16S rRNA Gene Sequence Similarity Research Articles

Streptomyces cylindrosporus sp. nov. and Streptomyces spinosisporus sp. nov.: two new endophytic actinobacteria isolated from the roots of Barleria lupulina Lindl.

Two endophytic actinobacteria, designated as strains 7R015T and 7R016T, were isolated from the roots of Barleria lupulina collected in Thailand. The morphological characteristics and results of chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains represented members of the genus Streptomyces. They contained ll-diaminopimelic acid in the peptidoglycan. Ribose and glucose were detected as the whole-cell sugars. MK-9(H4), MK-9(H6) and MK-9(H8), were found as the membrane menaquinone. The predominant cellular fatty acids detected were iso-C16 : 0 and anteiso-C15 : 0. The genomes of both strains harboured biosynthetic gene clusters for melanin, terpene, lanthipeptide, polyketides, non-ribosomal peptide synthetase, siderophore and ectoine. The 16S rRNA gene sequence of 7R015T showed the highest similarity to that of Streptomyces pseudovenezuelae DSM 40212T (98.6 %), Streptomyces cyaneus NRRL B2296T (98.6 %) and Streptomyces curacoi DSM 40107T (98.6 %). Strain 7R016T showed the highest 16S rRNA gene sequence similarity to Streptomyces gilvifuscus NBRC 110904T (98.2 %), which is lower than the threshold value for 16S rRNA gene sequence similarity for differentiation at the species level (98.65 %). Comparative genome analysis revealed that the genomes of 7R015T, 7R016T and the closely related type strains had an average nucleotide identity (ANI) of less than 95 % and a digital DNA-DNA hybridisation (dDDH) of less than 70 %, the thresholds for species demarcation. On the basis of the results of the polyphasic study, strains 7R015T and 7R016T represent novel species of the genus Streptomyces and are named herein as Streptomyces cylindrosporus sp. nov. (=NBRC 115200T = TBRC 14542T) for strain 7R015T and Streptomyces spinosisporus sp. nov. (=NBRC 115201T = TBRC 14543T) for strain 7R016T.

Baekduia alba sp. nov., a novel representative of the order Solirubrobacterales isolated from temperate grassland soil.

Strain 0141_2T was isolated from a temperate grassland soil in Germany and was found to be affiliated with the order Solirubrobacterales. It is most closely related to Baekduia soli BR7-21T, with 98.1 % 16S rRNA gene sequence similarity. Cells are rod-shaped, non-motile, stain Gram-positive and can have multiple vesicles in the cell surface. Polyhydroxybutyrate is accumulated within the cells. Catalase- and oxidase-positive. It is a mesophilic aerobe and grows best around neutral to slightly acidic pH in R2A medium. The major fatty acids are C18 : 1 ω9c, iso-C16 : 0, C18 : 0, C16 : 0, C16 : 1 ω7c and C17 : 1 ω8c. Diphosphatidylglycerol is present. The predominant respiratory quinone is MK-7(H4). Meso-diaminopimelic acid is the diagnostic diamino acid in the cell-wall peptidoglycan. The G+C content of genomic DNA is 72.9 mol%. Based on the results of phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the novel species Baekduia alba sp. nov. with the type strain 0141_2T (=DSM 104299T=LMG 30000T=CECT 9239T).

Paenibacillus agricola sp. nov., isolated from agricultural soil

A white-coloured, rod-shaped, motile, aerobic, and Gram-stain-positive bacterial strain S3N08T was isolated from agricultural soil. The strain grew at temperature 10-40°C, at 0-1.0% (w/v) NaCl concentration, and at pH 6.5-8.0. Catalase was negative and oxidase was positive. The phylogenetic analysis inferred that the strain S3N08T belonged to the genus Paenibacillus, with the closest relative being Paenibacillus periandrae PM10T (95.6% 16S rRNA gene sequence similarity). The only menaquinone was MK-7 and the major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylglycerol, and phosphatidylethanolamine. The predominant fatty acids were antiso-C15:0, C16:0, and iso-C15:0. The DNA G + C content was 45.1%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain S3N08T and with closest members were < 72.0% and < 19.0%, respectively. Altogether, the phylogenetic, genomics, phenotypic, and chemotaxonomic evidence illustrated in this study suggested that strain S3N08T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agricola sp. nov. is proposed. The type strain is S3N08T (= KACC 19666T = NBRC 113430T).

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota

Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.

Georgenia halotolerans sp. nov., a halotolerant actinobacterium isolated from Taklamakan desert soil.

A Gram-stain-positive, aerobic, non-motile, non-spore-forming and rod-shaped actinobacterium, designated strain 10Sc9-8T, was isolated from Taklamakan desert soil sampled in the Xinjiang Uygur Autonomous Region, China. Strain 10Sc9-8T grew at 8‒37 °C (optimum, 28‒30 °C), pH 6.0‒10.0 (optimum, pH 7.0-8.0) and in the presence of 0‒15 % (w/v) NaCl (optimum, 0-3 %). Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 10Sc9-8T was affiliated with members of the genus Georgenia and showed the highest 16S rRNA gene sequence similarity to Georgenia yuyongxinii Z443T (97.4 %). Phylogenomic analysis based on the whole genome sequences indicated that strain 10Sc9-8T should be assigned into the genus Georgenia. The average nucleotide identity and digital DNA-DNA hybridization values calculated from the whole genome sequences indicated that strain 10Sc9-8T was clearly separated from other closely related species of the genus Georgenia with values below the thresholds for species delineation. Chemotaxonomic analyses showed that the cell-wall peptidoglycan was in a variant of A4α type with an interpeptide bridge comprising l-Lys-l-Ala-Gly-l-Asp. The predominant menaquinone was MK-8(H4). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, several unidentified phospholipids, glycolipids and one unidentified lipid. The major fatty acids were anteiso-C15 : 0, anteiso-C15 : 1 A and C16 : 0. The genomic DNA G+C content was 72.7 mol%. On the basis of phenotypic, phylogenetic and phylogenomic data, strain 10Sc9-8T represents a novel species of the genus Georgenia, for which the name Georgenia halotolerans sp. nov. is proposed. The type strain is 10Sc9-8T (=JCM 33946T=CPCC 206219T).

Chitinolyticbacter albus sp. Nov., A Novel Chitin-Degrading Bacterium Isolated from Ancient Wood Rhizosphere Soil.

In this study, a novel aerobic mesophilic bacterial strain with capable of degrading chitin, designated YIM B06366T, was isolated and classified. The rod-shaped, Gram-stain-negative, on-spore-forming bacterium originated from rhizosphere soil sample collected in Kunming City, Yunnan Province, southwest PR China. Strain YIM B06366T exhibited growth at temperatures between 20 and 35 °C (optimum, 30 °C) and at pH 6.0-8.0 (optimum, pH 6.0). The analysis of 16S rRNA gene sequence similarity revealed that strain YIM B06366T was most closely related to type strain Chitinolyticbacter meiyuanensis SYBC-H1T (98.9%). Phylogenetic analysis based on genome data indicated that strain YIM B06366T should be assigned to the genus Chitinolyticbacter. The Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) values between strain YIM B06366T and the reference strain Chitinolyticbacter meiyuanensis SYBC-H1T were 84.4% and 27.7%, respectively. The major fatty acids included Summed Feature 3 (C16:1 ω6c/C16:1 ω7c), Summed Feature 8 (C18:1 ω6c/C18:1 ω7c), and C16:0. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipids, and two unidentified phospholipids. The predominant menaquinone was Q-8, and the genomic DNA G + C content was 64.1%. Considering the polyphasic taxonomic evidence, strain YIM B06366T is proposed as a novel species within the genus Chitinolyticbacter, named Chitinolyticbacter albus sp. nov. (type strain YIM B06366T = KCTC 92434T = CCTCC AB 2022163T).

Stakelama marina sp. nov., isolated from seawater of the Tangyin hydrothermal field in the Okinawa Trough.

A Gram-stain-negative, strictly aerobic, rod-shaped and non-flagellated marine bacterium, designated strain LXI357T, was isolated from deep-sea water sampled at the Tangyin hydrothermal field in the Okinawa Trough. The growth temperature range was 20-45 °C (optimum, 28 °C). Strain LXI357T was also able to grow at pH 5.0-7.5 (optimum, pH 6.0-7.0) and in the presence of 0.5-11 % (optimum, 7%, w/v) NaCl. Strain LXI357T was oxidase-negative and catalase-positive. The predominant fatty acids were C18 : 1 ω7c and C16 : 0. The major polar lipids of strain LXI357T contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, sphingoglycolipid, diphosphatidylglycero and an unidentified aminolipid. Based on the results of 16S rRNA gene sequence analysis, strain LXI357T belonged to the genus Stakelama and was most closely related to Stakelama flava CBK3Z-3T (96.28%, 16S rRNA gene sequence similarity), followed by Stakelama algicida Yeonmyeong 1-13T (95.67%), Stakelama pacifica JLT832T (95.46%) and Sphingosinicella vermicomposti YC7378T (95.43%). Genome relatedness between strain LXI357T and Stakelama flava CBK3Z-3T was computed using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, with values of 76.02, 20.9 and 71.1 %, respectively. The genomic DNA G+C content of strain LXI357T is 64.1 mol%. In addition, strain LXI357T has multiple genes related to sulphur metabolism, including genes encoding for the Sox system. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain LXI357T from its closest phylogenetic neighbours. According to the results of polyphasic analyses, strain LXI357T is considered to represent a novel species of the genus Stakelama, for which the name Stakelama marina sp. nov. is proposed. The type strain is LXI357T (=MCCC 1K06076T=KCTC 82726T).

Thermalbibacter longus gen. nov., sp. nov., isolated from a hot spring.

An isolate, designated CFH 74404T, was recovered from a hot spring in Tengchong, Yunnan province, PR China. Phylogenetic analysis indicated that the isolate belongs to the family Thermomicrobiaceae and showed the highest 16S rRNA gene sequence similarity to Thermorudis peleae KI4T (93.6 %), Thermorudis pharmacophila WKT50.2T (93.1 %), Thermomicrobium roseum DSM 5159T (92.0 %) and Thermomicrobium carboxidum KI3T (91.7 %). The average amino acid identity and average nucleotide identity values between strain CFH 74404T and the closest relatives were 42.0-75.9 % and 67.0-77.3 %, respectively. Cells of strain CFH 74404T stained Gram-positive and were aerobic, non-motile and short rod-shaped. Growth occurred at 20-65 °C (optimum, 55 °C), pH 6.0-8.0 (optimum, pH 7.0) and with up to 2.0 % (w/v) NaCl (optimum 0-1.0 %, w/v). The predominant respiratory quinone was MK-8. The major fatty acids (>10 %) were C18 : 0 (50.8 %) and C20 : 0 (16.8 %). The polar lipid profile of strain CFH 74404T included diphosphatidylglycerol, four unidentified phosphoglycolipids, phosphatidylinositol and three unidentified glycolipids. The G+C content of the genomic DNA was determined to be 67.1 mol% based on the draft genome sequence. On the basis of phenotypic, phylogenetic and genotypic analyses, it is concluded that strain CFH 74404T represents a new species of a novel genus Thermalbibacter of the family Thermomicrobiaceae, for which the name Thermalbibacter longus gen. nov., sp. nov. is proposed. The type strain is CFH 74404T (=KCTC 62930T=CGMCC 1.61585T).

Protaetiibacter mangrovi sp. nov., isolated from mangrove soil.

A novel Gram-stain-positive, aerobic, non-flagellated and rod-shaped actinobacterium, designated 10F1B-8-1T, was isolated from mangrove soil sampled at Futian Mangrove Nature Reserve, China. The isolate was able to grow at 10-40 °C (optimum 30-32 °C), at pH 6-8 (optimum 7) and in the presence of 0-6% (w/v) NaCl (optimum 0%). Strain 10F1B-8-1T shared the highest 16S rRNA gene sequence similarity to Protaetiibacter larvae NBRC 113051T (98.3%), followed by Protaetiibacter intestinalis NBRC 113050T (98.2%). Phylogenetic trees based on 16S rRNA gene sequences and the core proteomes exhibited that strain 10F1B-8-1T formed a new phyletic line in the clade of genus Protaetiibacter, indicating that this strain belonged to the genus Protaetiibacter. Strain 10F1B-8-1T showed low average nucleotide identity (<84%) and digital DNA-DNA hybridization values (<27%) with closely related taxa, suggesting that strain 10F1B-8-1T was a hitherto undescribed species of the genus Protaetiibacter. Strain 10F1B-8-1T contained D-2,4-diaminobutyric acid as the diagnostic diamino acid, and the peptidoglycan type was characterized as type B2β. The major fatty acids were iso-C16:0, anteiso-C15:0 and anteiso-C17:0. The major menaquinones were MK-13 and MK-14. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and five unidentified lipids. Notably, the ethyl acetate extracts of strain 10F1B-8-1T showed effective antibacterial activity against Bacillus subtilis CPCC 100029 and Escherichia coli △tolC. According to the polyphasic data, strain 10F1B-8-1T should be classified as a novel species of the genus Protaetiibacter, for which the name Protaetiibacter mangrovi sp. nov. is proposed, with the type strain 10F1B-8-1T (=JCM 33142T = CPCC 205428T).

Antribacter soli sp. nov., a novel actinobacterium isolated from soils of weathering dolomite.

Strain KLBMP 9083T, a novel actinobacterium, was isolated from weathered soils collected from a karst area in Anshun, Guizhou Province, PR China. The taxonomic position of strain KLBMP 9083T was studied using the polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain KLBMP 9083T formed a stabilized monophyletic clade with its closest relative strain Antribacter gilvus CGMCC 1.13856T (98.4 % 16S rRNA gene sequence similarity). The peptidoglycan hydrolysates contained alanine, glutamic acid, threonine and lysine. The polar lipids were composed of diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The predominant menaquinones were MK-9(H8) (87.1 %), MK-9(H6) (7.3 %) and MK-9(H4) (5.6 %). The major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 72.3 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between strain KLBMP 9083T and A. gilvus CGMCC 1.13856T were 23.4 and 79.9 %, respectively. On the basis of morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 9083T represents a novel species of the genus Antribacter, for which the name Antribacter soli sp. nov. is proposed. The type strain is KLBMP 9083T (=CGMCC 4.7737T=NBRC 115577T).

Parathalassolituus penaei gen. nov., sp. nov., a novel member of the family Oceanospirillaceae isolated from a coastal shrimp pond in Guangxi, PR China.

A Gram-stain-negative, strictly aerobic, rod-shaped and motile bacterium with bipolar flagella, designated G-43T, was isolated from a surface seawater sample collected from an aquaculture in Guangxi, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain G-43T was most closely related to the family Oceanospirillaceae and distantly to the most closely related genera Venatorbacter and Thalassolituus (95.52 % and 94.45-94.76 % 16S rRNA gene sequence similarity, respectively), while similarity values to other Oceanospirillaceae type strains were lower than 94.0 %. Strain G-43T was found to grow at 4-30 °C (optimum, 25-28 °C), pH 6-9.0 (optimum, pH 7.0) and with 0-4.0 % NaCl (w/v; optimum at 2 % NaCl). Chemotaxonomic analysis of strain G-43T indicated that the sole respiratory quinone was ubiquinone-8, the predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, aminolipid, diphosphatidylglycerol, phospholipids and an unidentified lipid. The G+C content of the genomic DNA was 55.4 mol%. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrate that strain G-43T represents a novel species in a novel genus within the family Oceanospirillaceae, for which the name Parathalassolituus penaei gen. nov., sp. nov. is proposed. Strain G-43T (=KCTC 72750T= CCTCC AB 2022321T) is the type and only strain of Parathalassolituus penaei.

A novel strictly anaerobic sulfate-reducing diazotrophic bacterium Fundidesulfovibrio terrae sp. nov., isolated from paddy soil.

A strictly anaerobic sulfate-reducing strain, designated SG127T, was isolated from paddy soil. SG127T showed the highest 16S rRNA gene sequence similarity to the type strain of Fundidesulfovibrio magnetotacticus (98.2 %). A phylogenetic tree based on 16S rRNA gene sequences indicated that SG127T clustered with members of the genus Fundidesulfovibrio. Growth of SG127T was observed at 20-37 °C (optimum, 30 °C), pH 5.5-9.0 (optimum, 7.0-8.0) and with 0-0.2 % (w/v) NaCl (optimally without NaCl). SG127T contained MK-7 as the only menaquinone and anteiso-C15 : 0, anteiso-C17 : 1ω9c, C18 : 0, iso-C14 : 0, iso-C15 : 0, iso-C16:0, iso-C16 : 1H, iso-C18 : 1H and summed feature nine as the major fatty acids. The genomic DNA G+C content of SG127T was 64.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SG127T and the closely related Fundidesulfovibrio magnetotacticus were 78.5% and 23.2 %, respectively, which were lower than the cut-off values (ANI 95-96% and dDDH 70 %) for prokaryotic species delineation. SG127T had desulfoviridin, possessed nitrogen fixation genes (nifHDK) and actively fixed nitrogen according to the acetylene reduction assay. On the basis of these results, strain SG127T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio terrae sp. nov. is proposed. The type strain is SG127T (= GDMCC 1.3137T = JCM 35589T).

Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil.

Four novel bacterial strains, designated RBB1W86T, RXD159T, RBB189T and RLT163T, were isolated from subtropical forest soil of the Nanling National Nature Reserve located in Guangdong Province, PR China. 16S rRNA gene phylogeny indicated their affiliation to the genus Dyella, among which strains RBB1W86T and RXD159T were closely related to Dyella halodurans CGMCC 1.15435T with 16S rRNA gene sequence similarities of 98.8 and 99.5 %, respectively, and strains RBB189T and RLT163T were closely related to Dyella tabacisoli CGMCC 1.16273T (98.8 %) and Dyella japonica JCM 21530T (99.4 %), respectively. Phylogenomic analysis based on 92 core genes showed consistent phylogeny with the 16S rRNA gene phylogeny for strains RBB1W86T, RBB189T and RLT163T, while strain RXD159T showed a closer relationship with D. tabacisoli CGMCC 1.16273T and strain RBB189T. The genome-derived average nucleotide identity (ANI) values between the newly isolated strains and their closely related species were 70.18‒90.20 %, and the corresponding digital DNA-DNA hybridization (dDDH) values were 20.80‒40.30 %. Meanwhile, the ANI and dDDH values between each pair of the newly isolated strains were 75.80‒79.77 % and 21.30‒23.30 %, respectively. They all took iso-C15 : 0 and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1 ω9c) as the major fatty acids. Moreover, C16 : 0, iso-C16 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) were also variously distributed as major components. They all took ubiquinone 8 as the only predominant respiratory quinone and phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Phosphatidylmethylethanolamine was only present in strain RBB189T as another major component. Based on the results of phenotypic, genotypic and chemotaxonomic analyses, the newly isolated strains could be clearly distinguished from their closely related species and should represent four distinct novel species of the genus Dyella, for which the names Dyella humicola sp. nov. (type strain RBB1W86T=GDMCC 1.1901T=KACC 21988T), Dyella subtropica sp. nov. (type strain RXD159T=GDMCC 1.1902T=KACC 21989T), Dyella silvatica sp. nov. (type strain RBB189T=GDMCC 1.1900T=KACC 21990 T) and Dyella silvae sp. nov. (type strain RLT163T=GDMCC 1.1916T=KACC 21991T) are proposed.

Desulfatitalea alkaliphila sp. nov., an alkalipilic sulfate- and arsenate- reducing bacterium isolated from a terrestrial mud volcano.

A novel alkaliphilic sulfate-reducing bacterium, strain M08butT, was isolated from a salsa lake of terrestrial mud volcano (Taman Peninsula, Russia). Cells were rod-shaped, motile and Gram-stain-negative. The temperature range for growth was 15-42°C (optimum at 30°C). The pH range for growth was 7.0-11.0, with an optimum at pH 8.5-9.0 Strain M08butT used sulfate, thiosulfate, sulfite, dimethyl sulfoxide and arsenate as electron acceptors. Acetate, formate, butyrate, fumarate, succinate, glycerol and pyruvate were utilized as electron donors with sulfate. Fermentative growth was observed with fumarate, pyruvate, crotonate. Strain M08butT grew chemolithoautotrophically with H2 and CO2. The G + C content of the genomic DNA was 60.1%. The fatty acid profile of strain M08butT was characterized by the presence of anteiso-C15:0 as the major component (68.8%). The closest phylogenetic relative of strain M08butT was Desulfatitalea tepidiphila (the order Desulfobacterales) with 96.3% 16S rRNA gene sequence similarity. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M08butT is considered to represent a novel species of the genus Desulfatitalea, with proposed name Desulfatitalea alkaliphila sp. nov. The type strain of Desulfatitalea alkaliphila is M08butT (= KCTC 25382T = VKM B-3560T = DSM 113909T = JCM 39202T = UQM 41473T).

Cellulosimicrobium fucosivorans is a later heterotypic synonym of Cellulosimicrobium composti.

The taxonomic relationship of Cellulosimicrobium fucosivorans SE3T and Cellulosimicrobium composti BIT-GX5T was re-evaluated. The type strains of the two species shared 99.9 % 16S rRNA gene sequence similarity, and whole genome sequence comparisons showed that the two species shared a 86.3 % digital DNA‒DNA hybridization (dDDH) value, a 98.5 % average nucleotide identity (ANI) score and a 98.2 % average amino acid identity (AAI) value. These values were higher than the recommend novel species recognition threshold values of 16S rRNA gene similarity of 98.6 %, dDDH cutoff value of 70 %, and ANI and AAI cutoff values of 95-96 %. In addition, the phylogenetic tree based on the 16S rRNA gene sequences as well as the phylogenomics tree based on whole genomes supported these two strains being closely related. Based on the principle of priority, we propose that Cellulosimicrobium fucosivorans is a later heterotypic synonym of Cellulosimicrobium composti.

Marinobacter panjinensis sp. nov., a moderately halophilic bacterium isolated from sea tidal flat environment.

Two moderately halotolerant bacterium strains, designated PJ-16T and PJ-38, were isolated from a tidal flat of the red beach in Panjin City, Liaoning Province, PR China. Cells were found to be Gram-stain-negative, aerobic, motile, rod-shaped with a single polar flagellum. Optimum growth of strain PJ-16T occurred at 30 °C, pH 7.0 and 0.2-8.0 % (w/v) NaCl, and strain PJ-38 at 30 °C, pH 6.0-7.0 and 0.2-8.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PJ-16T was most closely related to Marinobacter denitrificans KCTC 62941T (99.2 % 16S rRNA gene sequence similarity), Marinobacter algicola DSM 16394T (98.6 %), Marinobacter salarius JCM 19399T (98.4 %) and Marinobacter confluentis KCTC 42705T (98.2 %), and strain PJ-38 was most closely related to M. denitrificans KCTC 62941T (99.1 %), M. algicola DSM 16394T (98.6 %), M. salarius JCM 19399T (98.4 %) and M. confluentis KCTC 42705T (98.1 %). The G+C content of the genomic DNA of strain PJ-16T based on its draft genomic sequence was 57.4 mol%. The major cellular fatty acids of strain PJ-16T were C16 : 0, C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω9c. The major respiratory quinone of PJ-16T was ubiquinone-9 and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The results of the phenotypic, phylogenetic and genomic analyses revealed that strains PJ-16T and PJ-38 represent a novel species of the genus Marinobacter, and the name Marinobacter panjinensis sp. nov. is proposed. The type strain is PJ-16T (= CGMCC 1.13694T= KCTC 72023T).

Sulfurospirillum oryzae sp. nov., A Novel Nitrogen-Fixing Bacterium Isolated from Paddy Soil

An anaerobic, Gram-staining-negative, rod shaped, nitrogen-fixing strain designed SG202T, was isolated from paddy soil collected from Fujian Province in China. Strain SG202T showed the highest 16S rRNA gene sequence similarity with the type strain Sulfurospirillum multivorans DSM 12446T (98.5%). Phylogenetic trees based on 16S rRNA gene sequences and conserved core genes from genomes indicated that strain SG202T branched with members of the genus Sulfurospirillum. Growth was observed at 25-37 °C (optimum 30 °C), pH 6.0-10.5 (optimum 7.5), and 0-0.6% (w/v) NaCl (optimum 0.2%). Strain SG202T contained MK-6 as the menaquinone and C16:1ω7c (40.6%), C16:0 (33.3%), C18:1ω7c (13.6%) and C14:0 (9.0%) as the major fatty acids. The genomic DNA G+C content was 39.0%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG202T and its closely related species S. multivorans DSM 12446T, Sulfurospirillum halorespirans DSM 13726T, Sulfurospirillum arsenophilum DSM 10659T and Sulfurospirillum diekertiae ACSDCET were 81.3, 81.5, 84.4, 82.2% and 24.5, 24.5, 27.9, 25.2%, respectively. All these values were lower than the recommended species delineation thresholds of ANI (95-96%) and dDDH (70%). Strain SG202T possessed core genes (nifHDK) of nitrogen fixation, and nitrogenase activities (3470.45 μmol C2H4 g-1 protein h-1) was examined using the acetylene reduction assay. Based on the observed physiological properties, chemotaxonomic characteristics and genome analysis, strain SG202T is recognized as a novel species of the genus Sulfurospirillum, for which the name Sulfurospirillum oryzae sp. nov. is proposed. The type strain is SG202T (= GDMCC 1.3379T= JCM 35596T).

Micromonospora solifontis sp. nov., an actinobacterium isolated from hot spring soil.

An actinobacterium strain, PPF5-17T, was isolated from hot spring soil collected from Chiang Rai province, Thailand. The strain exhibited morphological and chemotaxonomic properties similar to those of members of the genus Micromonospora. Colonies of PPF5-17T were strong pinkish red and turned black after sporulation in ISP 2 agar medium. Cells formed single spores directly on the substrate mycelium. Growth was observed from 15 to 45 °C and at pH 5-8. Maximum NaCl concentration for growth was 3 % (w/v). PPF5-17T was found to have meso-diaminopimelic acid, xylose, mannose and glucose in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides were observed as the membrane phospholipids. MK-10(H6), MK-9(H6), MK-10(H4) and MK-9(H4) were the major menaquinones. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0. PPF5-17T shared the highest 16S rRNA gene sequence similarity with Micromonospora fluminis LMG 30467T (99.3 %). A genome-based taxonomic study revealed that PPF5-17T was closely related to Micromonospora aurantinigra DSM 44815T in the phylogenomic tree with an average nucleotide identity by blast (ANIb) of 87.7 % and a digital DNA-DNA hybridization (dDDH) value of, 36.1 % which were below the threshold values for delineation of a novel species. Moreover, PPF5-17T could be distinguished from its closest neighbours, M. fluminis LMG 30467T and M. aurantinigra DSM 44815T, with respect to a broad range of phenotypic properties. Thus, PPF5-17T represents a novel species, for which the name Micromonospora solifontis sp. nov. is proposed. The type strain is PPF5-17T (= TBRC 8478T = NBRC 113441T).

Lederbergia citrea sp. nov., isolated from citrus rhizosphere.

Three Gram-positive-staining strains FJAT-49754T, FJAT-49682 and FJAT-49731 were isolated from the citrus rhizosphere soil sample. These strains showed the highest 16S rRNA gene sequence similarity with the type strain of Lederbergia panacisoli (97.8-97.9 %). The 16S rRNA gene sequence similarities between strains FJAT-49754T, FJAT-49682, and FJAT-49731 were 99.9 %. The average nucleotide identity (ANI) values between strains FJAT-49754T, FJAT-49682 and FJAT-49731 were above 96 %, while the ANI values with the members of the genus Lederbergia were below 95 %, which were below the cut-off level for prokaryotic species delineation. The above results suggest that strains FJAT-49754T, FJAT-49682 and FJAT-49731 belong to a novel species of the genus Lederbergia. Growth of strain FJAT-49754T was observed at 10-40 °C (optimum at 30 °C, pH 6.0-10.0 (optimum at pH 8.0), and NaCl tolerance up to 7 % (w/v) (optimum at 1 %). MK-7 was the only menaquinone detected in strain FJAT-49754T, and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids of strain FJAT-49754T were anteiso-C15 : 0, iso-C15 : 0, and C16 : 0. The genomic DNA G+C content of strain FJAT-49754T was 38.7 %. Based on the above results, strain FJAT-49754T represents a novel species of the genus Lederbergia, for which the name Lederbergia citrea sp. nov., is proposed. The type strain is FJAT-49754T (=CCTCC AB 2019211T=LMG 31589T).

Genome analysis-based union of the genera Youhaiella and Paradevosia, and proposal that Methyloterrigena soli Kim et al. 2016 is a later heterotypic synonym of Paradevosia shaoguanensis Geng et al. 2015.

Phylogenetic tree analysis of Youhaiella tibetensis F4T, Paradevosia shaoguanensis J5-3T and Methyloterrigena soli M48T based on 16S rRNA gene sequences revealed that the three genera did not form distinct and independent monophyletic clusters. The 16S rRNA gene sequence similarities were all higher than 99 % between each pair of the three type strains. Average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and 16S rRNA gene sequence similarity between Paradevosia shaoguanensis J5-3T and Methyloterrigena soli M48T showed that they represented the same species. Physiological and biochemical characteristics of these three strains were similar, such as motility by polar flagella, major respiratory quinone, polar lipids, and fatty acids. Polygenetic trees and other characteristic comparative analysis revealed the need to merge the genera Youhaiella and Paradevosia into one genus.