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Lee H, Chaudhary DK, Lee KE, Cha IT, Chi WJ, Kim DU. Microbacterium humicola sp. nov., Microbacterium terrisoli sp. nov., Paenibacillus pedocola sp. nov., Paenibacillus silviterrae sp. nov., Flavobacterium terrisoli sp. nov., and Aquabacterium humicola sp. nov., isolated from soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39120518 DOI: 10.1099/ijsem.0.006486] [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: 08/10/2024] Open
Abstract
Four Gram-stain-positive and two Gram-stain-negative bacterial strains, designated as W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T, were isolated from soil samples collected from the Republic of Korea. The 16S rRNA gene sequence analysis showed that strains W4T and FW7T belonged to the genus Microbacterium, strains TW48T and UW52T were affiliated to the genus Paenibacillus, strain PT-3T was related to the genus Flavobacterium, and strain RJY3T was associated with the genus Aquabacterium. The closest phylogenetic taxa to W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T were Microbacterium bovistercoris NEAU-LLET (97.7 %), Microbacterium protaetiae DFW100M-13T (97.9 %), Paenibacillus auburnensis JJ-7T (99.6 %), Paenibacillus allorhizosphaerae JJ-447T (95.7 %), Flavobacterium buctense T7T (97.1 %), and Aquabacterium terrae S2T (99.5 %), respectively. Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and related reference type strains were <95.0 % and <70.0 %, respectively. The major cellular fatty acid in strains W4T, FW7T TW48T, and UW52T was antiso-C15 : 0. Similarly, strain PT-3T revealed iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH as its principal fatty acids. On the other hand, RJY3T exhibited summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), and C12 : 0 as its predominant fatty acids. Overall, the polyphasic taxonomic data indicated that strains W4T, FW7T, TW48T, UW52T, PT-3T, and RJY3T represent novel species within the genera Microbacterium, Paenibacillus, Flavobacterium, and Aquabacterium. Accordingly, we propose the names Microbacterium humicola sp. nov., with the type strain W4T (=KCTC 49888T=NBRC 116001T), Microbacterium terrisoli sp. nov., with the type strain FW7T (=KCTC 49859T=NBRC 116000T), Paenibacillus pedocola sp. nov., with the type strain TW48T (=KCTC 43470T=NBRC 116017T), Paenibacillus silviterrae sp. nov., with the type strain UW52T (=KCTC 43477T=NBRC 116018T), Flavobacterium terrisoli sp. nov., with the type strain PT-3T (=KCTC 92106T=NBRC 116012T), and Aquabacterium humicola sp. nov., with the type strain RJY3T (=KCTC 92105T=NBRC 115831T).
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Affiliation(s)
- Hyosun Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Microbiology, Pukyong National University, Busan, 48513, Republic of Korea
| | - Ki-Eun Lee
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Won-Jae Chi
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Dong-Uk Kim
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju, 26339, Republic of Korea
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Wu Y, Yang Y, Wan M, Chen L, Yuan Y, He J, Zhang B. Paenibacillus glufosinatiresistens sp. nov., a glufosinate-resistant bacterium isolated from sludge. Int J Syst Evol Microbiol 2024; 74. [PMID: 38305710 DOI: 10.1099/ijsem.0.006259] [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: 02/03/2024] Open
Abstract
A Gram-stain-positive bacterium capable of resisting 5.0 mM glufosinate, designated strain YX-27T, was isolated from a sludge sample collected from a factory in Wuxi, Jiangsu, PR China. Cells were rod-shaped, facultatively anaerobic, endospore-forming, and motile by peritrichous flagella. Growth was observed at 15-42 °C (optimum at 30 °C), pH 4.0-8.0 (optimum pH 7.0-7.5) and with 0-2.5% NaCl (w/v; optimum, 0.5 %). Strain YX-27T could tolerate up to 6.0 mM glufosinate. Strain YX-27T showed the highest 16S rRNA gene sequence similarity to Paenibacillus tianjinensis TB2019T (96.17 %), followed by Paenibacillus odorifer DSM 1539T (96.15 %), Paenibacillus sophorae S27T (96.04 %), Paenibacillus apii 7124T (96.02 %) and Paenibacillus stellifer DSM 14472T (95.87 %). The phylogenetic tree based on genome and 16S rRNA gene sequences indicated that strain YX-27T was clustered in the genus Paenibacillus but formed a separate clade. The genome size of YX-27T was 5.22 Mb with a G+C content of 57.5 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between the genomes of strain YX-27T and 12 closely related type strains ranged from 70.8 to 74.8% and 19.8 to 23.0 %, respectively. The major cellular fatty acids were C16 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were one diphosphatidylglycerol, one phosphatidylethanolamine, one phosphatidylglycerol, one phospholipid, four aminophospholipids and four unidentified lipids. The predominant respiratory quinone was MK-7. Based on phylogenetic, genomic, chemotaxonomic and phenotypic data, strain YX-27T was considered to represent a novel species for which the name Paenibacillus glufosinatiresistens sp. nov. is proposed, with YX-27T (=MCCC 1K08803T= KCTC 43611T) as the type strain.
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Affiliation(s)
- Yan Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yuwen Yang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Minglai Wan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Le Chen
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
| | - Ye Yuan
- Cuiying Honors College, Lanzhou University, Lanzhou 730000, Gansu, PR China
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Baolong Zhang
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, PR China
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Long Y, Li Y, Wang G, Jin J, Mao M, Gao L, Liu G, Fan G, Yu Z. Paenibacillus polygoni sp. nov., an endophytic bacterium isolated from Polygonum lapathifolium L. in wetland. Int J Syst Evol Microbiol 2023; 73. [PMID: 38015052 DOI: 10.1099/ijsem.0.006185] [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: 11/29/2023] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, yellowish and glossy strain, C31T, was isolated from a wetland plant Polygonum lapathifolium L. located south of Poyang Lake, Jiangxi Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C31T showed similarity values of lower than 97.0 % to other type species belonging to the genus Paenibacillus. The genomic average nucleotide identity values between strain C31T and its reference type species ranged from 68.9-70.9 % and the digital DNA-DNA hybridization values were lower than 27.8 %. The genomic DNA G+C content of strain C31T was 41.9 mol%. The optimal growth temperature, pH and NaCl concentration were 37 °C, pH 7 and 0.5 %, respectively. The major cellular fatty acids (>5.0 %) of strain C31T were anteiso-C15 : 0 (73.7 %), anteiso-C17 : 0 (8.4 %) and iso-C15 : 0 (5.2 %). The polar lipids of strain C31T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and unidentified phospholipids. The respiratory quinone was MK-7. Based on these phylogenetic and phenotypic characterizations, strain C31T represents a novel species within the genus Paenibacillus. Therefore, the proposed name for this newly identified species is Paenibacillus polygoni sp. nov. and the type strain is C31T (=CCTCC AB 2022349T=KCTC 43565T).
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Affiliation(s)
- Yong Long
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Yansheng Li
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guanghua Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Jian Jin
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Mengfan Mao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Lizheng Gao
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
| | - Guihua Liu
- Key Laboratory of Poyang Lake Wetland and Watershed Research (Jiangxi Normal University), Ministry of Education, Nanchang 330022, PR China
| | - Guoquan Fan
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province 150086, PR China
| | - Zhenhua Yu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 138 Haping Road, Harbin 150081, PR China
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Paenibacillus arenilitoris sp. nov., isolated from seashore sand and genome mining revealed the biosynthesis potential as antibiotic producer. Antonie Van Leeuwenhoek 2022; 115:1307-1317. [PMID: 36018400 DOI: 10.1007/s10482-022-01773-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
Abstract
Strain IB182493T, a marine, aerobic, Gram-stain-negative and motile bacterium, was isolated from seashore sand of South China Sea. Cells grew optimally at 25-30 °C, pH 7.0-8.0 and with 2-4% NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus, and was most closely related to Paenibacillus harenae DSM 16969 T (similarity 96.6%) and Paenibacillus alkaliterrae DSM 17040 T (similarity 96.1%). The chemotaxonomic characteristics of strain IB182493T included MK-7 as the predominant isoprenoid quinone, anteiso-C15:0 and iso-C16:0 as the major cellular fatty acids and meso-diaminopimelic acid as the diagnostic diaminoacid in cell wall peptidoglycan. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. The DNA G + C content of strain IB182493T was 56.2 %. The values of whole genome average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the isolate and the closely related type strains were less than 84.7% and 23.6%, respectively. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness and genomic data, we named the strain as Paenibacillus arenilitoris sp. nov. and proposed that strain IB182493T (= MCCC 1K04626T = JCM 34215 T) in the genus Paenibacillus represents a novel species.
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Wu N, Gao H, Xu Q, Zhang Z. Characterization and Whole-Genome Analysis of a Zearalenone-Degrading Stappia sp. WLB 29. Curr Microbiol 2022; 79:179. [PMID: 35508673 DOI: 10.1007/s00284-022-02874-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
Zearalenone (ZEN) is a widely distributed mycotoxin that frequently contaminates crops and animal feed. Our previous studies showed that a new strain, Stappia sp. WLB 29 with a 97.47% of similarity to Stappia indica B106T, isolated from the soil samples in the rhizosphere of the crops in Xinjiang, was capable of effectively degrading ZEN in minimal medium. In this study, we determined the complete genomic sequence of the Stappia sp. WLB 29 (Genbank accession number: JALBGD000000000; BioProject ID in GenBank is PRJNA814005). The total length of all sequences was 4,745,415 bp with a GC content of 67.08%. Moreover, the genome-wide analysis showed the presence of laccase- and peroxiredoxin-encoding genes in Stappia sp. WLB 29, which may be associated with ZEN degradation. The genome sequence of Stappia sp. WLB 29 reported here will serve as a reference for comparative genomic studies of ZEN degradation in the feed and food industry.
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Affiliation(s)
- Na Wu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Huihui Gao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Qing Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Zhidong Zhang
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, China.
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Jiang Y, Peng Y, Shin HH, Kim HJ, Kim KH, Jiang L, Lee J, Li Z. Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii. Arch Microbiol 2022; 204:185. [PMID: 35182244 DOI: 10.1007/s00203-022-02797-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
A bacterial strain, designated J12C1-MA-4T, was isolated from liquid culture of the dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and a 92 core gene set suggested that the strain J12C1-MA-4T belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represents a taxon separated from other genera. 16S rRNA gene sequence of the strain J12C1-MA-4T showed high similarities to Loktanella ponticola KCTC 42133T (95.7%), Pseudooctadecabacter jejudonensis KCTC 32525T (95.5%) and Jannaschia helgolandensis KCTC 12191T (95.3%). The genome length of strain J12C1-MA-4T was 3,621,968 bp with a DNA G + C content of 64.48 mol%. The major cellular fatty acids of strain J12C1-MA-4T were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) (> 10%). Phosphatidylglycerol (PG), phosphatidylcholine (PC), phospholipids (PL), lipids 1 (L1) and aminolipid (AL) were shown to be the major polar lipids. The sole predominant isoprenoid quinone was Q-10. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain J12C1-MA-4T represent a novel species in the novel genus of the family Rhodobacteraceae, with the proposed name Gymnodinialimonas ceratoperidinii gen. nov., sp. nov.. The type strain is J12C1-MA-4T (=KCTC 82770T =GDMCC 1.2729T).
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Affiliation(s)
- Yue Jiang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.,Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Yuxin Peng
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Hyeon Ho Shin
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje, 53201, Republic of Korea
| | - Hyun Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje, 53201, Republic of Korea
| | - Ki-Hyun Kim
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Lingmin Jiang
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Jiyoung Lee
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea.
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