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Agafonova NV, Belova AA, Kaparullina EN, Tarlachkov SV, Kopitsyn DS, Machulin AV, Doronina NV. Ancylobacter radicis sp. nov., a novel aerobic methylotrophic bacteria associated with plants. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01850-z. [PMID: 37270429 DOI: 10.1007/s10482-023-01850-z] [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: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
The two novel bacterial strains, designated as VTT and ML, were isolated from roots of cinquefoil (Potentilla sp.) and leaves of meadow-grass (Poa sp.) on the flooded bank of lake, respectively. These isolates were Gram-negative, non-spore-forming, non-motile, rod-shaped cells, utilized methanol, methylamine, and polycarbon compounds as carbon and energy sources. In the whole-cell fatty acid pattern of strains prevailed C18:1ω7c and C19:0cyc. Based on the phylogenetic analysis of 16S rRNA gene sequences, strains VTT and ML were closely related to the representatives of the genus Ancylobacter (98.3-98.5%). The assembled genome of strain VTT has a total length of 4.22 Mbp, and a G + C content is 67.3%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain VTT and closely related type strains of genus Ancylobacter were 78.0-80.6%, 73.8-78.3% and 22.1-24.0%, respectively, that clearly lower than proposed thresholds for species. On the basis of the phylogenetic, phenotypic, and chemotaxonomic analysis, isolates VTT and ML represent a novel species of the genus Ancylobacter, for which the name Ancylobacter radicis sp. nov. is proposed. The type strain is VTT (= VKM B-3255T = CCUG 72400T). In addition, novel strains were able to dissolve insoluble phosphates, to produce siderophores and plant hormones (auxin biosynthesis). According to genome analysis genes involved in the biosynthesis of siderophores, polyhydroxybutyrate, exopolysaccharides and phosphorus metabolism, as well as the genes involved in the assimilation of C1-compounds (natural products of plant metabolism) were found in the genome of type strain VTT.
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Affiliation(s)
- Nadezhda V Agafonova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia.
| | - Alina A Belova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia
| | - Elena N Kaparullina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia
| | - Sergey V Tarlachkov
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia
| | | | - Andrey V Machulin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia
| | - Nina V Doronina
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center «Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences», Prospect Nauki, 5, Pushchino, Moscow Region, 142290, Russia
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Qu L, Dai K, Wang J, Cao L, Rao Z, Han R. Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita. Front Microbiol 2023; 14:1168179. [PMID: 37303801 PMCID: PMC10247985 DOI: 10.3389/fmicb.2023.1168179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops. Methods To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods. Results Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents. Discussion These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.
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Liu C, Yan P, Liu Z, Zhang J, Zhang G, Cui L. Strip intercropping with local crops increased Aconitum carmichaeli yield and soil quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1147671. [PMID: 36938055 PMCID: PMC10020659 DOI: 10.3389/fpls.2023.1147671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Aconitum carmichaeli Debx. is a traditional Chinese medicine that is cultivated in China and Japan. However, the monoculturing of this herb substantially decreases soil quality. Therefore, scientific planting management is crucial for resolving the current problems in the cultivation of A. carmichaeli. In this study, we conducted a comparative study on the soil environmental characteristics, herb growth and quality of A. carmichaeli intercropping with five local crops in two different areas. Herb growth and quality, including biomass and secondary metabolites, and rhizosphere soil environmental characteristics were measured. The results showed that the intercropping with the five local crops substantially improved the A. carmichaeli biomass and polysaccharide content, decreased the disease index, and altered three monoester diterpenoid alkaloids and three diester diterpenoid alkaloids accumulations. The intercrops also increased the soil pH, nitrogen-cycling-gene abundances, and potentially beneficial microorganism abundances, and it also changed the soil nutrient levels. Moreover, these intercropping patterns could alleviate the continuous cropping obstacles of A. carmichaeli. According to a comprehensive evaluation of the A. carmichaeli growth and quality, as well as the soil quality, the best intercropping systems were the A. carmichaeli intercropping with rice, maize, and peanut. In summary, the strip-intercropping systems could improve the A. carmichaeli growth and soil quality, and be beneficial to the sustainable ecological planting of A. carmichaeli.
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Affiliation(s)
- Chen Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Pengdong Yan
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Zhenyu Liu
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jianglan Zhang
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guoyan Zhang
- Chenggu County Qunli Traditional Chinese Medicine Cooperative, Chenggu, China
| | - Langjun Cui
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi’an, China
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Wang P, Sheng H, Zheng K, Hong Y, Debnath SC, Yan C, Li K, Chen G, Xu J, Wu F, Guo Z, Zheng D. Ancylobacter gelatini sp. nov., isolated from beach sediment of Zhairuo Island, China. Arch Microbiol 2022; 204:430. [PMID: 35759057 DOI: 10.1007/s00203-022-03048-9] [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: 04/14/2022] [Accepted: 06/03/2022] [Indexed: 12/01/2022]
Abstract
A Gram-negative, aerobic, non-motile, oxidase-positive, catalase-positive, methyl red-positive, and lipase-negative bacterium, designated A5.8T, was isolated from beach sediment of Zhairuo Island located in the East China Sea. Growth occurred at 10-40 °C (optimum, 30 °C), pH 5.5-9.5 (optimum, 7.5), and 0-2% NaCl (optimum, 1.5%). Based on 16S rRNA gene sequence analysis, strain A5.8T belongs to the genus Ancylobacter, sharing the highest similarity with Ancylobacter aquaticus JCM 20518T (98.0%). Its polar lipids mainly consist of phosphatidylethanolamine (PE) and phosphatidylcholine (PC). The predominant fatty acids are summed feature 8 (C18:1ω7c and/or C18:1ω6c, 91.0%), and the major respiratory quinone is Q-10. The DNA G + C content is 67.2 mol%. Based on above analysis, as well as digital DNA-DNA hybridization (22.5-22.9%) and average nucleotide identity (83.0-83.6%) of strain A5.8T with reference type strains of the genus Ancylobacter, strain A5.8T was suggested to represent a novel species of the genus Ancylobacter, for which the name Ancylobacter gelatini sp. nov. is proposed. The type strain is A5.8T (= MCCC 1K07167T = LMG 32566T).
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Affiliation(s)
- Pinmei Wang
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Huan Sheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Kaiwen Zheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Yi Hong
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058, China
| | - Sanjit Chandra Debnath
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China.,Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4HB, Devon, UK
| | - Cen Yan
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Kejing Li
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Gen Chen
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Jinzhong Xu
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China
| | - Fabai Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China
| | - Zhen Guo
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058, China.
| | - Daoqiong Zheng
- State Key Laboratory of Motor Vehicle Biofuel Technology, Ocean College, Zhejiang University, Zhoushan, 316021, China. .,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311200, China.
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