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Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine

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Two rod-shaped, non-motile bacteria were isolated from two separate salt mines in Yunnan, south-western China. These strains, designated YIM D15T and YIM J21T, were Gram-negative and moderately halophilic. The two strains required 6–10 % NaCl (w/v; optimal) for growth. The DNA G+C contents of strains YIM D15T and YIM J21T were 49.0 mol% and 48.4 mol%, respectively. The predominant isoprenoid quinone was MK-7. The polar lipid profiles of strains YIM D15T and YIM J21T were composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unknown polar lipids and one glycolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c/10 methyl-C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct clade with the genus Fodinibius (in the phylum Bacteroidetes ) and were related to the species Fodinibius salinus , with sequence similarities of 91.9–92.4 %. Analyses of 16S rRNA gene sequences revealed that strains YIM D15T and YIM J21T were related to each other (97.3 % sequence similarity). The DNA–DNA hybridization relatedness between the two isolates was 34 %. On the basis of the phylogenetic analysis, DNA–DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM D15T and YIM J21T should be classified as members of a novel genus and as two novel species, for which the names Aliifodinibius roseus gen. nov., sp. nov. (type strain YIM D15T = ACCC 10715T = KCTC 23442T) and Aliifodinibius sediminis sp. nov. (type strain YIM J21T = ACCC 10714T = DSM 21194T) are proposed.

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While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by δ-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines.

Although Halomonas phages belonging to the families Myoviridae and Siphoviridae have been reported, no virulent Halomonas siphoviruses are known. In this study, a virulent bacteriophage, QHHSV-1, of the family Siphoviridae that specifically infects H. ventosae QH52-2 was isolated from the Qiaohou salt mine. Restriction analysis indicated that QHHSV-1 is a dsDNA virus with a genome size of 33.5-39.5 kb. Transmission electron microscopy showed that QHHSV-1 is a typical representative of the Siphoviridae, with an icosahedral head (47 nm in diameter) and a non-contractile tail (75 nm in length). We also assessed the adsorption rate of QHHSV-1 for the host bacterium and found significant inhibition after the addition of 10 mM CaCl2. Based on a one-step growth curve, we determined a latent period of 30 min and a burst size of 73 PFU/infected cell. At the optimal pH of 8.0, 25.9 and 15.2 % of the phages survived after a 60-min incubation at 50 and 60 °C, respectively. Phage replication was possible at a wide range of salt concentrations, from 2.0 to 20 % (w/v), with an optimum concentration of 5 %. The survival of QHHSV-1 at different salt concentrations decreased with time and 25 % survival after 25 days at 30 % salt concentration.

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1 ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 10.7 %) and C17 : 1 ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).