Family Ectothiorhodospiraceae Research Articles

Spiribacter halobius sp. nov., a novel halophilic Gammaproteobacterium with a relatively large genome

Spiribacter is the most abundant bacterial genus in the intermediate-salinity zones of hypersaline environments. However, Spiribacter strains are extremely difficult to isolate in pure culture. Therefore, the characteristics, genome features, and adaption mechanisms that allow Spiribacter strains to thrive in highly saline conditions are largely unknown. Here, we show that Spiribacter is predominant in brines from marine solar salterns and sulfate-type salt lakes with intermediate to saturated salinities. Using a high-salt medium, we isolated a novel strain, Spiribacter halobius E85T, which possesses a relatively large and distinct genome. The genome of strain E85T has a length of 4.17 Mbp, twice that of other Spiribacter species genomes and the largest described genome within the family Ectothiorhodospiraceae. Comparative genomic analyses indicate that approximately 50% of E85T genes are strain-specific, endowing functional differences in its metabolic capabilities, biosynthesis of compatible solutes, and transport and pumping of solutes into the cell from the environment. Hundreds of insertion sequences result in many pseudogenes and frequent gene fragment rearrangements in the E85T genome. Dozens of genomic islands, which show a significant preference for replication, recombination and repair, and cell motility and may have been gained from other bacterial species, are scattered in the genome. This study provides important insights into the general genetic basis for the abundance of Spiribacter in hypersaline environments and the strain-specific genome evolutionary strategies of strain E85T.

Bacterial diversity and microbial functional responses to organic matter composition and persistent organic pollutants in deltaic lagoon sediments

Lagoons in river deltas are highly productive systems that receive high loads of organic matter and nutrients. Among the major environmental stress factors and human health-related issues, the anthropogenic contamination is of particular concern, since coastal lagoons are intensively exploited for aquaculture activities. Although microbial communities constitute the most abundant fraction of the benthic biomass, also providing valuable ecosystem services, the links between sediment quality and microbial processes were largely disregarded. In this study, we aimed to elucidate whether different levels of riverine influence could provide favourable or adverse environmental conditions to sustain microbial diversity and processes. Sediments collected from four lagoons of the Po River delta were analysed to assess biochemical composition (biopolymeric carbon, Bio-PC), target organic pollutants (polycyclic aromatic hydrocarbons, PAHs; nonylphenols; bisphenol A), and microbial community properties (bacterial community composition, prokaryotic biomass, prokaryotic carbon production rate, PCP, community respiration rate, CR, extracellular enzyme activities, EEAs). The major physical and chemical sediment properties allowed identifying two statistically distinct groups of sediments with relatively low (LI) and high (HI) riverine influence. HI sediments were characterised by higher Bio-PC and PAHs concentrations, along with relatively high PAHs potential toxicity estimated by the Toxic Equivalent concentration approach. Contrasting results were obtained by linking the occurrence of dominant bacterial taxa (i.e.,Desulfobulbaceae and Desulfobacteraceae families) to sediment contamination patterns. Notably, the increasing pollution levels were likely to positively affect the occurrence of the Desulfuromonadales Sva1033 family, whereas detrimental effects were found against the family Ectothiorhodospiraceae. In addition, the concurrent increase of PCP/CR ratio along with key EEAs, highlighted that the benthic microbial community could consistently contribute to accelerate the degradation of persistent organic pollutants, with potential implication on the sediment self-purification processes.

Bacterial Communities of Microbial Mats of the White Sea Supralittoral and of the Littoral of the Lakes Separated from the Sea

Conditions of formation and phylogenetic composition were studied for pigmented biofilms and microbial mats of the Kandalaksha Bay (White Sea) supralittoral and of the littoral of the lakes separated from the sea. During the sampling period, salinity was 15 to 26 g/L, except for several desalinated salt marsh sites (4‒11 g/L); the temperature was 9‒12°C. The species composition and structure of benthic phototrophic communities were affected by severe climatic conditions of the area, including low average annual temperature and freezing of the littoral zones. Application of Next-generation sequencing of the 16S rRNA gene V3-V4 regions combined with microscopy of the samples and obtained cultures for analysis of the biodiversity of microbial communities resulted in improved understanding of diversity of both oxygenic and anoxygenic bacteria in the Kandalaksha Bay littoral. No significant differences were revealed in species composition of microbial mats from salt marshes and shallow sites of the lakes of marine origin. Members of the phyla Bacteroidetes (up to 36%) and Proteobacteria (up to 67%) predominated in the mats and biofilms. The share of phototrophic bacteria was 0.3–18%. Oxygenic phototrophs (cyanobacteria Phormidium, Oscillatoria, Spirulina, and Anabaena, as well as diatoms) predominated in the phototrophic community. The species number of anoxygenic phototrophic bacteria did not exceed 5% of all prokaryotes. These were mainly mesophilic marine species of purple sulfur bacteria of the genera Thiorhodococcus and Thiocapsa. No members of the family Ectothiorhodospiraceae, which are typical of microbial mats from southern seas, were found in subpolar microbial mats. Nonsulfur purple bacteria and aerobic anoxygenic phototrophic bacteria were mostly similar to the known marine species. Green sulfur bacteria (salt-water Prosthecochloris and Сhlorobium species) were detected in two coastal mat samples from meromictic lakes. Anoxygenic filamentous phototrophic bacteria, which occurred in almost all benthic phototrophic communities, were represented by new phylotypes.

Taxonomic and metabolic shifts in the Coorong bacterial metagenome driven by salinity and external inputs

The Coorong estuary lies at the terminus of Australia’s largest river system, the Murray-Darling; both are strongly influenced by human activities; including farming and extensive flow modification. Metagenomic approaches were used to determine the planktonic bacterial community composition and potential metabolic function at two extremes in the Coorong, the river mouth which exhibits marine-like salinity, and the hypersaline upper-reaches of the estuary. Significant shifts in taxa and metabolic function were seen between the two sites. The river mouth exhibited an increase in abundance of Rhodobacteriaceae and Alteromonadaceae; families readily able to adapt to change in nutrient conditions; and the potentially pathogenic families Brucellaceae, Enterobacteriaceae and Vibrionaceae. Metabolisms over-represented include motility and chemotaxis, RNA metabolism and membrane transport, all of which are involved in actively searching for and obtaining nutrients. Also over-represented were metabolisms involved in population succession and stress response. An over-representation of taxa and metabolisms indicative of environmental change is reflective of anthropogenically affected riverine input. In the hypersaline upper reaches of the estuary, the halophilic family Ectothiorhodospiraceae was over-represented, as were the families Flavobacteriaceae, Cytophagaceae and Nocardioidaceae, members of which are able to survive over a wide salinity range. Metabolisms over-represented here were reflective of increased bacterial growth, characteristic of hypersaline environments, and included DNA metabolism, nucleotide and nucleoside synthesis and cell cycle. Coorong metagenomes clustered taxonomically and metabolically with other planktonic metagenomes, but remained an outlier of this group with only 71% and 84% similarity, respectively. This indicates that the Coorong exhibits a unique planktonic bacterial community that is influenced by riverine input at the river mouth and salinity in the upper-reaches.

Natronospira proteinivora gen. nov., sp. nov, an extremely salt-tolerant, alkaliphilic gammaproteobacterium from hypersaline soda lakes.

Brine samples from Kulunda Steppe soda lakes (Altai, Russia) were inoculated into a hypersaline alkaline mineral medium with β-keratin (chicken feather) as a substrate. The micro-organisms dominating the enrichment culture were isolated by limiting serial dilution on the same medium with casein as a substrate. The cells of strain BSker1T were motile, curved rods. The strain was an obligately aerobic heterotroph utilizing proteins and peptides as growth substrates. The isolate was an obligate alkaliphile with a pH range for growth from pH 8.5 to 10.25 (optimum at pH 9.5), and it was extremely salt tolerant, growing with between 1 and 4.5 M total Na+ (optimally at 2-2.5 M). BSker1T had a unique composition of polar lipid fatty acids, dominated by two C17 species. The membrane polar lipids included multiple unidentified phospholipids and two aminolipids. According to phylogenetic analysis of the 16S rRNA gene sequence, the isolate forms a novel branch within the family Ectothiorhodospiraceae (class Gammaproteobacteria) with the highest sequence similarity to the members of this family being 91 %. On the basis of distinct phenotypic and genotypic properties, strain BSker1T (=JCM 31341T=UNIQEM U1008T) is proposed to be classified as a representative of a novel genus and species, Natronospira proteinivora gen. nov., sp. nov.

Halofilum ochraceum gen. nov., sp. nov., a gammaproteobacterium isolated from a marine solar saltern.

A Gram-stain-negative, oxidase-negative, catalase-positive, facultative anaerobe, designated XJ16T, was isolated from a marine solar saltern on the coast of Weihai, China. Cells of strain XJ16T were long and rod-shaped. The colonies were ochre in colour and were able to reduce nitrate to nitrite. Optimal growth occurred at 33-37 °C (range, 20-45 °C) and in the presence of 8-10 % (w/v) NaCl (range, 2-20 %). The pH range for growth was found to be 6.5-9.5, with optimum growth at pH 7.5-8.0. Phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain XJ16T was related to the phylum Proteobacteria. The most closely related neighbours were species of the genus Thioalkalivibrio, and the 16S rRNA gene sequence of strain XJ16T shared 93.1 % similarity with that of Thioalkalivibrio sulfidiphilus HL-EbGr7T and 93.0 % similarity with that of Thioalkalivibrio denitrificans ALJDT. The G+C content of the genomic DNA was 65.9 mol% (HPLC). The sole respiratory quinone was Q-8, and the predominant cellular fatty acids (>10 %) were iso-C15 : 0 2-OH/C16 : 1ω7c, C18 : 0 and C16 : 0 10-CH3. The predominant polar lipids in strain XJ16T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Based on these phylogenetic, physiological and biochemical characteristics, strain XJ16T should be classified representing a novel species of a new genus within the family Ectothiorhodospiraceae, for which the name Halofilum ochraceum gen. nov., sp. nov. is proposed. The type strain of the type species is XJ16T (=KCTC 42259T=MCCC 1H00120T=CICC 23817T).

Arsenite as an Electron Donor for Anoxygenic Photosynthesis: Description of Three Strains of Ectothiorhodospira from Mono Lake, California and Big Soda Lake, Nevada.

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243T, and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.

Spiribacter roseus sp. nov., a moderately halophilic species of the genus Spiribacter from salterns.

Four pink-pigmented, non-motile, Gram-staining-negative and moderately halophilic curved rods, designated strains SSL50T, SSL25, SSL97 and SSL4, were isolated from a saltern located in Isla Cristina, Huelva, south-west Spain. Phylogenetic analyses based on 16S rRNA gene sequences showed that they were members of the genus Spiribacter, most closely related to Spiribacter curvatus UAH-SP71T (99.3-99.5 % sequence similarity) and Spiribacter salinus M19-40T (96.5-96.7 %). Other related strains were Alkalilimnicola ehrlichii MLHE-1T (95.1-95.3 %), Arhodomonas recens RS91T (95.1-95.2 %) and Arhodomonas aquaeolei ATCC 49307T (95.0-95.1 %), all members of the family Ectothiorhodospiraceae. The major fatty acids were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0 and C12 : 0. The DNA G+C range was 64.0-66.3 mol%. The DNA-DNA hybridization values between strains SSL50T, SSL25, SSL97, SSL4 and S. piribacter. curvatus UAH-SP71T were 37-49 %. The average nucleotide identity (ANIb) values between the genome of strain SSL50T and those of the two other representatives of the genus Spiribacter, S. curvatus UAH-SP71T and S. salinus M19-40T, were 82.4 % and 79.1 %, respectively, supporting the proposal of a novel species of the genus Spiribacter. On the basis of the polyphasic analysis, the four new isolates are considered to represent a novel species of the genus Spiribacter, for which the name Spiribacter roseus sp. nov. is proposed. The type strain is SSL50T (=CECT 9117T=IBRC-M 11076T).

Spiribacter curvatus sp. nov., a moderately halophilic bacterium isolated from a saltern.

A novel pink-pigmented bacterial strain, UAH-SP71T, was isolated from a saltern located in Santa Pola, Alicante (Spain) and the complete genome sequence was analysed and compared with that of Spiribacter salinus M19-40T, suggesting that the two strains constituted two separate species, with a 77.3% ANI value. In this paper, strain UAH-SP71T was investigated in a taxonomic study using a polyphasic approach. Strain UAH-SP71T was a Gram-stain-negative, strictly aerobic, non-motile curved rod that grew in media containing 5-20% (w/v) NaCl (optimum 10% NaCl), at 5-40 °C (optimum 37 °C) and at pH 5-10 (optimum pH 8). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed thatstrain UAH-SP71T is a member of the genus Spiribacter, showing a sequence similarity of 96.5% with Spiribacter salinus M19-40T. Other related species are also members of the family Ectothiorhodospiraceae, including Arhodomonas recens RS91T (95.5% 16S rRNA gene sequence similarity), Arhodomonas aquaeolei ATCC 49307T (95.4 %) and Alkalilimnicola ehrlichii MLHE-1T (94.9 %). DNA-DNA hybridization between strain UAH-SP71T and Spiribacter salinus M19-40T was 39 %. The major cellular fatty acids of strain UAH-SP71T were C18 : 1ω6c and/or C18 : 1ω7c, C16 : 0, C16 : 1ω6c and/or C16 : 1ω7c, C10 : 0 3-OH and C12 : 0, a pattern similar to that of Spiribacter salinus M19-40T. Phylogenetic, phenotypic and genotypic differences between strain UAH-SP71T and Spiribacter salinus M19-40T indicate that strainUAH-SP71T represents a novel species of the genus Spiribacter, for which the name Spiribacter curvatus sp. nov. is proposed. The type strain is UAH-SP71T (5CECT8396T5DSM 28542T).

Inmirania thermothiophila gen. nov., sp. nov., a thermophilic, facultatively autotrophic, sulfur-oxidizing gammaproteobacterium isolated from a shallow-sea hydrothermal vent.

A novel thermophilic, facultatively autotrophic bacterium, strain S2479T, was isolated from a thermal spring located in a tidal zone of a geothermally heated beach (Kuril Islands, Russia). Cells of strain S2479T were rod-shaped and motile with a Gram-negative cell-wall type. The temperature range for growth was 35-68 °C (optimum 65 °C), and the pH range for growth was pH 5.5-8.8 (optimum pH 6.5). Growth of strain S2479T was observed in the presence of NaCl concentrations ranging from 0.5 to 3.5 % (w/v) (optimum 1.5-2.0 %). The strain oxidized sulfur and thiosulfate as sole energy sources for autotrophic growth under anaerobic conditions with nitrate as electron acceptor. Strain S2479T was also capable of heterotrophic growth by reduction of nitrate with oxidation of low-chain fatty acids and a limited number of other carboxylic acids or with complex proteinaceous compounds. Nitrate was reduced to N2. Sulfur compounds were oxidized to sulfate. Strain S2479T did not grow aerobically during incubation at atmospheric concentration of oxygen but was able to grow microaerobically (1 % of oxygen in gas phase). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the family Ectothiorhodospiraceae, order Chromatiales, class Gammaproteobacteria. On the basis of phylogenetic and phenotypic properties, strain S2479T represents a novel species of a new genus, for which the name Inmirania thermothiophila gen. nov., sp. nov. is proposed. The type strain of the type species is S2479T ( = DSM 100275T = VKM B-2962T).

Halopeptonella vilamensis gen. nov, sp. nov., a halophilic strictly aerobic bacterium of the family Ectothiorhodospiraceae.

A Gram-negative, halophilic, heterotrophic, rod-shaped, non-spore-forming bacterium (SV525T) was isolated from the sediment of a hypersaline lake located at 4600 m above sea level (Laguna Vilama, Argentina). Strain SV525T was strictly aerobic and formed pink-to-magenta colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), at pH levels 6.0–8.5 (optimum 7.0) and at NaCl concentrations of 7.5–25 % (w/v) with an optimum at 10–15 % (w/v). The strain required sodium and magnesium but not potassium ions for growth. Grows with tryptone, or Bacto Peptone as sole carbon and energy source and requires yeast extract for growth. It produced catalase and oxidase. The predominant ubiquinone was Q-8 and the major fatty acids comprised C18:1 ω7c, C16:0 and C18:0. The DNA G+C content was 60.4 mol% and its polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and a phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene indicated that strain SV525T belongs to the family Ectothiorhodospiraceae within the class Gammaproteobacteria. On the basis of phylogenetic and phenotypic data, SV525T represents a novel genus and species, for which the name Halopeptonella vilamensis gen. nov., sp. nov. is proposed. The type strain is SV525T (=DSM 21056T =JCM 16388T =NCIMB 14596T).

Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae.

Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile 'Thiobacillus prosperus' DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that 'Thiobacillus prosperus' DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T ( = JCM 30709T) and that it becomes the type strain of the type species of this genus.

Impact of petroleum hydrocarbon contamination on the indigenous soil microbial community

Changes in the microbial community structure in agricultural soils and soils contaminated with hydrocarbons were evaluated using the culture-independent method of 16S rRNA gene sequence analysis. The bacterial composition was more diverse in the agricultural soil (AS) samples in terms of number of species and Shannon diversity index [6.6 vs. 1.94 for the hydrocarbon-contaminated soil (HCS)]. Twelve known bacterial groups were identified in the AS: Proteobacteria (41 % of bacterial community), Actinobacteria (34 %), Acidobacteria (5 %), Firmicutes (4 %), Chloroflexi (4 %), Bacteroidetes (3 %), Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Armatimonadetes, Cyanobacteria, TM7 and Archaea (the latter 7 each accounting for 1–2%) . In comparison, the clonal library from the HCS samples included members from only five groups: Proteobacteria (85 %) and Bacteriodetes, Actinobacteria, Chloroflexi and Verrucomicrobia (the latter four collectively accounting for 15 %). The family Ectothiorhodospiraceae was the most dominant family within the Proteobacteria isolated from the HCS. These microbes are known to synthesize a number of biotechnologically useful products, such as polyhydroxyalkanoates and ectoines, and their dominance in the sampled area suggests the possibility of discovering better adapted novel genes of commercial importance, especially since the site had high alkaline and saline characteristics. Soils (arid, alpine and polar) which are nutrient and moisture limited are typically often dominated by Actinobacteria that are well adapted to low-resource environments and do not show major changes in community structure as a result of hydrocarbon contamination.

Maricoccus atlantica gen. nov. sp. nov., isolated from deep sea sediment of the Atlantic Ocean

A taxonomic study was carried out on strain 22II-S10r2(T), which was isolated from the deep sea sediment of the Atlantic Ocean using oil-degrading enrichment. The bacterium was Gram-negative, oxidase positive and catalase negative, spherical in shape, and motile by polar flagella. Growth was observed at salinities of 0.5-7 % and at temperatures of 10-41 °C. The isolate was capable of aesculin hydrolysis, but unable to reduce nitrate to nitrite or degrade Tween 80 or gelatine. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S10r2(T) belonged to the family Ectothiorhodospiraceae, with highest sequence similarity to Thioalkalivibrio sulfidiphilus HL-EbGR7(T) (90.9 % similarity). The principal fatty acids were Sum In Feature 8 (C18:1 ω7c/ω6c (29.9 %), C18:1 ω9c (13.5 %), C16:1 ω5c (12.3 %), C12:03OH (6.8 %), C18:1 ω5c (5.7 %) and C16:0 (5.3 %). The G+C content of the chromosomal DNA was 60.7 mol%. The respiratory quinone was determined to be Q-7 (25 %) and Q-8 (75 %). Phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid, glycolipid, three phospholipids and lipid were present. The strain was aerobic, non-phototrophic and non-chemolithoautotrophic. The combined genotypic and phenotypic data show that strain 22II-S10r2(T) represents a novel species within a novel genus, for which the name Maricoccus atlantica gen. nov. sp. nov. is proposed, with the type strain 22II-S10r2(T) (=CGMCC NO.1.12317(T) = LMG 27155(T) = MCCC 1A09384(T)).

Arhodomonas recens sp. nov., a halophilic alkane-utilizing hydrogen-oxidizing bacterium from the brines of flotation enrichment of potassium minerals

A halophilic nonpigmented rod-shaped (0.8–1.0 × 2.0–2.5 μm), gram-negative bacterium with a single polar flagellum (strain RS91) was isolated from acidic brines of flotation enrichment of potassium minerals (Silvinit Co., Solikamsk, Russia). The strain grew in the media with 2 to 25% NaCl (optimum at 10–12%), 20–45°C (optimum at 37°C), and pH 5.5–8.5 (optimum 6.5–7.5). It was an aerobe or facultative anaerobe incapable of fermentation. The strain was characterized by the absence of growth on glucose, fructose, and citrate, extensive aerobic growth on n-hexadecane and in the mineral medium with H2 + O2 + CO2 in the gas phase, anaerobic nitrate reduction with acetate or hydrogen (under H2 + CO2 + N2), and variable fatty acid composition. The DNA G+C content was 68.2 mol %. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that while strain RS91 was most closely related to Arhodomonas aquaeolei HA-1T (98.3%) and Nitrococcus mobilis (98.1%), it was only remotely related to the halophilic phototroph Halorhodospira halophila (90.6%). Based on the combination of its phenotypic and genotypic characteristics, the organism was classified as a new species of the genus Arhodomonas, family Ectothiorhodospiraceae with the proposed name Arhodomonas recens sp. nov. The type strain is RS91T (= IEGM 796T = VKPM B-11280T).

Complete genome sequence of Thioalkalivibrio sp. K90mix.

Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix 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 wastewater and gas streams.

Ectothiorhodospira magna sp. nov., a new large alkaliphilic purple sulfur bacterium

Two strains of purple sulfur bacteria of the family Ectothiorhodospiraceae were isolated from moderately saline steppe lakes (with pH above 9.0) of the Transbaikal region (strain B7-7) and Mongolia (strain M10). The cells of the novel strains were spiral-shaped, 2.0–3.2 × 9.6–20.0 μm, motile due to a polar tuft of flagella. Photosynthetic pigments were represented by bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Photosynthetic membranes were represented by long strands of lamellae distributed throughout the whole cell; unlike most Ectothiorhodospiraceae species, the membranes were not packed into regular stacks. Bacteria were capable of weak growth on sulfide and slow grow on hydrogen under photoautotrophic conditions. The best growth was noted on sulfide in the presence of acetate and bicarbonate. Thiosulfate did not stimulate phototrophic growth, even in the presence of organic substrates. The new isolates were alkaliphiles growing at a pH optimum of 9–10. Growth was possible within a salinity range of 0–80 g/l NaCl, with an optimum at 5–15 g/l NaCl. The morphology, the structure of the photosynthetic apparatus (strands of lamellae), and the physiology of the new strains were similar to those of Thiorhodospira sibirica. However, analysis of the 16S rRNA gene sequences demonstrated that the studied isolates were closely related to the type strain Ectothiorhodospira shaposhnikovii (99% similarity) of the family Ectothiorhodospiraceae, whereas the level of similarity between the new strains and Thiorhodospira sibirica was only 94–95%. According to the results of DNA-DNA hybridization, the DNA-DNA homology level between the tested strains was almost 100%; the similarity between the new isolates and the type strain Ectothiorhodospira shaposhnikovii was only 58%. The isolates differed from other representatives of the genus Ectothiorhodospira in the structure of the gene encoding the key enzyme of autotrophic CO2 fixation, ribulose-1,5-bisphosphate carboxylase (RuBisCo), which was similar to the RuBisCo genes of members of another family of sulfur bacteria, Chromatiaceae. The new isolates of purple bacteria were described as a new species of the genus Ectothiorhodospira, Ect. magna sp. nov. with the type strain B7-7T (= VKM B-2537 = DSM 22250).

Communities of anoxygenic phototrophic bacteria in the saline soda lakes of the Kulunda steppe (Altai Krai)

The saline soda lakes of the Kulunda steppe (Altai krai) are small and shallow; they are characterized by a wide range of salinity and alkalinity, as well as by the extreme instability of their water and chemical regimes. Accumulations of anoxygenic phototrophic bacteria (APB) visible to the unaided eye were noted only in several lakes with high rates of sulfate reduction in their bottom sediments. However, enumeration of APB cells by inoculation revealed their presence in all 17 lakes. APB cell numbers varied from 103 to 109 CFU cm−3. In the APB communities of all lakes, purple sulfur bacteria of the family Ectothiorhodospi- raceae were predominant. In 14 out of the 17 lakes, purple nonsulfur bacteria of the family Rhodobacteraceae were also detected (103–107 CFU cm−3). Purple sulfur bacteria of the family Chromatiaceae were less abundant: Halochromatium sp. (104–107 CFU cm−3) were found in six lakes, while Thiocapsa sp. (104 CFU cm3) were detected in one lake. On the whole, the APB communities of the soda lakes of the Kulunda steppe were characterized by the low diversity and evenness of their species compositions, as well as by the pronounced dominance of the members of the family Ectothiorhodospiraceae. There was no correlation between the structures of the APB communities and alkalinity. However, the dependence of the species composition of APB (mainly ectothiorhodospiras) on water mineralization was revealed. High mineralization (above 200 g l−1) was a limiting factor that affected the APB communities on the whole, restricting the APB species diversity to extremely halophilic bacteria of the genus Halorhodospira.

Phylogeny and evolution of the family Ectothiorhodospiraceae based on comparison of 16S rRNA, cbbL and nifH gene sequences

The occurrence of genes encoding nitrogenase and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) was investigated in the members of the family Ectothiorhodospiraceae. This family forms a separate phylogenetic lineage within the Gammaproteobacteria according to 16S rRNA gene sequence analysis and mostly includes photo- and chemoautotrophic halophilic and haloalkaliphilic bacteria. The cbbL gene encoding the large subunit of 'green-like' form I RubisCO was found in all strains, except the type strains of Alkalispirillum mobile and Arhodomonas aquaeolei. The nifH gene encoding nitrogenase reductase was present in all investigated species of the phototrophic genera Ectothiorhodospira, Halorhodospira and Thiorhodospira, but not of the genus Ectothiorhodosinus. Unexpectedly, nifH fragments were also obtained for the chemotrophic species Thioalkalispira microaerophila and Alkalilimnicola halodurans, for which diazotrophic potential has not previously been assumed. The cbbL-, nifH- and 16S rRNA gene-based trees were not highly congruent in their branching patterns since, in the 'RubisCO' and 'nitrogenase' trees, representatives of the Ectothiorhodospiraceae are divided in a number of broadly distributed clusters and branches. However, the data obtained may be regarded as evidence of the monophyletic origin of the cbbL and nifH genes in most species within the family Ectothiorhodospiraceae and mainly corresponded to the current taxonomic structure of this family. The cbbL phylogeny of the chemolithoautotrophic sulfur-oxidizers Thioalkalivibrio nitratireducens and Thioalkalivibrio paradoxus and the nitrifier Nitrococcus mobilis deviated significantly from the 16S-rRNA gene-based phylogeny. These species clustered with one of the duplicated cbbL genes of the purple sulfur bacterium Allochromatium vinosum, a member of the family Chromatiaceae.

Acetonitrile degradation under haloalkaline conditions by Natronocella acetinitrilica gen. nov., sp. nov.

Nitriles are important environmental compounds, both as natural products and industrial pollutants. Until now, there have been no data on the possibility of microbial nitrile degradation at high pH/salt conditions. Acetonitrile (CH(3)C(triple bond)N) is the simplest organic nitrile. Here, evidence is provided of microbial utilization of acetonitrile as a carbon, energy and nitrogen source at extremely high pH and moderate salinity. Positive enrichment cultures with acetonitrile at pH 10 and salt content equivalent to 0.6 M total Na(+) were obtained from mixed sediment samples from soda lakes, but not from soda soils. Purification of these cultures resulted in the isolation of two bacterial strains capable of growth with acetonitrile as sole carbon, energy and nitrogen source under haloalkaline conditions. Apart from acetonitrile, the bacteria also grew with propionitrile. Nitrile hydrolysis to acetamide was identified as the rate-limiting step of acetonitrile degradation via the nitrile hydratase/amidase pathway. The new bacteria belonged to moderately salt-tolerant obligate alkaliphiles with optimum growth at pH 10 and 0.5 M total Na(+). The cells were yellow-coloured due to a high concentration of carotenoids dominated by zeaxanthin. Phylogenetic analysis placed the isolates into a new lineage within the family Ectothiorhodospiraceae in the Gammaproteobacteria. On the basis of unique phenotypic properties and their separate phylogenetic position, the new bacteria are placed into a new genus and species for which the name Natronocella acetinitrilica gen. nov., sp. nov is proposed.