Taxogenomics of the Genus Cyclobacterium: Cyclobacterium xiamenense and Cyclobacterium halophilum as Synonyms and Description of Cyclobacterium plantarum sp. nov.

The genus Cyclobacterium belongs to the phylum Bacteroidetes and includes eight species. Our study, based on the genomic parameters in silico DNA-DNA hybridization (GGDC), average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that all current species of Cyclobacterium belong to this genus and constitute a coherent phylogenomic group, but with species forming two separate branches. In addition, the genome-based analyses revealed that Cyclobacterium xiamenense and Cyclobacterium halophilum are members of the same species. Besides, we carried out a taxonomic characterization of the new strain GBPx2T, isolated from the halophytic plant Salicornia sp. Analysis of its 16S rRNA gene sequence showed the highest sequence similarity (97.5%) to Cyclobacterium lianum HY9T. Percentages of GGDC and OrthoANI between strain GBPx2T and species of the genus Cyclobacterium were lower than the threshold value for species delineation. The DNA G+C content was 43.0 mol%. The polar lipids included phosphatidylethanolamine as well as one unidentified phospholipid and four unidentified lipids, and its major cellular fatty acids were iso-C15:0 and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The only quinone present was menaquinone 7. Based on a combination of phenotypic, chemotaxonomic, and phylogenomic features, the GBPx2T strain represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium plantarum sp. nov. is proposed. The type strain of Cyclobacterium plantarum is GBPx2T (= IBRC-M 10634T = LMG 28551T).

Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland.

A Gram-stain-positive, endospore-forming rod-shaped non-motile, moderately halophilic and alkaliphilic bacterium, strain GASy1T, was isolated from a water sample from Gomishan, a marine wetland in Iran. GASy1T required at least 0.5 % (w/v) NaCl for growth and was able to grow at NaCl concentrations of up to 15 % (w/v), with optimum growth occurring at 5 % (w/v) NaCl. The optimum pH and temperature for growth were pH 8.5-9.0 and 30 °C, respectively, while it was able to grow over a pH range and a temperature range of 7.5-10.0 and 4-40 °C, respectively. GASy1T was catalase-positive and oxidase-negative. Analysis of 16S rRNA gene sequences revealed that GASy1T represents a member of the genus Salipaludibacillus, family Bacillaceae within the order Bacillales, showing 97.4 % sequence similarity to Salipaludibacillus neizhouensis JSM 071004T, and 96.2 and 95.7 % sequence similarity to Salipaludibacillus agaradhaerens AC 13T and Salipaludibacillus aurantiacus S9T, respectively. The DNA G+C content of GASy1T was 38.8 mol%. The polar lipids of the strain were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids and its major cellular fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C15 : 0. The isoprenoid quinone was MK-7. DNA-DNA hybridization experiments revealed a low level of relatedness between GASy1T and Salipaludibacillus neizhouensis IBRC-M 10892T (18 %). On the basis of a combination of phenotypic, chemotaxonomic and phylogenetic features, GASy1T represents a novel species of the genus Salipaludibacillus, for which the name Salipaludibacillus halalkaliphilus sp. nov. is proposed. The type strain of Salipaludibacillus halalkaliphilus is GASy1T (=IBRC M 10902T=LMG 28385T).

Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano.

The application of tandem MALDI-TOF MS screening with 16S rRNA gene sequencing of selected isolates has been demonstrated to be an excellent approach for retrieving novelty from large-scale culturing. The application of such methodologies in different hypersaline samples allowed the isolation of the culture-recalcitrant Salinibacter ruber second phylotype (EHB-2) for the first time, as well as a new species recently isolated from the Argentinian Altiplano hypersaline lakes. In this study, the genome sequences of the different species of the phylum Rhodothermaeota were compared and the genetic repertoire along the evolutionary gradient was analyzed together with each intraspecific variability. Altogether, the results indicated an open pan-genome for the family Salinibacteraceae, as well as the codification of relevant traits such as diverse rhodopsin genes, CRISPR-Cas systems and spacers, and one T6SS secretion system that could give ecological advantages to an EHB-2 isolate. For the new Salinibacter species, we propose the name Salinibacter altiplanensis sp. nov. (the designated type strain is AN15T=CECT 9105T=IBRC-M 11031T).

Aliidiomarina sedimenti sp. nov., a haloalkaliphilic bacterium in the family Idiomarinaceae.

A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0-10 and 4-40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria, family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12-14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA-DNA relatedness between GBSy1T and Aliidiomarina marisDSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina. On the basis of evidence from this study, a novel species of the genus Aliidiomarina, Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.

Aliidiomarina iranensis sp. nov., a haloalkaliphilic bacterium from a coastal-marine wetland.

A novel Gram-stain-negative, straight rod-shaped, non-pigmented, slightly halophilic and alkaliphilic bacterium, designated strain GBPy7T, was isolated from a sample of the coastal-marine wetland Gomishan in Iran. Cells of strain GBPy7T were motile. Growth occurred on media with 1-15 % (w/v) NaCl (optimum 3 %), at pH 7-10 (optimum pH 8.5) and at 4-45 °C (optimum 37 °C). Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that strain GBPy7T belonged to the family Idiomarinaceae. Its closest relatives were Aliidiomarina shirensis AIST (98.1 % 16S rRNA gene sequence similarity) and other Aliidiomarina species (95.9-94.2 %), together with Idiomarina seosinensis CL-SP19T (94.3 %) and Idiomarina fontislapidosi F23T (94.3 %). The major cellular fatty acids of the isolate were iso-C15 : 0, iso-C17 : 0, iso-C17 : 1ω9c and C18 : 1ω7c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, one unknown phospholipid and one unknown aminophospholipid. Cells of strain GBPy7T contained ubiquinone Q-8. The G+C content of the genomic DNA of this strain was 51.6 mol%. The level of DNA-DNA relatedness between strain GBPy7T and A. shirensis IBRC-M 10414T was 21 %. The physiological, biochemical, genotypic and phylogenetic differences between strain GBPy7T and other previously described taxa indicate that the strain represents a novel species of the genus Aliidiomarina within the family Idiomarinaceae, for which the name Aliidiomarina iranensis sp. nov. is proposed. The type strain is GBPy7T ( = IBRC-M 10763T = CECT 8339T).

Salinispirillum marinum gen. nov., sp. nov., a haloalkaliphilic bacterium in the family 'Saccharospirillaceae'.

A novel Gram-staining-negative, motile, non-pigmented, facultatively anaerobic, spirillum-shaped, halophilic and alkaliphilic bacterium, designated strain GCWy1(T), was isolated from water of the coastal-marine wetland Gomishan in Iran. The strain was able to grow at NaCl concentrations of 1-10% (w/v) and optimal growth was achieved at 3% (w/v). The optimum pH and temperature for growth were pH 8.5 and 30 °C, while the strain was able to grow at pH 7.5-10 and 4-40 °C. Phylogenetic analysis based on the comparison of the 16S rRNA gene sequence placed the isolate within the class Gammaproteobacteria as a separate deep branch, with 92.1% or lower sequence similarity to representatives of the genera Saccharospirillum and Reinekea and less than 91.0% sequence similarity with other remotely related genera. The major cellular fatty acids of the isolate were C(18 : 1)ω7c, C(16:0) and C(17 : 0), and the major components of its polar lipid profile were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cells of strain GCWy1(T) contained the isoprenoid quinones Q-9 and Q-8 (81% and 2%, respectively). The G+C content of the genomic DNA of this strain was 52.3 mol%. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and phenotypic data, strain GCWy1(T) represents a novel species in a new genus in the family 'Saccharospirillaceae', order Oceanospirillales, for which the name Salinispirillum marinum gen. nov., sp. nov. is proposed. The type strain of the type species is GCWy1(T) ( = IBRC-M 10765(T) =CECT 8342(T)).

Pseudomonas salegens sp. nov., a halophilic member of the genus Pseudomonas isolated from a wetland.

A novel Gram-stain-negative, aerobic, non-endospore-forming, non-pigmented, rod-shaped, slightly halophilic bacterium, designated GBPy5(T), was isolated from aquatic plants of the Gomishan wetland, Iran. Cells of strain GBPy5(T) were motile. Growth occurred with between 1 and 10% (w/v) NaCl and the isolate grew optimally with 3% (w/v) NaCl. The optimum pH and temperature for growth of the strain were pH 8.0 and 30 °C, respectively, while it was able to grow over a pH range of 6.5-9.0 and a temperature range of 4-35 °C. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain GBPy5(T) is a member of the genus Pseudomonas forming a monophyletic branch. The novel strain exhibited 16S rRNA gene sequence similarity of 95.4% with type strains of Pseudomonas guariconensis PCAVU11(T) and Pseudomonas sabulinigri J64(T), respectively. The major cellular fatty acids of the isolate were C18:1ω7c (37.8%), C16:0 (14.9%), C16:1ω7c (12.9%), C12:0 3-OH (7.1%) and C12:0 (7.0%). The polar lipid pattern of strain GBPy5(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and one phospholipid. Ubiquinone 9 (Q-9) was the predominant lipoquinone. The G+C content of the genomic DNA of strain GBPy5(T) was 59.2 mol%. On the basis of the phenotypic and phylogenetic data, strain GBPY5(T) represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salegens sp. nov. is proposed. The type strain is GBPy5(T) ( = IBRC-M 10762(T) = CECT 8338(T)).

Cyclobacterium halophilum sp. nov., a marine bacterium isolated from a coastal-marine wetland.

A novel Gram-stain-negative, slightly halophilic bacterium, designated strain GASx41(T), was isolated from soil of the coastal-marine wetland Gomishan in Iran. Cells of strain GASx41(T) were curved, ring-like or horseshoe-shaped rods and non-motile. Strain GASx41(T) was strictly aerobic, and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 1-10% (w/v), with optimum growth occurring at 2.5-3% (w/v) NaCl. The optimum temperature and pH for growth were 25-30 °C and pH 7.5-8.0. On the basis of 16S rRNA gene sequence analysis, strain GASx41(T) was shown to belong to the genus Cyclobacterium within the phylum Bacteroidetes and showed closest phylogenetic similarity to 'Cyclobacterium jeungdonense' HMD3055 (98.0%). The DNA G+C content of strain GASx41(T) was 48.1 mol%. The major cellular fatty acids of strain GASx41(T) were iso-C15 : 0, summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), anteiso-C15 : 0 2-OH, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and its polar lipid pattern consisted of phosphatidylethanolamine, phosphatidylcholine and 12 unknown lipids. The only quinone present was menaquinone 7 (MK-7). All these features confirmed the placement of isolate GASx41(T) within the genus Cyclobacterium. On the basis of evidence from this study, a novel species of the genus Cyclobacterium, Cyclobacterium halophilum sp. nov., is proposed, with strain GASx41(T) ( = IBRC-M 10761(T) = CECT 8341(T)) as the type strain.