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Wang Y, Wang Y, Shang J, Wang L, Li Y, Wang Z, Zou Y, Cai W, Wang L. Redox gradients drive microbial community assembly patterns and molecular ecological networks in the hyporheic zone of effluent-dominated rivers. WATER RESEARCH 2024; 248:120900. [PMID: 38000224 DOI: 10.1016/j.watres.2023.120900] [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: 10/05/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
The impacts of effluent discharge on receiving waterbodies have been a research hotspot. Nonetheless, limited information is available on the microbial community assembly patterns in the hyporheic zones (HZ) responding to the changes in the microenvironments, e.g., solute transport and redox gradient variations. Using two representative effluent-dominated rivers as model systems, the spatio-temporal bacterial community dynamics and assembly patterns in oxic and suboxic zones in the shallow riverbed sediments were disentangled via null model- and neutral model-based approaches. Bacterial dynamics in community composition were observed driven by environmental filtering, i.e., impacts of environmental variables, more than geographic distances, i.e., the depths of sediments. The communities in samples collected in summer were largely shaped by stochasticity, in which homogeneous selection occupied a higher proportion in oxic (∼39%) than in suboxic zone (∼23%). Deterministic processes contributed to a more complex community structure for samples from oxic zones, whereas weakened the interspecies interactions in suboxic zones. The richness and abundances of non-neutral community were confirmed governing the deterministic assembly in oxic zones. Key species ascribed to 'connectors' and 'network hubs' dominated the community assembly variations in samples collected in winter, and in oxic zones, respectively. Significant positive relationships between β-nearest taxon index and dissolved organic nitrogen (DON) and nitrate highlighted their vital roles in community assembly via deterministic selective pressures in oxic zones. The significance thresholds of nitrogen species for community transition in winter (ΔDON: 2.81 mg-N/L, ΔNO3-: 1.09 mg-N/L) were lower than in summer, probably implying that stricter effluent quality standards should be established in colder seasons. Combined, our work poses first insights on the roles of redox zonation in driving microbial community assembly in HZ, which is of significance in guiding ecological remediation processes in effluent-dominated rivers.
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Affiliation(s)
- Yuming Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Yutao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Jiahui Shang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China.
| | - Ziyi Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, Jiangsu, 210098, PR China
| | - Yina Zou
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, China
| | - Wei Cai
- College of Environmental Science and Engineering, Yangzhou University, Huayang West Road #196, Yangzhou 225009, PR China
| | - Linqiong Wang
- College of Oceanography, Hohai University, Nanjing, Jiangsu, 210098, PR China
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Yang J, Xiang J, Xie Y, Yu K, Li P, Yew-Hoong Gin K, He Y. Antibiotic resistome associated with influencing factors in industrial-scale organic waste aerobic composting plants. BIORESOURCE TECHNOLOGY 2023:129354. [PMID: 37336453 DOI: 10.1016/j.biortech.2023.129354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
This study investigated the fate of antibiotic resistance genes (ARGs) and bacterial evolution in six industrial-scale organic wastes aerobic composting plants and identified key factors driving ARGs dynamics. A total of 226 ARGs and 46 mobile genetic elements (MGEs), mainly resistant to aminoglycoside and MLSB, were detected by high-throughput qPCR. Briefly, aerobic composting showed good performance in reducing the diversity and abundance of ARGs, where the total absolute abundance was reduced by 88.34%-97.08% except for cattle manures. Rapid composting may lead to a rebound of ARGs due to long-term storage compared to traditional composting. Hub ARGs and bacterial genera were screened out by co-occurrence patterns. As the dominant phyla in composting, the main potential hosts of ARGs were Firmicutes, Bacteroidota and Proteobacteria. Structural equation model indicated that MGEs and heavy metals were key factors affecting ARGs dynamics. In addition, nutrients and bacterial α-diversity can indirectly influence ARGs by affecting MGEs.
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Affiliation(s)
- Jun Yang
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Jinyi Xiang
- School of Medicine, Shanghai Jiao Tong University, 227 South Chongqing Road, Shanghai 200025, China
| | - Yu Xie
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Peng Li
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, Singapore 117576, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; China-UK Low Carbon College, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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3
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Flavobacterium hungaricum sp. nov. a novel soil inhabitant, cellulolytic bacterium isolated from plough field. Arch Microbiol 2022; 204:301. [PMID: 35524012 PMCID: PMC9076710 DOI: 10.1007/s00203-022-02905-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/15/2022]
Abstract
A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%). The highest ANI (83.3%) and dDDH (26.5%) values were found with Flavobacterium ginsenosidimutans THG 01 and Flavobacterium fluviale HYN0086T, respectively. The isolate is aerobic with rod-shaped cells, positive for catalase and negative for oxidase tests. The DNA G+C content is 34.7 mol%. The only isoprenoid quinone is menaquinone 6 (MK-6). The major fatty acids are iso-C15:0, summed feature 3 (C16:1ω7c/C16:1ω6c) and iso-C17:0 3OH. The major polar lipid is phosphatidylethanolamine. On the bases of phenotypic characteristics and analysis of 16S rRNA gene sequences, it is concluded that strain Kb82T represents a novel species in the Flavobacterium genus, for which the name Flavobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb82T (= LMG 31576T = NCAIM B.02635T).
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4
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LaFrentz BR, Králová S, Burbick CR, Alexander TL, Phillips CW, Griffin MJ, Waldbieser GC, García JC, de Alexandre Sebastião F, Soto E, Loch TP, Liles MR, Snekvik KR. The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare, Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare. Syst Appl Microbiol 2021; 45:126293. [PMID: 35026686 DOI: 10.1016/j.syapm.2021.126293] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 01/09/2023]
Abstract
Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT shared less than <98.8 % sequence identity to F. columnare ATCC 23463T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463T, genetic group 2 isolate AL-02-36T, genetic group 3 isolate 90-106T, and genetic group 4 isolate Costa Rica 04-02-TNT were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36T), F. davisii sp. nov. (90-106T), and F. oreochromis sp. nov. (Costa Rica 04-02-TNT) are proposed to represent genetic groups 2, 3, and 4, respectively.
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Affiliation(s)
- Benjamin R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States.
| | - Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Conner W Phillips
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, United States
| | - Geoffrey C Waldbieser
- Warmwater Aquaculture Research Unit, USDA-ARS, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, United States
| | - Julio C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Auburn, AL, United States
| | | | - Esteban Soto
- Department of Medicine & Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Kevin R Snekvik
- Washington Animal Disease Diagnostic Laboratory, Pullman, WA, United States; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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Ren L, Yan B, Kumar Awasthi M, Zhang J, Huang H, Zhang L, Luo L. Accelerated humification and alteration of microbial communities by distillers' grains addition during rice straw composting. BIORESOURCE TECHNOLOGY 2021; 342:125937. [PMID: 34543820 DOI: 10.1016/j.biortech.2021.125937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
This research explored the influence of distillers' grains amendment on the humification performance and microbial communities during rice straw composting. The composition of dissolved organic matter and maturity index were analyzed by the fluorescence excitation emission matrix spectroscopy and parallel factor analysis. High-throughput sequencing and redundancy analysis were employed for revealing the structure dynamics for microbial community and their shaping factors, respectively. Results indicated that addition of distillers' grains effectively increased the microbial activity, which was beneficial to the organic matter degradation and nitrogen conservation. Microbial community structures were significantly changed with different amendment strategies. Nitrate, water soluble carbon, organic matter, ammonium were the key parameters influencing the variation of bacterial community in different treatments. Water soluble carbon significantly affected the dominant fungal community dynamics. These results showed that addition of distillers' grains effectively improved the nutritional status and changed the microbial communities during rice straw composting.
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Affiliation(s)
- Liheng Ren
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Binghua Yan
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Jiachao Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China.
| | - Hongli Huang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Lihua Zhang
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Lin Luo
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [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: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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7
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Wang B, Chu S, Liu X, Zhang D, Chai X, Yang X, Zhi Y, Chi Y, Zhou P. Changes in soil bacterial and fungal communities in response to Bacillus megaterium NCT-2 inoculation in secondary salinized soil. PeerJ 2021; 9:e12309. [PMID: 34721987 PMCID: PMC8519178 DOI: 10.7717/peerj.12309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Background Secondary salinized soil in greenhouses often contains excess nitrate. Inoculation of Bacillus megaterium NCT-2 with nitrate assimilation ability represents an attractive approach for soil remediation. However, the effects of NCT-2 on the structure and function of soil microbial communities have not been explored. Methods Greenhouse experiments were carried out to investigate changes in soil properties, Brassica chinensis L. growth, bacterial, and fungal community structure and function in response to NCT-2 inoculation. Results The NCT-2 inoculant significantly reduced the nitrate content in B. chinensis and inhibited the rebound of soil nitrate in the later stage. The shifts of bacterial community structure and function by NCT-2 was negligible, and a greater disturbance of soil fungal community structure and function was observed, for example the strong inhibitory effect on ectomycorrhizal fungi. These results indicated that the NCT-2 inoculant likely achieved the remediation effect in secondary salinized soil by shifting fungal community. The present findings add to the current understanding of microbial interactions in response to bacterial inoculation and can be of great significance for the application of NCT-2 inoculants in secondary salinized soil remediation.
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Affiliation(s)
- Bin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Shaohua Chu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaorui Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaotong Chai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xijia Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yuee Zhi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yaowei Chi
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Pei Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Urban Agriculture, Ministry of Agriculture and Rural Affairs, Shanghai, China.,Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, China
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Yin Y, Yang C, Tang J, Gu J, Li H, Duan M, Wang X, Chen R. Bamboo charcoal enhances cellulase and urease activities during chicken manure composting: Roles of the bacterial community and metabolic functions. J Environ Sci (China) 2021; 108:84-95. [PMID: 34465440 DOI: 10.1016/j.jes.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 05/22/2023]
Abstract
Microbial enzymes are crucial for material biotransformation during the composting process. In this study, we investigated the effects of adding bamboo charcoal (BC) (i.e., at 5%, 10%, and 20% corresponding to BC5, BC10, and BC20, respectively) on the enzyme activity levels during chicken manure composting. The results showed that BC10 could increase the cellulose and urease activities by 56% and 96%, respectively. The bacterial community structure in BC10 differed from those in the other treatments, and Luteivirga, Lactobacillus, Paenalcaligenes, Ulvibacter, Bacillus, Facklamia, Pelagibacterium, Sporosarcina, Cellvibrio, and Corynebacterium had the most important roles in composting. Compared with other treatments, BC10 significantly enhanced the average rates of degradation of carbohydrates (D-xylose (40%) and α-D-lactose (44%)) and amino acids (L-arginine (16%), L-asparagine (14%), and L-threonine (52%)). We also explored the associations among the bacterial community and their metabolic functions with the changes in the activities of enzymes. Network analysis demonstrated that BC10 altered the co-occurrence patterns of the bacterial communities, where Ulvibacter and class Bacilli were the keystone bacterial taxa with high capacities for degrading carbon source, and they were related to increases in the activities of cellulase and urease, respectively. The results obtained in this study may help to further enhance the efficiency of composting.
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Affiliation(s)
- Yanan Yin
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Chao Yang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jingrui Tang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jie Gu
- College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Haichao Li
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Manli Duan
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region of China, Xi'an University of Technology, Xi'an 710048, China
| | - Xiaochang Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Rong Chen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; International S&T Cooperation Center for Urban Alternative Water Resources Development, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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9
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Yin Y, Gu J, Wang X, Zhang Y, Zheng W, Chen R, Wang X. Effects of rhamnolipid and Tween-80 on cellulase activities and metabolic functions of the bacterial community during chicken manure composting. BIORESOURCE TECHNOLOGY 2019; 288:121507. [PMID: 31128544 DOI: 10.1016/j.biortech.2019.121507] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/10/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Metabolism by microorganisms is the basis of composting. In this study, the dynamic changes in the enzyme activity levels, bacterial community structure, and metabolism functions were investigated during chicken manure composting with an added bio-surfactant (rhamnolipid) or chemical surfactant (Tween-80). The results showed that rhamnolipid and Tween-80 improved the quality of the finished compost in terms of the C/N ratio, water-soluble carbon content, germination index, E4/E6 ratio, and the cellulase activity, especially with Tween-80. Furthermore, the bacterial communities were determined by high-throughput sequencing, and their metabolism functions were evaluated using the PICRUSt and Biolog methods. Tween-80 greatly influenced the bacterial community structure, where it enhanced the abundances of bacteria that degrade cellulose and lignin (e.g., members of the order Bacillales) and the capacities for carbohydrate and amino acid metabolism. Network analysis also showed that the order Bacillales was closely related to the metabolism of characteristic carbon sources, especially carbohydrates.
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Affiliation(s)
- Yanan Yin
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China; College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China
| | - Jie Gu
- College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Xiaojuan Wang
- College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yajun Zhang
- College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Wei Zheng
- College of Resources and Environmental Sciences, Northwest A & F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Rong Chen
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China; International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, People's Republic of China
| | - Xiaochang Wang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China; International Science & Technology Cooperation Center for Urban Alternative Water Resources Development, Xi'an 710055, People's Republic of China
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11
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Lee Y, Jeon CO. Flavobacterium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2018; 68:1919-1924. [DOI: 10.1099/ijsem.0.002768] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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12
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Zhao JC, Cheng J, Zhang Q, Gao ZW, Zhang MY, Zhang YX. Flavobacterium artemisiae sp. nov., isolated from the rhizosphere of Artemisia annua L. and emended descriptions of Flavobacterium compostarboris and Flavobacterium procerum. Int J Syst Evol Microbiol 2018; 68:1509-1513. [DOI: 10.1099/ijsem.0.002701] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jian-Chao Zhao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Juan Cheng
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Qi Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Zi-Wei Gao
- Department of Biotechnology, School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Meng-Yue Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
| | - Yi-Xuan Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, PR China
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13
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Kim JJ, Marjerrison CE, Cornish Shartau SL, Brady AL, Sharp CE, Rijpstra WIC, Sinninghe Damsté JS, Schumann P, Grasby SE, Dunfield PF. Actinocrinis puniceicyclus gen. nov., sp. nov., an actinobacterium isolated from an acidic spring. Int J Syst Evol Microbiol 2017; 67:602-609. [DOI: 10.1099/ijsem.0.001667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Joong-Jae Kim
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Colbran E Marjerrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | | | - Allyson L Brady
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Christine E Sharp
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - W. Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Peter Schumann
- The Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Stephen E Grasby
- Geological Survey of Canada, Natural Resources Canada, Calgary, AB T2L 2A7, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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14
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Tortosa G, Castellano-Hinojosa A, Correa-Galeote D, Bedmar EJ. Evolution of bacterial diversity during two-phase olive mill waste ("alperujo") composting by 16S rRNA gene pyrosequencing. BIORESOURCE TECHNOLOGY 2017; 224:101-111. [PMID: 27931940 DOI: 10.1016/j.biortech.2016.11.098] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Microorganisms are the main contributing factor responsible for organic matter degradation during composting. In this research, the 454-pyrosequencing of the 16S rRNA gene was used to elucidate evolution of bacterial diversity during mesophilic, thermophilic and maturation composting stages of the two-phase olive mill waste ("alperujo"), the main by-product of the Spanish olive oil industry. Two similar piles were performance composting AL with sheep manure as bulking agent. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the main phyla found in genomic libraries from each composting phase. Shannon and Chao1 biodiversity indices showed a clear difference between the mesophilic/thermophilic and maturation phases, which was mainly due to detection of new genera. PCA analysis of the relative number of sequences confirmed maturation affected bacterial population structure, and Pearson correlation coefficients between physicochemical composting parameters and relative number of genera sequences suggest that Planomicrobium and Ohtaekwangia could be considered as biomarkers for AL composting maturation.
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Affiliation(s)
- Germán Tortosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, E-419, 18080-Granada, Spain.
| | - Antonio Castellano-Hinojosa
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, E-419, 18080-Granada, Spain
| | - David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, E-419, 18080-Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), Agencia Estatal CSIC, E-419, 18080-Granada, Spain
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15
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Hatayama K, Ushida A, Kuno T. Flavobacterium aquicola sp. nov., isolated from river water. Int J Syst Evol Microbiol 2016; 66:2789-2796. [DOI: 10.1099/ijsem.0.001057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kouta Hatayama
- Sagami Chemical Research Institute, Ayase, Kanagawa 252-1193, Japan
| | - Ayako Ushida
- Department of Life Science, College of Agriculture, Tamagawa University, Machida, Tokyo 194-8610, Japan
| | - Teruaki Kuno
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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16
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Sun JQ, Xu L, Liu M, Wang XY, Wu XL. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata. Int J Syst Evol Microbiol 2016; 66:1943-1949. [DOI: 10.1099/ijsem.0.000967] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji-Quan Sun
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
- College of Engineering, Peking University, Beijing 100871, PR China
| | - Lian Xu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Min Liu
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xin-Ying Wang
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, PR China
- Institute of Innovation (Baotou), Peking University, Baotou 014030, PR China
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Antibacterial activity of aquatic gliding bacteria. SPRINGERPLUS 2016; 5:116. [PMID: 26885469 PMCID: PMC4742450 DOI: 10.1186/s40064-016-1747-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 01/28/2016] [Indexed: 11/10/2022]
Abstract
The study aimed to screen and isolate strains of freshwater aquatic gliding bacteria, and to investigate their antibacterial activity against seven common pathogenic bacteria. Submerged specimens were collected and isolated for aquatic gliding bacteria using four different isolation media (DW, MA, SAP2, and Vy/2). Gliding bacteria identification was performed by 16S rRNA gene sequencing and phylogenetic analysis. Crude extracts were obtained by methanol extraction. Antibacterial activity against seven pathogenic bacteria was examined by agar-well diffusion assay. Five strains of aquatic gliding bacteria including RPD001, RPD008, RPD018, RPD027 and RPD049 were isolated. Each submerged biofilm and plastic specimen provided two isolates of gliding bacteria, whereas plant debris gave only one isolate. Two strains of gliding bacteria were obtained from each DW and Vy/2 isolation medium, while one strain was obtained from the SAP2 medium. Gliding bacteria strains RPD001, RPD008 and RPD018 were identified as Flavobacterium anhuiense with 96, 82 and 96 % similarity, respectively. Strains RPD049 and RPD027 were identified as F. johnsoniae and Lysobacter brunescens, respectively, with similarity equal to 96 %. Only crude extract obtained from RPD001 inhibited growth of Listeria monocytogenes (MIC 150 µg/ml), Staphylococcus aureus (MIC 75 µg/ml) and Vibrio cholerae (MIC 300 µg/ml), but showed weak inhibitory effect on Salmonella typhimurium (MIC > 300 µg/ml). Gliding bacterium strain RPD008 should be considered to a novel genus separate from Flavobacterium due to its low similarity value. Crude extract produced by RPD001 showed potential for development as a broad antibiotic agent.
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Flavobacterium notoginsengisoli sp. nov., isolated from the rhizosphere of Panax notoginseng. Antonie van Leeuwenhoek 2015; 108:545-52. [PMID: 26111850 DOI: 10.1007/s10482-015-0509-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Abstract
Two novel bacterial strains, designated SYP-B540(T) and SYP-B556, were isolated from rhizospheric soil of Panax notoginseng located at Yunnan Province, China. Both strains were Gram-staining negative, aerobic, non-motile, elongated rod shaped and yellow coloured. They grew optimally at 28 °C and pH 7.0. Analysis of 16S rRNA gene sequences showed that the two strains shared 99.8 % sequence similarity to each other, but lower than 97.6 % to the other known species of the genus Flavobacterium. The predominant respiratory quinone for the two strains was MK-6, and the major fatty acids were iso-C15:0 and summed Feature 3 (comprising 16:1 ω7c and/or 16:1 ω6c). The polar lipids consisted of phosphatidylethanolamine, two unidentified polar lipids and three unidentified amino-phospholipids. The DNA G+C contents of strains SYP-B540(T) and SYP-B556 were 33.3 and 32.7 mol%, respectively. In addition, the DNA-DNA hybridization values of strains SYP-B540(T) and SYP-B556 to their closest phylogenetic neighbors were significantly lower than 70 %. On the basis of the polyphasic taxonomy studies, strains SYP-B540(T) and SYP-B556 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium notoginsengisoli sp. nov. is proposed. The type strain is SYP-B540(T) (=KCTC 32505(T) = NBRC 110012(T) = BCRC 80724(T)).
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19
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Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field. Antonie van Leeuwenhoek 2013; 104:1029-37. [DOI: 10.1007/s10482-013-0023-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/30/2013] [Indexed: 11/25/2022]
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