Complete genome sequence of Hymenobacter sp. DG25A, a gamma radiation-resistant bacterium isolated from soil

Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea

Two novel Gram-stain-negative, non-motile, aerobic, rod-shaped, circular, convex, red-colored and UV-tolerant strains BT594^T and BT646^T were isolated from soil collected in Guri city (37° 36' 0″ N, 127° 9' 0″ E) and Gwangju city (37° 22' 0″ N, 127° 17' 0″ E), respectively, South Korea. 16S rDNA sequence analysis indicated that strains BT594^T and BT646^T belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes, kingdom Bacteria). The 16S rDNA gene sequence similarity between the two strains BT594^T and BT646^T was 96.2%. The strain BT594^T was closely related to Hymenobacter psychrotolerans Tibet-IIU11^T (97.0% 16S rDNA gene similarity) and Hymenobacter tibetensis XTM003^T (96.3%). The strain BT646^T was closely related to Hymenobacter psychrotolerans Tibet-IIU11^T (98.6%), Hymenobacter kanuolensis T-3 ^T (96.8%) and Hymenobacter perfusus LMG 26000 ^T (96.7%). The two strains were found to have the same quinone system, with MK-7 as the major respiratory quinone. The major polar lipids of strains BT594^T and BT646^T were phosphatidylethanolamine (PE) and aminophospholipids (APL). The major cellular fatty acids of strain BT594^T were anteiso-C_15:0 (17.9%), iso-C_15:0 (16.1%) and summed feature 3 (C_16:1 ω6c / C_16:1 ω7c) (10.0%). The major cellular fatty acids of strain BT646^T were summed feature 3 (C_16:1 ω6c / C_16:1 ω7c) (18.3%), C_16:0 (17.2%) and summed feature 4 (iso-C_17:1 I / anteiso-C_17:1 B) (14.5%). Based on the polyphasic analysis, strains BT594^T and BT646^T can be suggested as two novel bacterial species within the genus Hymenobacter and the proposed names are Hymenobacter guriensis and Hymenobacter duratus, respectively. The type strain of Hymenobacter guriensis is BT594^T (= KCTC 21863 ^T = NBRC 114853 ^T) and the type strain of Hymenobacter duratus is BT646^T (= KCTC 21915 ^T = NBRC 114854 ^T).

Methylobacterium radiodurans sp. nov., a novel radiation-resistant Methylobacterium

A Gram-negative, aerobic, flagellated, rod-shaped, and pink-pigmented bacterium, strain 17Sr1-43 ^T, was isolated from a soil sample collected in Nowongu, Seoul, Korea. The isolate could grow at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (optimum, pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum, 0%) with aeration. The major cellular fatty acids were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and summed feature 2 (iso-C_16:1 I and/or C_14:0 3-OH). The predominant respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and diphosphatidylglycerol. The G + C content of genomic DNA was 69.1 mol%. Strain 17Sr1-43 ^T was closely related to Methylobacterium gregans KACC 14808 ^T (98.4% 16S rRNA gene sequence similarity), Methylobacterium hispanicum KACC 11432 ^T (97.9%), and Methylobacterium phyllosphaerae CBMB27^T (96.1%). The complete genome of strain 17Sr1-43 ^T contains essential genes related to DNA repair processes including bacterial RecBCD dependent pathway and UmuCD system. Based on the phenotypic, genotypic, and chemotaxonomic characteristics, strain 17Sr1-43 ^T represents a novel species in the genus Methylobacterium, for which the name Methylobacterium radiodurans sp. nov. is proposed. The type strain is strain 17Sr1-43 ^T (= KCTC 52906 ^T = NBRC 112875 ^T).

Hymenobacter busanensis sp. nov., radiation-resistant species isolated from soil in South Korea

Two bacterial strains designated as MA3^T and BT182 were isolated from a soil sample in South Korea. Cells of the two strains were Gram-stain-negative, non-motile, rod-shaped and formed red colonies on R2A agar at 25 °C. The 16S rRNA genes of the two strains shared a sequence similarity of 99.8%. Both strains shared the highest 16S rRNA gene similarity of 96.8% with Hymenobacter edaphi NL^T, followed by Hymenobacter paludis KBP-30^T (96.3%), Hymenobacter coalescens WW84^T (96.3%) and Hymenobacter gummosus ANT-18^T (96.3%). Growth was observed at 15-37 °C (optimum 30 °C), pH 6-8 (optimum pH 7) and in the presence up to 1% NaCl. The genome size of strains MA3^T and BT182 is 4.9 Mb and 4.8 Mb, respectively. The genomic G + C content of both strains is 62.0 mol%. The main polar lipid of the strains was phosphatidylethanolamine, the only respiratory quinone detected was menaquinone-7 and the major fatty acids were anteiso-C_15:0, iso-C_15:0, summed feature 4 (iso-C_17:1 I/anteiso-C_17:1 B) and summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), supporting the affiliation of these strains with the genus Hymenobacter. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, strains MA3^T and BT182 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter busanensis is proposed. The type strain is MA3^T (= KCTC 72631^T = NBRC 114193^T).

Hymenobacter radiodurans sp. nov., isolated from soil in the Republic of Korea

A bacterial strain, designated 17J36-26^T, was isolated from the UV-irradiated soil from Jeju Island, South Korea. Cells are Gram negative, strictly aerobic, non-motile, non-spore forming, rod shaped, and catalase and oxidase positive. The major fatty acids of strain 17J36-26^T were summed feature 4 (17:1 iso I/17:1 anteiso B), summed feature 3 (16:1 ω6c/16:1 ω7c), C_16:1 ω5c and iso-C_15:0. The polar lipid profile contained phosphatidylethanolamine, unidentified aminophospholipid, phospholipids and four unidentified lipids. The G+C content of the strain 17J36-26^T was 62.6 mol%. The 16S rRNA gene sequence analysis showed that strain 17J36-26^T was phylogenetically related to Hymenobacter qilianensis DK6-37^T and Hymenobacter roseosalivarius AA718^T (97.5% and 96.8% sequence similarity, respectively). Strain 17J36-26^T showed resistance to UV radiation. Both average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains 17J36-26^T and type strains of Hymenobacter species were lower than the cut-off (≥ 95-96% for ANI and ≥ 70% for isDDH) to define a bacterial new species. The polyphasic approach using genotypic, phenotypic and chemotaxonomic data showed that strain 17J36-26^T could be distinguished from its phylogenetically related species, and thus, the strain representative of a novel species within the genus Hymenobacter, for which the name Hymenobacter radiodurans sp. nov. (type strain 17J36-26^T = KCTC 62269^T = JCM 33185^T) is proposed.

Azoarcus halotolerans sp. nov., a novel member of Rhodocyclaceae isolated from activated sludge collected in Hong Kong

A floc-forming bacterial strain, designated HKLI-1^T, was isolated from the activated sludge of a municipal sewage treatment plant in Hong Kong SAR, PR China. Cells of this strain were Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 18-37 °C (optimum, 28 °C), pH 5.5-9.0 (optimum, pH 7.5) and with 0-8.0 % (w/v) NaCl (optimum, 1-1.5 %) concentration. The major fatty acids of strain HKLI-1^T were C_16 : 0 and summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c). The polar lipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and three unidentified lipids. The DNA G+C content was 63.5 mol% from whole genomic sequence analysis. Based on the results of 16S rRNA gene sequences analysis, this strain should be assigned to the genus Azoarcus and is closely related to Azoarcus olearius DQS-4^T (94.93 % 16S rRNA gene sequence pairwise similarity), Azoarcus toluclasticus MF63^T (94.91 %) and Azoarcus communis SWub3^T (94.01 %), but separate from them by large distances in different phylogenetic trees. Based on whole genome analysis, the orthologous average nucleotide identity and in silico DNA-DNA hybridization values against four of the closest relatives were 73.03-74.83 and 17.2-23.0 %, respectively. The phylogenetic, genotypic, phenotypic and chemotaxonomic data demonstrated that strain HKLI-1^T could be distinguished from its phylogenetically related species, and that this strain represented a novel species within the genus Azoarcus, for which the name Azoarcus halotolerans sp. nov. is proposed. The type strain is HKLI-1^T (= 72659^T=CCTCC AB 2019312^T).

Rufibacter radiotolerans sp. nov., a novel gamma-radiation-resistant bacterium isolated from rice field

A red-pigmented isolate, designated DG31D^T, was isolated from the soil of a rice field in South Korea. Cells were strictly aerobic, short rod-shaped, Gram-negative, oxidase-positive, and catalase-positive. The major polar lipid was phosphatidylethanolamine (PE), and the predominant respiratory quinone was MK-7. DG31D^T showed high resistance to both the UV and gamma radiations. Based on the 16S rRNA gene sequence, strain DG31D^T was related to Rufibacter immobilis MCC P1^T (97.1%) and Rufibacter tibetensis 1351^T (96.5%). The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between the strain DG31D^T and the related Rufibacter sp. were between 74.1-77.6% and 19.9-21.9%, respectively. Strain DG31D^T grew between 15 and 30 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and tolerated up to 1.0% NaCl (w/v). The major cellular fatty acids of the novel strain were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and C_16:1 ω5c. Flexirubin-type pigments were absent. On the basis of the phenotypic, phylogenetic, and chemotaxonomic data, strain DG31D^T represents a novel species of the genus Rufibacter, for which the name Rufibacter radiotolerans sp. nov. is proposed. The type strain is DG31D^T (= JCM 19446^T = KCTC 32454^T).

Methylobacterium terricola sp. nov., a gamma radiation-resistant bacterium isolated from gamma ray-irradiated soil

A gamma radiation-resistant and pink-pigmented bacterial strain, designated as 17Sr1-39T, was isolated from a gamma ray-irradiated soil sample collected in the Republic of Korea. Cells were Gram-stain-negative, strictly aerobic, flagellated, asporogenous, rod-shaped and methylotrophic. Results of 16S rRNA gene sequence analysis showed that strain 17Sr1-39T was phylogenetically related to Methylobacterium currus PR1016AT (97.3 %), Methylobacterium aquaticum DSM 16371T (97.2 %), Methylobacterium platani PMB02T (97.0 %), Methylobacterium frigidaeris IER25-16T (96.6 %), Methylobacterium terrae 17Sr1-28T (96.6 %) and Methylobacterium organophilum JCM 2833T (93.4 %). The G+C content calculated based on the genome sequence was 70.4 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 17Sr1-39T and M. currus , M. aquaticum , M. platani , M. frigidaeris , M. terrae and M. organophilum were 77.3–89.9 and 22–38.2 %, respectively. The predominant fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the data from phenotypic tests and genotypic differences between strain 17Sr1-39T and its close phylogenetic relatives, strain 17Sr1-39T represented a new species belonging to the genus Methylobacterium , for which the name Methylobacterium terricola sp. nov. (=KACC 52905T=NBRC 112874T) is proposed.

Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island

A novel Gram-stain negative, aerobic, rod-shaped, non-motile and pink-coloured bacterium, designated strain 17J68-5^T, was isolated from soil in Jeju Island, Korea. The strain was found to grow at 18-37 °C (optimum 25 °C) in R2A medium at pH (6.0 to 7.5; optimum 6.5) in the presence of 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 17J68-5^T forms a distinct lineage within the family Hymenobacteraceae and is closely related to Hymenobacter daecheongensis DSM 21074^T (94.9% 16S rRNA gene sequence similarity), Hymenobacter rutilus K2-33028^T (94.6%) and Hymenobacter tibetensis XTM003^T (94.3%). The draft genome sequence of strain 17J68-5^Tis 5.1 Mb size. The calculated average nucleotide identity and the digital DNA-DNA hybridization between strain 17J68-5^T and closely related type strains were 81.3 to 84.1  % and 25.5 to 28.1%. The major cellular fatty acids (≥ 10%) of the strain 17J68-5^T were identified as summed feature 3 (C_16:1ω6c/C_16:1ω7c; 21.2%), iso-C_15:0 (19.1%), summed feature 4 (C_17:1 iso I/C_17:1 anteiso B; 17.9%) and C_16:1ω5c (13.1%). The predominant respiratory quinones were found to be menaquinone 7 and 6 (MK-7 and MK-6). The major polar lipid was found to be phosphatidylethanolamine. The genomic DNA G + C content based on the whole genome sequence is 59.6 mol %. The phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate 17J68-5^T represents a novel species within the genus Hymenobacter, for which the name Hymenobacter jejuensis sp. nov. is proposed. The type strain of Hymenobacter jejuensis is 17J68-5^T (= KCTC 62224^T = JCM 33182^T).

Community Ecology of Deinococcus in Irradiated Soil

Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We found the following: (1) Increasing radiation dose produced a major increase in relative abundance of Deinococcus, reaching ~ 80% of reads at the highest doses. Differing abundances of the various Deinococcus species in relation to exposure levels indicate distinct "radiation niches." At 3 kGy/h, a single OTU identified as D. ficus overwhelmingly dominated the mesocosms. (2) Corresponding published genome data show that the dominant species at 3 kGy/h, D. ficus, has a larger and more complex genome than other Deinococcus species with a greater proportion of genes related to DNA and nucleotide metabolism, cell wall, membrane, and envelope biogenesis as well as more cell cycle control, cell division, and chromosome partitioning-related genes. Deinococcus ficus also has a higher guanine-cytosine ratio than most other Deinococcus. These features may be linked to genome stability and may explain its greater abundance in this apparently competitive system, under high-radiation exposures. (3) Genomic analysis suggests that Deinococcus, including D. ficus, are capable of utilizing diverse carbon sources derived from both microbial cells killed by the radiation (including C5-C12-containing compounds, like arabinose, lactose, N-acetyl-D-glucosamine) and plant-derived organic matter in the soil (e.g., cellulose and hemicellulose). (4) Overall, based on its metagenome, even the most highly irradiated (3 kGy/h) soil possesses a wide range of the activities necessary for a functional soil system. Future studies may consider the resilience and sustainability of such soils in a high-radiation environment.

Paenibacillus albus sp. nov., a UV radiation-resistant bacterium isolated from soil in Korea

A novel Gram-stain-positive, motile, white color and endospore-forming bacterium, designated 18JY67-1^T, was isolated from soil in Jeju Island, Korea. The strain grow at 15-42 °C (optimum 30 °C) in R2A medium at pH (6.0-9.5) (optimum 7.5). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 18JY67-1^T formed a distinct lineage within the family Paenibacillaceae (order Bacillales, class Bacilli), and was closely related to Paenibacillus rhizoryzae (KP675984; 96.9% 16S rRNA gene sequence similarity). The major cellular fatty acids of the strain 18JY67-1^T were C_16:0 and anteiso-C_15:0. The predominant respiratory quinones were MK-7. The major polar lipid was identified as diphosphatidylglycerol. On the basis of phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate 18JY67-1^T represents a novel species within the genus Paenibacillus, for which the name Paenibacillus flavus sp. nov. is proposed. The type strain of Paenibacillus flavus is 18JY67-1^T (= KCTC 33959^T = JCM 33184^T).

Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil

Strain 17bor-2^T, a gamma-resistant, pink-to-red-coloured, aerobic, catalase-positive, oxidase-negative and Gram-stain-negative bacterium, was isolated from gamma ray-irradiated soil. The isolate grew aerobically at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (pH 6.5-7.5) and in the presence of 0-1 % (w/v) NaCl (0 % NaCl). Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 17bor-2^T belonged to the genus Deinococcus with a highest sequence similarity of 96.4 % to Deinococcus alpinitundrae ME-04-04-52^T. The major fatty acids of the strain were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and cyclo C17 : 0. The only respiratory quinone was MK-8. The major polar lipids of the strain were phosphoglycolipid, aminophospholipid and an unknown glycolipid. The DNA G+C content of strain 17bor-2^T was 62.8 mol%. On the basis of its phenotypic, genotypic and chemotaxonomic characteristics, strain 17bor-2^T should be classified as a novel species in the genus Deinococcus, for which the name Deinococcusirradiatisoli sp. nov. is proposed. The type strain is 17bor-2^T (=KCTC 33907^T=NBRC 113037^T).

Roseomonas radiodurans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil

A bacterial strain, designated 17Sr1-1^T, was isolated from gamma ray-irradiated soil. Cells of this strain were Gram-stain-negative, strictly aerobic, motile and non-spore-forming rods. Growth occurred at 18-42 ˚C and pH 6.0-8.0, but no growth occurred at 2 % NaCl concentration. The major fatty acids of strain 17Sr1-1^T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), iso-C17 : 1ω5c and C16 : 0. The polar lipid profile contained diphosphatidylglycerol, glycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified lipids. The G+C content of the genomic DNA of 17Sr1-1^T was 71.9 mol%. The 16S rRNA gene sequence analysis showed that strain 17Sr1-1^T was phylogenetically related to Roseomonas pecuniae N75^T and Roseomonas rosea 173-96^T (96.6 and 96.3 % sequence similarity, respectively). The genotypic and phenotypic data showed that strain 17Sr1-1^T could be distinguished from its phylogenetically related species, and that this strain represented a novel species within the genus Roseomonas, for which the name Roseomonas radiodurans sp. nov. (type strain 17Sr1-1^T=KCTC 52899^T=NBRC 112872^T) is proposed as the first reported gamma ray-resistant Roseomonas species.

Kurthia ruminicola sp. nov., isolated from the rumen contents of a Holstein cow

Gram-staining-positive, motile, rod-shaped bacteria, designated as H31022^T and H31024 was isolated from rumen contents of a Holstein cow. Optimum growth occurred at 25°C and pH 7.0 on R2A agar medium. Oxidase and catalase activities are positive. The 16S rRNA gene sequence (1,452 bp) of the new isolates revealed they belong to the genus Kurthia of the phylum Firmicutes. Highest gene sequence similarities were assessed to be with Kurthia massiliensis JC30^T (98.4%), Kurthia senegalensis JC8E^T (97.5%), and Kurthia populi 10y-14^T (97.4%). Kurthia sibirica DSM 4747^T (97.3%), Kurthia zopfii NBRC 101529^T (97.0%), and Kurthia gibsonii NCIMB 9758^T (96.7%). DNA G + C content of strains H31022^T and H31024 were 34.4% and 39.7%. Strains H31022^T and H31024 has the following chemotaxonomic characteristics; the major fatty acids are iso-C_15:0, iso-C_14:0 and anteiso-C₁₅; polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), unknown aminophospholipids (APL), unknown glycolipids (GL), unknown phospholipids (PL), and unknown polar lipids (L); the major quinone is MK-7. Based on polyphasic taxonomic analysis, strains H31022^T (= KCTC 33923^T = JCM 19640^T) and H31024 (= KCTC 33924^T = JCM 19641^T) identified a novel species in the genus Kurthia for which the name Kurthia ruminicola sp. nov. is proposed.