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1 Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
2 Department of Environmental Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
3 Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Meckenheimer Allee 168, D-53115 Bonn, Germany
4 DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
Correspondence
D. Yu. Sorokin
soroc{at}inmi.host.ru or
D.Y.Sorokin{at}tnw.tudelft.nl
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The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains HGD 3T and HGD 1-3T are DQ072718 and DQ072719, respectively.
Present address: Instituto de Agroquímica y Tecnologìa de Alimentos (IATA), Apdo. 73, 46100 Burjassot, Valencia, Spain. 
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). The opportunistic strategy is represented here by the moderately halophilic/extremely salt-tolerant Halomonas species (Gammaproteobacteria) that are better adapted to fluctuating salinity, whereas an extremely halophilic phenotype able to compete with the haloarchaea at salt-saturating conditions is very rare among the eubacteria (Ventosa et al., 1998). One possibility by which the eubacteria can compete with the haloarchaea for organic electron donors is their capacity to denitrify using simple organic electron donors produced in anaerobic sediments (such as acetate), since this potential is much more common for bacteria than for archaea (Zumft, 1997). Denitrification at extremely high salt concentrations represents an important function both for natural hypersaline habitats and as a potential application in the biological treatment of high-salt industrial waste rich in nitrate (Clifford & Liu, 1993). Furthermore, as mentioned above, the extremely halophilic eubacteria with a salt range for growth equal to that of haloarchaea, in contrast to moderate halophiles, are currently only poorly characterized. Here we report the results of the characterization of a group of gammaproteobacteria that persistently dominated in enrichment cultures at 4–5 M NaCl with acetate as electron donor/carbon source and nitrate/N2O as electron acceptor, inoculated with sediments from hypersaline lakes in Central Asia.
Dry steppe areas in south-western Siberia and north-eastern Mongolia harbour numerous small, hypersaline chloride–sulfate lakes, with a salt concentration approaching saturation. We investigated more than 20 such lakes in the Kulunda Steppe (Altai, Russia) stretching over 800 km along the central eastern border of Kazachstan, and two lakes in the north-eastern Mongolian steppe. Sediment samples from the Kulunda lakes were combined in six groups according to the salt content, which varied from 10 to 38 % (w/v). The salt content of the Mongolian lakes was 20–25 %. The pH ranged from 7·5 to 8·2 and the dominant ions were Na+, Cl– and 
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Extremely halophilic denitrifying bacteria were enriched and isolated in pure culture using the following mineral base medium (g l–1): NaCl, 240; K2HPO4, 2·5; (NH4)2SO4, 0·5. The pH was adjusted to 7·2. After sterilization, the medium was supplemented with 10 mM sodium acetate, 0·1 g yeast extract l–1, 2 mM MgCl2.6H2O and 1 ml l–1 of a trace metal solution (Pfennig & Lippert, 1966). KNO3 (5 mM) or N2O (50 mM) was used as the electron acceptor. The medium was made anoxic by five sequential cycles of evacuation–flushing with argon. Incubation was performed in 100 ml serum bottles sealed with butyl rubber stoppers, with 80 ml medium at 30 °C. Growth was monitored by measuring optical density at 600 nm and qualitative tests for nitrate/nitrite (Merck). After several 1 : 100 transfers and serial dilutions, pure cultures were isolated from single colonies on solid medium with the same composition as the base medium except that the NaCl concentration was reduced to 2 M. The plates were incubated in closed jars under argon or argon plus 10 % N2O in the presence of an oxygen-scavenging catalyst (AnaeroGen; Oxoid).
Nitrogen and sulfur compounds and protein were analysed as described previously (Sorokin et al., 2001). Intracellular compatible solutes were extracted and analysed following a modification of the methods described by Galinski & Herzog (1990). Phase-contrast micrographs were obtained using a Zeiss Axioplan Imaging 2 microscope. Cells were fixed with glutaraldehyde (final 3 %, v/v) for electron microscopy and positively contrasted with 1 % (w/v) uranyl acetate. Isolation of DNA and subsequent determination of the G+C content and DNA–DNA hybridization were performed by using the thermal denaturation/reassociation technique (Marmur, 1961; De Ley et al., 1970). Respiratory lipoquinones and polar lipids were extracted and analysed as described by Tindall (1990). Fatty acid methyl esters were obtained from freeze-dried whole cells using the method of Labrenz et al. (1998). The fatty acid methyl esters were separated and identification was confirmed by GC–MS, as described previously (Strömpl et al., 1999). DNA was obtained by standard phenol/chloroform extraction for amplification and sequencing of 16S rRNA genes. The 16S rRNA genes were selectively amplified using primers 5'-AGAGTTTGATCCTGGCTCAG-3' (forward) and 5'-TACGGTTACCTTGTTACGACTT-3' (reverse). PCR products were purified from low-melting-point agarose using the Wizard PCR-Prep kit (Promega), according to the manufacturer's instructions. Almost complete sequencing (1400–1450 nucleotides) was performed using the Promega Silver sequencing kit, according to the manufacturer's instructions with minor modifications. Phylogenetic analysis based on nucleotide sequences of 16S rRNA genes was performed using various treeing algorithms realized in the TREECON (Van de Peer & De Wachter, 1994) and PHYLIP (Felsenstein, 1989) software packages. Pairwise evolutionary distances (expressed as estimated changes per 100 nucleotides) were computed using the Jukes and Cantor method (Jukes & Cantor, 1969). The resulting phylogenetic tree was constructed by using the neighbour-joining method. Bootstrap analysis (100 replications) was used to validate the reproducibility of the branching pattern of the trees.
Anaerobic enrichments with acetate and nitrate at moderate salinity (2 M NaCl), inoculated with the sediment samples from hypersaline lakes in Altai and Mongolia, resulted in the domination of Halomonas spp. (identified by partial 16S rRNA gene sequencing; data not shown). In contrast, in most of the enrichments at 4 M NaCl the halomonads were out-competed by other gammaproteobacteria. These enrichments were the source of four pure cultures of extremely halophilic denitrifiers, three with nitrate and one with N2O as electron acceptor. Strains HGD 2, HGD 3T (nitrate) and HGDK 5 (N2O) were represented by vibrio-to-short spirilla (Fig. 1a) that were motile with a single polar flagellum (Fig. 2a). They showed high DNA–DNA hybridization values with each other (>80 %), indicating species-level relatedness. Strain HGD 1-3T (nitrate) is a long, flexible, non-motile rod (Figs 1b and 2b). It showed only 15–20 % DNA–DNA hybridization with the vibrio-shaped strains, indicating low genetic relatedness (and differences at the genomic level).
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One of the main properties of halophilic bacteria is their ability to accumulate large amounts of haloprotecting osmolytes (compatible solutes) during growth in high salt. In members of the Gammaproteobacteria, the most common osmolytes are represented by glycine betaine and ectoines (Galinski, 1995). Analysis of strains HGD 3T and HGD 1-3T demonstrated the presence of both osmolytes with domination of the former. When grown in 4 M NaCl aerobically with acetate, cells of strains HGD 3T and HGD 1-3T contained 22 and 17·7 % glycine betaine and 2·8 and 3·1 % ectoine (weight per weight dry cells), respectively. This differentiates the new isolates from the moderately halophilic Halomonas species, which contain ectoine and hydroxyectoine as the dominant osmolytes (Wohlfarth et al., 1990).
16S rRNA gene sequence analysis placed strains HGD 3T and HGD 1-3T in a cluster with the moderately halophilic bacterium Pseudomonas halophila DSM 3050 (Anzai et al., 2000), which was isolated from the Great Salt Lake, Utah (Fendrich, 1988) (Fig. 3). However, phenotypic comparison of our isolates with the original description of P. halophila demonstrated large differences. In fact, the properties of the vibrio-shaped isolates showed a better match with the phenotype of Halovibrio variabilis (Fig. 1c
), an extremely halophilic bacterium that was isolated from the same lake and described together with P. halophila by the same author (Fendrich, 1988). Strain DSM 3051 was later reclassified, on the basis of 16S rRNA gene sequence data, as Halomonas variabilis (Dobson et al., 1993; Dobson & Franzmann, 1996). Therefore, we suspected that the two halophiles from the Great Salt Lake, P. halophila and Halovibrio variabilis, represented by strains DSM 3050 and DSM 3051, respectively, may not correspond with their original descriptions. To verify this hypothesis, both strains were obtained from the DSMZ, cultivated and cross-compared with the new isolates and with their original descriptions. The results (Table 1) confirmed our suspicion that strain DSM 3050 (Fig. 1c), deposited under the name P. halophila, in fact matches the original description of the extremely halophilic Halovibrio variabilis, whereas strain DSM 3051 (deposited as Halomonas variabilis) matches the original description of the moderately halophilic P. halophila. There was only one important difference between our vibrio-shaped isolates and the original description of Halovibrio variabilis, namely that the latter was described as an obligate aerobe. On checking the ability of strain DSM 3050 to grow anaerobically with acetate and nitrate in 2–4 M NaCl, a positive result was obtained, although the strain grew less actively than the new isolates and the intermediate nitrite was never reduced completely. Apparently, this important feature was overlooked by Fendrich (1988). Also, we were unable to confirm the presence of proteolytic activity in strain DSM 3050, nor was it detected in the new isolates. Franzmann & Tindall (1990) have also reported on the chemical composition of P. halophila and Halovibrio variabilis, which confirmed their allocation to different higher taxa within the Proteobacteria.
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The respiratory lipoquinones of all three isolates and DSM 3050 comprised only ubiquinones, with ubiquinone 9 predominating. The polar lipids of all three isolates and DSM 3050 were virtually identical to the pattern reported previously by Franzmann & Tindall (1990), with diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified amino-positive phospholipid comprising the major components. The fatty acid compositions of the isolates and DSM 3050 are given in Table 2.
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; Yi et al., 2003; Yoon et al., 2004a, b; Lee et al., 2001). This is indicative of the fact that the 16S rRNA gene sequence data may not resolve absolute branching order and that the groupings should be given more significance than branching order. DSM 3050 and the novel strains all produced ubiquinone 9 as the sole respiratory quinone, a feature which they share with members of the genera Marinobacter, Pseudomonas, Halomonas, Cobetia, Carnimonas, Zymobacter, Hahella and Zooshikella (Garriga et al., 1998; Franzmann & Tindall, 1990; Okamoto et al., 1993; Baik et al., 2005; Yi et al., 2003). It should be noted that members of the genera Microbulbifer and Marinobacter also produce ubiquinone 8 (Yoon et al., 2004a, b). Although the polar lipids phosphatidylglycerol and phosphatidylethanolamine are widely distributed in the Gammaproteobacteria, the presence of an unidentified aminophospholipid appears to be characteristic. The latter lipid is not present in Marinobacter hydrocarbonoclasticus (Spröer et al., 1998) and is also not a significant component of members of the genus Alcanivorax examined to date (B. J. Tindall, unpublished data). The polar lipid pofiles of members of the genera Halomonas and Cobetia are more complex (Franzmann & Tindall, 1990). The polar lipid compositions of members of the genera Microbulbifer, Hahella and Zooshikella have not been reported to date. The fatty acids were characterized by the presence of straight-chain saturated and unsaturated components, with 16 : 0 and various isomers of 16 : 1 and 18 : 1 predominating. However, the dominance of such fatty acids is fairly typical of a large number of taxa within the Betaproteobacteria and Gammaproteobacteria and discrimination at the genus level depends on the evaluation of the other components. All strains contained a 3-OH 12 : 0 fatty acid, which appeared to be exclusively ester-linked, whereas the presence of 3-OH 14 : 0, which appeared to be amide-linked, was characteristic of strains HGD 3T, DSM 3050 and HGDK 5. In contrast, strain HGD 1-3T contained a 3-OH 14 : 1 fatty acid, which appeared to be ester- and amide-linked in the ratio 1 : 2. The presence of both ester-linked and amide-linked fatty acids is in contrast to the presence of 3-OH 12 : 0 in Marinobacter hydrocarbonoclasticus, which appears to be exclusively amide-linked (Spröer et al., 1998). The presence of an amide-linked 3-OH 12 : 0 in other members of the genus Marinobacter (Romanenko et al., 2005; Yoon et al., 2004b) may be inferred from the work of Gorshkova et al. (2003). 3-OH 12 : 0 also appears to be present in members of the genera Alcanivorax, Hahella and Zooshikella (Liu & Shao, 2005; Baik et al., 2005; Yi et al., 2003), although no data are available to date on the nature of the chemical linkage. The absence of this fatty acid in Alcanivorax borkumensis is simply due to the fact that Yakimov et al. (1998) only examined a selected lipid fraction, which would not have included the lipopolysaccharide. Members of the genus Pseudomonas contain both 3-OH 10 : 0 (ester-linked) and 3-OH 12 : 0 (amide-linked) (see Wilkinson, 1988 for an overview; Vancanneyt et al., 1996). In addition, some species of this genus also contain a 2-OH 12 : 0 fatty acid (Vancanneyt et al., 1996). Carnimonas nigrificans contains a 3-OH 14 : 0 and a 2-OH 12 : 0 fatty acid (Garriga et al., 1998; C. Belloch and B. J. Tindall, unpublished), whereas members of the genera Halomonas, Chromohalobacter, Cobetia and Zymobacter contain 3-OH 12 : 0, which appears to be both amide- and ester-linked (C. Belloch and B. J. Tindall, unpublished). Members of the genus Zooshikella contain 3-OH 10 : 0, 3-OH 12 : 0 and small amounts of 3-OH 12 : 1 (Yi et al., 2003), whereas members of the genus Hahella contain 3-OH 12 : 0 (Lee et al., 2001; Baik et al., 2005). These differences are probably due to differences in the structures of the lipopolysaccharides, but this would need to be verified by independent research. The distribution of the various unsaturated fatty acids also appears to be indicative of differences between strains HGD 3T, HGD 1-3T and DSM 3050, as well as between members of the genera Halomonas, Cobetia, Carnimonas, Zymobacter (Franzmann & Tindall, 1990; Garriga et al., 1998; Okamoto et al., 1993), Marinobacter (Gorshkova et al., 2003; Romanenko et al., 2005; Spröer et al., 1998; Yoon et al., 2004b) and Alcanivorax. Whereas 16 : 1
7c and 18 : 17c appear to predominate in members of the genera Zooshikella, Halomonas, Cobetia, Carnimonas, Zymobacter and Alcanivorax, these two fatty acids are also present in members of the genera Marinobacter and Hahella (Baik et al., 2005), but 16 : 19c and 18 : 19c generally predominate in members of these genera. The patterns in strains HGD 3T and DSM 3050 are similar to those of members of the genera Hahella and Marinobacter, but strain HGD 1-3T does not appear to contain either 16 : 17c or 16 : 19c. Members of the genus Microbulbifer are characterized by the presence of largely iso- and straight-chain saturated fatty acids, as well as 3-OH 10 : 0 and 3-OH iso-11 : 0 (Yoon et al., 2004a). Taken together, the chemical compositions of the novel isolates provide a useful dataset for distinguishing between the strains examined here and the members of those genera that share a high degree of 16S rRNA gene sequence similarity. These similarities and differences provide evidence in support of the use of the chemical composition of the cell to investigate evolutionary relationships within the prokaryotes (Tindall, 1994).
Overall, the data presented demonstrate that the novel, extremely halophilic gammaproteobacteria isolated from hypersaline lakes in Central Asia include two different groups. The three vibrio-shaped strains are closely related to the extremely halophilic bacterium originally described as Halovibrio variabilis, but currently listed under the name P. halophila (DSM 3050). This indicates that the circumscription of the species P. halophila does not coincide with the properties of the type (and only) strain of this species, DSM 3050. The same is true of the circumscription of the species Halovibrio variabilis (which is considered to be a member of the genus Halomonas) and the properties of its type (and only) strain, DSM 3051. Under Rule 18g of the Bacteriological Code (Lapage et al., 1992), such matters must be referred to the Judicial Commission and in an accompanying paper we have outlined the problem in detail, together with a formal request that DSM 3050 be recognized as the type strain of Halovibrio variabilis (Sorokin & Tindall, 2006). This would also have the effect of placing the type strain of that species and the genus Halovibrio outside of the genus Halomonas. Any novel species placed in the same genus as DSM 3050 would consequently be placed in the genus Halovibrio and not in a new genus. While the status of the genus name Halovibrio and the species name Halovibrio variabilis depends on the way the problem with the strains DSM 3050 and DSM 3051 is handled by the Judicial Commission, it also creates a problem for the recognition of a novel species that is to be placed in the same genus as DSM 3050.
On the basis of phenotypic and genetic properties, the new vibrio-shaped denitrifying isolates are clearly similar in their properties to the published description of Halovibrio variabilis (Fendrich, 1988) and to DSM 3050. However, these isolates are also clearly members of a novel species. A consequence of species names being combinations is that a novel species must by definition be placed in a genus. In this particular case, we consider that we are justified in providing the following solution. The novel species should be placed in the genus whose circumscription corresponds with that of the novel strains, i.e. the genus Halovibrio. However, this also depends on the Judicial Commission accepting that DSM 3050 fits the circumscription of Halovibrio variabilis and designating this as the type strain of the species. Consequently, although we have provided a formal description for a novel species within the genus Halovibrio, which conforms to the present Rules of the Bacteriological Code, we also recognize that this name anticipates the action of the Judicial Commission and that the name cannot currently be considered to be validly published, as outlined in Rule 28b (2) of the Bacteriological Code (Lapage et al., 1992). Equally, in submitting a Request for an Opinion, this would also preclude that DSM 3050 be placed in a new genus until the Judicial Commission has published its Opinion. Both aspects are dealt with in an accompanying paper (Sorokin & Tindall, 2006).
Below we present formal descriptions of the vibrio-shaped strains as representing a novel species of the genus Halovibrio, Halovibrio denitrificans sp. nov., and an emended description of the genus Halovibrio. In addition, the rod-shaped, extremely halophilic, denitrifying strain HGD 1-3T is proposed to represent a new genus and species, Halospina denitrificans gen. nov., sp. nov.
Emended description of the genus Halovibrio
The emended description is based on data collected during this study and on data published previously by Franzmann & Tindall (1990) using DSM 3050 (=P. halophila).
The description is based on data published by Fendrich (1988) on DSM 3050. In addition, ubiquinone 9 is the major respiratory lipoquinone, the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified amino-positive phospholipid. The Rf of this latter compound is important. Fatty acids present are 10 : 0, 12 : 0, 3-OH 12 : 0 (ester-linked), 14 : 1, 3-OH 14 : 0 (amide-linked), 16 : 19c, 16 : 0, 18 : 19c, 18 : 0, and 10-methyl 18 : 0. 16 : 17c and 18 : 17c may be present in varying amounts. The genus comprises two species, Halovibrio variabilis Fendrich 1989 and Halovibrio denitrificans.
Description of Halovibrio denitrificans sp. nov.
Halovibrio denitrificans (de.ni.tri'fi.cans. N.L. v. denitrifico to denitrify; N.L. part. adj. denitrificans denitrifying).
Cells are vibrios or short spirilla, motile with a single polar flagellum, 0·5–0·8x1·5–4 µm; in old cultures the cell edges become transparent. Extremely halophilic with NaCl range for growth between 2·0 and 5 M and an optimum at 2·0–2·5 M. Facultatively anaerobic. Grows anaerobically with nitrate as electron acceptor and short-chain fatty acids as electron donors/carbon source, producing nitrite and N2O as intermediates. Sugars are not utilized. Some strains can grow with N2O as electron acceptor. Oxidizes thiosulfate to tetrathionate during aerobic heterotrophic growth. Produces glycine betaine (major) and ectoine (minor) as compatible solutes. The chemical composition is identical to that given in the emended genus description. The G+C content of the DNA is 61·8±0·5 mol% (Tm).
The type strain, HGD 3T (=DSM 15503T=UNIQEM U232T), was isolated from sediments of the hypersaline lake Barun-Davst-Nur in north-eastern Mongolia.
Description of Halospina gen. nov.
Halospina [Ha.lo.spi'na. Gr. n. hals, halos salt; L. n. spina spine; N.L. masc. n. Halospina a salt (loving) spine (long thin rod)].
Rod-shaped, Gram-negative, extremely halophilic gammaproteobacteria, with highest 16S rRNA gene sequence similarity to members of the halophilic genera Marinobacter and Alcanivorax. Facultatively anaerobic. Produce glycine betaine (major) and ectoine (minor) as compatible solutes. Ubiquinone 9 is the major respiratory lipoquinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified amino-positive phospholipid. The Rf of this latter compound is important. Fatty acids present are 10 : 0, 12 : 0, 3-OH 12 : 0 (ester-linked), 14 : 1, 3-OH 14 : 1 (ester- and amide-linked), two different 16 : 1 isomers, 16 : 0, 18 : 19c, 18 : 0 and 10-methyl 18 : 0. The G+C content of the DNA of the type species is 60±0·5 mol% (Tm). Habitats are hypersaline lakes. The type and only species is Halospina denitrificans.
Description of Halospina denitrificans sp. nov.
Halospina denitrificans (de.ni.tri'fi.cans. N.L. v. denitrifico to denitrify; N.L. part. adj. denitrificans denitrifying).
Cells are long, flexible, non-motile rods with tapered edges, 0·7–1·0x3–7 µm. Extremely halophilic with NaCl range for growth between 2·0 and 5 M and an optimum at 2·5–3·0 M. Facultatively anaerobic. Grows aerobically and anaerobically with nitrate as electron acceptor and short-chain fatty acids as electron donors/carbon source, producing nitrite and N2O as intermediates. Sugars are not utilized. Oxidizes thiosulfate to tetrathionate during aerobic heterotrophic growth. Produces glycine betaine (major) and ectoine (minor) as compatible solutes. The chemical composition is identical to that given in the genus description. The G+C content of the DNA is 60·1±0·5 mol% (Tm).
The type strain, HGD 1-3T (=DSM 15505T=UNIQEM U233T), was isolated from sediments of a hypersaline salt lake in Kulunda Steppe (Altai, Russia).
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