Skip to main content


Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake


Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This organism was sequenced as part of the community science program at the DOE Joint Genome Institute.


Soda lakes are characterized by a high and stable pH (>9) due to the presence of molar concentrations of soluble carbonates as the dominant anions and a moderate to high salinity [1]. They are found in arid zones in many parts of the world, for example, in the Kulunda Steppe in Russia, North-Eastern China, the Rift Valley in Africa and the arid regions of California and Nevada (e.g., Mono Lake, Big Soda Lake). Despite their (extremely) haloalkaline character, these environments harbor a rich microbial diversity that is responsible for driving highly active biogeochemical cycles [2], of which the sulfur cycle is the most active. Our current research focuses on a group of chemolithoautotrophic sulfur-oxidizing bacteria that belong to the genus Thioalkalivibrio in the class Gammaproteobacteria . These organisms are of interest because of their role in the oxidative part of the sulfur cycle in soda lakes [3] and their application in the sustainable removal of sulfur from wastewater and gas streams [4]. To better understand the success of this group of organisms, we have sequenced the genomes of a large number of Thioalkalivibrio isolates. Here we present the genome sequence of T. paradoxus ARh 1T (= DSM 13531T = JCM 11367T ).

Organism information

Classification and features

This obligate aerobic and haloalkaliphilic strain, which was isolated from a mixed sample of sediments from Kenyan soda lakes, is a non-motile coccoid rod forming intracellular sulfur as an obligate intermediate during oxidation of thiosulfate and thiocyanate (Fig. 1). It is an obligate chemolithoautotroph, capable of using a variety of reduced, inorganic sulfur compounds, including sulfide, thiosulfate and polysulfide, as electron donor for carbon fixation. It can also oxidize CS2 (carbon disulfide). Of special interest is its ability to grow with thiocyanate (NCS) as electron donor, with a relatively high growth rate of 0.08–0.1 h−1 in continuous culture, compared to 0.01–0.015 h- 1 for growth on thiosulfate [5]. Phylogenetic analysis based on 16S rRNA sequences shows that T. paradoxus is closely related to Thioalkalivibrio nitratireducens ALEN 2T (Fig. 2). An overview of basic features of the organism is provided in Table 1.

Fig. 1

Thin section electron microscopy photographs of cells of strain ARh 1T grown with thiocyanate in batch (a) and chemostat (b) cultures at pH 10 and 0.6 M total Na+. S(in) - intracellular sulfur globe; S(out) - excreted sulfur globe damaging the cell membrane and the wall; N - nucleoid; C - carboxysomes

Fig. 2

Phylogenetic tree, based on 16S rRNA sequences, of Thioalkalivibrio and various members of the Ectothiorhodospiraceae family. ARB [22] was used for tree construction and MEGA6 [23] for the bootstrap analysis. Alphaproteobacteria were used as the outgroup and pruned from the finished tree

Table 1 Classification and general features of Thioalkalivibrio paradoxus ARh 1 T [24]

Genome sequencing information

Genome project history

In order to better understand the diversity within the genus Thioalkalivibrio , as well as their biogeochemical role in soda lakes, a large number of isolates (approximately 70) was sequenced at the Joint Genome Institute. The full genome of the type strain of Thioalkalivibrio paradoxus presented here contains 3.8 million basepairs. Sequencing was performed at the JGI under project number 401912 and the sequence data was subsequently released in Genbank on December 31, 2013. A project overview is provided in Table 2.

Table 2 Project information
Table 3 Genome statistics

Growth conditions and genomic DNA preparation

A buffer using sodium carbonate and bicarbonate, with a total salt concentration of 0.6 M Na+, was used for cultivation of the organism; the energy source was thiosulfate (40 mM). After harvesting, the cells were stored at −80 °C for further processing. Genomic DNA was extracted using a standard chloroform-phenol-isoamyl alcohol mixture, followed by ethanol precipitation. After vacuum drying, the pellet was dissolved in water and the quantity and quality of the DNA determined using the JGI-provided Mass Standard Kit.

Genome sequencing and assembly

The draft genome of Thioalkalivibrio paradoxus ARh 1T was generated at the DOE Joint Genome Institute (JGI) using Illumina data [6]. For this genome, we constructed and sequenced an Illumina short-insert paired-end library with an average insert size of 270 bp which generated 18,589,770 reads and an Illumina long-insert paired-end library with an average insert size of 7,058.67 +/–3247.54 bp which generated 20,051,794 reads totaling 5,796 Mbp of Illumina data (unpublished, Feng Chen). All general aspects of library construction and sequencing performed at the JGI can be found at The initial draft assembly contained 83 contigs in 11 scaffolds. The initial draft data was assembled with ALLPATHS [7], version 39750, and the consensus was computationally shredded into 10 Kbp overlapping fake reads (shreds). The Illumina draft data was also assembled with Velvet, version 1.1.05 [8], and the consensus sequences were computationally shredded into 1.5 Kbp overlapping fake reads (shreds). The Illumina draft data was assembled again with Velvet using the shreds from the first Velvet assembly to guide the next assembly. The consensus from the second Velvet assembly was shredded into 1.5 Kbp overlapping fake reads. The fake reads from the ALLPATHS assembly and both Velvet assemblies and a subset of the Illumina CLIP paired-end reads were assembled using parallel phrap, version 4.24 (High Performance Software, LLC). Possible mis-assemblies were corrected with manual editing in Consed [911]. Gap closure was accomplished using repeat resolution software (Wei Gu, unpublished), and sequencing of bridging PCR fragments with Sanger and/or PacBio (unpublished, Cliff Han) technologies. A total of 50 additional sequencing reactions were completed to close gaps and to raise the quality of the final sequence. The size of the genome is 3.8 Mb and the final assembly is based on 5,796 Mbp of Illumina draft data, which provides an average 1,486X coverage of the genome.

Genome annotation

The assembled sequence was annotated using the JGI prokaryotic annotation pipeline [12] and was further reviewed using the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [13]. Genes were identified using Prodigal [14], followed by manual curation using GenePRIMP [15]. Predicted CDSs were translated and used to search the NCBI non-redundant, UniProt, TIGRFam, Pfam, KEGG, COG and InterPro databases. The tRNAScanSE tool [16] was used to detect tRNA genes and ribosomal RNA genes were detected using models contructed from SILVA [17]. Other RNA genes were predicted using Rfam profiles in Infernal [18]. CRISPR elements were detected using CRT [19] and PILER-CR [20]. Further annotation was performed using the Integrated Microbial Genomics (IMG) platform [21].

Genome properties

The finished genome with a G + C percentage of 66.06 % comprises a single chromosome of approximately 3.8 Mb (Fig. 3). There are 3557 genes of which 3,500 are protein-coding genes (a summary of genome properties is shown in Table 3). Approximately two-thirds of the protein coding genes could be assigned to a COG functional category (Table 4).

Fig. 3

Genome map of Thioalkalivibrio paradoxus ARh 1T. From outer to inner ring: genes on the forward strand; genes on the reverse strand; RNA genes (tRNA: green; rRNA: red; other: black); GC content and GC skew

Table 4 Number of genes associated with the 25 general COG functional categories


The availability of high-quality genomic sequences of the type strains of Thioalkalivibrio , the dominant genus of sulfur-oxidizing bacteria in soda lakes, is an invaluable tool for gaining a more complete understanding of the biogeochemistry of these extreme environments. Additionally, this information may provide new insights into the exact mechanisms of adaptation these bacteria have evolved to not only survive, but thrive in this habitat. Finally, the genome may contain clues that will help improve the existing biotechnological applications of this organism in bioremediation.


  1. 1.

    Kempe S, Kazmierczak J. Soda Lakes. In: Reitner J, Thiel V, editors. Encyclopedia of Geobiology. Netherlands: Springer; 2011.

  2. 2.

    Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G. Microbial diversity and biogeochemical cycling in soda lakes. Extremophiles. 2014;18:791–809.

  3. 3.

    Sorokin DY, Banciu H, Robertson LA, Kuenen JG, Muyzer G. Halophilic and haloalkaliphilic sulfur-oxidizing bacteria from hypersaline habitats and soda lakes. In: Rosenberg E, editor. The Prokaryotes - Prokaryotic Physiology and Biochemistry. Berlin-Heidelberg: Springer; 2013. p. 530–51.

  4. 4.

    Sorokin DY, van den Bosch PLF, Abbas B, Janssen AJH, Muyzer G. Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors. Appl Microbiol Biotechnol. 2008;80:965–75.

  5. 5.

    Sorokin DY, Tourova TP, Lysenko AM, Mityushina LL, Kuenen JG. Thioalkalivibrio thiocyanoxidans sp. nov. and Thioalkalivibrio paradoxus sp. nov., novel alkaliphilic, obligately autotrophic, sulfuroxidizing bacteria capable of growth on thiocyanate, from soda lakes. Int J Syst Evol Microbiol. 2002;52:657–64.

  6. 6.

    Bennett S. Solexa Ltd. Pharmacogenomics. 2004;5:433–8.

  7. 7.

    Gnerre S, MacCallum I, Przybylski D, Ribeiro F, Burton J, Walker B, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011;108:1513–8.

  8. 8.

    Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–9.

  9. 9.

    Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 1998;8:175–85.

  10. 10.

    Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8:186–94.

  11. 11.

    Gordon D, Abajian C, Green P. Consed: a graphical tool for sequence finishing. Genome Res. 1998;8:195–202.

  12. 12.

    Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009;1:63–7.

  13. 13.

    Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25:2271–8.

  14. 14.

    Hyatt D, Chen G, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119–30.

  15. 15.

    Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010;7:455–7.

  16. 16.

    Lowe TM, Eddy SR. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res. 1997;25:955–64.

  17. 17.

    Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucl Acids Res. 2007;35:7188–96.

  18. 18.

    Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25:1335–7.

  19. 19.

    Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209.

  20. 20.

    Edgar RC. PILER-CR. fast and accurate identification of CRISPR repeats. BMC Bioinformatics. 2007;8:18.

  21. 21.

    Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Pillay M, et al. IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res. 2014;42:D560–7.

  22. 22.

    Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, et al. ARB: a software environment for sequence data. Nucl Acids Res. 2004;32:1363–71.

  23. 23.

    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013;30:2725–9.

  24. 24.

    Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. Towards a richer description of our complete collection of genomes and metagenomes “Minimum Information about a Genome Sequence ” (MIGS) specification. Nat Biotechnol. 2008;26:541–7.

  25. 25.

    Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.

  26. 26.

    Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.

  27. 27.

    Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2005; 55:2235–2238.

  28. 28.

    Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.

  29. 29.

    Garrity GM, Bell JA, Lilburn T. Order I. Chromatiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s Manual of Systematic Bacteriology, Volume 2, Part B. 2nd ed. New York: Springer; 2005. p. 1.

  30. 30.

    Imhoff JF. Reassignment of the Genus Ectothiorhodospira Pelsh 1936 to a new family, Ectothiorhodospiraceae fam. nov., and emended description of the Chromatiaceae Bavendamm 1924. Int J Syst Evol Microbiol. 1984;34:338–9.

  31. 31.

    Sorokin DY, Lysenko AM, Mityushina LL, Tourova TP, Jones BE, Rainey FA, et al. Thioalkalimicrobium aerophilum gen. nov., sp. nov. and Thioalkalimicrobium sibericum sp. nov., and Thioalkalivibrio versutus gen. nov., sp. nov., Thioalkalivibrio nitratis sp. nov. and Thioalkalivibrio denitrificans sp. nov., novel obligately alkaliphilic and obligately chemolithoautotrophic sulfur-oxidizing bacteria from soda lakes. Int J Syst Evol Microbiol. 2001;51:565–80.

  32. 32.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.

Download references


The work conducted by the U.S. 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. Tom Berben and Gerard Muyzer are supported by ERC Advanced Grant PARASOL (No. 322551). Dimitry Sorokin is supported by RBFR Grant 13–04–00049.

Author information

Correspondence to Gerard Muyzer.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

TB drafted this manuscript, with GM and DS providing critical review and discussion. DS was responsible for cultivation and DNA extraction. Sequencing and annotation were performed at the JGI by NI, AP, NK, LAG and TW. All authors approve of the final version.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, 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 ( applies to the data made available in this article, unless otherwise stated.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Berben, T., Sorokin, D.Y., Ivanova, N. et al. Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1T, an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake. Stand in Genomic Sci 10, 105 (2015) doi:10.1186/s40793-015-0097-7

Download citation


  • Haloalkaliphilic
  • Soda lakes
  • Sulfur-oxidizing bacteria
  • Thiocyanate