16S rRNA Gene Sequence Similarity Research Articles

Pseudomonas benzopyrenica sp. nov., isolated from soil, exhibiting high-efficiency degradation of benzo(a)pyrene.

A Gram-negative, yellow-pigmented, aerobic and rod-shaped bacterium, designated as strain BaP3T, was isolated from the soil. Strain BaP3T grew at 16-37℃ (optimum, 30 °C) and pH 6.0-8.0 (optimum, pH 7.0). Additionally, strain BaP3T could tolerate NaCl concentrations in the range 0-6 % (optimum, 1%). Moreover, strain BaP3T was motile by flagella. The phylogenetic analysis of 16S rRNA sequences showed that strain BaP3T belonged to the genus Pseudomonas, and the sequence was most closely related to Pseudomonas oryzihabitans CGMCC 1.3392T and Pseudomonas psychrotolerans DSM 15758T, with 99.66 % sequence similarity. Pseudomonas rhizoryzae RY24T was the next closely related species, exhibiting 99.38 % 16S rRNA gene sequence similarity. The DNA-DNA hybridization and average nucleotide identity values between strain BaP3T and its closely related types were below 50 and 92 %, respectively. Both results were below the cut-off for species distinction. The genomic DNA G+C content of strain BaP3T was 65.30 mol%. The predominant quinone in strain BaP3T was identified as ubiquinone Q-9. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. These results indicated that strain BaP3T represents a novel species in the genus Pseudomonas. The type strain is BaP3T (CCTCC AB 2022379T=JCM 35914T), for which the name Pseudomonas benzopyrenica sp. nov. is proposed.

Psychromarinibacter sediminicola sp. nov., a novel moderately halophilic, metabolically diverse bacterium isolated from a solar saltern sediment, and comparison between members of family Roseobacteraceae.

Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. This study compared and analyzed the phylogenetic, genomic, biochemical, and chemo taxonomical properties of seven species from three genera (Psychromarinibacter, Lutimaribacter, and Maritimibacter) of the family Roseobacteraceae. Moreover, a novel strain, named C21-152T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) between genomes of the novel strain and Psychromarinibacter halotolerans MCCC 1K03203T were 97.19, 78.49, 73.45, and 21.90%, respectively. Genome sequencing of strain C21-152T revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152T was resistant to many antibiotics and had the ability to survive below 13% salinity. This strain had versatile survival strategies in saline environments including salt-in, compatible solute production and compatible solute transport. Some of its physiological features enriched and complemented the knowledge of the characteristics of the genus Psychromarinibacter. Optimum growth of strain C21-152T occurred at 37℃, with 5-6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152T should represent a novel specie of the genus Psychromarinibacter, for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152T (= MCCC 1H00808T = KCTC 92746T = SDUM1063002T).

Description of Tellurirhabdus bombi sp. nov., Isolated from Bumblebee.

A Gram-stain-negative, aerobic, non-motile, and rod-shaped bacterium, designated IE-0392T, was isolated from a bumblebee. The 16S rRNA gene sequence (highest 16S rRNA gene sequence similarity with the type strain of Tellurirhabdus rosea (90.0%) and phylogenetic analysis suggest that strain IE-0392T was a member of the genus Tellurirhabdus. Strain IE-0392T optimally grew at 25℃ and pH 7.0. Menaquinone 7 (MK-7) was the only isoprenoid quinone present in strain IE-0392T. The major fatty acids (> 10%) of strain IE-0392T were iso-C15:0, C16:1 ω5c, and iso-C17:0 3-OH. The polar lipids of strain IE-0392T were phosphatidylethanolamine, phosphatidylserine, unidentified aminophospholipids, unidentified aminolipid, unidentified phospholipid, and unidentified lipids. The genomic DNA G + C content of strain IE-0392T was 48.8%. The amino acid identity (AAI) and the average nucleotide identity (ANI) values suggest that strain IE-0392T is a novel member of the genus Tellurirhabdus. The results suggest that strain IE-0392T represents a novel species of the genus Tellurirhabdus, for which the name Tellurirhabdus bombi sp. nov., is proposed. The type strain is IE-0392T (= GDMCC 1.2794T = JCM 35040T).

Planobacterium oryzisoli sp. nov., a novel bacterium isolated from roots of rice plant.

A Gram-negative, aerobic, short rod-shaped, non-motile, non-spore forming bacterium, designated strain GCR5T, was isolated from soil of paddy field. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GCR5Tbelongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490T (96.1%, 16S rRNA gene sequence similarity). Colonies on R2A were white but they turn into bright yellow after exponential growth. They produce carotenoid pigment after 5-6days of incubation, before that carotenoid pigment was not found. The major isoprenoid quinone was MK-6, and major cellular fatty acids were iso-C15:0, anteiso-C15:0 and iso-C17:0 3OH. Polar lipids include phosphatidylethanolamine, three unidentified phosphoglycolipids, three unidentified glycolipids, one unidentified aminophosphoglycolipid and five unidentified polar lipids. The strain GCR5T was found to have a 2,106,200bp linear genome with G + C content of 43.7%. The ANI, dDDH and AAI values between the strain GCR5T and the type strains of phylogenetically related species were 60.2-71.1%, 19-24.3%, and 60.2-69.6%, respectively. The strain designated GCR5T produced indole acetic acid (IAA) in the presence of tryptophan only, and auxin responsive genes and tryptophan biosynthesis genes were found in its genome. Based on its polyphasic characteristics, strain GCR5T represents a novel species within the genus Planobacterium, for which the name Planobacterium oryzisolisp. nov. was proposed. The type strain is GCR5T (= KCTC 82713T = TISTR 2996T = TBRC 15746T).Repositories: The draft genome and 16S rRNA gene sequences of strain GCR5T have been deposited at GenBank/EMBL/DDBJ under accession numbers JADKYY000000000 and MN955408, respectively.

Pseudokordiimonas caeni gen. nov., sp. nov., isolated from activated sludge.

A bacterial strain designated as LB-31T was isolated from activated sludge. Strain LB-31T was Gram-stain-negative, non-spore-forming and rod-shaped with a single polar flagellum. The isolate grew at 15-37 °C, pH 5.5-8.5 and 0.5-8.5 % (w/v) NaCl. Genome sequencing revealed a genome size of 3.55 Mb, a G+C content of 61.1 mol% and 3222 protein-coding genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LB-31T formed a phyletic lineage that was distinct from the three known genus within the family Kordiimonadaceae. The 16S rRNA gene sequence similarity of strain LB-31T to all recognized bacterial species was no more than 94 %. Average nucleotide identity and digital DNA-DNA hybridization values between strain LB-31T and its phylogenetic neighbours were below 72 and 22 %, respectively. The average amino acid identity values for strain LB-31T and its closed phylogenetic neighbours Kordiimonas and Eilatimonas were below 63%, supporting that strain LB-31T was a member of a novel genus. The predominant respiratory quinone is Q-10, the fatty acid profile predominantly consisted of iso-C17 : 1 ω9c, iso-C17 : 0, iso-C15 : 0 and summed feature 3 (comprising iso-C15 : 02-OH/C16 : 1 ω7c), and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The combined genotypic and phenotypic data show that strain LB-31T represents a novel species of a novel genus in the family Kordiimonadaceae, for which the name Pseudokordiimonas caeni gen. nov., sp. nov. is proposed. The type strain of Pseudokordiimonas caeni is LB-31T (=GDMCC 1.3625T=KCTC 92687T).

Alkalicoccobacillus porphyridii sp. nov., isolated from a marine red alga, reclassification of Shouchella plakortidis and Shouchella gibsonii as Alkalicoccobacillus plakortidis comb. nov. and Alkalicoccobacillus gibsonii comb. nov., and emended description of the genus Alkalicoccobacillus Joshi et al. 2022.

A Gram-stain-positive alkali-tolerant and strictly aerobic bacterium, designated strain P16T, was isolated from a marine red alga, Porphyridium cruentum, in the Yellow Sea, Republic of Korea. Cells were motile rods with peritrichous flagella and exhibited catalase and oxidase activities. The optimal growth of strain P16T was observed to occur at 30 °C and pH 8.0 and in the presence of 2.0 % (w/v) NaCl. Menaquinone-7 was identified as the sole respiratory quinone. Strain P16T contained anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major cellular fatty acids and polar lipids, respectively. The G+C content of strain P16T was 40.8 mol%. Strain P16T was most closely related to Shouchella plakortidis P203T, Shouchella gibsonii DSM 8722T and Alkalicoccobacillus murimartini LMG 21005T with 98.1, 98.1 and 98.0 % 16S rRNA gene sequence similarities, respectively. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that strain P16T, S, plakortidis, S. gibsonii and A. murimartini formed a single phylogenetic lineage cluster, and genomic relatedness analyses showed that they are different species. Based on phylogenetic, phenotypic, chemotaxonomic and molecular features, strain P16T represents a novel species of the genus Alkalicoccobacillus, for which the name Alkalicoccobacillus porphyridii sp. nov. is proposed. The type strain is P16T (=KACC 19520T=JCM 32931T). In addition, S. plakortidis and S. gibsonii are reclassified as Alkalicoccobacillus plakortidis comb. nov. (type strain P203T=DSM 19153T=NCIMB 14288T) and Alkalicoccobacillus gibsonii comb. nov. (type strain PN-109T=ATCC 700164T=DSM 8722T=KCCM 41407T), respectively.

Thiovibrio frasassiensis gen. nov., sp. nov., an autotrophic, elemental sulphur disproportionating bacterium isolated from sulphidic karst sediment, and proposal of Thiovibrionaceae fam. nov.

A novel, autotrophic, mesophilic bacterium, strain RS19-109T, was isolated from sulphidic stream sediments in the Frasassi Caves, Italy. The cells of this strain grew chemolithoautotrophically under anaerobic conditions while disproportionating elemental sulphur (S0) and thiosulphate, but not sulphite with bicarbonate/CO2 as a carbon source. Autotrophic growth was also observed with molecular hydrogen as an electron donor, and S0, sulphate, thiosulphate, nitrate and ferric iron as electron acceptors. Oxygen was not used as an electron acceptor and sulphide was not used as an electron donor. Weak growth was observed with sulphate as an electron acceptor and organic carbon as an electron donor and carbon source. The strain also showed weak growth by fermentation of tryptone. It grew at pH 5.5–7.5 (optimum, pH 7.0), 4–35 °C (optimum, 30 °C) and between 0–1.7 % NaCl. Strain RS19-109T was found to be phylogenetically distinct based on 16S rRNA gene sequence similarity (89.2 %) to its closest relative, Desulfurivibrio alkaliphilus AHT2T. The draft genome sequence for strain RS19-109T had average nucleotide identity, average amino acid identity and in silico DNA–DNA hybridization values of 72.2, 63.0 and 18.3 %, respectively, compared with the genome sequence of D. alkaliphilus AHT2T. On the basis of its physiological and genomic properties, strain RS19-109T is proposed as the type strain of a novel species of a novel genus, Thiovibrio frasassiensis gen. nov., sp. nov. A novel family, Thiovibrionaceae fam. nov., is proposed to accommodate Thiovibrio within the order Desulfobulbales . Strain RS19-109T has been deposited at the DSMZ-German Collection of Microorganisms and Cell Cultures (=DSM 115074T) and the American Type Culture Collection (=ATCC TSD-325T).

Pontibacterium sinense sp. nov., a nitrate-reducing and thiosulphate-oxidizing bacterium, isolated from coastal sediment.

A novel bacterial strain, N1Y112T, was isolated from coastal sediment collected in Weihai, PR China. This Gram-stain-negative, facultatively anaerobic, motile rod-shaped bacterium exhibited the ability to oxidize thiosulphate to sulphate and reduce nitrate to ammonia through its Sox system and nitrate reduction pathway, respectively. The strain grew at 20-35 °C (optimum, 28 °C), pH 6.0-10.0 (optimum, pH 7.5) and in the presence of 1.0-5.0 % (w/v) NaCl (optimum, 3.0 %). Major fatty acids present in the strain included summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. Its polar lipid profile consisted of one phosphatidylethanolamine, two unknown aminolipids, one aminophosphoglycolipid, one diphosphatidylglycerol, one phosphatidylglycerol, two unknown phospholipids and two unknown lipids. Strain N1Y112T contained ubiquinone-7 and ubiquinone-8 as isoprenoid quinones, with a genomic G+C content of 50.6 mol%. Based on phylogenetic analysis, strain N1Y112T clustered with Pontibacterium granulatum JCM 30316T being its closest relative at 97.1 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA-DNA hybridization values were 77.1 and 20.7 %, respectively, which suggest significant differences between genomes of N1Y112T and P. granulatum JCM 30316T. Based on the findings from its phenotypic, genotypic and phylogenetic analyses, N1Y112T is considered to represent a novel species of the genus Pontibacterium, for which the name Pontibacterium sinense sp. nov. is proposed. The type strain is N1Y112T (=KCTC 72927T=MCCC 1H00429T).

Saccharopolyspora oryzae sp. nov., isolated from rhizosphere soil of the wild rice species Oryza rufipogon.

A novel actinobacterium, designated as strain WRP15-2T, was isolated from rhizosphere soil of rice plant (Oryza rufipogon). The strain was Gram-stain-positive, aerobic, and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain WRP15-2T fell into the genus Saccharopolyspora. The strain shared the highest 16S rRNA gene sequence similarity with the type strains Saccharopolyspora kobensis JCM 9109T (99.1%), Saccharopolyspora indica VRC122T (98.9%), and Saccharopolyspora antimicrobica DSM 45119T (98.7%). However, the digital DNA-DNA hybridization and average nucleotide identity values among these strains confirmed that the microorganism represented a novel member of the genus Saccharopolyspora. Chemotaxonomic data revealed that strain WRP15-2T possessed MK-9(H4) as the predominant menaquinone. It contained meso-diaminopimelic acid as the diagnostic diaminopimelic acid and arabinose, galactose, and ribose as predominant whole-cell sugars. The detected phospholipids were dominated by phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxy-phosphatidylmethylethanolamine, and phosphatidylcholine. The predominant cellular fatty acids were iso-C16:0, C16:0, and iso-C15:0. The G + C content of the genomic DNA was 69.5%. Based on these genotypic and phenotypic data, it is supported that strain WRP15-2T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora oryzae sp. nov. is proposed. The type strain is WRP15-2T ( = TBRC 15728T = NBRC 115560T).

Paraburkholderia flagellata sp. nov. and Paraburkholderia adhaesiva sp. nov., two novel species isolated from forest soil in Dinghushan Biosphere Reserve in Guangdong, China.

Two Gram-stain-negative, aerobic, motile and short rod strains, designated 4D117T and ZD32-2T, were isolated from the forest soils. Strains 4D117T and ZD32-2T grew optimally at pH 4.0-6.5, 20-33°C and pH 4.5-7.0, 33°C, respectively, and both at 0.5% (w/v) NaCl concentration. Strains 4D117T and ZD32-2T shared the highest 16S rRNA gene sequence similarity with P. acidiphila 7Q-K02T(99.1%) and P. ferrariae NBRC 106233T (98.7%), respectively. The genome size and G + C contents of strains 4D117T and ZD32-2T were 9,002,095bp, 62.9% and 6,974,420bp, 61.7%, respectively. The dDDH and ANI values between strains 4D117T, ZD32-2T and closely related Paraburkholderia species were in the ranges of 21.9-51.6% and 82.9-94.4%, and 81.7% and 25.4% between themself, respectively. Functional genomic analysis showed both strains were capable of degrading contaminants, such as benzoate, anthranilic acid and catechol for 4D117T, and benzene and catechol for ZD32-2T, indicating that they may have potentials for soil pollutant treatment. The main polar lipids of strains 4D117T and ZD32-2T were phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain 4D117T contained C16:0, C19:0 cyclo ω8c and C18:1 ω7c and/or C18:1 ω6c, while strain ZD32-2T had C16:0 and C17:0 cyclo as their major cellular fatty acids (> 10%). Based on the phenotypic characters and genomic data, strains 4D117T and ZD32-2T represent two novel species of genus Paraburkholderia, for which the names Paraburkholderia flagellata sp. nov. (type strain 4D117T = GDMCC 1.2617T = NBRC 115278T) and Paraburkholderia adhaesiva sp. nov. (type strain ZD32-2T = GDMCC 1.2622T = NBRC 115282T) are proposed.

Faecalibacterium hominis Liu et al. 2023 is a later heterotypic synonym of Faecalibacterium duncaniae Sakamoto et al. 2022.

A strain of the recently validated species Faecalibacterium hominis shares 99.0 % 16S rRNA gene sequence similarity with the type strain of Faecalibacterium duncaniae. The aim of this study was to evaluate the taxonomic relationship between F. hominis and F. duncaniae. F. duncaniae JCM 31915T showed 73.0 % digital DNA-DNA hybridization (dDDH) value with F. hominis JCM 39347T. The average nucleotide identity (ANI) value between these two strains was 96.7 %. These results indicate that F. duncaniae JCM 31915T and F. hominis JCM 39347T represent members of the same species. Based on these data, we propose Faecalibacterium hominis as a later heterotypic synonym of Faecalibacterium duncaniae. An emended description is provided.

Poseidonibacter ostreae sp. nov., Isolated from the Gut of Ostrea from the Seomjin River

Three Gram-negative strains, SJOD-M-6T, SJOD-M-5, and SJOD-M-33, were isolated from Ostrea denselamellosa. These strains are oxidase- and catalase-positive coccoids that thrive aerobically. The three strains shared 100.0% 16S rRNA gene sequence similarity and showed average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 99.7–99.8% and 93.8–96.8%, suggesting that they belonged to the same species. Phylogenetic analysis based on the 16S rRNA gene revealed that all three isolates belong to the genus Poseidonibacter. Their closest neighbors were Poseidonibacter parvus LPB0137T (98.8%), Poseidonibacter antarcticus SM1702T (98.7%), and Poseidonibacter lekithochrous LFT 1.7T (95.5%). However, the ANI and dDDH values between SJOD-M-6T (the representative strain of the novel species) and its closest phylogenetic relatives fell well below the established cut-off values of <95% (ANI) and <70% (dDDH) for species delineation. Furthermore, several phenotypic traits distinguish the novel strains from their closest relatives. Based on the combined genotypic and phenotypic data, strains SJOD-M-6T, SJOD-M-5, and SJOD-M-33 are classified as novel species within the genus Poseidonibacter. We propose the name Poseidonibacter ostreae sp. nov. for this novel species, with the type strain being SJOD-M-6T (=KCTC 72758T = NBRC 114334T = FBCC-B685).

Vogesella aquatica sp. nov. and Vogesella margarita sp. nov., isolated from rivers in Southwest China.

Eight Gram-stain-negative, aerobic, short rod-shaped and motile strains (DC21WT, LYT5WT, LYT10W, LYT16W, LYT22W, LYT23W, LYT24W and SH7W) were isolated from rivers in Southwest China. Comparisons based on the 16S rRNA gene sequences showed that strain DC21WT shared the highest 16S rRNA gene sequence similarity (99.6 %) with Vogesella mureinivorans 389T, strain LYT5WT shared 99.2 % with Vogesella fluminis Npb-07T, and the other isolated strains took Vogesella indigofera DSM 3303T as their most similar strain, respectively. The phylogenetic trees reconstructed based on the 16S rRNA gene sequences also supported that strains V. mureinivorans 389T, V. fluminis Npb-07T and V. indigofera DSM 3303T were the closest neighbours of the isolated strains. The phylogenomic tree showed similar phylogenetic relationships among these strains. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains DC21WT, LYT5WT and other related strains were less than 93.7 and 53.7 %, respectively. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains LYT10W, LYT16W, LYT22W, LYT23W, LYT24W, SH7W and V. indigofera DSM 3303T ranged from 94.8 to 97.2 % and from 59.8 to 74.9 %, respectively. Although these values were located in the transition region of species demarcation, their similar phenotypic, biochemical and genotypic characteristics supported that these six strains should be assigned to the species V. indigofera. Comparative genomic analyses showed that only V. indigofera DSM 3303T harboured 19 genes encoding the Type VI secretion system. Combining above descriptions, strains DC21WT and LYT5WT should represent two independent novel species of the genus Vogesella, for which the names Vogesella aquatica sp. nov. (type strain DC21WT=GDMCC 1.3220T=KCTC 92556T) and Vogesella margarita sp. nov. (type strains LYT5WT=GDMCC 1.3213T=KCTC 92549T) are proposed, respectively.

Chryseobacterium herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau.

A non-motile, Gram-staining-negative, orange-pigmented bacterium called herbae pc1-10T was discovered in Tibet in the soil around Pyrola calliantha H. Andres' roots. The isolate thrived in the temperature range of 10-30 °C (optimal, 25 °C), pH range of 5.0-9.0 (optimum, pH = 6.0), and the NaCl concentration range of 0-1.8% (optimal, 0%). The DNA G+C content of the novel strain was 37.94 mol%. It showed the function of dissolving organophosphorus, acquiring iron from the environment by siderophore and producing indole acetic acid. Moreover, the genome of strain herbae pc1-10T harbors two antibiotic resistance genes (IND-4 and AdeF) encoding a β-lactamase, and the membrane fusion protein of the multidrug efflux complex AdeFGH; antibiotic-resistance-related proteins were detected using the Shotgun proteomics technology. The OrthoANIu values between strains Chryseobacterium herbae pc1-10T; Chryseobacterium oleae CT348T; Chryseobacterium kwangjuense KJ1R5T; and Chryseobacterium vrystaatense R-23566T were 90.94%, 82.96%, and 85.19%, respectively. The in silico DDH values between strains herbae pc1-10T; C. oleae CT348T; C. kwangjuense KJ1R5T; and C. vrystaatense R-23566T were 41.7%, 26.6%, and 29.7%, respectively. Chryseobacterium oleae, Chryseobacterium vrystaatense, and Chryseobacterium kwangjuense, which had 16S rRNA gene sequence similarity scores of 97.80%, 97.52%, and 96.75%, respectively, were its closest phylogenetic relatives. Chryseobacterium herbae sp. nov. is proposed as the designation for the strain herbae pc1-10T (=GDMCC 1.3255 = JCM 35711), which represented a type species based on genotypic and morphological characteristics. This study provides deep knowledge of a Chryseobacterium herbae characteristic description and urges the need for further genomic studies on microorganisms living in alpine ecosystems, especially around medicinal plants.

Mariniradius sediminis sp. nov., a multi-xenobiotics degrading genes harbouring bacterium isolated from sediment of river.

A Gram-stain-negative, strictly aerobic, non-motile, catalase- and oxidase-positive, pink and rod-shaped strain, designated RY-2T, was isolated from sediment of Fuyang River located in Wuqiang County, Hengshui City, Hebei Province, PR China. The strain grew at 25-45 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, pH 7.0) and in the presence of 0-1.5 % (w/v) NaCl (optimum, 1 %). From the phylogenetic analysis of the 16S rRNA gene sequence, strain RY-2T was affiliated to the genus Mariniradius, and had the highest 16S rRNA gene sequence similarity to Mariniradius saccharolyticus JCM 17389T (98.3 %) and the similarity values between strain RY-2T and other type strains was all below 89.3 %. The genome size of strain RY-2T was 4.75 Mb and the DNA G+C content was 46.6 %. Values of digital DNA-DNA hybridization and average nucleotide identity between strain RY-2T and the reference strain were 63.2 and 95.5 %, respectively. The major fatty acids (≥5.0 %) were iso-C15 : 0 (37.9 %), summed feature 9 (8.4 %, iso-C17 : 1 ω9c and/or C16 : 010-methyl), anteiso-C15 : 0 (8.2 %), iso-C17 : 0 3-OH (7.6 %) and summed feature 4 (5.2 %, iso-C17 : 1 I and/or anteiso-C17 : 1 B) and its sole menaquinone was MK-7. The polar lipids consisted of phosphatidylethanolamine, an unknown phosphoglycolipid, an unidentified phospholipid, two unidentified aminolipids, three unidentified glycolipids and nine unidentified lipids. Based on the results of biochemical, physiological, phylogenomic and chemotaxonomic analyses, strain RY-2T is considered to represent a novel species of the genus Mariniradius within the family Cyclobacteriaceae, for which the name Mariniradius sediminis sp. nov. is proposed. The type strain is RY-2T (=GDMCC 1.2781T=JCM 35631T).

Description and genome-wide analysis of Profundicola chukchiensis gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea.

Two Gram-negative, aerobic halophilic non-motile strains designated KMM 9713 and KMM 9724T were isolated from the bottom sediments sampled from the Chukchi Sea in the Arctic Ocean, Russia. The novel strains grew in 0.5-5% NaCl, at 7-42°C, and pH 5.5-10.5. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences revealed that strains KMM 9713 and KMM 9724T were close to each other and shared the highest 16S rRNA gene sequence similarity of 91.28% with the type strain Ornithobacterium rhinotracheale DSM 15997T and 90.15-90.92% with the members of the genus Empedobacter in the family Weeksellaceae. Phylogenetic trees indicated that strains KMM 9713 and KMM 9724T formed a distinct line adjacent to their relative O. rhinotracheale DSM 15997T. The average nucleotide identity values between strain KMM 9724T and O. rhinotracheale DSM 15997T, Empedobacter brevis NBRC 14943T, and Moheibacter sediminis CGMCC 1.12708T were 76.73%, 75.78%, and 74.65%, respectively. The novel strains contained the predominant menaquinone MK-6 and the major fatty acids of iso-C17:0 3-OH, iso-C15:0 followed by iso-C17:1ω6. Polar lipids consisted of phosphatidylethanolamine, one an unidentified aminophospholipid, two unidentified aminolipids, and two or three unidentified lipids. The DNA G+C contents of 34.5% and 34.7% were calculated from genome sequence of the strains KMM 9713 and KMM 9724T, respectively. Based on the phylogenetic evidence and distinctive phenotypic characteristics, strains KMM 9713 and KMM 9724T are proposed to be classified as a novel genus and species Profundicola chukchiensis gen. nov., sp. nov. The type strain of Profundicola chukchiensis gen. nov., sp. nov. is strain KMM 9724T (= KACC 22806T).

Sporolactobacillus mangiferae sp. nov., a spore-forming lactic acid bacterium isolated from tree bark in Thailand.

A Gram-stain-positive, facultatively anaerobic and endospore-forming rod-shaped bacterium, designed strain CPB3-1T, was isolated from tree bark. This homofermentative strain produced dl-lactic acid from glucose. It grew at 20-45 °C, pH 4.0-9.5 and in 0-3.0 % (w/v) NaCl. It contained meso-diaminopimelic acid in cell-wall peptidoglycan and had menaquinone with seven isoprene units (MK-7) as the predominant component. The major fatty acid was anteiso-C17 : 0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown lipid. Based on the results of 16S rRNA gene sequence analysis, strain CPB3-1T belonged to the genus Sporolactobacillus and was closely related to Sporolactobacillus kofuensis DSM 11701T and Sporolactobacillus spathodeae BK117-1T (both 96.7 % similarity), Sporolactobacillus inulinus NRIC 1133T and Sporolactobacillus terrae DSM 11697T (both 96.6 % similarity), and Sporolactobacillus shoreicorticis MK21-7T, Sporolactobacillus laevolacticus DSM 442T, Sporolactobacillus shoreae BK92T and Sporolactobacillus pectinivorans GD201205T (all 95.8-96.5 % similarity). The draft genome of strain CPB3-1T contained 2 930 919 bps with 3117 coding genes. The DNA G+C content was 45.1 mol%. The digital DNA-DNA hybridization values between strain CPB3-1T and closely related type strains were 19.2-24.0 %. The average nucleotide identity (84.0-87.6 %) and average amino acid identity (66.5-76.3 %) values were lower than the cut-off values for species delineation. Strain CPB3-1T was clearly distinguished from related Sporolactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and the results of draft genome analysis. Therefore, the strain represents a novel species of the genus Sporolactobacillus, for which the name Sporolactobacillus mangiferae sp. nov. is proposed. The type strain is CPB3-1T (=JCM 35082T=TISTR 10004T).

Asticcacaulis aquaticus sp. nov., Asticcacaulis currens sp. nov. and Asticcacaulis machinosus sp. nov., isolated from streams in PR China.

Three Gram-stain-negative, aerobic, rod-shaped, stalked and motile strains with a polar flagellum (BYS171WT, DXS10WT and LKC15WT) were isolated from streams in PR China. Comparisons based on 16S rRNA gene sequences showed that strains BYS171WT and DXS10WT had the highest 16S rRNA gene sequence similarities (98.1 and 98.6 %, respectively) to Asticcacaulis excentricus CB 48T, and strain LKC15WT showed 99.6 % similarity to Asticcacaulis endophyticus ZFGT-14T. These three strains showed 16S rRNA gene sequence similarities of less than 96.9 % to other species of the genus Asticcacaulis. A phylogenetic tree reconstructed based on 16S rRNA gene sequences also showed that strains BYS171WT and DXS10WT took A. excentricus CB 48T as their closest neighbour, and strain LKC15WT formed a tight cluster with A. endophyticus ZFGT-14T. The phylogenomic tree also showed that these three strains belong to the genus Asticcacaulis and form a distinct clade with the species of the genus Asticcacaulis. The major cellular fatty acids of these three strains were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and 11-methyl C18 : 1 ω7c. Their polar lipids mainly consisted of phosphatidylglycerol, unidentified glycolipids and nitrogen-containing phosphoglycolipids. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains BYS171WT, DXS10WT, LKC15WT and other related strains were less than 87.2 % and 34.0 %, respectively, indicating that these three strains should represent three independent novel species of the genus Asticcacaulis, for which the names Asticcacaulis aquaticus sp. nov. (type strain BYS171WT=GDMCC 1.3226T=KCTC 92612T), Asticcacaulis currens sp. nov. (type strain DXS10WT=GDMCC 1.3224T=KCTC 92543T) and Asticcacaulis machinosus sp. nov. (type strain LKC15WT=GDMCC 1.3225T=KCTC 92544T) are proposed.

Description and Genomic Characteristics of Weissella fermenti sp. nov., Isolated from Kimchi.

A Gram-positive, non-motile, and non-spore-forming lactic acid bacterium, designated as BK2T, was isolated from kimchi, a Korean traditional fermented vegetable food, and the taxonomic characteristics of strain BK2T, along with strain LMG 11983, were analyzed. Both strains optimally grew at 30°C, pH 7.0, and 1.0% NaCl. Cells of both strains were heterofermentative and facultatively anaerobic rods, demonstrating negative reactions for catalase and oxidase. Major fatty acids (>10%) identified in both strains were C18:1 ω9c, C16:0, and summed feature 7 (comprising C19:1 ω6c and/or C19:1 ω7c). The genomic DNA G+C contents of both strains were 44.7 mol%. The 16S rRNA gene sequence similarity (99.9%), average nucleotide identity (ANI; 99.9%), and digital DNA-DNA hybridization (dDDH; 99.7%) value between strains BK2T and LMG 11983 indicated that they are different strains of the same species. Strain BK2T was most closely related to Weissella confusa JCM 1093T and Weissella cibaria LMG 17699T, with 100% and 99.4% 16S rRNA gene sequence similarities, respectively. However, based on the ANI and dDDH values (92.3% and 48.1% with W. confusa, and 78.4% and 23.5% with W. cibaria), it was evident that strain BK2T represents a distinct species separate from W. confusa and W. cibaria. Based on phylogenetic, phenotypic, and chemotaxonomic features, strains BK2T and LMG 11983 represent a novel species of the genus Weissella, for which the name Weissella fermenti sp. nov. is proposed. The type of strain is BK2T (=KACC 22833T=JCM 35750T).

Rubellimicrobium arenae sp. nov., isolated from desert soil.

Two Gram-stain-negative strains, designated as SYSU D00286T and SYSU D00782, were isolated from a sand sample collected from the Kumtag Desert in Xinjiang, north-west China. Cells were aerobic, non-motile and positive for both oxidase and catalase. Growth occurred at 4-37 °C (optimum, 28-30 °C), pH 6.0-7.0 (optimum, pH 7.0) and NaCl concentration of 0-1.5 % (w/v; optimum, 0%). Growth was observed on Reasoner's 2A agar and nutrient agar, but not on Luria-Bertani agar and trypticase soy agar. The polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-10 and the major fatty acids (>10 %) were C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The 16S rRNA gene sequence similarity between strains SYSU D00286T and SYSU D00782 was 100%, and their average nucleotide identity (ANI), average amino acid identity and (AAI) digital DNA-DNA hybridization (dDDH) values were all 100.0 %. Phylogenetic analysis indicated that these two strains belong to the same species of the genus Rubellimicrobium and show the highest sequence similarity to Rubellimicrobium rubrum KCTC 72461T (98.2 %) and Rubellimicrobium roseum CCTCC AA 208029T (97.5 %). The ANI, AAI and dDDH values between SYSU D00286T (as well as SYSU D00782) and the other five Rubellimicrobium type strains were all less than or equal to 83.2, 80.1 and 23.6 %, respectively. Based on their phylogenetic, phenotypic and chemotaxonomical features, strains SYSU D00286T and SYSU D00782 represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium arenae sp. nov. is proposed. The type strain is SYSU D00286T (=MCCC 1K04981T=CGMCC 1.8626T=KCTC 82271T).