1
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OuYang YT, Lv AP, Liu L, Li TT, Zhou Y, She TT, Cao LX, Jiao JY, Wang S, Li WJ. Isoptericola croceus sp. nov., a novel actinobacterium isolated from saline-alkali soil. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01849-6. [PMID: 37247101 DOI: 10.1007/s10482-023-01849-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023]
Abstract
A novel actinomycete, designated strain q2T, was isolated from the saline-alkaline soil, collected from Daqing, Heilongjiang province, China. The results of phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain q2T belongs to the genus Isoptericola, and showed the highest sequence similarity to Isoptericola halotolerans KCTC 19046T (98.48%) and Isoptericola chiayiensis KCTC 19740T (98.13%), respectively. The average nucleotide identity values between strain q2T and other members of the genus Isoptericola were lower than 95% recommended for distinguishing novel prokaryotic species. Cells of strain q2T were Gram-staining-positive, aerobic, non-motile, rod-shaped and non-spore-forming. Colonies of strain q2T were golden-yellow pigmented, tidy edged and smooth surfaced. Growth occurred at 15-37 °C (optimum, 29 °C), pH 7.0-10.0 (optimum, pH 8.0). The predominant respiratory quinones were MK-9(H4) and MK-9(H2). The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositol mannoside. The peptidoglycan compositions were L-alanine, D-aspartic, L-glutamic acid and L-lysine (type A4α). The major cellular fatty acids (> 10%) were anteiso-C15:0, iso-C15:0, and anteiso-C17:0. The G+C content of the genomic DNA was determined to be 69.7%. Based on the phenotypic, physiological, genotypic, and phylogenetic data, strain q2T represents a novel species of the genus Isoptericola, for which the name Isoptericola croceus sp. nov. is proposed. The type strain is q2T (= GDMCC 1.2923T = KCTC 49759T).
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Affiliation(s)
- Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ai-Ping Lv
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ting-Ting Li
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Yi Zhou
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Ting-Ting She
- School of Biology and Food Engineering, Guangdong University of Education, Guangzhou, 510303, People's Republic of China
| | - Li-Xiang Cao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation and Utilization/Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin, 150086, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
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Monteiro FAC, Bezerra SGDS, Castro LGZD, Oliveira FADS, Normando LRO, Melo VMM, Hissa DC. Neotropical Frog Foam Nest’s Microbiomes. Microorganisms 2023; 11:microorganisms11040900. [PMID: 37110323 PMCID: PMC10146838 DOI: 10.3390/microorganisms11040900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Amphibian foam nests are unique microenvironments that play a crucial role in the development of tadpoles. They contain high levels of proteins and carbohydrates, yet little is known about the impact of their microbiomes on tadpole health. This study provides a first characterization of the microbiome of foam nests from three species of Leptodactylids (Adenomera hylaedactyla, Leptodactylus vastus, and Physalaemus cuvieri) by investigating the DNA extracted from foam nests, adult tissues, soil, and water samples, analyzed via 16S rRNA gene amplicon sequencing to gain insight into the factors driving its composition. The results showed that the dominant phyla were proteobacteria, bacteroidetes, and firmicutes, with the most abundant genera being Pseudomonas, Sphingobacterium, and Paenibacillus. The foam nest microbiomes of A. hylaedactyla and P. cuvieri were more similar to each other than to that of L. vastus, despite their phylogenetic distance. The foam nests demonstrated a distinct microbiome that clustered together and separated from the microbiomes of the environment and adult tissue samples. This suggests that the peculiar foam nest composition shapes its microbiome, rather than vertical or horizontal transference forces. We expanded this knowledge into amphibian foam nest microbiomes, highlighting the importance of preserving healthy foam nests for amphibian conservation.
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Shang J, Xu L, Yang R, Zhao Y, Tang SK, Sun JQ. Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996. Syst Appl Microbiol 2022; 45:126351. [PMID: 35905572 DOI: 10.1016/j.syapm.2022.126351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 10/17/2022]
Abstract
Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.
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Affiliation(s)
- Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rui Yang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yang Zhao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China.
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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Xu L, Shang J, Tian J, Sun JQ, Shen B. Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005443] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, non-motile, strictly aerobic, yellow-coloured, rod-shaped bacterial strains, designated LR1S40T and M4N3S171T, were isolated from rhizosphere and bulk saline soil of Suaeda salsa collected in Inner Mongolia, China. Phylogenetic trees based on 16S rRNA gene and whole genome sequences showed that the two strains clustered tightly with strains of the genus
Ruania
. Strains LR1S40T and M4N3S171T had 95.5% 16S rRNA gene similarity to each other, and strain LR1S40T had 98.8, 98.7, 97.4 and <97.0% similarity to
Ruania alkalisoli
RN3S43T,
Ruania rhizosphaerae
LNNU 22110T,
Ruania alba
YIM 93306T and all other current type strains, while strain M4N3S171T had 98.6 and <97.0% similarity to
R. alba
YIM 93306T, and all other current type strains, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values of LR1S40T and M4N3S171T with each other and to the other type strains of
Ruania
were well below the threshold values (95% for ANIb, 70% for dDDH) for differentiating a species. Diphosphatidylglycerol and phosphatidylglycerol were the major polar lipids in both strains. The predominant menaquinone in both strains was both MK-8. The genome of strain LR1S40T consisted of a 3557440 bp circular chromosome, with a G+C content of 71.1 mol%, while the genome of strain M4N3S171T consisted of 4270413 bp, with a G+C content of 67.6 mol%. The phylogenetic, physiological and phenotypic characteristics allowed discrimination of the two strains from their relatives. The names Ruania suaedae sp. nov. [type strain LR1S40T (=CGMCC 1.19028T=KCTC 49726T)] and Ruania halotolerans sp. nov. [type strain M4N3S171T (=CGMCC 1. 19142T=KCTC 49727T)] are therefore proposed. During the publication of
Haloactinobacterium kanbiaonis
,
Haloactinobacterium glacieicola
(type strain T3246-1T), which was selected as the reference strain for the identification of
H. kanbiaonis
, was reclassified as
Occultella glacieicola
. The two phylogenetic trees showed that
H. kanbiaonis
HY164T tightly clustered with
Occultella aeris
F300T, and had the highest 16S rRNA gene similarity (99.8%) to
O. aeris
F300T. Based on the phylogenetic analysis and the publication record,
Haloactinobacterium kanbiaonis
should be reclassified as Occultella kanbiaonis comb. nov.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Jing Tian
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
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Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria–Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1
ω6c and/or C16 : 1
ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus
Sphingobacterium
and had the highest sequence similarity to
Sphingobacterium tabacisoli
h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain C459-1T and
S. tabacisoli
h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other
Sphingobacterium
species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus
Sphingobacterium
, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.
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Tóth Á, Máté R, Kutasi J, Tóth E, Bóka K, Táncsics A, Nagy I, Kovács G, Kosztik J, Bata-Vidács I, Kukolya J. Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium. Int J Syst Evol Microbiol 2021; 71. [PMID: 34779758 DOI: 10.1099/ijsem.0.005105] [Citation(s) in RCA: 4] [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 Gram-reaction-negative bacterial strain, designated Kb22T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C15:0 (28.4%), summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) (25.7 %) and iso-C17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22T (=LMG 31574T=NCAIM B.02638T).
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Affiliation(s)
- Ákos Tóth
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Rózsa Máté
- BioFil Microbiological, Biotechnological and Biochemical Ltd., Budapest, Hungary
| | - József Kutasi
- BioFil Microbiological, Biotechnological and Biochemical Ltd., Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Kovács
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,University of Sopron, Sopron, Hungary
| | - Judit Kosztik
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Ildikó Bata-Vidács
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - József Kukolya
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
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Tóth Á, Bata-Vidács I, Kosztik J, Máté R, Kutasi J, Tóth E, Bóka K, Táncsics A, Nagy I, Kovács G, Kukolya J. Sphingobacterium pedocola sp. nov. a novel halotolerant bacterium isolated from agricultural soil. Antonie van Leeuwenhoek 2021; 114:1575-1584. [PMID: 34363180 PMCID: PMC8448689 DOI: 10.1007/s10482-021-01623-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
Abstract
A Gram-reaction-negative halotolerant bacterial strain, designated Ka21T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, highest similarity was found with Sphingobacterium alkalisoli Y3L14T (96.72%). Cells were observed to be aerobic, non-motile rods. The isolate was found to be able to grow between 0 and 10% of NaCl concentration. The assembled genome of strain Ka21T has a total length of 5.2 Mb with a G + C content of 41.0 mol%. According to the genome analysis, Ka21T encodes several glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in the soil. Based on phenotypic characteristics and phylogenetic analysis, it is concluded that strain Ka21T represents a novel species in the Sphingobacterium genus for which the name Sphingobacterium pedocola sp. nov. is proposed. The type strain of the species is strain Ka21T (= LMG 31575T = NCAIM B.02636T).
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Affiliation(s)
- Ákos Tóth
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary.
| | - Ildikó Bata-Vidács
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Judit Kosztik
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Rózsa Máté
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - József Kutasi
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,Institute of Biochemistry, Biological Research Centre, Eötvös Lorand Research Network, Szeged, Hungary
| | - Gábor Kovács
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,University of Sopron, Sopron, Hungary
| | - József Kukolya
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
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Sun JQ, Yiayeng PE, Xu L, Huang XX, Li Y. Ruania alkalisoli sp. nov., Isolated from Saline-Alkaline Soil. Curr Microbiol 2021; 78:3285-3291. [PMID: 34164698 DOI: 10.1007/s00284-021-02579-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022]
Abstract
A Gram-positive, strictly aerobic, ivory-colored, rod-shaped bacterial strain, designated RN3S43T, was isolated from saline-alkaline soil, in Tumd Right Banner, Inner Mongolia, China. Strain RN3S43T grew at 10-40 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 9.0), and 0-12.5% NaCl (optimum 2-4%). It was positive to oxidase, catalase, urease, and nitrate reductase. The methyl red and Voges-Proskauer tests were negative. The phylogenetic trees based on the 16S rRNA gene sequences and genome both showed that strain RN3S43T clustered with Ruania alba YIM 93306 T and shared 95.5% and < 95.0% of 16S rRNA gene similarities with R. alba YIM 93306 T and all the other type strains. MK-8 was the major respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and an unidentified lipid were the major polar lipids. The major fatty acids were anteiso-C15:0 and iso-C15:0. The genome consisted of a 4,448,708-bp circular chromosome, with a G+C content of 68.2%, predicting 3,911 coding sequence genes, 44 tRNA genes and two rRNA operons. The average nucleotide identity (ANI), amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values of strain RN3S43T to R. alba YIM 93306T were 79.0%, 79.2%, and 23.4%, respectively. The results of phylogenetic, physiological, and phenotypic tests allowed the discrimination of strain RN3S43T from its phylogenetic relatives. Ruania alkalisoli sp. nov. is therefore proposed, and the type strain is RN3S43T (=CGMCC 1.18652T = KCTC 49471T).
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Affiliation(s)
- Ji-Quan Sun
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
| | - Pa Eryang Yiayeng
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Xian Huang
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Yan Li
- Institute of Environment and Ecology & Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
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9
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Zhang XF, Shi R, Chen M, Zhou XK, Wei YQ, Cha QY, Li N, Su YX, Ma L, Mo MH, Cao Y. Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida. Int J Syst Evol Microbiol 2021; 71. [PMID: 34047689 DOI: 10.1099/ijsem.0.004823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30-37 ℃, at pH 7.0 and with 0-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611T showed the highest degree of 16S rRNA gene sequence similarity to Sphingobacterium olei HAL-9T (97.0 %), followed by Sphingobacterium alkalisoli Y3L14T (95.8 %). The respiratory quinone of strain 1.3611T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C15 : 0 (41.3 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 22.1 %) and iso-C17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611T and S. olei HAL-9T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611T (=KCTC 62980T=CCTCC AB 2018349T) as the type strain.
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Affiliation(s)
- Xiao-Fei Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Rui Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Min Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Xing-Kui Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yu-Qian Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Qi-Yan Cha
- Kunming Center for Disease Control and Prevention, Kunming, 650228, PR China
| | - Ni Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yuan-Xiao Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Li Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Ming-He Mo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Yi Cao
- Guizhou Academy of Tobacco Science, Guiyang, 550081, PR China
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10
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Zhang R, Dong N, Shen Z, Zeng Y, Lu J, Liu C, Zhou H, Hu Y, Sun Q, Cheng Q, Shu L, Cai J, Chan EWC, Chen G, Chen S. Epidemiological and phylogenetic analysis reveals Flavobacteriaceae as potential ancestral source of tigecycline resistance gene tet(X). Nat Commun 2020; 11:4648. [PMID: 32938927 PMCID: PMC7494873 DOI: 10.1038/s41467-020-18475-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/25/2020] [Indexed: 11/25/2022] Open
Abstract
Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet(X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X). Emergence of tigecycline-resistance tet(X) genes is of concern. Here, the authors determine tet(X) prevalence in more than 6,000 clinical Gram-negative bacterial isolates collected between 1994 to 2019 in hospitals in China and suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance genes.
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Affiliation(s)
- Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Jiauyue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Yanyan Hu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Qipeng Cheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, China
| | - Lingbing Shu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Jiachang Cai
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China.
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.
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11
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Complete Genome Sequence of Sphingobacterium psychroaquaticum Strain SJ-25, an Aerobic Bacterium Capable of Suppressing Fungal Pathogens. Curr Microbiol 2019; 77:115-122. [PMID: 31646352 DOI: 10.1007/s00284-019-01789-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/04/2019] [Indexed: 01/22/2023]
Abstract
Using antagonistic bacterium is an effective method to control plant disease by fungal pathogens. An aerobic bacterium designated SJ-25, capable of suppressing Fusarium graminearum, Exserohilum turcicum, Pythium aphanidermatum, and Cochliobolus sativus, was isolated from farmland soil. The phylogenetic analysis revealed that strain SJ-25 belongs to the species of Sphingobacterium psychroaquaticum. The genome of strain SJ-25 consists of a 4,396,535-bp chromosome with a G+C content of 41.7 mol%; including 3696 CDS, 64 tRNA genes and six rRNA operons. Genomic analysis revealed that its genome contains multiple genes responsible for biosynthesis of siderophore, methyl 4-hydroxybenzoate, chitinase, giving strain SJ-25 the antagonistic ability on fungi pathogen. Strain SJ-25 harbors sets genes responsible for production of 2, 3-butanediol and salicylic acid, which could elicit the induced systemic resistance of the host plant. This genome sequence could be used as a basis material for further exploration of antagonistic mechanisms on fungi, widening our understanding of the ecological role of the genus Sphingobacterium in farmland ecosystem.
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12
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Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2019; 69:1870-1874. [DOI: 10.1099/ijsem.0.003148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Cheng JF, Guo JX, Bian YN, Chen ZL, Li CL, Li XD, Li YH. Sphingobacterium athyrii sp. nov., a cellulose- and xylan-degrading bacterium isolated from a decaying fern (Athyrium wallichianum Ching). Int J Syst Evol Microbiol 2019; 69:752-760. [DOI: 10.1099/ijsem.0.003231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jian Fei Cheng
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Jie Xi Guo
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
- 2College of Teacher Education, Capital Normal University, Beijing 100048, PR China
| | - Yan Nan Bian
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Zhi Ling Chen
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Chun Li Li
- 3New Technique Centre, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xue Dong Li
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
| | - Yan Hong Li
- 1College of Life Sciences, Capital Normal University, Beijing 100048, PR China
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14
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Lee Y, Jin HM, Jung HS, Jeon CO. Sphingobacterium humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2017; 67:4632-4638. [PMID: 28945541 DOI: 10.1099/ijsem.0.002345] [Citation(s) in RCA: 9] [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 Gram-stain-negative, facultatively aerobic bacterium, designated strain D1T, was isolated from soil in South Korea. Cells of strain D1T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1T formed a phyletic lineage with Sphingobacterium hotanense XH4T within the genus Sphingobacterium. Strain D1T was most closely related to S. hotanense XH4T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603T (97.2 %), and the DNA-DNA relatedness level between strain D1T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1T (=KACC 18595T=JCM 31225T).
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Affiliation(s)
- Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyun Mi Jin
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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