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

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 piscis sp. nov., isolated from a fish pond

Bacterial strain NST-14T, isolated from a freshwater fish pond in Taiwan, was characterized using a polyphasic taxonomy approach. The strain was Gram-stain-negative, strictly aerobic, non-motile, rod-shaped and formed pink colonies. Optimal growth occurred at 30 °C, pH 7 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain NST-14T formed a phylogenetic lineage in the genus Hymenobacter . Analysis of 16S rRNA gene sequences showed that strain NST-14T had the highest similarity to Hymenobacter actinosclerus CCUG 39621T (97.7%), Hymenobacter amundsenii P5136T (97.3%) and Hymenobacter humicola P6312T (96.9%). Strain NST-14T showed 75.1–85.3 % average nucleotide identity, 73.7–89.8 % average amino acid identity and 14.5–26.0 % digital DNA–DNA hybridization with the type strains of other closely related Hymenobacter species. Strain NST-14T contained iso-C15 : 0, C16 : 1  ω5c and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) as the predominant fatty acids. The major hydroxyl fatty acids were iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The polar lipids were phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminophospholipids, one unidentified aminolipid, two unidentified phospholipids and three unidentified lipids. The major polyamine was homospermidine. The major isoprenoid quinone was MK-7. The DNA G+C content of the genomic DNA was 62.4 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain NST-14T should be classified as a novel species of the genus Hymenobacter , for which the name Hymenobacter piscis sp. nov. is proposed. The type strain is NST-14T (=BCRC 81249T=LMG 31686T).

Hymenobacter taeanensis sp. nov., radiation resistant bacterium isolated from coastal sand dune

An aerobic, Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, and light pink-colored bacterial strain, designated TS19^T, was isolated from a sand sample obtained from a coastal sand dune after exposure to 3 kGy of gamma radiation. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the isolate was a member of the genus Hymenobacter and was most closely related to H. wooponensis WM78^T (98.3% similarity). Strain TS19^T and H. wooponensis showed resistance to gamma radiation with D₁₀ values (i.e., the dose required to reduce the bacterial population by tenfold) of 7.3 kGy and 3.5 kGy, respectively. The genome of strain TS19^T consists of one contig with 4,879,662 bp and has a G + C content of 56.2%. The genome contains 3,955 protein coding sequences, 44 tRNAs, and 12 rRNAs. The predominant fatty acids of strain TS19^T were iso-C_15:0, summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B), summed feature 3 (C_16:1 ω6c and/or C_16:1 ω7c), and C_16:1 ω5c. The major polar lipids were phosphatidylethanolamine, and one unidentified aminophospholipid. The main respiratory quinone was menaquinone-7. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain TS19^T represents a novel species, for which the name Hymenobacter taeanensis sp. nov. is proposed. The type strain is TS19^T (= KCTC 72897^T = JCM 34023^T).

Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica

A rod-shaped and Gram-stain-negative bacterial strain 9A^T, was isolated from an air sample collected at King George Island, maritime Antarctica. Phylogenetic analysis based on 16S rRNA gene sequence reveals that strain 9A^T belongs to the genus Hymenobacter and shows the highest similarity to Hymenobacter coccineus CCM 8649^T (96.8 %). The DNA G+C content based on the draft genome sequence is 64.9 mol%. Strain 9A^T is strictly aerobic, psychrophilic, catalase-positive, oxidase-positive and non-motile. Growth is observed at 0-20 °C (optimum 10 °C), pH 6.0-8.0 (optimum pH 7.0), and in the absence of NaCl. The predominant menaquinone of strain 9A^T is MK-7 and the major fatty acids comprise Summed Feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c; 25.2 %), iso-C_15 : 0 (23.2 %), C_16 : 1  ω5c (11.6 %), Summed Feature 4 (anteiso-C_17 : 1 B/iso-C_17 : 1 I) (9.6 %) and anteiso-C_15 : 0 (9.6 %). The polar lipid profile consists of the major lipid phosphatidylethanolamine and moderate to minor amounts of phosphatidylserine, unidentified aminolipids, aminophospholipids, aminophosphoglycolipids, polar lipids lacking a functional group and an unidentified phospholipid and a glycolipid. In the polyamine pattern sym-homospermidine is predominant. On the basis of the results obtained, strain 9A^T is proposed as a novel species of the genus Hymenobacter, for which the name Hymenobacter caeli sp. nov. is suggested. The type strain is 9A^T (=CCM 8971^T=LMG 32109^T=DSM 111653^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 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 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 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).