Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 6C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47-50 6C and pH 7.0-7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7-100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes. The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2 T and Phycisphaera mikurensis FYK2301M01 T with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842 T , 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842 T (5VKM B-2832. We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.Thermophilic micro-organisms represent diverse phylogenetic lineages of prokaryotes, including new deep ones (Cole et al., 2013; Kawaichi et al., 2013;Podosokorskaya et al., 2013). Some phylogenetic groups inhabiting thermal environments contain only thermophiles, while others contain organisms with different temperature characteristics (Lebedinsky et al., 2007). Thermophilic representatives are now found even in bacterial phyla previously considered to contain only mesophilic prokaryotes, such as the phylum Acidobacteria (Losey et al., 2013). Another example is the phylum Planctomycetes. Analysis of the diversity and distribution of this group in thermal environments based on environmental molecular data revealed several phylogenetic groups of the phylum Planctomycetes most frequently detected in these habitats (A. Yu. Merkel and others, unpublished results). Several isolates from different terrestrial and subsurface thermal habitats were obtained, enriched and/or isolated in pure cultures and identified as members of the new genus 'Thermogutta' (Slobodkina et al., 2014) which is part of the Pirellula-Blastopirellula-Rhodopirellula cluster. These organisms, together with a representative of the genus 'Thermopirellula' (name not validly published; Liu et al., 2012), are to our knowledge the first thermophilic representatives of the phylum Planctomycetes.Abbreviation: ECL, equivalent chain length.
The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.
Schlesner & Stackebrandt, 1986), which has 11 genera that accommodate 19 species. Metabolically, planctomycetes are divided into two separate groups: aerobic organotrophs utilizing diverse mono-, diand polysaccharides and obligately anaerobic lithoautotrophic anammox bacteria. The latter group is represented by many genera, but none of these micro-organisms so far has been isolated in pure culture (Ward et al., 2006). Isolates of the phylum Planctomycetes maintained in laboratory cultures are mesophiles and neutrophiles. At the same time, the 16S rRNA genes of planctomycetes have been detected in different thermal natural and industrial environments: terrestrial hot springs, oilfields and waste-degrading reactors (Hugenholtz et al., 1998;Lau et al., 2009;Nazina et al., 2006;Sekiguchi et al., 1998). Yet to date, no thermophilic members of the Planctomycetes with a growth optimum above 50 u C have been described. In this study we report the isolation and characterization of two novel thermophilic planctomycetes from terrestrial and subterranean habitats. Strain R1T was isolated from a terrestrial sample of water and microbial mat (pH 7.3, 46 u C) that was collected in 2012 from a hot spring (Kunashir Island, Kurils, Russia). Strain SBP2T was isolated from a subterranean sample (pH 8.8, 32 u C) that was collected in 2011 from fracture water in an existing borehole at 1375 m below the shaft collar of the Beatrix gold mine (SibanyeGold, Free State, Abbreviation: CFA, cellular fatty acid.The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains R1T and SBP2 T are KC867694 and KC867695, respectively.
Sediments from six soda lakes of the Kulunda Steppe (Altai, Russia) and from hypersaline alkaline lakes of Wadi Natrun (Egypt) were analyzed for the presence of cbb and aclB genes encoding key enzymes Ci assimilation (RuBisCO in Calvin-Benson and ATP citrate lyase in rTCA cycles, respectively). The cbbL gene (RuBisCO form I) was found in all samples and was most diverse, while the cbbM (RuBisCO form II) and aclB were detected only in few samples and with a much lower diversity. The cbbL libraries from hypersaline lakes were dominated by members of the extremely haloalkaliphilic sulfur-oxidizing Ectothiorhodospiraceae, i.e. the chemolithotrophic Thioalkalivibrio and the phototrophic Halorhodospira. In the less saline soda lakes from the Kulunda Steppe, the cbbL gene comprised up to ten phylotypes with a domination of members of a novel phototrophic Chromatiales lineage. The cbbM clone libraries consisted of two major unidentified lineages probably belonging to chemotrophic sulfur-oxidizing Gammaproteobacteria. One of them, dominating in the haloalkaline lakes from Wadi Natrun, was related to a cbbM phylotype detected previously in a hypersaline lake with a neutral pH, and another, dominating in lakes from the Kulunda Steppe, was only distantly related to the Thiomicrospira cluster. The aclB sequences detected in two samples from the Kulunda Steppe formed a single, deep branch in the Epsilonproteobacteria, distantly related to Arcobacter sulfidicus.
A moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain HRh1T, was obtained from mixed sediment samples from hypersaline chloride–sulfate lakes in the Kulunda Steppe, in south-western Siberia (Russia), using aerobic enrichment culture at 1 M NaCl with thiocyanate as substrate. Cells of the isolate were short, non-motile rods with a Gram-negative type of cell wall. The bacterium was an obligate aerobe capable of chemolithoautotrophic growth with thiocyanate and thiosulfate. With thiosulfate, it grew at NaCl concentrations of 0.2–3.0 M (optimum 0.5 M) and at pH 6.3–8.0 (optimum pH 7.3–7.5). During growth on thiocyanate, cyanate was identified as an intermediate. The dominant cellular fatty acids were C16 : 0 and C18 : 1 ω7. Phylogenetic analysis based on 16S rRNA gene sequencing placed the isolate in the class Gammaproteobacteria as an independent lineage, with an unclassified marine sulfur-oxidizing bacterium as the closest culturable relative (93 % sequence similarity). A single cbbL gene (coding for the key enzyme of the Calvin–Benson cycle of autotrophic CO2 assimilation) with relatively low similarity to any homologous genes found in chemolithoautotrophs was detected in strain HRh1T. On the basis of our phenotypic and phylogenetic analysis, the halophilic isolate is proposed to represent a new genus and novel species, Thiohalobacter thiocyanaticus gen. nov., sp. nov. The type strain of Thiohalobacter thiocyanaticus is HRh1T (=DSM 21152T =UNIQEM U249T).
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