Nocardiopsis changdeensis sp. nov., an endophytic actinomycete isolated from the roots of Eucommia ulmoides Oliv

Mo, Ping; Li, Kaiqin; Zhou, Jinhua; Zhou, Fumin; He, Jiang; Zou, Wansheng; Gao, Jian

doi:10.1038/s41429-023-00596-0

Cited by 11 publications

(5 citation statements)

References 40 publications

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“…The genome sequencing of strain HUAS 11-8 T was completed by using a Nanopore PromethION sequencing system at Wuhan Benagen Technology Co., Ltd. (Hubei, China). Genomic DNA extraction and PCR conditions of the 16S rRNA gene were carried out using the method described by Mo et al (2023) . The 16S rRNA gene of strain HUAS 11-8 T was amplified using universal primers (27F and 1492R) ( Lane, 1991 ).…”

Section: Methodsmentioning

confidence: 99%

New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis

Deng,

Fu,

et al. 2024

Front. Microbiol.

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At present, it is widely believed that a 95–96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA–DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95–96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.

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Section: Methodsmentioning

confidence: 99%

New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis

Deng,

Fu,

et al. 2024

Front. Microbiol.

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“…The genomic DNA extraction, PCR system and PCR amplification procedure were carried out as described by Mo et al [28]. The amplified fragments were detected by agarose gel electrophoresis and shipped to Sangon Biotech Co., Ltd (Shanghai, PR China) for sequencing.…”

Section: S Rrna Gene Phylogenymentioning

confidence: 99%

Kitasatospora cathayae sp. nov., a novel endophytic actinomycete isolated from the leaves of Cathaya argyrophylla

Zheng,

Mo,

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Strain HUAS 3-15T was isolated from the leaves of Cathaya argyrophylla collected from Chenzhou, Hunan Province, PR China. The main fatty acids (>5.0 %) of the strain were anteiso-C15 : 0, C16 : 0, C18 : 1 ω9c, iso-C16 : 0, summed feature 5 (C18 : 2 ω6,9c/C18 : 0 ante), iso-C15 : 0 and anteiso-C17 : 0. MK-9(H6), MK-9(H8) and MK-9(H4) were detected as respiratory quinones. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. Galactose, glucose and ribose were also present in the cell wall. The major polar lipids consisted of diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidylinositol mannosides and unidentified phospholipids. The DNA G+C content of the genome sequence, consisting of 8 860 963 bp, is 72.4 mol%. blast analysis based on 16S rRNA gene sequences revealed that the strain belongs to the genus Kitasatospora, with 99.37, 99.03, 98.95, 98.68 and 98.67 % sequence similarity to Kitasatospora aureofaciens ATCC 10762T, Kitasatospora viridis DSM 44826T, Kitasatospora xanthocidica NBRC 13469T, Kitasatospora aburaviensis NRRL B-2218T and Kitasatospora kifunensis IFO 15206T, respectively. Phylogenetic trees based on 16S rRNA gene and whole-genome sequences demonstrated that strain HUAS 3-15T formed a well‐supported cluster with K. aureofaciens ATCC 10762T. Further genomic characterization through average nucleotide identity (ANIb/m) and digital DNA–DNA hybridization analysis between strain HUAS 3-15T and K. aureofaciens ATCC 10762T showed values of 90.62/92.55 % and 45.3 %, respectively, lower than the 95–96 % ANI threshold and 70.0 % cutoff used as guideline values for species delineation in bacteria. Furthermore, the differences between the strain and its phylogenomic neighbour in terms of physiological (e.g. sole carbon source growth) and chemotaxonomic (e.g. cellular fatty composition) characteristics further supported this conclusion. Consequently, we concluded that strain HUAS 3-15T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora cathayae sp. nov. is proposed. The type strain is HUAS 3-15T (=MCCC 1K08542T=JCM 36274T).

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“…has been used to treat various diseases since ancient times [ 51 ]. The research group led by Mo et al [ 52 , 53 ] isolated two new species of Nocardia sp. from the leaves and roots of Eucommia ulmoides Oliv.…”

Section: Medicinal Plants and Their Cultivable Endophyte Resourcesmentioning

confidence: 99%

“…Actinomycetes of other genera can also be isolated from medicinal plants, but the number is relatively small compared with Streptomyces. Many studies have isolated new species of bioactive endophytic actinomycetes from medicinal plants, which greatly expanded microbial resources and laid a foundation for the industrial application of actinomycetes [ 52 , 53 , 58 , 60 , 61 ]. The results of endophyte isolation from medicinal plants in recent years are shown in Table 3 .…”

Section: Medicinal Plants and Their Cultivable Endophyte Resourcesmentioning

confidence: 99%

Cultivable Endophyte Resources in Medicinal Plants and Effects on Hosts

Wang

Zhang

Hao

et al. 2023

Life

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With the increasing demand for medicinal plants and the increasing shortage of resources, improving the quality and yield of medicinal plants and making more effective use of medicinal plants has become an urgent problem to be solved. During the growth of medicinal plants, various adversities can lead to nutrient loss and yield decline. Using traditional chemical pesticides to control the stress resistance of plants will cause serious pollution to the environment and even endanger human health. Therefore, it is necessary to find suitable pesticide substitutes from natural ingredients. As an important part of the microecology of medicinal plants, endophytes can promote the growth of medicinal plants, improve the stress tolerance of hosts, and promote the accumulation of active components of hosts. Endophytes have a more positive and direct impact on the host and can metabolize rich medicinal ingredients, so researchers pay attention to them. This paper reviews the research in the past five years, aiming to provide ideas for improving the quality of medicinal plants, developing more microbial resources, exploring more medicinal natural products, and providing help for the development of research on medicinal plants and endophytes.

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Nocardiopsis changdeensis sp. nov., an endophytic actinomycete isolated from the roots of Eucommia ulmoides Oliv

Cited by 11 publications

References 40 publications

Kitasatospora cathayae sp. nov., a novel endophytic actinomycete isolated from the leaves of Cathaya argyrophylla

Cultivable Endophyte Resources in Medicinal Plants and Effects on Hosts

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