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 ß-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.

Chitinophaga chungangae sp. nov., isolated from a Korean grape garden and its potential to biosynthesize ginsenoside Rg2.

A ginsenoside Rg2-producing, Gram stain-negative, aerobic, catalase and oxidase-positive, rod-shaped, non-motile and orange pigmented novel bacterium designated strain MAH-28 T was isolated from soil sample of a grape garden. Strain MAH-28 T hydrolyzed aesculin, casein and DNA. Flexirubin-type pigments are present. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MAH-28 T formed a cluster within the genus Chitinophaga and the most close relatives were Chitinophaga alhagiae T22T (98.9% 16S rRNA gene sequence similarity), Chitinophaga humicola Ktm-2 T (98.8%), Chitinophaga barathri YLT18T (98.3%) and Chitinophaga lutea ZY74T (97.4%). The novel strain MAH-28 T has a draft genome size of 6,043,180 bp (14 contigs), annotated with 4,863 protein-coding genes, 53 tRNA and 6 rRNA genes. The ANI and dDDH values between strain MAH-28 T and the closely related type strains were in the range of 76.0-83.4% and 20.3-26.7%, respectively. The novel strain MAH-28 T was able to synthesize ginsenoside Rg2 from major ginsenoside Re. The genome annotation revealed 152 carbohydrate genes which may involve with the synthesis of ginsenoside Rg2. The respiratory quinone of strain MAH-28 T was MK-7 and the dominant cellular fatty acids were C15:0 iso, C16:1 ω5c and C17:0 iso 3-OH. The DNA G + C content of strain MAH-28 T was 53.3 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic studies, strain MAH-28 T represents a new member of genus Chitinophaga for which the name Chitinophaga chungangae sp. nov. is proposed with type strain MAH-28 T (= KACC 19968 T = CGMCC 1.16605 T).

Sphingomonas horti sp. nov., a novel bacterial species isolated from soil of a tomato garden.

A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical, and 0.2-0.7 mm in diameter when grown on Luria-Bertani agar for 2 days. Strain MAH-20T grows at 15-40 °C (optimum growth temperature 30-32 °C), at pH 5.0-10.0 (optimum growth pH 7.0) and at 0-2.0% NaCl. The strain showed positive activity for both oxidase and catalase tests. Cells were able to hydrolyze starch, DNA, urea, gelatin, L-arginine, and Tween 20. According to the 16S rRNA gene sequence similarity, the strain MAH-20T was identified as a new member of the genus Sphingomonas and had the close sequence similarity with Sphingomonas changbaiensis V2M44T (98.9%) and Sphingomonas tabacisoli X1-8T (98.1%). The genomic ANI value between strain MAH-20T and S. changbaiensis NBRC 104936T was 84.4%. The novel strain MAH-20T has a draft genome size of 3,350,026 bp (25 contigs), annotated with 3210 protein-coding genes, 46 tRNA, and 3 rRNA genes. The genomic DNA G + C content of isolate was 67.3 mol%, the predominant quinone was ubiquinone 10 and the major fatty acids were C16:0, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). On the basis of DNA-DNA hybridization results, phenotypic, genotypic, and chemotaxonomic data, the isolated strain MAH-20T represents a novel species, for which the name Sphingomonas horti sp. nov. is proposed, with MAH-20T as the type strain (= KACC 19746T = CGMCC1.13658T).

Flavobacterium agri sp. nov., a novel bacterial species isolated from rhizospheric soil of Coriandrum sativum.

A Gram-stain-negative, strictly aerobic, cream yellow colored, non-motile, rod-shaped bacterial strain, designated MAH-1T was isolated from rhizospheric soil of Coriandrum sativum. A polyphasic taxonomic study was performed on the isolated strain. Optimal growth occurred at 28-30 °C, pH 6.5 and 0% NaCl. The strain showed activity for both catalase and oxidase tests. Cell growth occurs on R2A agar, nutrient agar and Luria-Bertani agar. Cells were able to hydrolyze starch, aesculin, gelatin, and Tween 20. Alignment of 16S rRNA gene sequences indicated that strain MAH-1T was associated with the genus Flavobacterium and was most closely related to Flavobacterium longum YIT 12745T (94.5% sequence similarity) and Flavobacterium caeni LM5T (93.0%). Strain MAH-1T had a genome size of 3,975,600 bp. Genome contained 67 contigs encoded by 3,522 protein-coding genes with 38 tRNA and 6 rRNA genes. The genomic DNA G + C contents of strain MAH-1T was 47.1 mol %. The genomic ANI and dDDH values between strain MAH-1T and one of the close relatives F. caeni LM5T were 72.2 and 18.8%, respectively. The major fatty acids were C15:0 iso, C16:0 iso and C15:0 anteiso. The predominant respiratory quinone was menaquinone 6 (MK-6). Based on physiological, biochemical and phylogenetic data for this isolate, it was confirmed that strain MAH-1T was affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium agri sp. nov. is proposed. The type strain is MAH-1T (= KACC 19300T = CGMCC 1.16617T).

Fluviicola chungangensis sp. nov., a bacterium isolated from rice field.

A Gram-stain negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-3T, was isolated from soil sample of a rice field. The colonies were orange pigmented, smooth, circular and 0.4-0.9 mm in diameter when grown on R2A agar for 3 days. Strain MAH-3T was found to grow at 10-40 °C (optimum 30 °C), pH 6.0-8.0 (optimum 7.0) and in the presence of 0-1.0% NaCl (optimum 0%). Cell growth occurs on R2A agar and Luria-Bertani agar, but not on nutrient agar, tryptone soya agar and MacConkey agar. Cells were positive for catalase test but negative for oxidase test. Cells were able to hydrolyze casein, gelatin, DNA and Tween 80. 16S rRNA gene sequence analysis revealed that strain MAH-3T was most closely related to the genus Fluviicola and exhibited the highest sequence similarity to Fluviicola hefeinensis MYL-8T (97.4%), Fluviicola taffensis RW262T (96.2%) and Fluviicola kyonggii CA-1T (95.6%). Strain MAH-3T had a genome size of 4,271,694 bp and the genomic DNA G + C content was determined to be 41.7 mol%. The genome contained 19 contigs encoded by 3,664 protein-coding genes with 34 tRNA and 4 rRNA genes. The genomic ANI value between strain MAH-3T and one of the closely related type strains, F. taffensis DSM 16823T was 76.2%. The predominant isoprenoid quinone of isolated strain MAH-3T was menaquinone-6 (MK-6). The major fatty acids were identified as C15:0 iso, C15:0 2OH and C17:0 iso 3OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies and DNA-DNA hybridization results, the isolated strain MAH-3T represents a novel species, for which the name Fluviicola chungangensis sp. nov. is proposed, with MAH-3T as the type strain (= KACC 19742T = CGMCC 1.13750T).

Mucilaginibacter corticis sp. nov., isolated from bark of Pinus koraiensis.

A gram-stain negative, aerobic, non-motile and rod-shaped novel bacterial strain, designated MAH-19T, was isolated from bark of Pinus koraiensis. The colonies were observed to be light pink coloured, smooth, circular and 0.3-0.7 mm in diameter when grown on R2A agar for 2 days. Strain MAH-19T was found to be able to grow at 10-35 °C (optimum 28-30 °C), at pH 6.0-8.0 (optimum 7.0) and at 0-0.5% NaCl (optimum 0%). Cell growth occurs on nutrient agar and R2A agar. The strain was found to be positive for both catalase and oxidase tests. Cells are able to hydrolyse aesculin and Tween 20, but not casein, gelatin, starch, L-tyrosine, DNA, L-arginine, urea or Tween 80. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Mucilaginibacter and to be closely related to Mucilaginibacter panaciglaebae BXN5-31T (97.4% similarity), Mucilaginibacter antarcticus S14-88T (97.2%) and Mucilaginibacter ximonensis XM-003T (97.1%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-19T and its close phylogenetic neighbours was below 45.0%. The novel strain MAH-19T has a draft genome size of 5,335,442 bp (14 contigs), annotated with 4963 protein-coding genes, 44 tRNA and 6 rRNA genes. The genomic DNA G+C content was determined to be 42.7 mol%. The predominant isoprenoid quinone of strain MAH-19T was identified as MK-7. The major fatty acids were identified as C15:0 iso and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c). The DNA-DNA hybridization results and results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain MAH-19T represents a novel species within the genus Mucilaginibacter, for which the name Mucilaginibacter corticis sp. nov. is proposed, with MAH-19T (= KACC 19745T = CGMCC1.13657T) as the type strain.

Sphingobium chungangianum sp. nov., isolated from rhizosphere of Pinus koraiensis.

A novel Gram-staining negative, yellow-pigmented, non-motile, aerobic and rod-shaped bacterium, designated MAH-11T, was isolated from rhizosphere of Pinus koraiensis and was characterised by using a polyphasic taxonomic approach. The colonies were smooth, circular and 0.3-1.0 mm in diameter when grown on R2A agar for 3 days. The strain was positive for both catalase and oxidase tests. Optimum growth temperature and pH were 28-30 °C and 7.0, respectively. Cell growth occurs on R2A agar, nutrient agar, Luria-Bertani agar and tryptone soya agar but not on MacConkey agar. The novel strain was found to be able to hydrolyse esculin but not casein, gelatin, starch, L-tyrosine, DNA, L-arginine, urea, Tween 20 and Tween 80. On the basis of 16S rRNA gene sequence analysis, strain MAH-11T belongs to the genus Sphingobium and is closely related to Sphingobium quisquiliarum P25T (98.1%), Sphingobium vermicomposti VC-230T (97.8%), Sphingobium mellinum WI4T (97.5%), Sphingobium barthaii KK22T (97.2%) and Sphingobium fuliginis TKPT (97.2%). In DNA-DNA hybridization tests, the DNA relatedness values between strain MAH-11T and its close phylogenetic neighbors were below 45.0%. The DNA G+C content was 64.5 mol% and the predominant respiratory quinone was identified as ubiquinone-10. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The DNA-DNA hybridization results in combination with chemotaxonomic and physiological data demonstrated that strain MAH-11T represents a novel species within the genus Sphingobium, for which the name Sphingobium chungangianum is proposed. The type strain is MAH-11T (= KACC 19836T = CGMCC 1.13749T).

Mucilaginibacter formosus sp. nov., a bacterium isolated from road-side soil.

A Gram-stain negative, aerobic, non-motile and rod-shaped novel bacterial strain, designated as MAH-5T, was isolated from a road-side soil sample and was characterised by using a polyphasic taxonomic approach. The colonies were observed to be yellowish orange in colour, smooth, circular and 0.3-0.7 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-5T was found to be able to grow at 15-35 °C and at pH 4.0-8.0. The strain was observed to be positive for both the catalase and oxidase tests. Cells were found to be able to hydrolyse aesculin, gelatin and starch. By 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Mucilaginibacter and to be closely related to Mucilaginibacter panaciglaebae BXN5-31T (98.35%), Mucilaginibacter soyangensis HME6664T (97.82%), Mucilaginibacter antarcticus S14-88T (97.49%) and Mucilaginibacter ximonensis XM-003T (97.06%). In DNA-DNA hybridization tests, the DNA relatedness values between strain MAH-5T and its close phylogenetic neighbors were below 45.0%. The genomic DNA G + C content of strain MAH-5T was determined to be 41.5 mol% and the predominant isoprenoid quinine was identified as MK-7. The major fatty acids were identified as C15:0 iso and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c). The genetic characteristics, in combination with chemotaxonomic and physiological data, demonstrated that the isolated strain MAH-5T represents a novel species within the genus Mucilaginibacter, for which the name Mucilaginibacter formosus sp. nov. is proposed, with MAH-5T as the type strain (= KACC 19291T = CGMCC1.16489T).

Microvirga rosea sp. nov.: a nanoparticle producing bacterium isolated from soil of rose garden.

A Gram-stain negative, aerobic, non-motile, and rod-shaped novel bacterial strain, designated MAH-2T, was isolated from a soil sample of rose garden and was characterized using a polyphasic approach. The colonies were light pink color, smooth, circular and 0.2-0.6 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-2T grows at 15-40 °C (optimum growth temperature 30 °C), at pH 5.0-7.0 (optimum growth pH 6.5) and at 0-2% NaCl (optimum 0-0.5%). Cell growth occurs on nutrient agar and R2A agar but not on tryptone soya agar, luria-bertani agar and MacConkey agar. The strain was positive for both catalase and oxidase tests. The strain was able to synthesis of silver nanoparticles. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Microvirga and was most closely related to Microvirga soli R491T (96.7% sequence similarity), Microvirga subterranea Fail4T (96.4%), Microvirga guangxiensis 25BT (96.0%) and Microvirga aerophila 5420S-12T (95.9%). The genomic DNA G + C content of isolated strain was determined to be 62.5 mol% and the predominant isoprenoid quinone was Q-10. The major fatty acids were identified as summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c) and C19:0 cyclo ω8c. On the basis of these phenotypic, genotypic, and chemotaxonomic studies and DNA-DNA hybridization results, the isolated strain MAH-2T represents a novel species, for which the name Microvirga rosea sp. nov. is proposed, with MAH-2T as the type strain (= KACC 19290T = CGMCC1.16488T).

Sphingobium tyrosinilyticum sp. nov., a tyrosine hydrolyzing bacterium isolated from Korean radish garden.

A yellow-pigmented novel bacterial strain, MAH-12T, was isolated from a soil sample of Korean radish garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, non-motile and rod-shaped. The strain was aerobic, catalase positive, optimum growth temperature and pH were 28-30 °C and 6.0, respectively. The novel strain is able to hydrolyze L-tyrosine, starch, esculin and 4-nitrophenyl-ß-D-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-12T belongs to the genus Sphingobium and is most closely related to several Sphingobium type strains (97.2-97.8%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-12T and its closest phylogenetic neighbors was below 45.0%. The DNA G + C content was 64.0 mol% and the predominant respiratory quinone was ubiquinone-10. The major cellular fatty acids were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C16:0. The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-12T represented a novel species within the genus Sphingobium, for which the name Sphingobium tyrosinilyticum is proposed. The type strain is MAH-12T (= KACC 19297T = CGMCC 1.16225T). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain MAH-12T is KY964278 and the digital protologue database taxon number of strain MAH-12T is TA00463.

Luteibacter pinisoli sp. nov., a casein degrading bacterium isolated from rhizospheric soil of Pinus koraiensis.

A yellow pigmented, Gram-staining negative, motile and rod-shaped novel bacterial strain, designated MAH-14T was isolated from rhizospheric soil and was characterized using a polyphasic approach. The isolated strain was aerobic, oxidase and catalase were positive, optimum growth temperature and pH were 28-30 °C and 6.5, respectively. The novel strain is able to hydrolyze casein, starch, esculin, gelatin, L-tyrosine, DNA, tween 80, tween 20, L-arginine and 4-nitrophenyl-BD-galactopyranoside. On the basis of 16S rRNA gene sequence analysis, strain MAH-14T belongs to the genus Luteibacter and is most closely related to Luteibacter yeojuensis R2A16-10T (98.5%), Luteibacter anthropi CCUG 25036T (98.4%) and Luteibacter rhizovicinus LJ96T (98.3%). In DNA-DNA hybridization experiments, the DNA relatedness between strain MAH-14T and its closest phylogenetic neighbor was below 45.0%. The predominant respiratory quinone and the DNA G + C content of the novel strain were ubiquinone-8 and 63.5 mol%, respectively. The novel strain MAH-14T is able to produce flexirubin-type pigments. The major cellular fatty acids were C15:0 iso, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (C17:1 iso ω9c and/or C16:0 10-methyl). The DNA-DNA hybridization results and results of the genotypic analysis in combination with chemotaxonomic and physiological data revealed that strain MAH-14T represented a novel species within the genus Luteibacter, for which the name Luteibacter pinisoli, is proposed. The type strain is MAH-14T (= KACC 19298T = CGMCC 1.16227T).

Caenispirillum humi sp. nov., a bacterium isolated from the soil of Korean pine garden.

A novel bacterial strain MAH-8T was isolated from a soil sample of a Korean pine garden and was characterized using a polyphasic approach. Cells were Gram-staining negative, pinkish yellow colored, motile and vibrio-shaped. The strain was aerobic and catalase, oxidase positive, optimum growth temperature and pH were 28-30 °C and 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain MAH-8T belongs to the genus Caenispirillum and is most closely related to Caenispirillum bisanense KCTC 12839T (98.14%), Caenispirillum deserti KCTC 42064T (96.35%), and Caenispirillum salinarum JCM 17360T (95.76%). In DNA-DNA hybridization tests, the DNA relatedness between strain MAH-8T and its closest phylogenetic neighbor was below 45.0%. The DNA G + C content was 70.5 mol% and the predominant respiratory quinone was ubiquinone-10. Flexirubin-type pigments were present and the major cellular fatty acids were C18:1 ω7c/C18:1 ω6c, C16:1 ω7c/C16:1 ω6c and C16:0. The results of DNA-DNA hybridization and genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain MAH-8T represented a novel species within the genus Caenispirillum, for which the name Caenispirillum humi, is proposed. The type strain is MAH-8T (= KACC 19294T = CGMCC 1.16224T). The NCBI GenBank Accession Number for the 16S rRNA gene sequence of strain MAH-8T is KY964275.