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"Thioalkalivibrio Sulfidophilus" HL-Ebgr7 Classification and Features Has Rod-Shaped, Elongated Cells with a Polar Flagel- “T

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UvA-DARE (Digital Academic Repository) Complete genome sequence of Thioalkalivibrio sulfidophilus HL-EbGr7 Muyzer, G.; Sorokin, D.Y.; Mavromatis, K.; Lapidus, A.; Clum, A.; Ivanova, N.; Pati, A.; d' Haeseleer, P.; Woyke, T.; Kyrpides, N.C. DOI 10.4056/sigs.1483693 Publication date 2011 Document Version Final published version Published in Standards in Genomic Sciences Link to publication Citation for published version (APA): Muyzer, G., Sorokin, D. Y., Mavromatis, K., Lapidus, A., Clum, A., Ivanova, N., Pati, A., d' Haeseleer, P., Woyke, T., & Kyrpides, N. C. (2011). Complete genome sequence of Thioalkalivibrio sulfidophilus HL-EbGr7. Standards in Genomic Sciences, 4(1), 23-35. https://doi.org/10.4056/sigs.1483693 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:24 Sep 2021 Standards in Genomic Sciences (2011) 4:23-35 DOI:10.4056/sigs.1483693 Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7 Gerard Muyzer1*, Dimitry Yu Sorokin1,2, Konstantinos Mavromatis3, Alla Lapidus3, Alicia Clum3, Natalia Ivanova3, Amrita Pati3, Patrick d'Haeseleer4, Tanja Woyke3, Nikos C. Kyrpides3 1Department of Biotechnology, Delft University of Technology, Delft, The Netherlands 2Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia 3Joint Genome Institute, Walnut Creek, California, USA 4Joint Bioenergy Institute, California, USA *Corresponding author: Gerard Muyzer Keywords: haloalkaliphilic, sulfide, thiosulfate, sulfur-oxidizing bacteria (SOB) “Thioalkalivibrio sulfidophilus” HL-EbGr7 is an obligately chemolithoautotrophic, haloalkali- philic sulfur-oxidizing bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we re- port the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases. Introduction “Thioalkalivibrio sulfidophilus” HL-EbGr7 is an obli- hydrogen sulfide is stripped from the gas phase gately chemolithoautotrophic SOB using CO2 as a into an alkaline solution, which is subsequently carbon source and reduced inorganic sulfur com- transferred to a bioreactor where Thioalkalivibrio pounds as an energy source. It belongs to the genus oxidizes HS- almost exclusively to elemental sulfur Thioalkalivibrio. This genus is characterized by at a low red-ox potential [21]. Removal of toxic obligate haloalkaliphily and forms a monophyletic sulfide is needed, not only for a clean and healthy group within the family Ectothiorhodospiraceae. environment, but also to protect gas turbines from The genus currently includes nine validly described corrosion. In contrast to chemical desulfurization species [1] and many yet uncharacterized isolates processes, such as the ‘Claus-process’, biological [2,3]. The members are slow growing and well- removal is cheaper, cleaner and more sustainable, adapted to hypersaline (up to salt saturation) and as the produced hydrophilic bio-sulfur is a better alkaline (up to pH 10.5) conditions. They can oxid- fertilizer and fungicide than the chemically pro- ize sulfide, thiosulfate, elemental sulfur, sulfite and duced crystalline hydrophobic sulfur. polythionates (see Table 1 for summary). Moreo- To get insight into the molecular mechanism by ver, some species can reduce nitrate, nitrite or nitr- which Thioalkalivibrio strains adapt to haloalkaline ous oxide [17,18] or utilize thiocyanate (SCN-) as an conditions (i.e., pH 10 and up to 4 M of Na+) identifi- energy and nitrogen source [19,20]. Genetic diver- cation of the genes that are involved in these adapta- sity analysis of 85 Thioalkalivibrio strains isolated tions is needed. The most important issues are sul- from different soda lakes located in Mongolia, fide specialization, carbon assimilation at high pH Kenya, California, Egypt and south Siberia, indi- and bioenergetic adaptation to high salt/high pH. In cated a high genetic diversity and an endemic cha- addition, information on the genome might help in racter, i.e., the majority of the genotypes (85.9%) optimizing the sulfur removal process. Here we were found to be unique to one region [15]. present a summary classification and a set of fea- Apart from their role in the sulfur cycle of soda tures for “T. sulfidophilus” HL-EbGr7, together with lakes, Thioalkalivibrio species also play a key role in the description of the genomic sequencing and anno- the sustainable removal of sulfide from wastewater tation. and gas streams. In this so-called ‘Thiopaq-process’, The Genomic Standards Consortium "Thioalkalivibrio sulfidophilus" HL-EbGr7 Classification and features has rod-shaped, elongated cells with a polar flagel- “T. sulfidophilus” HL-EbGr7 was isolated from a lum (Figure 1b and c). The strain is obligately al- full-scale Thiopaq bioreactor in the Netherlands kaliphilic with a pH optimum of 9.5. It can tolerate a salinity of 1.5 M (optimum at 0.4 M) of total so- used to remove H2S from biogas [21]. The reactor biomass had a very peculiar property, which made dium, sulfide concentrations up to 5 mM and a it different from the usual SOB biomass, i.e., an temperature up to 40°C. It utilizes ammonium and almost complete sulfide specialization and no thi- urea, but not nitrate or nitrite, as a N-source. On osulfate-oxidizing activity. This was probably the the basis of 16S rRNA gene sequencing the strain result of a very low red-ox potential at which the belongs to the Gammaproteobacteria with Thioal- reactor was operated. Therefore, the dominant kalivibrio denitrificans as the closest, described SOB could originally be enriched only with sulfide species (Figure 2). Despite this relation, strain HL- as substrate in cylinders with agarose-stabilized EbGr7 cannot grow anaerobically with NOx. Both medium containing opposing gradients of oxygen phylogeny and specific physiology indicate that and sulfide [Figure 1a, 22]. Subsequently, the this strain represents a novel species within the strain was purified using serial dilutions in gra- genus Thioalkalivibrio for which a tentative spe- dient cultures and finally from a colony on solid cies epithet “sulfidophilus” is proposed. medium with sulfide at micro-oxic conditions. It Figure 1. a, Enrichment of “Thioalkalivibrio sulfidophilus” HL-EbGr7 in a gradient culture, whereby sulfide is diffusing from an agarose plug in the bottom of the cylinder and O2 from the top. The bacterial cells ac- cumulate in a dense band at the most favorable sulfide and oxygen concentration. b, phase-contrast microphotograph; c, electron micro- scopy microphotograph of a total cell preparation contrasted with phosphotungstic acid. 24 Standards in Genomic Sciences Muyzer et al. Table 1. Features of “Thioalkalivibrio sulfidophilus” strain HL-EbGR7 according to the MIGS recommendations [4]. MIGS ID Property Term Evidence code Current classification Domain Bacteria TAS [5] Phylum Proteobacteria TAS [6] Class Gammaproteobacteria TAS [7,8] Order Chromatiales TAS [7,9] Family Ectothiorhodospiraceae TAS [10] Genus Thioalkalivibrio TAS [11-13] Species “Thioalkalivibrio sulfidophilus” HL-EbGR7 NAS Gram stain negative TAS [2] Cell shape rod-shaped TAS [2] Motility motile TAS [2] Sporulation non-sporulating TAS [2] Temperature range Mesophile TAS [2] Optimum temperature 34 TAS [2] MIGS-6.3 Salinity range 0.2-1.5M Na+ (opt.0.4 M) TAS [2] MIGS-22 Oxygen requirement microaerophilic TAS [2] - Carbon source HCO3 TAS [2] Energy source Sulfide/polysulfide, thiosulfate, sulfur TAS [2] MIGS-6 Habitat Alkaline bioreactors; soda lakes TAS [2] MIGS-15 Biotic relationship free-living TAS [2] MIGS-14 Pathogenicity none NAS Biosafety level 1 TAS [14] Isolation Thiopaq bioreactor TAS [15] MIGS-4 Geographic location Eerbeek, The Netherlands TAS [15] MIGS-5 Sample collection time 2005 NAS MIGS-4.1 Latitude 52.11 TAS [16] MIGS-4.2 Longitude 6.07 TAS [16] MIGS-4.3 Depth Not applicable MIGS-4.4 Altitude Sea level NAS Evidence codes - IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from of the Gene Ontology project. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements. Genome sequencing information Genome project history Strain HL-EbGr7 was selected for
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