes, and 52 RNAs. A total of 26 pseudogenes were identified. The majority of the protein-coding genes (72.9%) were assigned with a putative function while those remaining were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Schumacher W, Kroneck PMH, Pfennig N. Comparative systematic study on “Spirillum” 5175, Campylobacter and Wolinella species. Arch Microbiol 1992; 158:287–293 doi:10.1007/BF00245247.
Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed
Schumacher W, Kroneck P. Anaerobic energy metabolism of the sulfur-reducing bacterium “Spirillum” 5175 during dissimilatory nitrate reduction to ammonia. Arch Microbiol 1992; 157:464–470. doi:10.1007/BF00249106
Liao PC, Huang BH, Huang S. Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding. Microb Ecol 2007; 54:497–507. PubMed doi:10.1007/s00248-007-9217-2
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Stamatakis A, Hoover P, Rougemont J. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
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
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.
Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Springer, New York, 2001, p. 119–169.
Garrity GM, Bell JA, Lilburn T. Order I. Campylobacterales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Springer, New York, 2005, p. 1145.
Vandamme P, De Ley J. Proposal for a new family, Campylobacteraceae. Int J Syst Bacteriol 1991; 41:451–455.
Kodama Y, Ha LT, Watanabe K. Sulfurospirillum cavolei sp. nov., a facultatively anaerobic sulfur-reducing bacterium isolated from an underground crude oil storage cavity. Int J Syst Evol Microbiol 2007; 57:827–831. PubMed doi:10.1099/ijs.0.64823-0
Biological Agents. Technical rules for biological agents www.baua.de TRBA 466.
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. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Zöphel A, Kennedy MC, Beinert H, Kroneck PM. Investigations on microbial sulfur respiration. Isolation, purification, and characterization of cellular components from Spirillum 5175. Eur J Biochem 1991; 195:849–856. PubMed doi:10.1111/j.1432-1033.1991.tb15774.x
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 ε-Proteobacteria. Int J Syst Bacteriol 1999; 49:1177–1180. PubMed
Eisenmann E, Beuerle J, Sulger K, Kroneck P, Schumacher W. Lithotrophic growth of Sulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia. Arch Microbiol 1995; 164:180–185. doi:10.1007/BF02529969
Straub KL, Schink B. Ferrihydrite-dependent growth of Sulfurospirillum deleyianum through electron transfer via sulfur cycling. Appl Environ Microbiol 2004; 70:5744–5749. PubMed doi:10.1128/AEM.70.10.5744-5749.2004
Zöphel A, Kennedy MC, Beinert H, Kroneck PMH. Investigations on microbial sulfur respiration. Activation and reduction of elemental sulfur in several strains of eubacteria. Arch Microbiol 1988; 150:72–77.
Wolfe RS, Pfennig N. Reduction of sulfur by spirillum 5175 and syntrophism with Chlorobium. Appl Environ Microbiol 1977; 33:427–433. PubMed
Einsle O, Messerschmidt A, Stach P, Bourenkov GP, Bartunik HD, Huber R, Kroneck PMH. Structure of cytochrome c nitrite reductase. Nature 1999; 400:476–480. PubMed doi:10.1128/AEM.70.10.5744-5749.2004
Schumacher W, Kroneck PMH. Dissimilatory hexaheme c nitrite reductase of “Spirillum” strain 5175: purification and properties. Arch Microbiol 1991; 156:70–74. doi:10.1007/BF00418190
Stach P, Einsle O, Schumacher W, Kurun E.M.H. Kroneck P. Bacterial cytochrome c nitrite reductase: new structural and functional aspects. J Inorg Biochem 2000; 79:381–385. PubMed doi:10.1016/S0162-0134(99)00248-2
Clarke TA, Hemmings AM, Burlat B, Butt JN, Cole JA, Richardson DJ. Comparison of the structural and kinetic properties of the cytochrome c nitrite reductases from Escherichia coli, Wolinella succinogenes, Sulfurospirillum deleyianum and Desulfovibrio desulfuricans. Biochem Soc Trans 2006; 34:143–145. PubMed doi:10.1042/BST0340143
Luijten MLGC, Weelink SAB, Godschalk B, Langenhoff AAM, Eekert MHA, Schraa G, Stams AJM. Anaerobic reduction and oxidation of quinone moieties and the reduction of oxidized metals by halorespiring and related organisms. FEMS Microbiol Ecol 2004; 49:145–150. PubMed doi:10.1016/j.femsec.2004.01.015
Collins MD, Widdel F. Respiratory quinones of sulphate-reducing and sulphur-reducing bacteria: a systematic investigation. Syst Appl Microbiol 1986; 8:8–18.
Luijten MLGC, de Weert J, Smidt H, Boschker HTS, de Vos WM, Schraa G, Stams AJM. Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. Int J Syst Evol Microbiol 2003; 53:787–793. PubMed doi:10.1099/ijs.0.02417-0
List of media used at DSMZ for cell growth: http://www.dsmz.de/microorganisms/media_list.php
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ. A phylogeny-driven genomic encyclopedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12–20. doi:10.4056/sigs.761
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. BMC Bioinformatics 2010; 11:119.
Pati A, Ivanova N, Mikhailova, N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. Nat Methods (in press).
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Petra Aumann in cultivation of the strain and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1 and SI 1352/1-2.