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Gu M, Lv S, Hu M, Yang Z, Xiao Y, Wang X, Liang P, Zhang L. Sphingomonas bacteria could serve as an early bioindicator for the development of chlorantraniliprole resistance in Spodoptera frugiperda. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105891. [PMID: 38685253 DOI: 10.1016/j.pestbp.2024.105891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
The fall armyworm (Spodoptera frugiperda) was found to have invaded China in December 2018, and in just one year, crops in 26 provinces were heavily affected. Currently, the most effective method for emergency control of fulminant pests is to use of chemical pesticides. Recently, most fall armyworm populations in China were begining to exhibite low level resistance to chlorantraniliprole. At present, it is not possible to sensitively reflect the low level resistance of S. frugiperda by detecting target mutation and detoxification enzyme activity. In this study we found that 12 successive generations of screening with chlorantraniliprole caused S. frugiperda to develop low level resistance to this insecticide, and this phenotype was not attribute to genetic mutations in S. frugiperda, but rather to a marked increase in the relative amount of the symbiotic bacteria Sphingomonas. Using FISH and qPCR assays, we determined the amount of Sphingomonas in the gut of S. frugiperda and found Sphingomonas accumulation to be highest in the 3rd-instar larvae. Additionally, Sphingomonas was observed to provide a protective effect to against chlorantraniliprole stress to S. frugiperda. With the increase of the resistance to chlorantraniliprole, the abundance of bacteria also increased, we propose Sphingomonas monitoring could be adapted into an early warning index for the development of chlorantraniliprole resistance in S. frugiperda populations, such that timely measures can be taken to delay or prevent the widespread propagation of resistance to this highly useful agricultural chemical in S. frugiperda field populations.
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Affiliation(s)
- Meng Gu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shenglan Lv
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Mengfan Hu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ziyi Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuying Xiao
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuegui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; College of Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Pei Liang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Lei Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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2
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Li Q, Zhou Q, Chen Y, Hu K, Sarrà M, Li J, Liu A, Zou L, Liu S. Whole-genome sequencing of Sphingobium baderi SC-1 and identification of a crucial 3-phenoxybenzoic acid-degrading gene. Front Microbiol 2024; 15:1361335. [PMID: 38646623 PMCID: PMC11026547 DOI: 10.3389/fmicb.2024.1361335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
As an efficient degradation strain, Sphingobium baderi SC-1 can breakdown 3-phenoxybenzoic acid (3-PBA) with high proficiency. To investigate the internal factors that regulate this process, we conducted whole-genome sequencing and successfully identified the pivotal 3-PBA-degrading gene sca (1,230 bp). After sca was expressed in engineered bacteria, a remarkable degradation efficiency was observed, as 20 mg/L 3-PBA was almost completely decomposed within 24 h. The phenol was formed as one of the degradation products. Notably, in addition to their ability to degrade 3-PBA, the resting cells proficiently degraded 4'-HO-3-PBA and 3'-HO-4-PBA. In conclusion, we successfully identified and validated sca as the pivotal enzyme responsible for the efficient degradation of 3-PBA from Sphingomonas baderi, providing a crucial theoretical foundation for further explorations on the degradation potential of SC-1.
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Affiliation(s)
- Qin Li
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Qiao Zhou
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Yuan Chen
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Montserrat Sarrà
- Departament d’Enginyeria Química, Biològica i Ambiental, Escola d’Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Likou Zou
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya’an, Sichuan, China
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3
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De Castro O, Avino M, Carraturo F, Di Iorio E, Giovannelli D, Innangi M, Menale B, Mormile N, Troisi J, Guida M. Profiling microbial communities in an extremely acidic environment influenced by a cold natural carbon dioxide spring: A study of the Mefite in Ansanto Valley, Southern Italy. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13241. [PMID: 38407001 PMCID: PMC10895555 DOI: 10.1111/1758-2229.13241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
The Ansanto Valley's Mefite, one of the Earth's largest non-volcanic CO2 gas emissions, is distinguished by its cold natural carbon dioxide springs. These emissions originate from the intricate tectonics and geodynamics of the southern Apennines in Italy. Known for over two millennia for its lethal concentration of CO2 and other harmful gases, the Mefite has a reputation for being toxic and dangerous. Despite its historical significance and unique geological features, there is a lack of information on the microbial diversity associated with the Mefite's gas emissions. This study presents an integrated exploration of the microbial diversity in the mud soil, using high-throughput sequencing of 16S rRNA (Prokaryotes) and ITS2 (Fungi), alongside a geochemical site characterisation. Our findings reveal that the Mefite's unique environment imposes a significant bottleneck on microbial diversity, favouring a select few microbial groups such as Actinobacteria and Firmicutes for Prokaryotes, and Basidiomycota for Fungi.
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Affiliation(s)
- Olga De Castro
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- Botanical GardenNaplesItaly
| | - Mariano Avino
- Department of Biochemistry and Functional GenomicsSherbrooke UniversitySherbrookeQuebecCanada
| | | | | | - Donato Giovannelli
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- National Research CouncilInstitute of Marine Biological Resources and Biotechnologies—CNR‐IRBIMAnconaItaly
- Department of Marine and Coastal ScienceRutgers UniversityNew BrunswickNew JerseyUSA
- Marine Chemistry & Geochemistry DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
- Earth‐Life Science InstituteTokyo Institute of TechnologyTokyoJapan
| | - Michele Innangi
- EnvixLab, Department of Biosciences and TerritoryUniversity of Molise Contrada Fonte LapponePesche (IS)Italy
| | - Bruno Menale
- Department of BiologyUniversity of Naples Federico IINaplesItaly
- Botanical GardenNaplesItaly
| | - Nicolina Mormile
- Department of BiologyUniversity of Naples Federico IINaplesItaly
| | - Jacopo Troisi
- European Biomedical Research Institute of Salerno (EBRIS)SalernoItaly
- Theoreo srlMontecorvino Pugliano (SA)Italy
| | - Marco Guida
- Department of BiologyUniversity of Naples Federico IINaplesItaly
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Chen X, Li YD, Liu XM, Gao L, Zhou XK, Dong LM, Du G, Habib N, Li WJ, Duan YQ. Simplicispira sedimenti sp. nov., isolated from a sediment of drainage ditch in winery. Antonie Van Leeuwenhoek 2024; 117:13. [PMID: 38170218 DOI: 10.1007/s10482-023-01899-w] [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: 10/12/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024]
Abstract
A Gram-stain-negative, motile (by single polar flagellum) and rod-shaped bacterium, designated W1-6T, was isolated from a sediment of drainage ditch in winery in Guiyang, south-western China. Strain W1-6T showed the highest 16S rRNA gene sequence similarities with the type strain of Acidovorax wautersii (98.1%) and Simplicispira lacusdiani (97.9%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain W1-6T was placed adjacent to the members of the genus Simplicispira and formed a separat subclade. Cells showed oxidase and catalase negative reactions. The only respiratory quinone detected was ubiquinone-8 (Q-8). Summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) were predominant cellular fatty acids (> 10%) of strain W1-6T. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and five unidentified phospholipids were found in the polar lipid extraction. The genomic DNA G + C content was 65.6%. Strain W1-6T shared the highest digital DNA-DNA hybridization [dDDH, (27.6%)] and average nucleotide identity [ANI (84.3%)] values with the type strain of S. lacusdiani. The dDDH and ANI values were below the cutoff level (dDDH 70%; ANI 95-96%) for species delineation. The polyphasic characteristics indicated that the strain W1-6T represents a novel species of the genus Simplicispira, for which the name Simplicispira sedimenti sp. nov. is proposed. The type strain is W1-6T (= CGMCC 1.16274T = NBRC 115624T).
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Affiliation(s)
- Xing Chen
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Yuan-Dong Li
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Xiu-Ming Liu
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Li Gao
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Li-Min Dong
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China
| | - Gang Du
- School of Life Sciences, Yunnan Minzu University, Kunming, 650031, People's Republic of China
| | - Neeli Habib
- Department of Microbiology, Shaheed Benazir Bhutto Women University Peshawar, Peshawar, KPK, 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, People's Republic of China.
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, People's Republic of China.
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Tian M, Zhang W, Zhang G, Bahadur A, Wu S, Yu X, Wu Y, Jia P, Chen T, Liu G. A novel UV-resistant bacterium Sphingomonas endolithica sp. nov., and genomic analysis, isolated from the north slope of Mount Everest. Antonie Van Leeuwenhoek 2023; 117:5. [PMID: 38153511 DOI: 10.1007/s10482-023-01903-3] [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: 07/17/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Gram-stain-negative, aerobic, rod-shaped, non-motile bacterium strain ZFBP2030T was isolated from a rock on the North slope of Mount Everest. This strain contained a unique ubiquinone-10 (Q-10) as a predominant respiratory quinone. Among the tested fatty acids, the strain contained summed feature 8, C14:0 2OH, and C16:0, as major cellular fatty acids. The polar lipid profile contained phosphatidyl glycerol, phosphatidyl ethanolamine, three unidentified phospholipids, two unidentified aminolipids, and six unidentified lipids. The cell-wall peptidoglycan was a meso-diaminopimelic acid, and cell-wall sugars were ribose and galactose. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain ZFBP2030T was a member of the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas aliaeris DH-S5T (97.9%), Sphingomonas alpina DSM 22537T (97.3%) and Sphingomonas hylomeconis CCTCC AB 2013304T (97.0%). The 16S rRNA gene sequence similarity between ZFBP2030T and other typical strains was less than 97.0%. The average amino acid identity values, average nucleotide identity, and digital DNA-DNA hybridization values between strain ZFBP2030T and its highest sequence similarity strains were 56.9-79.9%, 65.1-82.2%, and 19.3-25.8%, respectively. The whole-genome size of the novel strain ZFBP2030T was 4.1 Mbp, annotated with 3838 protein-coding genes and 54 RNA genes. Moreover, DNA G + C content was 64.7 mol%. Stress-related functions predicted in the subsystem classification of the strain ZFBP2030T genome included osmotic, oxidative, cold/heat shock, detoxification, and periplasmic stress responses. The overall results of this study clearly showed that strain ZFBP2030T is a novel species of the genus Sphingomonas, for which the name Sphingomonas endolithica sp. nov. is proposed. The type of strain is ZFBP2030T (= EE 013T = GDMCC 1.3123T = JCM 35386T).
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Affiliation(s)
- Mao Tian
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 320 Donggang West Road, Lanzhou, 730000, Gansu Province, China.
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 320 Donggang West Road, Lanzhou, 730000, Gansu Province, China
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiyu Wu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xue Yu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 320 Donggang West Road, Lanzhou, 730000, Gansu Province, China
| | - Yujie Wu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Puchao Jia
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, 320 Donggang West Road, Lanzhou, 730000, Gansu Province, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Guangxiu Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu Province, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
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Sakda P, Xiang X, Song Z, Wu Y, Zhou L. Impact of Season on Intestinal Bacterial Communities and Pathogenic Diversity in Two Captive Duck Species. Animals (Basel) 2023; 13:3879. [PMID: 38136916 PMCID: PMC10740475 DOI: 10.3390/ani13243879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Vertebrates and their gut bacteria interact in complex and mutually beneficial ways. The intestinal microbial composition is influenced by several external influences. In addition to food, the abiotic elements of the environment, such as temperature, humidity, and seasonal fluctuation are also important determinants. Fecal samples were collected from two captive duck species, Baikal teal (Sibirionetta formosa) and common teal (Anas crecca) across four seasons (summer, autumn, winter, and spring). These ducks were consistently fed the same diet throughout the entire experiment. High throughput sequencing (Illumina Mi-seq) was employed to analyze the V4-V5 region of the 16sRNA gene. The dominant phyla in all seasons were Proteobacteria and Firmicutes. Interestingly, the alpha diversity was higher in winter for both species. The NMDS, PCoA, and ANOSIM analysis showed the distinct clustering of bacterial composition between different seasons, while no significant differences were discovered between duck species within the same season. In addition, LefSe analysis demonstrated specific biomarkers in different seasons, with the highest number revealed in winter. The co-occurrence network analysis also showed that during winter, the network illustrated a more intricate structure with the greatest number of nodes and edges. However, this study identified ten potentially pathogenic bacterial species, which showed significantly enhanced diversity and abundance throughout the summer. Overall, our results revealed that season mainly regulated the intestinal bacterial community composition and pathogenic bacteria of captive ducks under the instant diet. This study provides an important new understanding of the seasonal variations in captive wild ducks' intestinal bacterial community structure. The information available here may be essential data for preventing and controlling infections caused by pathogenic bacteria in captive waterbirds.
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Affiliation(s)
- Patthanan Sakda
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Xingjia Xiang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
| | - Zhongqiao Song
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
| | - Yuannuo Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (P.S.); (Z.S.); (Y.W.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Chizhou 247230, China
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Siddiqi MZ, Rajivgandhi G, Faiq M, Im WT. Isolation and Characterization of Sphingomonas telluris, Sphingomonas caseinilyticus Isolated from Wet Land Soil. Curr Microbiol 2023; 80:264. [PMID: 37386175 DOI: 10.1007/s00284-023-03339-4] [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] [Accepted: 05/22/2023] [Indexed: 07/01/2023]
Abstract
Two novel bacterial strains, designated as SM33T and NSE70-1T, were isolated from wet soil in South Korea. To get the taxonomic positions, the strains were characterized. The genomic information (both 16S rRNA gene and draft genome sequence analysis) show that both novel isolates (SM33T and NSE70-1T) belong to the genus Sphingomonas. SM33T share the highest 16s rRNA gene similarity (98.2%) with Sphingomonas sediminicola Dae20T. In addition, NSE70-1T show 96.4% 16s rRNA gene similarity with Sphingomonas flava THG-MM5T. The draft genome of strains SM33T and NSE70-1T consist of a circular chromosome of 3,033,485 and 2,778,408 base pairs with DNA G+C content of 63.9, and 62.5%, respectively. Strains SM33T and NSE70-1T possessed the ubiquinone Q-10 as the major quinone, and a fatty acid profile with C16:0, C18:1 2-OH, C16:1 ω7c/C16:1 ω6c (summed feature 3) and C18:1 ω7c/C18:1 ω6c (summed feature 8) as major fatty acids. The major polar lipids of SM33T and NSE70-1T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine, respectively. Moreover, genomic, physiological, and biochemical results allowed the phenotypic and genotypic differentiation of strains SM33T and NSE70-1T from their closest and other species of the genus Sphingomonas with validly published names. Therefore, the SM33T and NSE70-1T represent novel species of the genus Sphingomonas, for which the name Sphingomonas telluris sp. nov. (type strain SM33T = KACC 22222T = LMG 32193T), and Sphingomonas caseinilyticus (type strain NSE70-1T = KACC 22411T = LMG 32495T).
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea
| | - Govindan Rajivgandhi
- 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
| | - Muhammad Faiq
- Department of Food Science and Technology, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- AceEMzyme Co., Ltd., Academic Industry Cooperation, Room 403, 327 Jungang-ro, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
- HK Ginseng Research Center, 327 Jungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea.
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8
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Siddiqi MZ, Rajivgandhi G, Lee SY, Im WT. Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land. Int J Syst Evol Microbiol 2023; 73. [PMID: 37216283 DOI: 10.1099/ijsem.0.005884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Four novel bacterial strains, designated as RG327T, SE158T, RB56-2T and SE220T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas. The draft genomes of RG327T, SE158T, RB56-2T and SE220T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C16 : 0, C17 : 1ω6c, C18 : 1 2-OH, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327T, SE158T, RB56-2T and SE220T to the genus Sphingomonas. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327T, SE158T, RB56-2T and SE220T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas, for which the names Sphingomonas anseongensis sp. nov. (RG327T = KACC 22409T = LMG 32497T), Sphingomonas alba sp. nov. (SE158T = KACC 224408T = LMG 324498T), Sphingomonas brevis (RB56-2T = KACC 22410T = LMG 32496T) and Sphingomonas hankyongi sp. nov., (SE220T = KACC 22406T = LMG 32499T) are proposed.
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Affiliation(s)
- Muhammad Zubair Siddiqi
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
| | - Govindan Rajivgandhi
- 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 YatSen University, Guangzhou 510275, PR China
| | - Soon-Youl Lee
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Jungang-ro Anseong-si, Gyeonggi-do 17579, Republic of Korea
- HK Ginseng Research Center, Hankyong National University, 327 Jungang-ro Anseong-si, Gyonggi-do, 13449, Republic of Korea
- AceEMzyme Co., Ltd., Room 733, 815 Daewangpangyo-ro, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13449, Republic of Korea
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Sorouri B, Rodriguez CI, Gaut BS, Allison SD. Variation in Sphingomonas traits across habitats and phylogenetic clades. Front Microbiol 2023; 14:1146165. [PMID: 37138640 PMCID: PMC10150699 DOI: 10.3389/fmicb.2023.1146165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available Sphingomonas genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between Sphingomonas habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that Sphingomonas strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes. Sphingomonas strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that Sphingomonas gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about Sphingomonas and facilitate applications in bioremediation.
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Affiliation(s)
- Bahareh Sorouri
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
- *Correspondence: Bahareh Sorouri,
| | - Cynthia I. Rodriguez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, United States
- Department of Earth System Science, University of California Irvine, Irvine, CA, United States
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10
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Kim I, Chhetri G, So Y, Jung Y, Park S, Seo T. Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots. Arch Microbiol 2022; 205:16. [PMID: 36477930 DOI: 10.1007/s00203-022-03360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Three bacterial strains, designated RP10T, RMG20T, and MG17T, were isolated from Liriope platyphylla fruit (strain RP10T), soil (RMG20T), and Tagetes patula roots (MG17T) collected in Goyang, Republic of Korea. The 16S rRNA gene sequences revealed that strains RP10T, RMG20T, and MG17T were closely related to Sphingomonas melonis DSM 14444 T (highest similarity of the strain RP10T), Sphingomonas asaccharolytica DSM 10564 T (strain RMG20T), and Sphingomonas suaedae JCM 33850 T (strain MG17T) with 98.0-99.0% highest sequence similarity. The 16S rRNA gene sequences similarity between strains RP10T, RMG20T, and MG17T was 96.6-97.4%. Strains RP10T, RMG20T, MG17T, and the closely related type strains have digital DNA-DNA hybridization and average nucleotide identity values of 19.4-65.3% and 74.0-95.7%, respectively. Based on phylogenetic, biochemical, chemotaxonomic, and phenotypic data, strains RP10T, RMG20T, and MG17T are considered to represent novel species of the genus Sphingomonas, for which the name Sphingomonas liriopis sp. nov. (type strain RP10T = KACC 22357 T = TBRC 15161 T), Sphingomonas donggukensis sp. nov. (type strain RMG20T = KACC 22358 T = TBRC 15162 T), and Sphingomonas tagetis sp. nov. (type strain MG17T = KACC 22355 T = TBRC 15160 T), are proposed.
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, 10326, Republic of Korea.
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11
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Jeon D, Jiang L, Peng Y, Seo J, Li Z, Park SH, Jeong RD, Park SJ, Jeong JC, Lee J. Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. 'Cheungsam'. Int J Syst Evol Microbiol 2022; 72. [PMID: 36260506 DOI: 10.1099/ijsem.0.005566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4T is related to species of the genus Sphingomonas, and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244T and Sphingomonas leidyi DSM 4733T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4T and S. kyenggiensis KCTC 42244T, and S. leidyi DSM 4733T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C14 : 0 2-OH, C16 : 0, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4T (=KCTC 92075T = GDMCC 1.3018T).
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Affiliation(s)
- Doeun Jeon
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Lingmin Jiang
- 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
| | - Jiyoon Seo
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Zhun Li
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Seung-Hwan Park
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Rae-Dong Jeong
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Ju Park
- Division of Biological Science, Wonkwang University, Iksan 54538, Republic of Korea
| | - Jae Cheol Jeong
- 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
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12
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Wang L, Zhang Q, Mei H, Cui X, Wang M, Zhu Y, Ji B, Wei Y. Different Distribution of Core Microbiota in Upper Soil Layer in Two Places of North China Plain. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2207220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Backgrounds:
Soils harbor diverse bacteria, and these bacteria play important roles in soil nutrition cycling and carbon storage. Numerous investigations of soil microbiota had been performed, and the core microbiota in different soil or vegetation soil types had been described. The upper layer of soil, as a source of organic matter, is important and affected by the habitats and dominant bacteria. However, the complexity of soil environments and relatively limited information of many geographic areas had attracted great attention on comprehensive exploration of soil microbes in enormous types of soil.
Methods:
To reveal the core upper layer soil microbiota, soil samples from metropolis and countryside regions in the North China Plain were investigated using high-throughput sequencing strategy.
Results:
The results showed that the most dominant bacteria are Proteobacteria (38.34%), Actinobacteria (20.56%), and Acidobacteria (15.18%). At the genus-level, the most abundant known genera are Gaiella (3.66%), Sphingomonas (3.6%), Acidobacteria Gp6 (3.52%), and Nocardioides (2.1%). Moreover, several dominant operational taxanomy units OTUs, such as OTU_3 and OTU_17, were identified to be associated with the soil environment. Microbial distributions of the metropolis samples were different from the countryside samples, which may reflect the environments in the countryside were more diverse than in the metropolis. Microbial diversity and evenness were higher in the metropolis than in the countryside, which might due to the fact that human activity increased the microbial diversity in the metropolis.
Conclusion:
The upper layer soil core microbiota of the North China Plain were complex, and microbial distributions in these two places might be mainly affected by the human activity and environmental factors, not by the distance. Our data highlights the upper layer soil core microbiota in North China Plain, and provides insights for future soil microbial distribution studies in central China.
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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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14
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Changes of Microbial Diversity in Rhizosphere of Different Cadmium-Gradients Soil under Irrigation with Reclaimed Water. SUSTAINABILITY 2022. [DOI: 10.3390/su14148891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Water scarcity and the uneven distribution of water resources in China have resulted in water shortages for agricultural irrigation in arid and semi-arid areas. Reclaimed water used for agricultural irrigation has become an effective solution in the context of the global water shortage. In order to improve soil productivity and solve the shortage of water resources, we carried out reclaimed water irrigation experiments on polluted soil. Compared with full irrigation treatments, the EC value of reclaimed water under deficit irrigation treatments decreased by 2.89–42.90%, and the content of organic matter increased by 6.31–12.10%. The proportion of Acidobacteria community in soils with different cadmium concentration gradients irrigated with reclaimed water ranged from 13.6% to 30.5%, its relative abundance decreased with the increase of soil cadmium concentration. In particular, the relative abundance of Pseudomonas pathogens in deficit irrigation treatments was lower than that of the full irrigation treatments. RDA analysis showed that the environmental factors that played a leading role in the change of microbial community structure were organic matter and pH. Furthermore, the metabolic function potential of the rhizosphere soil bacterial community in deficit irrigation treatments was higher than that of full irrigation treatments with reclaimed water. This study proved that reclaimed water irrigation for cadmium contaminated soil did not aggravate the pollution level and promoted the soil ecological environment with better microbial community diversity.
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15
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Ye C, Xian X, Bao R, Zhang Y, Feng M, Lin W, Yu X. Recovery of microbiological quality of long-term stagnant tap water in university buildings during the COVID-19 pandemic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150616. [PMID: 34592279 PMCID: PMC9752782 DOI: 10.1016/j.scitotenv.2021.150616] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 05/10/2023]
Abstract
Stagnant water can cause water quality deterioration and, in particular, microbiological contaminations, posing potential health risks to occupants. University buildings were unoccupied with little water usage during the COVID-19 pandemic. It's an opportunity to study microbiological quality of long-term stagnant water (LTSW) in university buildings. The tap water samples were collected for three months from four types of campus buildings to monitor water quality and microbial risks after long-term stagnation. Specifically, the residual chlorine, turbidity, and iron/zinc were disqualified, and the heterotrophic plate counts (HPC) exceeded the Chinese national standard above 100 times. It took 4-54 days for these parameters to recover to the routine levels. Six species of pathogens were detected with high frequency and levels (101-105 copies/100 mL). Remarkably, L. pneumophilia occurred in 91% of samples with turbidity > 1 NTU. The absence of the culturable cells for these bacteria possibly implied their occurrence in a viable but non-culturable (VBNC) status. The bacterial community of the stagnant tap water differed significantly and reached a steady state in more than 50 days. Furthermore, a high concentration of endotoxin (>10 EU/mL) was found in LTSW, which was in accordance with the high proportion of dead bacteria. The results suggested that the increased microbiological risks require more attention and the countermeasures before the building reopens should be taken.
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Affiliation(s)
- Chengsong Ye
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Xuanxuan Xian
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Ruihan Bao
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Yiting Zhang
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Mingbao Feng
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Wenfang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xin Yu
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China.
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Duan DY, Liu YK, Liu L, Liu GH, Cheng TY. Microbiome analysis of the midguts of different developmental stages of Argas persicus in China. Ticks Tick Borne Dis 2021; 13:101868. [PMID: 34800866 DOI: 10.1016/j.ttbdis.2021.101868] [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] [Received: 09/22/2020] [Revised: 09/25/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
Argas persicus is an ectoparasite of poultry. The bacterial community structure and the pathogenic bacteria associated with different developmental stages of A. persicus have implications for control. Argas persicus were collected from chickens in the city of Jiuquan in Gansu, China. Bacterial DNA was extracted from the midgut contents of blood engorged larvae, nymphs and adult females. The V3-V4 hypervariable regions of 16S rRNA genes were sequenced using the IonS5™XL platform. Identification of Rickettsia spp. and detection of Coxiella burnetii were performed using PCR on target genes. The bacterial diversity within larvae was the highest and the bacterial diversity within nymphs was greater than that of adults. At different classification levels, seven bacterial phyla were common phyla, 27 genera were common genera, and 18 species were common species in the three samples. At the phylum level, Proteobacteria showed a marked predominance in all samples. Rickettsia, Stenotrophomonas, Spiroplasma, and Coxiella were the dominant bacteria at the genus level. The Rickettsia species in A. persicus was identified as Rickettsia hoogstraalii and the Coxiella species was identified as a Coxiella-like endosymbiont. Additionally, some bacterial species such as Pseudomonas geniculata, Sphingomonas koreensis, and Acinetobacter haemolyticus were reported here for the first time in A. persicus.
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Affiliation(s)
- De-Yong Duan
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Yu-Ke Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Lei Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Guo-Hua Liu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China.
| | - Tian-Yin Cheng
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China.
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Kanatani JI, Watahiki M, Kimata K, Kato T, Uchida K, Kura F, Amemura-Maekawa J, Isobe J. Detection of Legionella species, the influence of precipitation on the amount of Legionella DNA, and bacterial microbiome in aerosols from outdoor sites near asphalt roads in Toyama Prefecture, Japan. BMC Microbiol 2021; 21:215. [PMID: 34273946 PMCID: PMC8285874 DOI: 10.1186/s12866-021-02275-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Background Legionellosis is caused by the inhalation of aerosolized water contaminated with Legionella bacteria. In this study, we investigated the prevalence of Legionella species in aerosols collected from outdoor sites near asphalt roads, bathrooms in public bath facilities, and other indoor sites, such as buildings and private homes, using amoebic co-culture, quantitative PCR, and 16S rRNA gene amplicon sequencing. Results Legionella species were not detected by amoebic co-culture. However, Legionella DNA was detected in 114/151 (75.5%) air samples collected near roads (geometric mean ± standard deviation: 1.80 ± 0.52 log10 copies/m3), which was comparable to the numbers collected from bathrooms [15/21 (71.4%), 1.82 ± 0.50] but higher than those collected from other indoor sites [11/30 (36.7%), 0.88 ± 0.56] (P < 0.05). The amount of Legionella DNA was correlated with the monthly total precipitation (r = 0.56, P < 0.01). It was also directly and inversely correlated with the daily total precipitation for seven days (r = 0.21, P = 0.01) and one day (r = − 0.29, P < 0.01) before the sampling day, respectively. 16S rRNA gene amplicon sequencing revealed that Legionella species were detected in 9/30 samples collected near roads (mean proportion of reads, 0.11%). At the species level, L. pneumophila was detected in 2/30 samples collected near roads (the proportion of reads, 0.09 and 0.11% of the total reads number in each positive sample). The three most abundant bacterial genera in the samples collected near roads were Sphingomonas, Streptococcus, and Methylobacterium (mean proportion of reads; 21.1%, 14.6%, and 1.6%, respectively). In addition, the bacterial diversity in outdoor environment was comparable to that in indoor environment which contains aerosol-generating features and higher than that in indoor environment without the features. Conclusions DNA from Legionella species was widely present in aerosols collected from outdoor sites near asphalt roads, especially during the rainy season. Our findings suggest that there may be a risk of exposure to Legionella species not only in bathrooms but also in the areas surrounding asphalt roads. Therefore, the possibility of contracting legionellosis in daily life should be considered. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02275-2.
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Affiliation(s)
- Jun-Ichi Kanatani
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan.
| | - Masanori Watahiki
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan
| | - Keiko Kimata
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan
| | - Tomoko Kato
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan
| | - Kaoru Uchida
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan
| | - Fumiaki Kura
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640, Tokyo, Japan
| | - Junko Amemura-Maekawa
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, 162-8640, Tokyo, Japan
| | - Junko Isobe
- Department of Bacteriology, Toyama Institute of Health, 17-1 Nakataikoyama, 939-0363, Imizu-city, Toyama, Japan
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18
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Sharma M, Khurana H, Singh DN, Negi RK. The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 280:111744. [PMID: 33280938 DOI: 10.1016/j.jenvman.2020.111744] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.
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Affiliation(s)
- Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Durgesh Narain Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.
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Ruiz-Lopez S, Foster L, Boothman C, Cole N, Morris K, Lloyd JR. Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site. Front Microbiol 2020; 11:587556. [PMID: 33329459 PMCID: PMC7732693 DOI: 10.3389/fmicb.2020.587556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/26/2020] [Indexed: 11/29/2022] Open
Abstract
The use of nuclear power has been a significant part of the United Kingdom’s energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 104–106 mL–1 were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.
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Affiliation(s)
- Sharon Ruiz-Lopez
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Lynn Foster
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Chris Boothman
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Nick Cole
- Sellafield Ltd., Warrington, United Kingdom
| | - Katherine Morris
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
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20
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Madhaiyan M, Saravanan VS, Wirth JS, Alex THH, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji L. Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants. Antonie van Leeuwenhoek 2020; 113:1617-1632. [PMID: 32949307 DOI: 10.1007/s10482-020-01468-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = KACC 17594T).
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Affiliation(s)
- Munusamy Madhaiyan
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
| | | | - Joseph S Wirth
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, USA
| | - Tan Hian Hwee Alex
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Science, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - William B Whitman
- Department of Microbiology, University of Georgia, 527 Biological Sciences Building, Athens, GA, 30602-2605, USA
| | - Lianghui Ji
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.
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Characterization of vB_StuS_MMDA13, a Newly Discovered Bacteriophage Infecting the Agar-Degrading Species Sphingomonas turrisvirgatae. Viruses 2020; 12:v12080894. [PMID: 32824138 PMCID: PMC7472734 DOI: 10.3390/v12080894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 01/21/2023] Open
Abstract
Members of Sphingomonas genus have gained a notable interest for their use in a wide range of biotechnological applications, ranging from bioremediation to the production of valuable compounds of industrial interest. To date, knowledge on phages targeting Sphingomonas spp. are still scarce. Here, we describe and characterize a lytic bacteriophage, named vB_StuS_MMDA13, able to infect the Sphingomonas turrisvirgatae MCT13 type strain. Physiological characterization demonstrated that vB_StuS_MMDA13 has a narrow host range, a long latency period, a low burst size, and it is overall stable to both temperature and pH variations. The phage has a double-stranded DNA genome of 63,743 bp, with 89 open reading frames arranged in two opposite arms separated by a 1186 bp non-coding region and shows a very low global similarity to any other known phages. Interestingly, vB_StuS_MMDA13 is endowed with an original nucleotide modification biosynthetic gene cluster, which greatly differs from those of its most closely related phages of the Nipunavirus genus. vB_StuS_MMDA13 is the first characterized lytic bacteriophage of the Siphoviridae family infecting members of the Sphingomonas genus.
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Zhang H, Xu L, Zhang JX, Sun JQ. Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa. Int J Syst Evol Microbiol 2020; 70:3816-3823. [DOI: 10.1099/ijsem.0.004238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with
Sphingomonas turrisvirgatae
MCT13T and
Sphingomonas koreensis
JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to
S. koreensis
JSS-26T and
S. turrisvirgatae
MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C16 : 0 and C17 : 1
ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with
S. turrisvirgatae
MCT13T and
S. koreensis
JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus
Sphingomonas
, for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).
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Affiliation(s)
- Hui Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Jin-Xin Zhang
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
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23
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Zheng X, Liu G, Wang Z, Wang J, Zhang H, Liu B. Bacillus dafuensis sp. Nov., Isolated from a Forest Soil in China. Curr Microbiol 2020; 77:2049-2055. [PMID: 32382951 DOI: 10.1007/s00284-020-02014-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/24/2020] [Indexed: 11/29/2022]
Abstract
A Gram-staining-positive, motile, rod-shaped, aerobic bacterial strain FJAT-25496 T was isolated from a forest soil sample collected from Dafu County, Chengdu City, Sichuan Province, China. Strain FJAT-25496 T grew at 15-50 °C (optimum 35 °C), pH 6.0-10.0 (optimum 8.0), and NaCl tolerance of 0-4.0% (w/v) (optimum 0%). The strain contained iso-C15:0 and anteiso-C15:0 as the predominant cellular fatty acids as well as MK-7 as the only menaquinone. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidyl glycerol (PG). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FJAT-25496 T was a member of the genus Bacillus, and most closely related to Bacillus solani FJAT-18043 T (97.8%), Bacillus praedii FJAT-25547 T (97.8%), Bacillus depressus BZ1T (97.7%), Bacillus oceanisediminis H2T (97.7%), and Bacillus ciccensis 5L6T (97.6%). Based on complete genome comparisons between strain FJAT-25496 T and the type strains of its closely related species, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 73.4-76.3% and 21.7-23.2%, respectively. The genomic DNA G + C content of strain FJAT-25496 T was 36.9%. On the basis of phenotypic, phylogenetic, chemotaxonomic, and genomic features, strain FJAT-25496 T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus dafuensis sp. nov. is proposed. The type strain is FJAT-25496 T (= CCTCC AB 2019182 T = KCTC 43120 T).
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Affiliation(s)
- Xuefang Zheng
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | | | - Ziran Wang
- Dean of Department of Biochemistry and Biotechnology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Jieping Wang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Haifeng Zhang
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China
| | - Bo Liu
- Agrobiological Resource Research Institute, Fujian Academy of Agriculture Sciences, Fuzhou, 350003, China.
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24
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Cha I, Kang H, Kim H, Joh K. Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba. Int J Syst Evol Microbiol 2019; 69:3224-3229. [PMID: 31343398 DOI: 10.1099/ijsem.0.003613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain HMF7854T, isolated from a ginkgo tree, was an orange-pigmented, Gram-stain-negative, motile by means of a single flagellum, strictly aerobic, rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0-8.0 and 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF7854T belonged to the genus Sphingomonas and was most closely related to Sphingomonasagri HKS-06T (96.8 % sequence similarity). The major fatty acids were C17 : 1 ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 68.4 mol%. Thus, based on its phylogenetic, phenotypic and chemotaxonomic data, strain HMF7854T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasginkgonis sp. nov. is proposed. The type strain of the species is strain HMF7854T (=KCTC 62461T=NBRC 113337T).
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Affiliation(s)
- Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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25
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Sphingomonas aracearum sp. nov., isolated from rhizospheric soil of Araceae plants. Int J Syst Evol Microbiol 2019; 69:2972-2978. [DOI: 10.1099/ijsem.0.003477] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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26
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Distribution and characterization of N-acylhomoserine lactone (AHL)-degrading activity and AHL lactonase gene (qsdS) in Sphingopyxis. J Biosci Bioeng 2019; 127:411-417. [DOI: 10.1016/j.jbiosc.2018.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/27/2018] [Accepted: 10/07/2018] [Indexed: 11/18/2022]
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27
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Shi YL, Sun Y, Jiang ZM, Ruan ZY, Su J, Yu LY, Zhang YQ. Simplicispira lacusdiani sp. nov., a novel betaproteobacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2019; 69:129-133. [DOI: 10.1099/ijsem.0.003112] [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)
- Yun-Lei Shi
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Ye Sun
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Zhu-Ming Jiang
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Zhi-Yong Ruan
- 2Institute of Agricultural Resources and Regional Planning, CAAS, Beijing 100081, PR China
| | - Jing Su
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Li-Yan Yu
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
| | - Yu-Qin Zhang
- 1Chinese Academy of Medical Sciences and Peking Union Medical College, Institute of Medicinal Biotechnology, Beijing 100050, PR China
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28
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Whole-Genome Sequence of Sphingomonas sp. Strain FARSPH, a Novel Sf9 Insect Cell Culture Contaminant. Microbiol Resour Announc 2018; 7:MRA01128-18. [PMID: 30533768 PMCID: PMC6256503 DOI: 10.1128/mra.01128-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we report the whole-genome sequence of Sphingomonas sp. strain FARSPH, isolated from an insect cell line as a contaminant. FARSPH shared high identity with Sphingomonas melonis and Sphingomonas aquatilis strains. Due to this finding, we recommend taking this genus into consideration for cell culture quality control.
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29
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Sphingopyxis lindanitolerans sp. nov. strain WS5A3pT enriched from a pesticide disposal site. Int J Syst Evol Microbiol 2018; 68:3935-3941. [DOI: 10.1099/ijsem.0.003094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Thaller MC, D'Andrea MM, Marmo P, Civitareale C, Casu F, Migliore L. Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater. Int J Syst Evol Microbiol 2018; 68:2794-2799. [PMID: 30180924 DOI: 10.1099/ijsem.0.002896] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow pigmented and agar-pitting colony was isolated from a water sample obtained from a drainage ditch within a disused system of constructed wetlands. The strain was purified and named MCT13T. This rod-shaped, Gram-negative, oxidase- and catalase-positive, aerobic, non-spore-forming, and non-motile strain formed round colonies and grew optimally at pH 7.5±0.2, at 28-30 °C on LB agar, with 0-0.5 % NaCl. The 16S rRNA gene sequence analysis placed the MCT13T isolate within the Sphingomonas (sensu stricto) cluster. The DNA G+C content was 65.3 %. The only observed ubiquinone was Q10. The major fatty acids included C17 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major polyamine was spermidine. The 16S rRNA gene phylogenetic analysis performed on the whole sequence, showed the closest relative of MCT13T to be Sphingomonas koreensis (98.52 %); however, there are several genotypic and phenotypic differences between the novel isolate and the type strain JSS26T of S. koreensis. On the basis of these results, strain MCT13T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas turrisvirgatae sp. nov. is proposed. The type strain is MCT13T (=DSM 105457T=BAC RE RSCIC 7T).
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Affiliation(s)
| | - Marco Maria D'Andrea
- 2Department of Medical Biotechnologies, University of Siena, Siena, Italy.,1Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Pasquale Marmo
- 1Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Cinzia Civitareale
- 3Food Safety, Nutrition and Veterinary Public Health Department, Food Chemical Safety Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Casu
- 4The University of Auckland, 49 Symonds Street, Auckland, 1010, New Zealand
| | - Luciana Migliore
- 1Department of Biology, University of Rome Tor Vergata, Rome, Italy
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31
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Feng GD, Yang SZ, Zhu HH, Li HP. Emended descriptions of the species Sphingomonas adhaesiva Yabuuchi et al. 1990 and Sphingomonas ginsenosidimutans Choi et al. 2011. Int J Syst Evol Microbiol 2018; 68:970-973. [DOI: 10.1099/ijsem.0.002557] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guang-Da Feng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
| | - Song-Zhen Yang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Hua-Ping Li
- College of Agriculture, South China Agricultural University, Guangzhou 510642, PR China
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32
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Li L, Osman G, Salam N, Mohamed OA, Jiao J, Ma J, Asem MD, Xiao M, Li WJ. Limoniibacter endophyticus gen. nov., sp. nov., an alphaproteobacterium isolated from the roots of Limonium otolepis. Arch Microbiol 2018; 200:663-670. [PMID: 29356837 DOI: 10.1007/s00203-017-1472-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 11/26/2022]
Abstract
A Gram-negative bacterium, designated as strain YIM 690229T, was isolated from the roots of Limonium otolepis. The strain was able to grow at 10-40 °C (optimum, 28-37 °C), pH 6.0-8.0 (optimum, 7.0) and in the presence of up to 7% NaCl (w/v) (optimum, up to 2.5%). Comparative 16S rRNA gene sequence analysis revealed that strain YIM 690229T shared less than 93.9% sequence similarities with members within the order Rhizobiales, and was remotely related to members of the family Hyphomicrobiaceae. Strain YIM 690229T was characterized by the presence of Q-10 as the predominant respiratory lipoquinone. The major fatty acids (> 10%) detected were C18:1 ω7c, C16:0, anteiso-C15:0 and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanoamine and two unidentified lipids. The genomic DNA G + C content was 57.2 mol%. Data from this polyphasic taxonomy study suggested that strain YIM 690229T should be classified as a new species of a new genus within the family Hyphomicrobiaceae for which the name Limoniibacter endophyticus gen. nov., sp. nov., is proposed. The type species of the genus Limoniibacter gen. nov. is Limoniibacter endophyticus. The type strain of the species Limoniibacter endophyticus sp. nov. is YIM 690229T (= KCTC 42097T = JCM 30141T = CCTCC AB 2014130T = CGMCC 1.12906T).
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Affiliation(s)
- Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China
| | - Ghenijan Osman
- Xinjiang Institute of Microbiology, Xinjiang Academy of Agricultural Sciences, Ürümqi, 830091, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Osama Abdalla Mohamed
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China
- Environmental Science Department, Institute for Post Graduate of Environment Study, Arish University, North Sinai, 45511, Egypt
| | - Jianyu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jinbiao Ma
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China
| | - Mipeshwaree Devi Asem
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, 830011, People's Republic of China.
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Chaudhary DK, Kim J. Sphingopyxis nepalensis sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:364-370. [DOI: 10.1099/ijsem.0.002514] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Li Y, Ai MJ, Sun Y, Zhang YQ, Zhang JQ. Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2017; 67:3144-3149. [DOI: 10.1099/ijsem.0.001778] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong Li
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong Universit, Chengdu 610031, PR China
| | - Meng-Jie Ai
- Institute of Mediicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Ye Sun
- Institute of Mediicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Mediicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Jian-Qiang Zhang
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong Universit, Chengdu 610031, PR China
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Lee KC, Kim KK, Eom MK, Kim JS, Kim DS, Ko SH, Yang SH, Lee JS. Sphingomonas gotjawalisoli sp. nov., isolated from soil of a lava forest. Int J Syst Evol Microbiol 2017; 67:2975-2979. [PMID: 28820106 DOI: 10.1099/ijsem.0.002061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated SN6-9T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Strain SN6-9T was Gram-stain-negative, motile, oxidase- and catalase-negative, yellow-pigmented and rod-shaped. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids, Q-10 as the predominant isoprenoid quinone, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and two unidentified phospholipids as the polar lipids. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a separate lineage in the genus Sphingomonas. Based on the results from this polyphasic taxonomic study, it is concluded that strain SN6-9T represents a novel species in the genus Sphingomonas. The name Sphingomonas gotjawalisoli sp. nov. is proposed; the type strain is SN6-9T (=KCTC 52405T=NRRL B-65395T).
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Affiliation(s)
- Keun Chul Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Kwang Kyu Kim
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Jong-Shik Kim
- Gyeongbuk Institute for Marine Bioindustry, Uljin, 767-813, Republic of Korea
| | - Dae-Shin Kim
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 63341, Republic of Korea
| | - Suk-Hyung Ko
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 63341, Republic of Korea
| | - Seung-Hoon Yang
- World Heritage and Mt. Hallasan Research Institute, Jeju Special Self-Governing Province, 63341, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea.,University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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36
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Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017; 67:2834-2841. [DOI: 10.1099/ijsem.0.002029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Dong Lee
- Faculty of Science Education, Jeju National University, Jeju63243, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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37
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Ko Y, Hwang WM, Kim M, Kang K, Ahn TY. Sphingomonas silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:2704-2710. [DOI: 10.1099/ijsem.0.002001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yongseok Ko
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Woon Mo Hwang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Minsun Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
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Biocatalytic Asymmetric Synthesis of (1R, 2S)-N-Boc-vinyl-ACCA Ethyl Ester with a Newly Isolated Sphingomonas aquatilis. Appl Biochem Biotechnol 2017; 184:500-512. [DOI: 10.1007/s12010-017-2567-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/21/2017] [Indexed: 01/17/2023]
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Chaudhary DK, Dahal RH, Kim J. Sphingopyxis solisilvae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:1820-1826. [PMID: 28613148 DOI: 10.1099/ijsem.0.001869] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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Wang H, Xie C, Zhu P, Zhou NY, Lu Z. Two Novel Sets of Genes Essential for Nicotine Degradation by Sphingomonas melonis TY. Front Microbiol 2017; 7:2060. [PMID: 28144232 PMCID: PMC5239795 DOI: 10.3389/fmicb.2016.02060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/07/2016] [Indexed: 11/13/2022] Open
Abstract
Nicotine is a type of environmental pollutant present in the tobacco waste that is generated during tobacco manufacturing. Sphingomonas melonis TY can utilize nicotine as a sole source of carbon, nitrogen and energy via a variant of the pyridine and pyrrolidine pathway (the VPP pathway). In this study, we report the identification of two novel sets of genes, ndrA1A2A3, and ndrB1B2B3B4, which are crucial for nicotine degradation by strain TY. ndrA1A2A3 and ndrB1B2B3B4 exhibit similarity with both nicotine dehydrogenase ndh from Arthrobacter nicotinovorans and nicotine hydroxylase vppA from Ochrobactrum sp. SJY1. The transcriptional levels of ndrA1A2A3 and ndrB1B2B3B4 in strain TY were significantly upregulated in the presence of nicotine. Furthermore, ndrA1 or ndrB2 knockout resulted in a loss of the ability to degrade nicotine, whereas gene complementation restored the capacity of each mutant to utilize nicotine for growth. Biodegradation assays indicated that the mutant strains retained the ability to degrade the first intermediate in the pathway, 6-hydroxynicotine (6 HN). However, heterologous expression of ndrA1A2A3 and ndrB1B2B3B4 did not confer nicotine dehydrogenase activity to E. coli DH5α, Pseudomonas putida KT2440 or Sphingomonas aquatilis. These results provide information on the VPP pathway of nicotine degradation in S. melonis TY, and we conclude that these two sets of genes have essential functions in the conversion of nicotine to 6 HN in strain TY.
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Affiliation(s)
- Haixia Wang
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Cuixiao Xie
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Panpan Zhu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhenmei Lu
- Institute of Microbiology, College of Life Sciences, Zhejiang University Hangzhou, China
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Lee JH, Kim DI, Kang JW, Seong CN. Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. Int J Syst Evol Microbiol 2016; 66:5493-5499. [DOI: 10.1099/ijsem.0.001546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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42
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Liu B, Liu GH, Sengonca C, Schumann P, Lan JL, Chen DJ, Cui WD, Lin NQ. Paenibacillus solani sp. nov., isolated from potato rhizosphere soil. Int J Syst Evol Microbiol 2016; 66:4486-4491. [PMID: 27498790 DOI: 10.1099/ijsem.0.001378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, endospore-forming bacterium, designated FJAT-22460T, was isolated from a soil sample of a potato field in Xinjiang Autonomous Region, China. Cells were rods that were catalase-positive and motile by peritrichous flagella. The strain was found to grow at temperatures ranging from 10 to 40 °C (optimum 30 °C) and at pH 5.0-12.0 (optimum pH 7) with 0-5 % (w/v) NaCl (optimum 0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FJAT-22460T belonged to the genus Paenibacillus and exhibited 16S rRNA gene sequence similarities of 97.3, 97.2, 97.2 and 97.0 % with Paenibacillus glucanolyticus DSM 5162T, Paenibacillus lautus DSM 3035T, Paenibacillus lactis MB 1871T and Paenibacillus chibensis JCM 9905T, respectively. DNA-DNA relatedness of strain FJAT-22460T with Paenibacillus glucanolyticusDSM 5162T and Paenibacillus lautus DSM 3035T was 62.6 % and 33.3 %, respectively, lower than the 70 % accepted for species delineation. The menaquinone was identified as MK-7. The major fatty acids detected were anteiso-C15 : 0 (51.4 %), iso-C15 : 0 (5.3 %), C16 : 0 (12.1 %), iso-C16 : 0 (10.7 %) and anteiso-C17 : 0 (6.9 %). The DNA G+C content was determined to be 50.9 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate FJAT-22460T represents a novel species within the genus Paenibacillus, for which the name Paenibacillus solani sp. nov. is proposed. The type strain is FJAT-22460T (=DSM 100999T=CCTCC AB 2015207T).
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Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A, Bonn D-53115, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig 38124, Germany
| | - Jiang-Lin Lan
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - De-Ju Chen
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Wei-Dong Cui
- Microbiology, Institute of Applied for Microorganism of Xinjiang Academy of Agricultural Sciences, Urumchi, PR China
| | - Nai-Quan Lin
- Institute of Biological Control, Institute of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, PR China
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43
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Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li M. Sphingomonas faucium sp. nov., isolated from canyon soil. Int J Syst Evol Microbiol 2016; 66:2847-2852. [DOI: 10.1099/ijsem.0.001064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dongmei Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xin Jin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuelian Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yali Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Liling Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Steroidobacter flavus sp. nov., a microcystin-degrading Gammaproteobacterium isolated from soil. Antonie van Leeuwenhoek 2016; 109:1073-9. [PMID: 27151048 DOI: 10.1007/s10482-016-0706-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
A microcystin-degrading strain, designated CPCC 100154(T), was isolated from a forest soil sample collected from Hainan Island, South China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CPCC 100154(T) is affiliated to the family Sinobacteraceae in Gammaproteobacteria, with high 16S rRNA gene sequence similarities of 98.1, 96.6 and 96.6 % to Steroidobacter agariperforans JCM 18477(T), S. denitrificansis DSM 18526(T), and Povalibacter uvarum JCM 18749(T), respectively. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 100154(T) formed a stable phylogenetic subclade with S. agariperforans JCM 18477(T), which indicated that strain CPCC 100154(T) should be identified as a member of the genus Steroidobacter. The phylogenetic analysis based on partial gyrB gene sequences confirmed the affiliation of strain CPCC 100154(T) to the genus Steroidobacter. While the DNA-DNA hybridization value (47.0 ± 1.7 %) between the new isolate and its near phylogenetic neighbor S. agariperforans JCM 18477(T) was far below 70 %, which demonstrated that strain CPCC 100154(T) represents a different genomic species from S. agariperforans. The strain CPCC 100154(T) was found to be a Gram-stain negative, rod-shaped, motile with a polar flagellum, non-endospore-forming bacterium. Good growth was observed at 28-32 °C and pH 7.0-7.5. Polar lipids were identified to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a unidentified phospholipid, an aminophospholipid and an unidentified aminolipid. The polyamine pattern was determined to contain spermidine as the predominant polyamine, moderate amounts of putrescine as well as traces of sym-homospermidine and spermine. The respiratory quinone was identified as ubiquinone-8. The major cellular fatty acids were found to include summed feature 3 (C16: 1 ω7C/C16: 1 ω6C) (46.1 %) and C16: 0 (29.6 %). The genomic DNA G+C content was determined to be 64.4 mol%. On the basis of the above polyphasic taxonomy evidence, a novel species, Steroidobacter flavus sp. nov. is proposed. The type strain is CPCC 100154(T) (=DSM 23339(T) =CGMCC 1.10759(T)).
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45
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Zhou YX, Liu GH, Liu B, Chen GJ, Du ZJ. Bacillus mesophilus sp. nov., an alginate-degrading bacterium isolated from a soil sample collected from an abandoned marine solar saltern. Antonie van Leeuwenhoek 2016; 109:937-43. [PMID: 27084709 DOI: 10.1007/s10482-016-0692-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/28/2016] [Indexed: 11/28/2022]
Abstract
A novel Gram-stain positive, endospore-forming bacterium, designated SA4(T), was isolated from a soil sample collected from an abandoned marine solar saltern at Wendeng, Shandong Province, PR China. Cells were observed to be rod shaped, alginase positive, catalase positive and motile. The strain was found to grow at temperatures ranging from 15 to 40 °C (optimum 35 °C), and pH 5.0-11.0 (optimum pH 8.0) with 0-7.0 % (w/v) NaCl concentration (optimum NaCl 3.0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SA4(T) belongs to the genus Bacillus and exhibits 16S rRNA gene sequence similarities of 96.6, 96.5, 96.3 and 96.2 % with Bacillus horikoshii DSM 8719(T), Bacillus acidicola 105-2(T), Bacillus shackletonii LMG 18435(T) and Bacillus pocheonensis Gsoil 420(T), respectively. The menaquinone was identified as MK-7 and the major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15:0 (22.3 %), iso-C15:0 (22.6 %), iso-C16:0 (14.8 %) and iso-C14:0 (14.7 %). The DNA G+C content was determined to be 42.4 mol %. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate SA4(T) represents a novel species within the genus Bacillus, for which the name Bacillus mesophius sp. nov. is proposed. The type strain is SA4(T) (=DSM 101000(T)=CCTCC AB 2015209(T)).
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Affiliation(s)
- Yan-Xia Zhou
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, People's Republic of China
| | - Bo Liu
- Agricultural Bio-Resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350003, People's Republic of China.
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai, 264209, People's Republic of China.
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Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System Simulator. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00183-16. [PMID: 27034493 PMCID: PMC4816621 DOI: 10.1128/genomea.00183-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report the draft genomes of two Sphingopyxis sp. strains isolated from a chloraminated drinking water distribution system simulator. Both strains are ubiquitous residents and early colonizers of water distribution systems. Genomic annotation identified a class 1 integron (intI1) gene associated with sulfonamide (sul1) and puromycin (pac) antibiotic resistance genes.
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Jordaan K, Bezuidenhout CC. Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:5868-5880. [PMID: 26593724 DOI: 10.1007/s11356-015-5786-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
The aim of this study was to determine the impacts of anthropogenic disturbances on bacterial community composition in an urban river (Mooi River). Physico-chemical analysis, bacterial enumeration and 454-pyrosequencing were conducted on the Mooi River system upstream and downstream of an urban settlement in the North West Province, South Africa. Pyrosequencing and multivariate analysis showed that nutrient inputs and faecal pollution strongly impacted the physico-chemical and microbiological quality at the downstream sites. Also, bacterial communities showed higher richness and evenness at the downstream sites. Multivariate analysis suggested that the abundances of Betaproteobacteria, Epsilonproteobacteria, Acidobacteria, Bacteroidetes and Verrucomicrobia are related to temperature, pH, dissolved oxygen (DO), sulphate and chlorophyll-a levels. These results suggest that urbanisation caused the overall water quality of this river to deteriorate, which in turn affected the bacterial community composition. In addition, our work identified potential indicator groups that may be used to track faecal and organic pollution in freshwater systems.
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Affiliation(s)
- K Jordaan
- Unit for Environmental Science and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - C C Bezuidenhout
- Unit for Environmental Science and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom, 2520, South Africa.
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Wallner J, Frei R, Burkhalter F. A Rare Case of Peritoneal Dialysis-Associated Peritonitis with Sphingomonas koreensis. Perit Dial Int 2016; 36:224-5. [DOI: 10.3747/pdi.2015.00065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sphingomonas species are ubiquitous gram-negative, aerobic bacteria frequently found in aquatic environments such as drinking water and very seldom in hemodialysis fluids or supposedly sterile drug solutions. Human infections with the gram-negative Sphingomonas species are rare and peritonitis with these organisms even rarer. Here we report a case of polymicrobial peritonitis due to Sphingomonas koreensis and Escherichia coli in a patient undergoing peritoneal dialysis (PD).
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Affiliation(s)
- Julia Wallner
- Clinic for Transplant Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Reno Frei
- Division of Clinical Microbiology University Hospital Basel, Basel, Switzerland
| | - Felix Burkhalter
- Clinic for Transplant Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
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49
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Liu B, Liu GH, Sengonca C, Schumann P, Ge CB, Wang JP, Cui WD, Lin NQ. Bacillus solani sp. nov., isolated from rhizosphere soil of a potato field. Int J Syst Evol Microbiol 2015; 65:4066-4071. [DOI: 10.1099/ijsem.0.000539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, endospore-forming bacterium, designated strain FJAT-18043T, was isolated from a soil sample of a potato field in Xinjiang Autonomous Region, China. Cells were rods that were catalase-positive and motile by peritrichous flagella. The strain grew at 20–45 °C (optimum 35 °C), at pH 6.0–10.0 (optimum pH 9) and with 0–10 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FJAT-18043T belonged to the genus Bacillus and exhibited similarities of 97.7, 97.6, 97.2 and 97.2 % with Bacillus eiseniae A1-2T, Bacillus horneckiae DSM 23495T, Bacillus gottheilii WCC 4585T and Bacillus purgationiresistens DS22T, respectively. DNA–DNA relatedness between strain FJAT-18043T and B. eiseniae A1-2 T was lower than 70 % (36.1 %). The menaquinone was identified as MK-7 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids detected were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0, C16 : 0 and iso-C14 : 0. The DNA G+C content was 48.8 mol%. Phenotypic, chemotaxonomic and genotypic properties clearly indicated that isolate FJAT-18043T represents a novel species within the genus Bacillus, for which the name Bacillus solani sp. nov. is proposed. The type strain is FJAT-18043T ( = DSM 29501T = CCTCC AB 2014277T).
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Affiliation(s)
- Bo Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Guo-Hong Liu
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Cetin Sengonca
- Institute of Crop Sciences and Resource Conservation (INRES), University of Bonn, Meckenheimer Allee 166A, D-53115 Bonn, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ci-Bin Ge
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Jie-Ping Wang
- Agricultural Bio-resource Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350003, PR China
| | - Wei-Dong Cui
- Institute of Applied for Microorganism of Xinjiang Academy of Agricultural Sciences, PR China
| | - Nai-Quan Lin
- Institute of Plant Protection, Fujian Agriculture and Forestry University, PR China
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Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil. J Microbiol 2015; 53:673-7. [DOI: 10.1007/s12275-015-5132-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 07/31/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
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