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Wang X, Xiao Y, Deng Y, Sang X, Deng QL, Wang L, Yang YW, Zhang BH, Zhang YQ. Sphingomonas lacusdianchii sp. nov., an attached bacterium inhibited by metabolites from its symbiotic cyanobacterium. Appl Microbiol Biotechnol 2024; 108:309. [PMID: 38661971 PMCID: PMC11045571 DOI: 10.1007/s00253-024-13081-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 04/26/2024]
Abstract
An alpha-proteobacterial strain JXJ CY 53 T was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) collected from Lake Dianchi, China. JXJ CY 53 T was observed to be an aerobic, Gram-stain-negative, oval shaped, and mucus-secreting bacterium. It had C18:1ω7c and C16:0 as the major cellular fatty acids, Q-10 as the predominant ubiquinone, and sphingoglycolipid, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylmethylethanolamine as the polar lipids. The G + C content of DNA was 65.85%. The bacterium had 16S rRNA gene sequence identities of 98.9% and 98.7% with Sphingomonas panni DSM 15761 T and Sphingomonas hankookensis KCTC 22579 T, respectively, while less than 97.4% identities with other members of the genus. Further taxonomic analysis indicated that JXJ CY 53 T represented a new member of Sphingomonas, and the species epithet was proposed as Sphingomonas lacusdianchii sp. nov. (type strain JXJ CY 53 T = KCTC 72813 T = CGMCC 1.17657 T). JXJ CY 53 T promoted the growth of MF-905 by providing bio-available phosphorus and nitrogen, plant hormones, vitamins, and carotenoids. It could modulate the relative abundances of nonculturable bacteria associated with MF-905 and influence the interactions of MF-905 and other bacteria isolated from the cyanobacterium, in addition to microcystin production characteristics. Meanwhile, MF-905 could provide JXJ CY 53 T dissolved organic carbon for growth, and control the growth of JXJ CY 53 T by secreting specific chemicals other than microcystins. Overall, these results suggest that the interactions between Microcystis and its attached bacteria are complex and dynamic, and may influence the growth characteristics of the cyanobacterium. This study provided new ideas to understand the interactions between Microcystis and its attached bacteria. KEY POINTS: • A novel bacterium (JXJCY 53 T) was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) • JXJCY 53 T modulated the growth and microcystin production of MF-905 • MF-905 could control the attached bacteria by specific chemicals other than microcystins (MCs).
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Affiliation(s)
- Xin Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yao Xiao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xue Sang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Qing-Lin Deng
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Le Wang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Yi-Wen Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China
| | - Bing-Huo Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, 332000, China.
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Jiang L, Choe H, Peng Y, Jeon D, Cho D, Jiang Y, Lee JH, Kim CY, Lee J. Sphingomonas abietis sp. nov., an Endophytic Bacterium Isolated from Korean Fir. J Microbiol Biotechnol 2023; 33:1292-1298. [PMID: 37528562 PMCID: PMC10619552 DOI: 10.4014/jmb.2303.03017] [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: 03/14/2023] [Revised: 06/20/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023]
Abstract
PAMB 00755T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20°C, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755T was most closely related to Sphingomonas chungangi MAH-6T (97.7%) and Sphingomonas polyaromaticivorans B2-7T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C18:1ω7c and/or C18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755T as the type strain (= KCTC 92781T = GDMCC 1.3779T).
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Affiliation(s)
- Lingmin Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Present address: National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Hanna Choe
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yuxin Peng
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Donghyun Cho
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Yue Jiang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Biosystem and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Cha Young Kim
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Jiyoung Lee
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Biosystem and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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Yuan YH, Liu LX, Wang L, Dong GZ, Liu YG. Effects of different seasons on bacterial community structure in rose rhizosphere soil. Appl Microbiol Biotechnol 2022; 107:405-417. [DOI: 10.1007/s00253-022-12290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022]
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Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7T, RRHST34T and RHCKR47T, were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus
Sphingomonas
, among which both strains RHCKR7T and RRHST34T showed a close relationship with
Sphingomonas yunnanensis
YIM 003T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47T was most closely related to
Sphingomonas palmae
KACC 17591T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7T and RRHST34T were 90.43 and 40.80 %, respectively, and their most closely related type strain,
S. yunnanensis
YIM 003T, showed 90.43 % ANI and 40.7 % dDDH with RHCKR7T and 90.21 % and 42.9 % with RRHST34T, respectively, and the corresponding values between strain RHCKR47T and
S. palmae
KACC 17591T were 85.53 % and 29.30%, respectively. They all took C14 : 0 2-OH and summed feature 8 (C18 : 1
ω6c and/or C18 : 1
ω7c) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym-Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus
Sphingomonas
, for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7T (=GDMCC 1.2663T=JCM 34794T), RRHST34T (=GDMCC 1.2665T=JCM 34796T) and RHCKR47T (=GDMCC 1.2664T=JCM 34795T) as the type strains, respectively.
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Dong L, Li S, Lian WH, Wei QC, Mohamad OAA, Hozzein WN, Ahmed I, Li WJ. Sphingomonas arenae sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 35060847 DOI: 10.1099/ijsem.0.005195] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1 ω6c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).
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Affiliation(s)
- Lei Dong
- 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, PR China
| | - Shuai 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, PR China
| | - Wen-Hui Lian
- 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, PR China
| | - Qi-Chuang Wei
- 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, PR China
| | - Osama Abdalla Abdelshafy Mohamad
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Bio-Resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Park Road, Islamabad 45500, Pakistan
| | - 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, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2021; 71. [PMID: 33513088 DOI: 10.1099/ijsem.0.004600] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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