Hymenobacter crusticola sp. nov., isolated from biological soil crust

Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada

A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467^T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467^T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467^T is distinguishable from H. yonginensis based on average nucleotide identity (91.3 %) and digital DNA-DNA hybridization values (39.3 %). The major fatty acids (>10 %) of strain PAMC 29467^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_15 : 0 iso, C_16 : 1  ω5c and summed feature 4 (C_17 : 1 iso l and/or anteiso B). The major respiratory quinone was menaquinone-7. The genomic DNA G+C content was 61.5 mol%. Strain PAMC 29467^T was separated from the type species in the genus Hymenobacter by its distinct phylogenetic position and some physiological characteristics. As a result, a novel species is proposed, with the name Hymenobacter canadensis sp. nov. (type strain, PAMC 29467^T=KCTC 92787^T=JCM 35843^T).

Hymenobacter armeniacus sp. nov. and Hymenobacter montanus sp. nov., two radiation-resistant bacteria from soil

Two bacterial strains, designated BT189T and BT664T, were isolated from soil sampled in the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains BT189T and BT664T belonged to the genus Hymenobacter , family Hymenobacteraceae (order Cytophagales ). The 16S rRNA genes of the two strains shared a sequence similarity of 93.7 %. The closely related species of strain BT189T were Hymenobacter rubidus DG7BT (97.1 % 16S rRNA similarity) and Hymenobacter terrae DG7AT (96.7 %). The closest related species to strain BT664T were Hymenobacter sedentarius DG5BT (95.3 %) and Hymenobacter terrenus MIMtkLc17T (95.2 %). The genome sizes of strains BT189T and BT664T were 5 285 287 and 5 475 357 bp, respectively. The genomic DNA G+C contents of strains BT189T and BT664T were 63.2 and 59.3 mol%, respectively. The main fatty acids of strain BT189T were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1  ω6c/C16 : 1  ω7c), and those of strain BT664T were iso-C15 : 0, C16 : 1  ω5c and summed feature 3 (C16 : 1  ω6c/C16 : 1  ω7c). The main polar lipid in both strains was phosphatidylethanolamine and the predominant respiratory quinone was MK-7, supporting the affiliation of these strains with the genus Hymenobacter . Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Hymenobacter armeniacus BT189T (=KCTC 72341T=NBRC 114843T) and Hymenobacter montanus BT664T (KACC 21967T=NBRC 114856T), are proposed.

A Round Trip to the Desert: In situ Nanopore Sequencing Informs Targeted Bioprospecting

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies.

Hymenobacter puniceus sp. nov., radiation resistant bacteria isolated from soil in South Korea

Two novel Gram-negative bacterial strains BT190^T and BT191 were isolated from soil collected in Uijeongbu city (37°44'55″N, 127°02'20″E), Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains BT190^T and BT191 belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia). The level of 16S rRNA gene sequence similarity between the strains BT190^T and BT190 was 99.5%. The strains BT190^T and BT191 were closely related to Hymenobacter swuensis DY53^T (97.0% 16S rRNA gene similarity), Hymenobacter metallilatus 9PBR-2 ^T (96.8%), Hymenobacter tibetensis XTM003^T (96.8%) and Hymenobacter yonginensis HMD1010^T (96.6%). The genome size of strain BT190^T was 4,859,864 bp. The DNA G+C content of strain BT190^T was 55.3 mol%. Bacterial growth was observed at 4-30 °C (optimum 25 °C) and pH 6.0-9.0 (optimum, pH 6.0-7.0) on R2A agar. Colonies of strains BT190^T and BT191 were raised, smooth, circular and red-pink colored. The sole respiratory quinone of strain BT190^T was MK-7 and the predominant cellular fatty acids were iso-C_15:0, C_16:1 ω5c, summed feature 3 (C_16:1 ω6c / C_16:1 ω7c) and summed feature 4 (iso-C_17:1 I / anteiso-C_17:1 B). The major polar lipids of strain BT190^T were aminophospholipid (APL) and phosphatidylethanolamine (PE). Based on the chemotaxonomic, biochemical, and phylogenetic analysis, strains BT190^T and BT191 can be suggested as a novel bacterial species within the genus Hymenobacter, for which the name Hymenobacter puniceus sp. nov is proposed. The type strain of Hymenobacter puniceus is BT190^T (= KCTC 72342 ^T = NBRC 114860 ^T).

Hymenobacter citatus sp. nov., isolated from soil in South Korea

Two novel Gram-negative bacterial strains, BT507^T and BT506, were isolated from soil collected in Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both strains BT507^T and BT506 belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae; order Cytophagales; class Cytophagia). The 16S rRNA genes of the two strains shared a sequence similarity of 100.0%. Strains BT507^T and BT506 are closely related to Hymenobacter profundi M2^T (97.2% 16S rRNA gene similarity), Hymenobacter defluvii POA9^T (97.1%), and Hymenobacter tenuis POB6^T (95.3%). The genome size of strain BT507^T is 5,078,289 base pairs. Bacterial growth was observed at 10-37 °C (optimum 25 °C) and pH 6.0-8.0 (optimum pH 6.0). The primary cellular fatty acids of strain BT507^T are iso-C_15:0, C_16:1ω5c, and summed feature 3 (C_16:1ω6c/C_16:1ω7c). Its predominant respiratory quinone is MK-7. The primary polar lipids of strain BT507^T are lipid, aminophospholipid, and phosphatidylethanolamine. Based on the biochemical, chemotaxonomic, and phylogenetic analysis, strains BT507^T and BT506 can be described a novel bacterial species within the genus Hymenobacter, and the proposed name is Hymenobacter citatus. The type strain of H. citatus is BT507^T is KCTC 82115^T and NBRC 114850^T.

Hymenobacter baengnokdamensis sp. nov., Isolated from the Soil of a Crater Lake in Korea

An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and pink-colored bacterial strain, designated BRD72^T, was isolated from a crater lake (Baengnokdam) at the top of Mt. Hallasan in the Republic of Korea. Cells were catalase-positive and oxidase-negative. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and most closely related to Hymenobacter marinus KJ035^T (96.2% similarity). The isolate was found to produce carotenoid pigment, but not flexirubin-type pigment. The predominant fatty acids of strain BRD72^T were summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c, 21.6%), iso-C_15:0 (17.9%), anteiso-C_15:0 (13.3%) and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B, 11.3%). The major polar lipids were phosphatidylethanolamine, an unidentified amino lipid, and two unidentified aminophospholipids. The main respiratory quinone was menaquinone-7 (MK-7), and the main polyamine was homospermidine. The DNA G+C content was 59.8 mol%. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain BRD72^T represents a novel species, for which the name Hymenobacter baengnokdamensis sp. nov. is proposed. The type strain is BRD72^T (= KCTC 72649^T = JCM 33837^T).

Hymenobacter fodinae sp. nov. and Hymenobacter metallicola sp. nov., isolated from abandoned lead–zinc mine

Two novel strains, designated 92R-1T and 9PBR-1T, were isolated from abandoned lead–zinc ore collected in Meizhou, Guangdong Province, PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that they fell into the genus of Hymenobacte r and formed two distinct lineages. Strain 92R-1T was most closely related to Hymenobacter wooponensis JCM 19491T (98.7 %) and Hymenobacter gelipurpurascens LMG 21873T (98.5 %), while strain 9PBR-1T was most closely related to Hymenobacter chitinivorans LMG 21951T (99.0 %), Hymenobacter elongatus JCM 17223T (98.7 %) and Hymenobacter aquaticus JCM 31653T (98.1 %). Strain 92R-1Tshared average nucleotide identity values of 80.0–83.7 % and digital DNA–DNA hybridization values of 23.1–27.1 % with its closely related type strains, respectively, while strain 9PBR-1T shared corresponding values of 80.3–83.2 % and 23.6–26.7 % with its closely related type strains, respectively. The two novel strains could be clearly distinguished from their closely related type strains by enzyme activities and substrates assimilation, respectively. Both of them took iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and C16:1 ω5c as major fatty acids, and showed clear differences from their closely relatives in the contents of several components. They contained menaquinone 7 as the major respiratory quinone and phosphatidylethanolamine as the dominant polar lipid. The G+C contents of strains 92R-1T and 9PBR-1T were 56.7 and 59.5 mol%, respectively. The results clearly supported that strains 92R-1T and 9PBR-1T represent two distinct novel species within the genus Hymenobacter , for which the names Hymenobacter fodinae sp. nov. (type strain 92R-1T=GDMCC 1.1493T=JCM 32697T) and Hymenobacter metallicola sp. nov. (type strain 9PBR-1T=GDMCC 1.1491T=JCM 32698T) are proposed.

Hymenobacter lutimineralis sp. nov., belonging to the family Hymenobacteraceae, isolated from zeolite

A red-pigmented bacterial strain, designated KIGAM108^T, within the family Hymenobacteraceae was isolated from zeolite in the Gampo-41 mine of the Gyeongju, Republic of Korea. This strain was a Gram-negative, strictly aerobic, non-spore forming, rod-shaped bacterium. Phylogenetic analysis of the 16S rRNA gene sequence of strain KIGAM108^T found that it was related to the genus Hymenobacter, with similarities of 96.6, 96.4, 95.5, and 95.0% to H. fastidiosus VUG-A124^T, H. algoricola VUG-A23a^T, H. crusticola MIMBbqt21^T, and H. daecheongensis DSM 21074^T, respectively. Strain KIGAM108^T grew in the presence of 0-0.5% (w/v) NaCl at 4-37 °C and pH 6.0-10.0. This isolate contained MK-7 as a respiratory quinone. The polar lipids of strain KIGAM108^T were identified as phosphatidylethanolamine, two unidentified aminophospholipids, one unidentified phospholipid and five unidentified lipids. The major fatty acids profile showed summed feature 3 (C_16:1ω6c and/or C_16:1ω7c) (22.3%), anteiso-C_15:0 (17.1%), C_16:1ω5c (13.3%), and iso-C_15:0 (11.0%). The genomic DNA G + C content was 60.0 mol%. Based on the polyphasic taxonomic data, strain KIGAM108^T is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter lutimineralis sp. nov. is proposed. The type strain is KIGAM108^T (=KCTC 72263^T =JCM 33444^T).