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Zhang X, Duan XM, Cheng J, Qiao HJ, Dai YM. Hymenobacter endophyticus sp. nov., isolated from wheat leaf tissue. Int J Syst Evol Microbiol 2023; 73. [PMID: 38059799 DOI: 10.1099/ijsem.0.006197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023] Open
Abstract
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.
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Affiliation(s)
- Xue Zhang
- College of Animal Science and Technology, Hebei Normal University of Science &Technology, Qinhuangdao 066600, PR China
| | - Xue-Mei Duan
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Sichuan 610041, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jin Cheng
- College of Animal Science and Technology, Hebei Normal University of Science &Technology, Qinhuangdao 066600, PR China
| | - Hong-Jiao Qiao
- College of Animal Science and Technology, Hebei Normal University of Science &Technology, Qinhuangdao 066600, PR China
| | - Yu-Mei Dai
- College of Animal Science and Technology, Hebei Normal University of Science &Technology, Qinhuangdao 066600, PR China
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Kim Y, Subramanian P, Choi H, Weon HY, Kim S, Kwon SW, Lee D, Han BH, Hong SB, Heo J. 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. Int J Syst Evol Microbiol 2023; 73. [PMID: 37725077 DOI: 10.1099/ijsem.0.006026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
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.
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Affiliation(s)
- Yiseul Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Hyorim Choi
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seunghwan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Daseul Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Byeong-Hak Han
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Seung-Beom Hong
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeollabuk-do, Republic of Korea
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Kim W, Jang S, Chae N, Kim M, Yeh JY, Kim S, Lee YM. Hymenobacter canadensis sp. nov., isolated from freshwater of the pond in Cambridge Bay, Canada. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326606 DOI: 10.1099/ijsem.0.005913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
A Gram-stain-negative, aerobic, reddish-coloured, rod-shaped and non-motile strain PAMC 29467T, was isolated from freshwater of the pond in Cambridge Bay, Canada. Strain PAMC 29467T was closely related to Hymenobacter yonginensis (98.1 % 16S rRNA gene similarity). Genomic relatedness analyses showed that strain PAMC 29467T 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 29467T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso, C16 : 1 ω5c and summed feature 4 (C17 : 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 29467T 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 29467T=KCTC 92787T=JCM 35843T).
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Affiliation(s)
- Woohyun Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Seonghan Jang
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Namyi Chae
- Institutes of Life Sciences and Natural Resources, Korea University, Seoul 02841, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, 26 Songdomirae-ro, Yeonsu-gu, Incheon 21990, Republic of Korea
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Oh H, Lee HB, Kim MK. Hymenobacter lucidus sp. nov., and Hymenobacter nitidus sp. nov., isolated from soil. Arch Microbiol 2022; 204:697. [DOI: 10.1007/s00203-022-03244-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/27/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
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Paenibacillus farraposensis sp. nov., isolated from a root nodule of Arachis villosa. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain UY79T was isolated from a root nodule of Arachis villosa, collected at the Esteros de Farrapos National Park, Río Negro, Uruguay. Cells were non-motile Gram-variable rods with central to subterminal oval to ellipsoidal endospores that swell the sporangia. Growth was observed in the range of 15–42 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0–8.0) and with up to 3 % (w/v) NaCl (optimum, 1–2 %). Strain UY79T was facultative anaerobic, catalase-positive and oxidase-negative. According to the results of 16S rRNA gene sequence analysis, UY79T belongs to the genus
Paenibacillus
and is closely related to
P. ottowii
MS2379T,
P. peoriae
BD-57T,
P. polymyxa
ATCC 842T and
P. brasilensis
PB172T, exhibiting 99.4, 99.0, 99.0 and 98.9% sequence identity, respectively. Average nucleotide identity and digital DNA–DNA hybridization values with the most closely related type strains were 74.3–88.6% and 38.2–48.7 %, respectively. Major fatty acids (>10 %) were anteiso-C15:0, iso-C15:0, and C16 : 0. Menaquinones MK-7 and MK-6 were the only isoprenoid quinones detected. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. Spermidine was the predominant polyamine. The DNA G+C content based on the draft genome sequence was 46.34 mol%. Based on the current polyphasic study, UY79T represents a novel species of the genus
Paenibacillus
, for which the name Paenibacillus farraposensis sp. nov. is proposed. The type strain is UY79T (=CCM 9147T=CGMCC 1.19038T).
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Chen Y, Zhu L, Bai P, Cui S, Xin Y, Zhang Y, Zhang J. Hymenobacter terricola sp. nov., isolated from Antarctic soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005205] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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).
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Affiliation(s)
- Ya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Pengze Bai
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Siqi Cui
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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