Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov., isolated from soil and faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau

Two novel strain pairs (HM61T/HM23 and S-34T/S-58) were isolated from soil and the faeces of Tibetan antelope (Pantholops hodgsonii) collected at the Qinghai-Tibet Plateau of PR China. All four new isolates were aerobic, non-motile, Gram-stain-positive, catalase-positive, oxidase-negative, and short rod-shaped bacteria. The results of phylogenetic analysis based on the full-length 16S rRNA genes and 283 core genomic genes indicated that the four strains were separated into two independent branches belonging to the genus Nocardioides. Strains HM61T and HM23 were most closely related to Nocardioides pelophilus THG T63T (98.58 and 98.65 % 16S rRNA gene sequence similarity). Strains S-34T and S-58 were most closely related to Nocardioides okcheonensis MMS20-HV4-12T (98.89 and 98.89 % 16S rRNA gene sequence similarity). The G+C contents of the genomic DNA of strains HM61T and S-34T were 70.6 and 72.5 mol%, respectively. Strains HM61T, S-34T and the type strains of closely related species in the analysis had average nucleotide identity values of 75.4-90.5 % as well as digital DNA-DNA hybridization values between 20.1 and 40.8 %, which clearly indicated that the four isolates represent two novel species within the genus Nocardioides. The chemotaxonomic characteristics of strains HM61T and S-34T were consistent with the genus Nocardioides. The major fatty acids of all four strains were iso-C16 : 0, C17 : 1  ω8c or C18 : 1  ω9c. For strains HM61T and S-34T, MK-8(H4) was the predominant respiratory quinone, ll-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan, and the polar lipids profiles were composed of diphosphatidylglycerol and phosphatidylglycerol. Based on phylogenetic, phenotypic, and chemotaxonomic data, we propose that strains HM61T and S-34T represent two novel species of the genus Nocardioides, respectively, with the names Nocardioides bizhenqiangii sp. nov. and Nocardioides renjunii sp. nov. The type strains are HM61T (=GDMCC 4.343T=JCM 36399T) and S-34T (=CGMCC 4.7664T=JCM 33792T).

Roseateles subflavus sp. nov. and Roseateles aquae sp. nov., isolated from artificial pond water and Roseateles violae sp. nov., isolated from a Viola mandshurica root

Two novel strains, designated APW6T and APW11T, were isolated from artificial pond water, and one novel strain, designated PFR6T, was isolated from a Viola mandshurica root. These strains were found to be Gram-negative, rod-shaped, motile by means of flagella, and oxidase-positive. Growth conditions of the type strains were as follows: APW6T, 15-43 °C (optimum, 28 °C), pH 6.0-12.0 (optimum, pH 7.0), with no salinity; APW11T, 4-35 °C (optimum, 25 °C), pH 6.0-11.0 (optimum, pH 9.0), with 0-1 % NaCl (w/v, optimum 0 %); PFR6T, 10-38 °C (optimum 28 °C), pH 6.0-12.0 (optimum, pH 7.0), with 0-2 % NaCl (w/v; optimum, 0 %). Strains APW6T, APW11T, and PFR6T belonged to the genus Roseateles, having the most 16S rRNA gene sequence similarity to Roseateles saccharophilus DSM 654T (98.1 %), Roseateles oligotrophus CHU3T (98.7 %), and Roseateles puraquae CCUG 52769T (98.1 %). The estimated genome sizes of APW6T, APW11T, and PFR6T were 50 50 473, 56 70 008, and 52 16 869 bp, respectively and the G+C contents were 69.5, 66, and 68.5 mol%. The digital DNA-DNA hybridization, average amino acid identity, and average nucleotide identity values among the novel strains and related taxa were all lower than 22.4, 74.7, and 78.9 %, respectively. The predominant cellular fatty acids (>10 %) of all strains were summed feature 3 (comprising C16 : 1  ω6c and/or C16 : 1  ω7c) and C16 : 0. PFR6T also had summed feature 8 (comprising C18 :  1  ω7c and/or C18 :  1  ω6c) as a major fatty acid. The polar lipid profile of all strains contained phosphatidylethanolamine, phosphoaminoglycolipid, and phosphoglycolipid. The distinct phylogenetic, physiological, and chemotaxonomic features reported in this study indicate that strains APW6T, APW11T, and PFR6T represent novel species within the genus Roseateles, for which the names Roseateles subflavus sp. nov., with the type strain APW6T (=KACC 22877T=TBRC 16606T), Roseateles aquae sp. nov., with the type strain APW11T (=KACC 22878T=TBRC 16607T), and Roseateles violae sp. nov (=KACC 23257T=TBRC 17653T) are respectively proposed.

Pedobacter rhodius sp. nov. and Pedobacter punctiformis sp. nov., isolated from soil

Two Gram-staining negative, catalase- and oxidase-positive, pinkish-colored and rod-shaped strains, designated SJ11T and HCMS5-2 T, were isolated from soil in South Korea. The growth of strain SJ11T was observed from 15℃ to 35℃ (optimum, 30℃), from pH 6.0 to 11.0 (optimum, pH 6.0-7.0) and with NaCl 0-1% (w/v) (optimum, 0%) and that of strain HCMS5-2 T was observed from 4℃ to 40℃ (optimum, 25℃), from pH 6.0 to pH 8.0 (optimum, pH 7.0) and with NaCl 0-5% (w/v) (optimum, 0-1%). Phylogenetic analysis based on 16S rRNA gene sequences showed that both strains belonged to the genus Pedobacter. Strain SJ11T had the highest 16S rRNA similarities with Pedobacter jejuensis THG-DR3T (98.5%) and strain HCMS5-2 T had the highest similarities with Pedobacter nototheniae 36B243T (98.7%). The digital DNA-DNA hybridization value of strain SJ11T with Pedobacter jejuensis THG-DR3T was 23.6%, with an average nucleotide identity value of 79.6%, and that of strain HCMS5-2 T with Pedobacter nototheniae 36B243T was 26.4%, with an average nucleotide identity value of 83.1%. The predominant cellular fatty acids (> 10%) of SJ11T and HCMS5-2 T were iso-C15:0, summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) and iso-C17:0 3-OH. The genome size of strain SJ11T was approximately 4.7 Mb with a G + C content of 37.7% and that of strain HCMS5-2 T was approximately 4.1 Mb with a G + C content of 36.4%. The major polar lipid and respiratory quinone of SJ11T and HCMS5-2 T were phosphatidylethanolamine and menaquinone NK-7, respectively. Results of this study showed that strains SJ11T and HCMS5-2 T belonged to the genus Pedobacter as novel species, of which the name Pedobacter rhodius sp. nov., with the type strain SJ11T (= KACC 22884 T = TBRC 16597 T) and Pedobacter punctiformis sp. nov., with the type strain HCMS5-2 T (= KACC 22863 T = TBRC 16598 T) were respectively proposed.

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 GCR5T belongs to the genus Planobacterium and is related to Planobacterium taklimakanense NCTC 13490 T (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 5-6 days 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 2,106,200 bp 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 oryzisoli sp. nov. was proposed. The type strain is GCR5T (= KCTC 82713 T = TISTR 2996 T = TBRC 15746 T).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.

Nocardioides pini sp. nov. and Nocardioides pinisoli sp. nov., two novel actinomycetes isolated from Pinus densiflora

Two novel Gram-positive bacteria designated as strains STR2T and STR3T were isolated from the rhizosphere of a Pinus densiflora sample collected from Goyang-si, Republic of Korea. Strains STR2T and STR3T were aerobic, rod shaped, non-sporulated, catalase negative, oxidase negative and non-motile bacteria. They grew at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.0) and in the presence of 0-2% NaCl (optimum, 0 %, w/v). The chemotaxonomic and morphological characteristics of the novel strains were consistent with those of the members of Nocardioides. The phylogenetic analysis of the 16S rRNA gene sequences revealed that STR2T was closely related to N. cavernae YIM A1136T (99.3 %) and N. flavus Y4T (99.1 %), and STR3T was closely related to N. exalbidus DSM 22017T (99.0 %), N. baculatus G10T (98.8 %) and N. hwasunensis HFW-21T (98.7 %). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values of STR2T and STR3T with the most closely related strains that have publicly available whole genomes were 83.1-89.8 %, 80.9-89.6% and 26.2-39.1 %, respectively. The cell-wall peptidoglycan of strain STR2T and STR3T contained ll-diaminopimelic acid as the diagnostic amino acid. The major fatty acids in STR2T and STR3T were iso-C16 : 0 and C17 : 1 ω8c, and the predominant quinone was MK-8(H4). Their polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and other polar lipids. The draft genome sequences showed that the genomic DNA G+C content of STR2T and STR3T were both 72.2 mol%. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that STR2T and STR3T could represent novel Nocardioides species. Their proposed names were as follows: Nocardioides pini sp. nov. for strain STR2T (=KACC 22784T=TBRC 16336T) and Nocardioides pinisoli sp. nov. for strain STR3T (= KACC 22785T=TBRC 16337T).

Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil

Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4^T and GMJ5^T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4^T and GMJ5^T were both positive for catalase and oxidase. Strain PBS4-4^T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5^T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4^T and GMJ5^T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4^T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5^T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C_15 : 0 and summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c). Strain GMJ5^T had one other major fatty acid: iso-C_17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4^T and GMJ5^T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4^T (=KACC 22882^T=TBRC 17052^T) and the type strain of C. gilvum is GMJ5^T (=KACC 22883^T=TBRC 17053^T).

Chryseolinea lacunae sp. nov. and Piscinibacter lacus sp. nov. Isolated from Artificial Pond Water

Two Gram stain-negative bacterial strains designated Jin1^T and Jin2^T were isolated from artificial pond water in the Republic of Korea and investigated in the present study using a polyphasic taxonomic approach. Phylogenetic analysis of the 16S rRNA gene sequences indicated that these two strains belonged to the genera Chryseolinea and Piscinibacter due to their highest similarities with the 16S rRNA gene sequences of Chryseolinea serpens RYG^T (98.7%) and Piscinibacter aquaticus IMCC1728^T (97.1%), respectively. The dDDH and ANI values were 18.1-20.5% and 68.9-76.8% between whole-genome sequences of strain Jin1^T and type trains of the selected taxa, Chryseolinea species, and 20.1-20.2% and 75.5-76.1% between those of strain Jin2^T and the type strains of the selected taxa, Piscinibacter species, respectively. A threshold AAI value of 44.7-64.8% for the species boundary (95-96%) was established for strains Jin1^T, Jin2^T, and type strains of other species involved in the system incidence, which confirms that strains Jin1^T and Jin2^T represent two new species of the genera Chryseolinea and Piscinibacter, respectively. Based on the phylogenetic, chemotaxonomic, and phenotypic analyses, strains Jin1^T and Jin2^T represent novel species of the genera Chryseolinea and Piscinibacter, respectively, for which the names Chryseolinea lacunae sp. nov. (type strain Jin1^T = KCTC 82562^T = NBRC 114837^T) and Piscinibacter lacus sp. nov. (type strain Jin2^T = KCTC 82556^T = NBRC 114838^T) have been proposed.

Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils

Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4^T, JC52^T and PR3^T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4^T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201^T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80^T (97.2/-/18.2±1.2 %). Values for JC52^T with Paenibacillus validus NBRC 15382^T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352^T were 96.1, 72.1 and 19.3 %. Values for PR3^T with Paenibacillus ginsengiterrae DCY89^T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1^T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729^T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C_15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4^T, JC52^T and PR3^T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717^T=JCM 32775^T), Paenibacillus cremeus sp. nov. (=KACC 21221^T=NBRC 113867^T) and Paenibacillus terricola sp. nov. (=KACC 21455^T=NBRC 114385^T), respectively.

Characteristics and Biological Activity of Exopolysaccharide Produced by Lysobacter sp. MMG2 Isolated from the Roots of Tagetes patula

In the present study, exopolysaccharide (EPS) produced by Lysobacter sp. MMG2 (lyEPS) was characterized and purified. The lyEPS-producing strain Lysobacter sp. MMG2 was isolated from the roots of Tagetes patula. When lyEPS was produced in tryptic soy broth with 1% glucose and the lyophilized powder was measured, the yield was found to be 0.67 g/L. The molecular weight (Mw) of lyEPS was 1.01 × 105 Da. Its monosaccharide composition includes 84.24% mannose, 9.73% glucose, 2.55% galactose, 2.77% arabinose, 0.32% xylose, and 0.03% rhamnose. Scanning electron microscopy (SEM) revealed that lyEPS has various round and rough surfaces. Fourier-transform infrared (FTIR) analysis identified its carbohydrate polymer functional groups. Moreover, thermogravimetric analysis of lyEPS revealed two events of mass loss: the first was water loss, which resulted in 3.97% mass loss and the second event occurred at approximately 212 °C. lyEPS could inhibit biofilm-producing pathogenic bacteria without any antimicrobial activity. Furthermore, lyEPS at a concentration of 4 mg/mL could exhibit potent 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical-scavenging activity (89.25%). These results indicate that lyEPS could be a promising candidate for industrial development if its biological activity is further explored.