Marinobacter iranensis sp. nov., a slightly halophilic bacterium from a hypersaline lake.

A novel halophilic bacterium, strain 71-iT, was isolated from Inche-Broun hypersaline lake in Golestan province, in the north of Iran. It was a Gram-stain-negative, non-endospore forming, rod-shaped bacterium. It grew at 4-40 °C (optimum 30 °C), pH 6.0-11.0 (optimum pH 7.5) and with 0.5-15 % (w/v) NaCl [optimum 3 % (w/v) NaCl]. The results of phylogenetic analyses based on the 16S rRNA gene sequence comparison indicated its affiliation to the genus Marinobacter and the low percentage of identity with the most closely related species (97.5 %), indicated its placement as a novel species within this genus. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) analyses of this strain against closely related species confirmed its condition of novel taxon. On the other hand, the percentage of the average amino acid identity (AAI) affiliated strain 71-iT within the genus Marinobacter. The DNA G+C content of this isolate was 57.7 mol%. The major fatty acids were C16 : 0 and C16 : 1ω7c and/or C16 : 1 ω6c. Ubiquinone-9 was the major isoprenoid quinone and diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) were the main polar lipids of this strain. On the basis of the phylogenomic and phenotypic (including chemotaxonomic) features, we propose strain 71-iT (= IBRC M 11023T = CECT 30160T = LMG 29252T) as the type strain of a novel species within the genus Marinobacter, with the name Marinobacter iranensis sp. nov. Genomic detections of this strain in various metagenomic databases indicate that it is a relatively abundant species in environments with low salinities (approximately 5 % salinity), but not in hypersaline habitats with high salt concentrations.

Halomonas lysinitropha sp. nov., a novel halophilic bacterium isolated from a hypersaline wetland.

We carried out a polyphasic taxonomic study on a new halophilic strain designated 3(2)T, isolated from Meighan wetland, Iran. Cells of the novel strain were Gram-stain-negative, non-hemolytic, catalase- and oxidase-positive, rod-shaped, non-endospore-forming and motile. Cell growth occurred at 3-15 % NaCl (w/v; optimum, 5 %), pH 7.0-9.0 (optimum, pH 7.5-8.0) and 15-35 °C (optimum, 30 °C). 16S rRNA gene sequence comparisons confirmed the affiliation of strain 3(2)T to the class Gammaproteobacteria and the genus Halomonas with highest similarity to Halomonas daqiaonensis YCSA28T (98.4 %) and Halomonas ventosae Al12T (97.9 %). Experimental and in silico DNA-DNA hybridization values were 42.7 and 35.1% with H. daqiaonensis IBRC-M 10931T and 48 and 35.2% with H. ventosae IBRC-M 10566T, respectively, and indicated that they are different members of the same genus. The genome of the type strain was characterized by a size of 3.83 Mbp with 63 scaffolds and a G+C content of 64.8 mol%. Moreover, the average nucleotide identity values against H. ventosae Al12T and H. daqiaonensis YCSA28T were 88.8 and 88.5 %, respectively. The predominant respiratory quinone was Q-9 (92 %) with Q-8 (8 %) as a minor component. Major fatty acids were C16 : 0 cyclo, C19 : 0 ω8c, C16 : 1 ω7c and/or iso-C15:0 2-OH, C12 : 0 3-OH and C18 : 1 ω7c. The polar lipid profile of the strain contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphoaminoglycolipid and four unidentified phospholipids. According to our results, strain 3(2)T could be classified as a novel species in the genus Halomonas for which the name Halomonas lysinitropha sp. nov. is proposed. The type strain is 3(2)T (=IBRC M 10929T=LMG 29450T=CIP 111708T).

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).

Planomicrobium iranicum sp. nov., a novel slightly halophilic bacterium isolated from a hypersaline wetland.

A novel strain, designated as MX6T was isolated from Meighan wetland, in the centre of Iran. The cells were Gram-stain-positive, motile, coccoid to rod-shaped, oxidase- and catalase-positive. The strain grew optimally at 35 °C, 3 % (w/v) NaCl and pH 7-7.5. A polyphasic taxonomic study was undertaken in order to characterize the strain in detail. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that MX6T represented a member of the phylum Firmicutes, family Planococcaceae, genus Planomicrobium, and showed the highest similarity with Planomicrobium flavidum ISL-41T (98.2 %) and Planomicrobium psychrophilum CMC 53orT (98.0 %). The main polar lipids of MX6T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and seven unidentified phospholipids and its DNA G+C content was 45.5 mol%. Major cellular fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol, iso-C14 : 0, iso-C15 : 0 and iso-C16 : 0 and the predominant respiratory quinone was Q-8 (62 %). Experimental DNA-DNA hybridization between MX6T and Planomicrobium flavidum IBRC-M 11047T was 20 %, supporting the differential taxonomic status of MX6T as representing a different taxon. All these data indicate that MX6T represents a novel species of the genus Planomicrobium, for which the name Planomicrobium iranicum sp. nov. is proposed. The type strain is MX6T (=IBRC M 10928T=LMG 28548T).

Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake.

A moderately halophilic bacterium was isolated from a brine sample of a hypersaline lake, Aran-Bidgol, in Iran. The strain, designated J8BT, was Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, motile and produced cream colonies. Strain J8BT grew in NaCl at between 3.0-15.0 % (w/v) (optimally at 7.5 % NaCl, w/v), between pH 6.5-9.0 (optimally at pH 8.0) and between 20-45 °C (optimally at 35 °C). Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain J8BT is a member of the genus Oceanobacillus and most closely related to Oceanobacillus profundus CL-MP28T, Oceanobacillus polygoni SA9T and Oceanobacillus oncorhynchi R-2T (96.9 %, 96.3 % and 96.2 % similarities, respectively). The level of DNA-DNA relatedness between the novel isolate and O. profundus IBRC-M 10567T was 10 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid pattern of strain J8BT consisted of phosphatidylglycerol, diphosphatidylglycerol, five phospholipids, two aminolipids and two glycoaminolipids. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 39.2 mol%. Phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus halophilus sp. nov. is proposed. The type strain is strain J8BT ( = IBRC-M 10444T = DSM 23996T).

Salinithrix halophila gen. nov., sp. nov., a halophilic bacterium in the family Thermoactinomycetaceae.

A halophilic actinomycete, strain R4S8(T), was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30-50 °C (optimum 40 °C), pH 6-10 (optimum pH 7.0) and in the presence of 1-15 % (w/v) NaCl (optimum 3-5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8(T) contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8(T) belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269(T) (95.5 %) and Marininema mesophilum SCSIO 10219(T) (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8(T) represents a novel species in a new genus within the family Thermoactinomycetaceae, for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8(T) ( = IBRC-M 10813(T) = CECT 8506(T)).

Basidioascus persicus sp. nov., a yeast-like species of the order Geminibasidiales isolated from soil.

A novel species of basidiomycetes was isolated from kitchen garden soil in Shahryar city, Tehran province, Iran. Molecular and conventional methods were employed to identify and classify this single isolate. Morphologically, the isolate was considered yeast-like with hyaline and oval cells reproducing by monopolar budding, forming ballistoconidia, hyphae, arthroconidia and didymospores. Basidia and basidiospores resembling those produced by Basidioascus species were observed. Sequencing and Bayesian phylogenetic analysis of rRNA genes and the internal transcribed spacer region revealed its sister relationship to described species of the genus Basidioascus. Assimilation and fermentation tests, cell-wall carbohydrate analysis and enzyme activity tests were performed to provide insight into the metabolism of the isolate. Based on morphology, physiology and phylogeny of rRNA gene sequences, the isolate was shown to represent a novel species of the genus Basidioascus, described as Basidioascus persicus sp. nov. (holotype IBRC P1010180(T) = ex-type IBRC M30078(T) = isotype CBS 12808(T)). The MycoBank number of the novel species is MB 804703. An emended description of the genus Basidioascus is also provided.

Aliicoccus persicus gen. nov., sp. nov., a halophilic member of the Firmicutes isolated from a hypersaline lake.

A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76(T), was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76(T) grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5% (w/v) NaCl (optimal growth at 7.5%, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76(T) was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1%, to the type species of the genera Jeotgalicoccus, Salinicoccus and Nosocomiicoccus, respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76(T) were anteiso-C(15 : 0) and iso-C(15 : 0), and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94%), MK-5 (3%) and MK-7 (3%). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76(T) and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae, for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76(T) ( = CECT 8508(T) = DSM 28306(T) = IBRC-M 10081(T)).

Alloactinosynnema iranicum sp. nov., a rare actinomycete isolated from a hypersaline wetland, and emended description of the genus Alloactinosynnema.

A Gram-staining-positive actinobacterial strain, Chem10(T), was isolated from soil around Inche-Broun hypersaline wetland in the north of Iran. Strain Chem10(T) was strictly aerobic, and catalase- and oxidase-positive. The isolate grew with 0-3 % NaCl, at 20-40 °C and at pH 6.0-8.0. The optimum temperature and pH for growth were 30 °C and pH 7.0, respectively. The cell wall of strain Chem10(T) contained meso-diaminopimelic acid as diamino acid and galactose, ribose and arabinose as whole-cell sugars. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain Chem10(T) synthesized cellular fatty acids of the straight-chain saturated and mono-unsaturated, and iso- and anteiso-branched types C14 : 0, C16 : 0, iso-C16 : 1, anteiso-C17 : 0, iso-C16 : 0, iso-C14 : 0 and iso-C15 : 0, and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 70.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Chem10(T) belonged to the family Pseudonocardiaceae and showed the closest phylogenetic similarity to Alloactinosynnema album KCTC 19294(T) (98.3 %) and Actinokineospora cibodasensis DSM 45658(T) (97.9 %). DNA-DNA relatedness values between the novel strain and strains Alloactinosynnema album KCTC 19294(T) and Actinokineospora cibodasensis DSM 45658(T) were only 52 % and 23 %, respectively. On the basis of phylogenetic analysis, phenotypic characteristics and DNA-DNA hybridization data, a novel species of the genus Alloactinosynnema is proposed, Alloactinosynnema iranicum sp. nov. The type strain is Chem10(T) ( = IBRC-M 10403(T) = CECT 8209(T)). In addition, an emended description of the genus Alloactinosynnema is proposed.

Limimonas halophila gen. nov., sp. nov., an extremely halophilic bacterium in the family Rhodospirillaceae.

A novel, Gram-staining-negative, non-pigmented, rod-shaped, strictly aerobic, extremely halophilic bacterium, designated strain IA16(T), was isolated from the mud of the hypersaline Lake Aran-Bidgol, in Iran. Cells of strain IA16(T) were not motile. Growth occurred with 2.5-5.2 M NaCl (optimum 3.4 M), at pH 6.0-8.0 (optimum pH 7.0) and at 30-50 °C (optimum 40 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IA16(T) belonged in the family Rhodospirillaceae and that its closest relatives were Rhodovibrio sodomensis DSM 9895(T) (91.6 % sequence similarity), Rhodovibrio salinarum NCIMB 2243(T) (91.2 %), Pelagibius litoralis CL-UU02(T) (88.9 %) and Fodinicurvata sediminis YIM D82(T) (88.7 %). The novel strain's major cellular fatty acids were C19 : 0 cyclo ω7c and C18 : 0 and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, four unidentified phospholipids, three unidentified aminolipids and two other unidentified lipids. The cells of strain IA16(T) contained the ubiquinone Q-10. The G+C content of the novel strain's genomic DNA was 67.0 mol%. The physiological, biochemical and phylogenetic differences between strain IA16(T) and other previously described taxa indicate that the strain represents a novel species in a new genus within the family Rhodospirillaceae, for which the name Limimonas halophila gen. nov., sp. nov. is proposed. The type strain of Limimonas halophila is IA16(T) ( = IBRC-M 10018(T)  = DSM 25584(T)).