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Lee DH, Kim SB. Quorum Quenching Potential of Reyranella sp. Isolated from Riverside Soil and Description of Reyranella humidisoli sp. nov. J Microbiol 2024; 62:449-461. [PMID: 38814538 DOI: 10.1007/s12275-024-00131-2] [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] [Received: 10/10/2023] [Revised: 01/13/2024] [Accepted: 02/27/2024] [Indexed: 05/31/2024]
Abstract
Quorum quenching refers to any mechanism that inhibits quorum sensing processes. In this study, quorum quenching activity among bacteria inhabiting riverside soil was screened, and a novel Gram-stain-negative, rod shaped bacterial strain designated MMS21-HV4-11T, which showed the highest level of quorum quenching activity, was isolated and subjected to further analysis. Strain MMS21-HV4-11T could be assigned to the genus Reyranella of Alphaproteobacteria based on the 16S rRNA gene sequence, as the strain shared 98.74% sequence similarity with Reyranella aquatilis seoho-37T, and then 97.87% and 97.80% sequence similarity with Reyranella soli KIS14-15T and Reyranella massiliensis 521T, respectively. The decomposed N-acyl homoserine lactone was restored at high concentrations under acidic conditions, implying that lactonase and other enzyme(s) are responsible for quorum quenching. The genome analysis indicated that strain MMS21-HV4-11T had two candidate genes for lactonase and one for acylase, and expected protein structures were confirmed. In the quorum sensing inhibition assay using a plant pathogen Pectobacterium carotovorum KACC 14888, development of soft rot was significantly inhibited by strain MMS21-HV4-11T. Besides, the swarming motility by Pseudomonas aeruginosa PA14 was significantly inhibited in the presence of strain MMS21-HV4-11T. Since the isolate did not display direct antibacterial activity against either of these species, the inhibition was certainly due to quorum quenching activity. In an extended study with the type strains of all known species of Reyranella, all strains were capable of degrading N-acyl homoserine lactones (AHLs), thus showing quorum quenching potential at the genus level. This is the first study on the quorum quenching potential and enzymes responsible in Reyranella. In addition, MMS21-HV4-11T could be recognized as a new species through taxonomic characterization, for which the name Reyranella humidisoli sp. nov. is proposed (type strain = MMS21-HV4-11 T = KCTC 82780 T = LMG 32365T).
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Affiliation(s)
- Dong Hyeon Lee
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Zhang M, Song Q, Sang J, Li Z. Paenibacillus spongiae sp. nov. isolated from deep-water marine sponge Theonella swinhoei. Int J Syst Evol Microbiol 2023; 73. [PMID: 37910170 DOI: 10.1099/ijsem.0.006122] [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: 11/03/2023] Open
Abstract
A novel bacterial strain, designated as PHS-Z3T, was isolated from a marine sponge belonging to the genus Theonella on the Puerto Galera Deep Monkey, Philippines. Cells of PHS-Z3T were Gram-stain-positive, motile, oxidase- and catalase-positive, white-pigmented, spore-forming, short rods that could grow at 10-40 °C (optimum, 20 °C), pH 6.0-9.5 (optimum, pH 7.5) and with 2-16 % (w/v) NaCl (optimum, 7 %). The 16S rRNA gene sequence of PHS-Z3T showed 97.9 %, 96.7 %, and 96.2 % identities to Paenibacillus mendelii C/2T, Paenibacillus oenotherae DT7-4T and Paenibacillus aurantiacus RC11T, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PHS-Z3T formed an independent cluster with Paenibacillus mendelii C/2T. The total genome of PHS-Z3T was approximately 7 613 364 bp in size with a DNA G+C content of 51.6 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between PHS-Z3T and other type strains of species of the genus Paenibacillus were 68.0-81.4 % [ANI by blast (ANIb)], 83.0-88.0 % [ANI by MUMmer (ANIm)] and 12.7-32.1 % (dDDH). The dDDH and ANI values were below the standard cut-off criteria for delineation of bacterial species. The percentage of conserved proteins (POCP) values between the genome of PHS-Z3T and those of members of the genus Paenibacillus were 39.7-75.7 %, while the average amino acid identity (AAI) values were 55.9-83.7 %. The sole respiratory quinone in the strain was MK-7, and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The major polar lipids of PHS-Z3T consisted of diphosphatidylglycerol, phospholipid and phosphatidylglycerol. The characteristic amino acid in the cell wall of PHS-Z3T was diamino heptanoic acid (meso-DAP). On the basis of the molecular, physiological, biochemical and chemotaxonomic features, strain PHS-Z3T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus spongiae sp. nov. is proposed, with the type strain PHS-Z3T (=MCCC 1K07848T=KCTC 43443T).
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Affiliation(s)
- Mimi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Qianqian Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jin Sang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
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Kämpfer P, Lipski A, Lamothe L, Clermont D, Criscuolo A, McInroy JA, Glaeser SP. Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01852-x. [PMID: 37338631 PMCID: PMC10371898 DOI: 10.1007/s10482-023-01852-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - André Lipski
- Institut für Ernährungs- und Lebensmittelwissenschaften, Lebensmittelmikrobiologie und -hygiene, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lucie Lamothe
- CNRS, IFB-Core, UMS 3601, Institut Français de Bioinformatique, Evry, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - Dominique Clermont
- Institut Pasteur, CIP - Collection of Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Alexis Criscuolo
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université de Paris, 75015, Paris, France
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, Alabama, USA
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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Lee DH, Ra JS, Kim MJ, Kim SB. Micromonospora antibiotica sp. nov. and Micromonospora humidisoli sp. nov., two new actinobacterial species exhibiting antimicrobial potential. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two novel actinobacterial strains, designated MMS20-R2-23T and MMS20-R2-29T, were isolated from riverside soil and subjected to taxonomic characterization. Both strains were Gram-stain-positive, aerobic, non-motile and filamentous, and formed orange to strong orange-brown coloured colonies, which later turned black. Both strains grew optimally at mesophilic temperatures, neutral to slightly alkaline pH and in the absence of NaCl. Analysis of 16S rRNA gene sequences indicated that the two novel strains fell into phylogenetic clusters belonging to the genus
Micromonospora
. Strains MMS20-R2-23T and MMS20-R2-29T showed the highest 16S rRNA gene sequence similarity to
Micromonospora phytophila
SG15T (99.3 %) and
Micromonospora humida
MMS20-R1-14T (99.4 %), respectively. Based on the comparative genome analysis, strain MMS20-R2-23T had the highest orthologous average nucleotide identity (orthoANI) value of 92.70 % with
Micromonospora matsumotoense
DSM 44100T, and MMS20-R2-29T shared 94.99 % with
Micromonospora wenchangensis
CCTCC AA 2012002T. Besides, the digital DNA–DNA hybridization (dDDH) values of MMS20-R2-23T and MMS20-R2-29T with the same species were 47.6 and 59.2% respectively, which were also highest among the compared species, thus confirming the separation of each strain at species level from related species. The orthoANI and dDDH values between MMS20-R2-23T and MMS20-R2-29T were 92.18 and 44.9% respectively. The genomes of strains MMS20-R2-23T and MMS20-R2-29T were estimated as 7.56 Mbp and 7.13 Mbp in size, and the DNA G+C contents were 72.5 and 72.9 mol%, respectively. The chemotaxonomic properties of both strains were consistent with those of the genus. The novel strains showed antimicrobial activity against a broad range of microbes, in particular Gram-positive bacteria and yeasts. It is evident that each of the isolated strains merits recognition as representing novel species of
Micromonospora
, for which the names Micromonospora antibiotica sp. nov. (type strain=MMS20-R2-23T=KCTC 49542T=JCM 34495T) and Micromonospora humidisoli sp. nov. (type strain=MMS20-R2-29T=KCTC 49543T=JCM 34496T) are proposed.
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Affiliation(s)
- Dong Hyeon Lee
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Jun Sik Ra
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Min Ji Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99 Daehak-ro, Yuseong, Daejeon 34134, Republic of Korea
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Devi R, Kaur T, Kour D, Yadav A, Yadav AN, Suman A, Ahluwalia AS, Saxena AK. Minerals solubilizing and mobilizing microbiomes: A sustainable approaches for managing minerals deficiency in agricultural soil. J Appl Microbiol 2022; 133:1245-1272. [PMID: 35588278 DOI: 10.1111/jam.15627] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022]
Abstract
Agriculture faces challenges to fulfill the rising food demand due to shortage of arable land and various environmental stressors. Traditional farming technologies help in fulfilling food demand but they are harmful to humans and environmental sustainability. The food production along with agro-environmental sustainability could be achieved by encouraging farmers to use agro-environmental sustainable products such as biofertilizers and biopesticides consisting of live microbes or plant extract instead of chemical-based inputs. The ecofriendly formulations play a significant role in plant growth promotion, crop yield, and repairing degraded soil texture and fertility sustainably. Mineral solubilizing microbes that provide vital nutrients like phosphorus, potassium, zinc, and selenium are essential for plant growth and development and could be developed as biofertilizers. These microbes could be plant-associated (rhizospheric, endophytic, and phyllospheric) or inhabits the bulk soil, and diverse extreme habitats. Mineral solubilizing microbes from soil, extreme environments, surface and internal parts of the plant belong to diverse phyla such as Ascomycota, Actinobacteria, Basidiomycota, Bacteroidetes, Chlorobi, Cyanobacteria, Chlorophyta, Euryarchaeota, Firmicutes, Gemmatimonadetes, Mucoromycota, Proteobacteria, and Tenericutes. Mineral solubilizing microbes (MSMs) directly or indirectly stimulate plant growth and development either by releasing plant growth regulators; solubilizing phosphorus, potassium, zinc, selenium, and silicon; biological nitrogen fixation; and production of siderophores, ammonia, hydrogen cyanide, hydrolytic enzymes, and bioactive compound/secondary metabolites. Biofertilizer developed using mineral solubilizing microbes is an eco-friendly solution to the sustainable food production system in many countries worldwide. The present review deals with the biodiversity of mineral solubilizing microbes, and potential roles in crop improvement and soil well-being for agricultural sustainability.
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Affiliation(s)
- Rubee Devi
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Tanvir Kaur
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Divjot Kour
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Amrik Singh Ahluwalia
- Department of Botany, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kusmaur-275103, Mau, India
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Abstract
A novel Gram-stain-negative, rod-shaped, aerobic and motile bacterium designated strain UL073T was isolated from a forest soil of an island, and subjected to taxonomic characterization. Strain UL073T grew at 10–37 °C (optimum, 30 °C), at pH 5.0–10.0 (optimum, pH 7.0) and in the presence of 0–3 % NaCl (optimum, 0 %), respectively. Strain UL073T showed the highest sequence similarity to
Pseudomonas lalkuanensis
PE08T based on 16S rRNA gene analysis with a sequence similarity of 98.08 %, which was well below the suggested cutoff for species distinction. The 16S rRNA gene tree as well as the multilocus sequence analysis and genome-based trees indicated the independent taxonomic position of strain UL073T, and the orthologous average nucleotide identity and in silico DNA–DNA hybridization values between strain UL073T and related species were no higher than 84.7 and 28.3% respectively, thus confirming the distinctive taxonomic position of the strain. The chemotaxonomic properties were consistent with those of the genus, as the major fatty acids of the strain were a summed feature consisting of C18 : 1 ω7c/C18 : 1 ω6c (31.4 %), another summed feature consisting of C16 : 1 ω7c/C16 : 1 ω6c (23.1 %), and C16 : 0 (22.0 %), the major respiratory quinone was ubiquinone 9, and the major polar lipids were phosphatidylethanolamine and diphosphatidylglycerol. The genome size and DNA G+C content of strain UL073T were 4.87 Mbp and 65.9 mol%. On the basis of phenotypic and phylogenetic evidence, strain UL073T should be classified as representing a novel species of
Pseudomonas
, for which the name Pseudomonas insulae sp. nov. (type strain=UL073T=KCTC 82407T=JCM 34511T) is proposed.
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KIm KH, Seo YL, Baek JH, Jin HM, Jeon CO. Paenibacillus agri sp. nov., isolated from soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34435945 DOI: 10.1099/ijsem.0.004981] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strict aerobic bacterium, strain JW14T was isolated from soil in the Republic of Korea. Cells were Gram-stain-positive, non-endospore-forming and motile rods showing catalase-positive and oxidase-negative activities. Growth of strain JW14T was observed at 20-37 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and in the presence of 0-2.0% NaCl (optimum, 0%). Strain JW14T contained menaquinone-7 as the sole isoprenoid quinone, anteiso-C15:0, C16:0 and iso-C16 : 0 as the major fatty acids (>10.0%), and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and an unidentified lipid as the major polar lipids. The cell-wall peptidoglycan of strain JW14T contained meso-diaminopimelic acid. The DNA G+C content of strain JW14T calculated from the whole genome sequence was 48.1 mol%. Strain JW14T was most closely related to Paenibacillus graminis DSM 15220T with 97.4% 16S rRNA gene sequence similarity. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JW14T formed a distinct phyletic lineage from closely related type strains within the genus Paenibacillus. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain JW14T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus agri sp. nov. is proposed. The type strain is JW14T (=KACC 21840T=JCM 34279T).
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Affiliation(s)
- Kyung Hyun KIm
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ye Lin Seo
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do 37242, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Narsing Rao MP, Dong ZY, Kan Y, Zhang K, Fang BZ, Xiao M, Kang YQ, Li WJ. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil. Int J Syst Evol Microbiol 2020; 70:1048-1054. [DOI: 10.1099/ijsem.0.003870] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yu Kan
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Talent Base of Microbiology and Human health of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, PR China
| | - Kun Zhang
- School of Eco-environment Technology, Guangdong Industry Polytechnic, Guangzhou, 510300, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Ying-Qian Kang
- Key Laboratory of Medical Microbiology and Parasitology & Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Talent Base of Microbiology and Human health of Guizhou Province, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
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Dai X, Shi K, Wang X, Fan J, Wang R, Zheng S, Wang G. Paenibacillus flagellatus sp. nov., isolated from selenium mineral soil. Int J Syst Evol Microbiol 2018; 69:183-188. [PMID: 30461376 DOI: 10.1099/ijsem.0.003125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain DXL2T, a Gram-stain-negative, rod-shaped, endospore-forming, motile, aerobic bacterium, was isolated from selenium mineral soil. DXL2T had the highest 16S rRNA gene sequence similarities with those of Paenibacillus ginsengarviGsoil 139T (96.8 %), Paenibacillushemerocallicola DLE-12T (95.5 %) and Paenibacillus hodogayensisSGT (95.4 %). The genome size of DXL2T was 7.24 Mb, containing 6243 predicted protein-coding genes, with a DNA G+C content of 60.2 mol%. DXL2T contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0 and iso-C15 : 0. The major quinone was menaquinone 7. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two aminophospholipids, an unidentified aminolipid, phosphatidylmethylethanolamine, an unidentified glycolipid and an unidentified phospholipid. Compared with the other strains, DXL2T had a specific phospholipid and a specific aminolipid, it hydrolyzed Tween 40 and could not assimilate potassium gluconate. On the basis of the phenotypic, chemotaxonomic and phylogenetic results, strain DXL2T represents a novel species within the genus Paenibacillus, for which the name Paenibacillusflagellatus sp. nov. is proposed. The type strain is DXL2T (=KCTC 33976T=CCTCC AB 2018054T).
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Affiliation(s)
- Xingli Dai
- 1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Kaixiang Shi
- 1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin Wang
- 1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Jun Fan
- 2Tobacco Company of Enshi, Hubei Province, Enshi, Hubei 445000, PR China
| | - Rui Wang
- 2Tobacco Company of Enshi, Hubei Province, Enshi, Hubei 445000, PR China
| | - Shixue Zheng
- 1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Gejiao Wang
- 1State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
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Yun BR, Park S, Kim MK, Park J, Kim SB. Shewanella saliphila sp. nov., Shewanella ulleungensis sp. nov. and Shewanella litoralis sp. nov., isolated from coastal seawater. Int J Syst Evol Microbiol 2018; 68:2960-2966. [DOI: 10.1099/ijsem.0.002929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bo-Ram Yun
- 1Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- 2Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, Republic of Korea
| | | | - Min-Kyeong Kim
- 1Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Jisun Park
- 1Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Seung Bum Kim
- 1Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Park J, Kim MK, Yun BR, Han JH, Kim SB. Pseudogracilibacillus endophyticus sp. nov., a moderately thermophilic and halophilic species isolated from plant root. Int J Syst Evol Microbiol 2017; 68:165-169. [PMID: 29125459 DOI: 10.1099/ijsem.0.002475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive strain, designated DT7-02T, was isolated from the surface-sterilized root of Oenotherabiennis (evening primrose) and subjected to taxonomic characterization. Cells of DT7-02T were slender rod-shaped, motile by means of flagella, and oxidase- and catalase-positive. The colonies were circular, pinkish-yellow, opaque, glistering and 1-2 mm in diameter. The strain was moderately thermophilic and halophilic, as growth occurred at 20-44 °C (optimum 40 °C), pH 7-10 (optimum pH 8-9) and in the presence of 0-8 % of NaCl (optimum 4 %) in tryptic soy broth. The analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Pseudogracilibacillus of the family Bacillaceae, and the sequence similarity was 96.5 % with Pseudogracilibacillus auburnensis P-207T and 95.9 % with Pseudogracilibacillus marinus NIOT-bflm-S4T. Other related taxa were Ornithinibacillus contaminans DSM 22953T and Sinibacillus soli KCTC 33117T, with 16S rRNA gene sequence similarities of 95.4 and 94.3 %, respectively. The major cellular fatty acids of DT7-02T were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 35.1 mol%, and the respiratory quinone was MK-7. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The combination of chemotaxonomic properties enabled differentiation of DT7-02T from the other two species of the genus Pseudogracilibacillus. The results of phylogenetic, phenotypic and chemotaxonomic analyses demonstrate that strain DT7-02T (=KCTC 33854T=JCM 31192T) merits recognition as representing a novel species of the genus Pseudogracilibacillus, for which the name Pseudogracilibacillusendophyticus sp. nov. is proposed.
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Affiliation(s)
- Jisun Park
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Min-Kyeong Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Bo-Ram Yun
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
| | - Ji-Hye Han
- Bacterial Resources Research Team, Freshwater Bioresources Research Division, Nakdonggang National Institute of Biological Resources, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, 99 Daehak-Ro, Yuseong, Daejeon 34134, Republic of Korea
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12
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Zeng B, Zhao J, Guo W, Zhang S, Hua Y, Tang J, Kong F, Yang X, Fu L, Liao K, Yu X, Chen G, Jin L, Shuai S, Yang J, Si X, Ning R, Mishra S, Li Y. High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs. Front Microbiol 2017; 8:1929. [PMID: 29056930 PMCID: PMC5635199 DOI: 10.3389/fmicb.2017.01929] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/21/2017] [Indexed: 12/21/2022] Open
Abstract
While the skin microbiome has been shown to play important roles in health and disease in several species, the effects of altitude on the skin microbiome and how high-altitude skin microbiomes may be associated with health and disease states remains largely unknown. Using 16S rRNA marker gene sequencing, we characterized the skin microbiomes of people from two racial groups (the Tibetans and the Hans) and of three local pig breeds (Tibetan pig, Rongchang pig, and Qingyu pig) at high and low altitudes. The skin microbial communities of low-altitude pigs and humans were distinct from those of high-altitude pigs and humans, with five bacterial taxa (Arthrobacter, Paenibacillus, Carnobacterium, and two unclassified genera in families Cellulomonadaceae and Xanthomonadaceae) consistently enriched in both pigs and humans at high altitude. Alpha diversity was also significantly lower in skin samples collected from individuals living at high altitude compared to individuals at low altitude. Several of the taxa unique to high-altitude humans and pigs are known extremophiles adapted to harsh environments such as those found at high altitude. Altogether our data reveal that altitude has a significant effect on the skin microbiome of pigs and humans.
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Affiliation(s)
- Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Siyuan Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yutong Hua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jingsi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xuewu Yang
- Animal Husbandry and Technology Bureau of Daocheng County, Daocheng, China
| | - Lizhi Fu
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Kun Liao
- Pasturage Station of Tongjiang Agriculture Bureau, Bazhong, China
| | - Xianqiong Yu
- Animal Husbandry and Technology Bureau of Daocheng County, Daocheng, China
| | - Guohong Chen
- Animal Husbandry and Technology Bureau of Daocheng County, Daocheng, China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Surong Shuai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiandong Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaohui Si
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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13
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Zhang J, Ma XT, Gao JS, Zhao JJ, Yin HQ, Zhang CW, Zhang RJ, Zhang XX. Paenibacillus
oryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2016; 66:5000-5004. [DOI: 10.1099/ijsem.0.001459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jun Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- College of Life Science, The Yangtze University, Jingzhou 434025, PR China
| | - Xiao-Tong Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun-Sheng Gao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
- Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang 426182, PR China
| | - Juan-Juan Zhao
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Hua-Qun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, PR China
| | - Cai-Wen Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Rui-Jie Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiao-Xia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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14
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Sadaf K, Tushar L, Nirosha P, Podile AR, Sasikala C, Ramana CV. Paenibacillus arachidis sp. nov., isolated from groundnut seeds. Int J Syst Evol Microbiol 2016; 66:2923-2928. [DOI: 10.1099/ijsem.0.001124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- K. Sadaf
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - L. Tushar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - P. Nirosha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - A. R. Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad 500 085, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
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15
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Park J, Kim YR, Kim MK, Jo JH, Im WT, Kim SB. Humibacter soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:2509-2514. [PMID: 27081846 DOI: 10.1099/ijsem.0.001081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinobacterial strain, designated R1-20T, was isolated during a study of the bacterial diversity of the soil at a white heron nesting site. The isolate was non-motile, Gram-stain-positive and short rod-shaped. Colonies were dull white and convex with entire margin during the early stages of growth, and gradually became yellow. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter of the family Microbacteriaceae, as sequence similarity with its nearest neighbours was 97.16 % with Humibacter antriD7-27Tand 96.44 % with Humibacter albusDSM 18994T. However, the combination of cultural and physiological as well as chemotaxonomic properties clearly distinguished strain R1-20T from other Humibacter species. The DNA G+C content of strain R1-20T was 65.5 mol%, and the major respiratory isoprenoid quinone was menaquinone MK-11. The acyl group of the peptidoglycan was of acetyl type, and the diagnostic diamino acid was 2,4-diaminobutyric acid. Glutamic acid, alanine and glycine were also present in the cell wall. The major fatty acids of strain R1-20T were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain R1-20T merits recognition as a representative of a novel species of the genus Humibacter, for which the name Humibacter soli sp. nov. is proposed. The type strain is R1-20T (=KCTC 39614T=JCM 31015T).
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Affiliation(s)
- Jisun Park
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Yu Ri Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Min-Kyeong Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Jung Hun Jo
- Department of Biotechnology, Hankyoung National University, Anseong, South Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, Anseong, South Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
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16
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Guo GN, Zhou X, Zhao R, Chen XY, Chen ZL, Li XD, Li YH. Paenibacillus herberti sp. nov., an endophyte isolated from Herbertus sendtneri. Antonie van Leeuwenhoek 2015; 108:587-96. [PMID: 26155771 DOI: 10.1007/s10482-015-0514-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/17/2015] [Indexed: 11/26/2022]
Abstract
Strain R33(T), an endophyte recovered from Herbertus sendtneri, was identified as representing a novel species of the genus Paenibacillus by using a polyphasic taxonomic approach. The novel strain was observed to be a Gram-stain positive, aerobic, rod-shaped, motile and endospore-forming bacterium. The major polar lipids of strain R33(T) were identified as diphosphatidylglycerol, phosphatidylethanolamine, along with lesser amounts of phosphatidylglycerol, three unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The predominant isoprenoid quinone was identified as MK-7. The major fatty acids (>8.0 %) were found to be anteiso-C15:0 (40.0 %), C16:1 ω11c (9.4 %), C16:1 ω7c alcohol (8.5 %) and C16:0 (8.2 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The G+C content of genomic DNA was determined to be 56.9 mol%. The 16S rRNA gene sequence similarities of strain R33(T) to other Paenibacillus species ranged from 91.6 to 97.2 %, with high similarities to Paenibacillus humicus PC-147(T) and Paenibacillus pasadenensis SAFN-007(T). The phylogenetic analyses based on 16S rRNA gene sequences and the partial rpoB gene confirmed that strain R33(T) belongs to the genus Paenibacillus. However, strain R33(T) shows differential molecular characteristics compared to other related Paenibacillus species based on 16S rDNA-RFLP analyses; the DNA-DNA relatedness values between strain R33(T) and P. humicus PC-147(T), and that between strain R33(T) and P. pasadenensis SAFN-007(T), were 35.0 ± 2.0 and 41.4 ± 0.9 %, respectively. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain R33(T) is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus herberti is proposed (type strain R33(T) = CGMCC 1.15042(T) = DSM 29849(T)).
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Affiliation(s)
- Guan Nan Guo
- College of Life Science, Capital Normal University, Xisanhuan North Road 105, Haidian District, Beijing, 100048, China
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