Isolation and characterization of two new species, Hymenobacter mellowenesis sp. nov. and Hymenobacter aranciens sp. nov., from soil

Strains M29T and ASUV-10-1T, which are aerobic, non-flagellated, and Gram-stain-negative, were isolated from soil samples collected in Inje (37°57'49.1"N 128°19'53.7"E) and Cheonan City (36°48'47.1"N 127°05'22.4"E), South Korea. Phylogenetic analyses based on rRNA gene sequences revealed that strains M29T and ASUV-10-1T form a distinct branch within the family Hymenobacter (order Cytophagales, class Cytophagia). Strain M29T is most closely related to Hymenobacter rubidus DG7BT with a 16 S rRNA gene sequence similarity of 97.05%. Strain ASUV-10-1T shows closest genetic similarity to Hymenobacter frigidus B1789T (96.42%), Hymenobacter jeongseonensis BT683T (95.97%), and Hymenobacter terricola 3F2TT (95.65%). The optimal growth conditions for these strains are pH 7.0, no NaCl, and a temperature of 25 °C. The dominant cellular fatty acids identified in these strains are iso-C15:0, anteiso-C15:0, and Summed Feature 3 (C16:1ω 7c / C16:1ω 6c). Both strains predominantly contain MK-7 as the respiratory quinone. The major polar lipids in strains M29T and ASUV-10-1T are phosphatidylethanolamine, aminophospholipid, and aminolipid. Based on biochemical, chemotaxonomic, and phylogenetic data, it is evident that M29T and ASUV-10-1T represent new species within the genus Hymenobacter. The new species were classified based on biochemical and chemotaxonomic characteristics. The taxonomic classification of these species was conducted following the guidelines and protocols outlined in Bergey's Manual of Systematic Bacteriology. We followed the methods for determining physiological and biochemical characteristics, as well as chemotaxonomic markers such as fatty acid profiles, quinone types, and polar lipid compositions. We also compared with the results of carbohydrate utilization and enzyme activities results [Bergey 1994]. Therefore, we propose the names Hymenobacter mellowenesis for strain M29T (= KCTC 102056T = NBRC 116578T) and Hymenobacter aranciens for strain ASUV-10-1T (= KCTC 92969T = NBRC 116575T).

The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats

Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.

Hymenobacter endophyticus sp. nov., isolated from wheat leaf tissue

A bacterium, designated strain ZK17L-C2T, was isolated from the leaf tissues of wheat (Triticum aestivum) collected in Chengdu, Sichuan Province, PR China. It is aerobic, non-motile, Gram-negative, rod-shaped and red-to-pink in colour. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZK17L-C2T belonged to the genus Hymenobacter and was most closely related to Hymenobacter rigui KCTC 12533T (98.68 %) and Hymenobacter metallilatus 9PBR-2T (98.19 %). Digital DNA-DNA hybridization (dDDH) values between strain ZK17L-C2T and these two type strains were 26.6 and 26.5 %, and average nucleotide identity (ANI) values were 84.9 and 84.8 %, respectively; these values are lower than the proposed and generally accepted species boundaries for dDDH and ANI. The genomic DNA G+C content of strain ZK17L-C2T was 59.4 mol%. It can grow at pH 5.5-7.5 and 15-30 °C, which is different from the closely related type strains. The major fatty acids of strain ZK17L-C2T were iso-C15 : 0, C16 : 0 and C18 : 0. Overall, the results from biochemical, chemical taxonomy and phylogenetic analyses indicate that strain ZK17L-C2T (=CGMCC 1.19373T=KCTC 92184 T) represents a new species of the genus Hymenobacter, for which the name Hymenobacter endophyticus sp. nov. is proposed.

Five novel Hymenobacter species isolated from air: Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov

Five Hymenobacter strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus Hymenobacter. Digital DNA-DNA hybridization values and average nucleotide identities values for species delineation (70 and 95-96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus Hymenobacter for which we propose the names, Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov., with strains 5116 S-3T (=KACC 21925T=JCM 35216T), 5116 S-27T (=KACC 21926T=JCM 35217T), 5413 J-13T (=KACC 21928T=JCM 35219T), 5516 S-25T (=KACC 21931T=JCM 35222T) and 5420 S-77T (=KACC 21932T=JCM 35223T) as the type strains, respectively.

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 siberiensis sp. nov., isolated from a marine sediment of the East Siberian Sea and Hymenobacter psoromatis sp. nov., isolated from an Antarctic lichen

Gram-stain-negative, strictly aerobic, red-pink-coloured, rod-shaped and non-motile bacterial strains PAMC 29290, PAMC 29294T and PAMC 29296 were isolated from marine surface sediment sampled in the East Siberian Sea and strains PAMC 26553 and PAMC 26554T were obtained from an Antarctic lichen. Strains PAMC 29290, PAMC 29294T and PAMC 29296 were closely related to Hymenobacter artigasi (98.8 % 16S rRNA gene similarity), Hymenobacter antarcticus (97.3 %) and Hymenobacter glaciei (96.9 %), and PAMC 26553 and PAMC 26554T showed high similarity to Hymenobacter ginsengisoli (97.0 %), Hymenobacter rivuli (96.1 %) and Hymenobacter setariae (95.9 %). Genomic relatedness analyses showed that strains PAMC 29290, PAMC 29294T and PAMC 29296 could be distinguished from H. artigasi by average nucleotide identity (ANI; 93.1–93.2 %) and digital DNA–DNA hybridization (dDDH; 50.3–51.0 %) values. Strains PAMC 26553 and PAMC 26554T could be clearly distinguished from H. ginsengisoli with ANI values <79.8 % and dDDH values <23.3 %. The major fatty acids of strains PAMC 29290, PAMC 29294T and PAMC 29296 were C15 : 0 iso (21.0–26.0 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 17.4–18.2 %), C15 : 0 anteiso (12.7–19.1 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 8.6–16.1 %) and those of strains PAMC 26553 and PAMC 26554T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 20.7–22.2 %), C15 : 0 anteiso (17.5–19.7 %) and summed feature 4 (C17 : 1 iso I and/or anteiso B; 15.5–18.1 %). The major respiratory quinone was MK-7. The genomic DNA G+C contents were 60.6–60.8 mol%. The polar lipids of PAMC 29294T were found to consist of phosphatidylethanolamine, four unidentified aminolipids, an unidentified aminophospholipid and five unidentified lipids; those of PAMC 26554T were phosphatidylethanolamine, three unidentified aminolipids, four unidentified aminophospholipid and two unidentified lipids. The distinct phylogenetic position and some physiological characteristics distinguished the novel strains from closely related type strains in the genus Hymenobacter . Thus, two novel species are proposed, with the names Hymenobacter siberiensis sp. nov. (type strain, PAMC 29294T=KCTC 82466T=JCM 34574T) and Hymenobacter psoromatis sp. nov. (type strain, PAMC 26554T=KCTC 82464T=JCM 34572T), respectively.

Hymenobacter terricola sp. nov., isolated from Antarctic soil

Strain 3F2T was isolated from a soil sample obtained from the surface of Deception Island, Antarctica. The isolate was a Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, and its colonies were red to pink in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3F2T belonged to the genus Hymenobacter , family Hymenobacteraceae and was most closely related to Hymenobacter sedentarius DG5BT (97.0% sequence similarity), Hymenobacter soli PB17T (96.9%), Hymenobacter terrae DG7AT (96.8%) and Hymenobacter rufus S1-2-2-6T (96.5%). Growth occurred at 4–20 °C (optimum, 10 °C), up to 1.0 % (w/v) NaCl (optimum, 0%) and pH 6.0–8.0 (optimum, pH 7.0). The chemotaxonomic characteristics of strain 3F2T, which had MK-7 as its predominant menaquinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), iso-C15:0, anteiso-C15:0 and C16:1 ω5c as its major fatty acids, were consistent with classification in the genus Hymenobacter . The polar lipid profile of strain 3F2T comprised phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The genome of strain 3F2T was 6.56 Mbp with a G+C content of 61.5 mol%. Average nucleotide identity (ANI) values between 3F2T and the other species of the genus Hymenobacter were found to be low (ANIm <87.0%, ANIb <82.0% and OrthoANIu <83.0%). Furthermore, digital DNA–DNA hybridization and average amino acid identity values between strain 3F2T and the closely related species ranged from 20.0 to 26.3% and from 64.0 to 81.1 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain 3F2T represents a novel species within the genus Hymenobacter , for which the name Hymenobacter terricola sp. nov. is proposed. The type strain is 3F2T (=KCTC 72468T=CGMCC 1.13716T).

Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica

A group of four psychrotrophic bacterial strains was isolated on James Ross Island (Antarctica) in 2013. All isolates, originating from different soil samples, were collected from the ice-free northern part of the island. They were rod-shaped, Gram-stain-negative, and produced moderately slimy red-pink pigmented colonies on R2A agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, MALDI-TOF MS, rep-PCR analyses, chemotaxonomic methods and extensive biotyping was used to clarify the taxonomic position of these isolates. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to the genus Hymenobacter. The closest relative was Hymenobacter humicola CCM 8763^T, exhibiting 98.3 and 98.9% 16S rRNA pairwise similarity with the reference isolates P5342^T and P5252^T, respectively. Average nucleotide identity, digital DNA-DNA hybridization and core gene distances calculated from the whole-genome sequencing data confirmed that P5252^T and P5342^T represent two distinct Hymenobacter species. The menaquinone systems of both strains contained MK-7 as the major respiratory quinone. The predominant polar lipids for both strains were phosphatidylethanolamine and one unidentified glycolipid. The major components in the cellular fatty acid composition were summed feature 3 (C_16:1 ω7c/C_16:1ω6c), C_16:1ω5c, summed feature 4 (anteiso-C_17:1 B/iso-C_17:1 I), anteiso-C_15:0 and iso-C_{15 : 0} for all isolates. Based on the obtained results, two novel species are proposed, for which the names Hymenobacter terrestris sp. nov. (type strain P5252^T=CCM 8765^T=LMG 31495^T) and Hymenobacter lapidiphilus sp. nov. (type strain P5342^T=CCM 8764^T=LMG 30613^T) are suggested.

Hymenobacter artigasi sp. nov., isolated from air sampling in maritime Antarctica

A rod-shaped and Gram-stain-negative bacterial strain, 1B^T, was isolated from an air sample collected at King George Island, maritime Antarctica. Strain 1B^T is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth of strain 1B^T is observed at 0-20 °C (optimum, 10 °C), pH 6.0-8.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences places strain 1B^T within the genus Hymenobacter and shows the highest similarity to Hymenobacter antarcticus VUG-A42aa^T (97.5 %). The predominant menaquinone of strain 1B^T is MK-7 and the major fatty acids (>10 %) comprise summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c; 32.5 %), iso-C_15 : 0 (17.6 %) and anteiso C_15 : 0 (12.3 %). The polar lipid profile consists of the major compounds phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids and one unidentified phospholipid. The DNA G+C content based on the draft genome sequence is 61.2 mol%. Based on the data from the current polyphasic study, 1B^T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter artigasi sp. nov. is suggested. The type strain is 1B^T (=CCM 8970^T=CGMCC 1.16843^T).

Hymenobacter humicola sp. nov., isolated from soils in Antarctica

A set of three psychrotrophic bacterial strains was isolated from different soil samples collected at the deglaciated northern part of James Ross Island (Antarctica) in 2014. All isolates were rod-shaped, Gram-stain-negative, non-motile, catalase-positive and oxidase-negative, and produced moderately slimy red-pink pigmented colonies on Reasoner's 2A (R2A) agar. A polyphasic taxonomic approach based on 16S rRNA gene sequencing, whole-genome sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy methods and extensive biotyping using conventional tests and commercial identification kits was applied to the isolates in order to clarify their taxonomic position. Phylogenetic analysis based on the 16S rRNA gene showed that all isolates belonged to the genus Hymenobacter with the closest relative being Hymenobacter aerophilus DSM 13606^T, exhibiting 98.5 % 16S rRNA gene pairwise similarity to the reference isolate P6312^T. Average nucleotide identity values calculated from the whole-genome sequencing data proved that P6312^T represents a distinct Hymenobacter species. The major components of the cellular fatty acid composition were summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c), C_16 : 1 ω5c, summed feature 4 (C_17 : 1 anteiso B/iso I), C_15 : 0 anteiso and C_15 : 0 iso. The menaquinone system of strain P6312^T contained MK-7 as the major respiratory quinone. The predominant polar lipids were phosphatidylethanolamine and an unidentified phospholipid. Moderate to minor amounts of three unidentified polar lipids, four unidentified aminophospholipids, one unidentified glycolipid and one unidentified phospholipid were also present. Based on the obtained results, we propose a novel species for which the name Hymenobacterhumicola sp. nov. is suggested, with the type strain P6312^T (=CCM 8763^T=LMG 30612^T).

Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming bacterial strain, designated DK6-66^T, was isolated from subsurface sandstone sediment located in the Qilian Mountains in Qinghai Province, Northwest China. Strain DK6-66^T was found to grow optimally at pH 7.0 and 22 °C. The 16S rRNA gene sequence analysis indicated that strain DK6-66^T belonged to the genus Hymenobacter and clustered with the type strain of Hymenobacter arcticus, with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. The DNA G+C content was 60.4 mol%. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, anteiso-C17 : 1 B and/or iso-C17 : 1 I, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω5c. On the basis of phylogenetic and phenotypic data, strain DK6-66^T was classified in the genus Hymenobacter as a member of a novel species, for which the name Hymenobacterbucti sp. nov. is proposed. The type strain is DK6-66^T (=CGMCC 1.15795^T=KCTC 52629^T).

Hymenobacter pedocola sp. nov., a novel bacterium isolated from soil

Strain S12-2-1^T was isolated from a soil sample collected in the Gyeongsangnam-do province of the Republic of Korea. The isolate is a Gram-stain-negative, aerobic, short, rod-shaped bacterium, and its colonies are red to pink in colour. Analysis of the 16S rRNA gene identified strain S12-2-1^T as a member of the genus Hymenobacter in the family Cytophagaceae, with high levels of 16S rRNA gene sequence similarity to Hymenobacter arizonensis OR362-8^T (97.7 %), Hymenobacter sedentarius DG5B^T (97.4 %) and Hymenobacter humi DG31A^T (97.2 %). The isolate was positive for catalase and oxidase, but negative for acid production from glucose. The growth of strain S12-2-1^T was supported at 4-30 °C, pH 7-10 and in the presence of 0-0.5 % NaCl. Strain S12-2-1^T contained menaquinone-7 as the predominant respiratory quinone, sym-homospermidine as the major polyamine and iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids. Phosphatidylethanolamine was the major polar lipid. The genomic DNA G+C content was 58.7 mol%. Phenotypic and chemotaxonomic data supported the assignment of the isolate to the genus Hymenobacter. However, strain S12-2-1^T exhibited a relatively low level of DNA-DNA relatedness with H. humi (31.7 %), H. arizonensis (24.4 %) and H. sedentarius (21.3 %). Based on its phenotypic and genotypic properties, along with its phylogenetic distinctiveness, strain S12-2-1^T should be considered a novel species in the genus Hymenobacter, for which the name Hymenobacter pedocola sp. nov. is proposed. The type strain is S12-2-1^T (=KCTC 52730^T=JCM 32198^T).