Actinoplanes rishiriensis sp. nov., a novel motile actinomycete isolated by rehydration and centrifugation method

Yamamura, Hideki; Shimizu, Aya; Nakagawa, Youji; Hamada, Moriyuki; Otoguro, Misa; Tamura, Tomohiko; Hayakawa, Masayuki

doi:10.1038/ja.2012.8

Cited by 12 publications

(4 citation statements)

References 35 publications

(28 reference statements)

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“…The description is the same as for A. rishiriensis [58]. Phylogenetic and chemotaxonomic analysis strongly supported the placement of this species in the genus Paractinoplanes .…”

Section: Description Of Paractinoplanes Rishiriensis Comb Novmentioning

confidence: 70%

Phylogenomic analyses of the genus Actinoplanes: description of four novel genera

Roman,

Fedorenko,

Gromyko

2024

International Journal of Systematic and Evolutionary Microbiology

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The genus Actinoplanes comprises 57 species (in February 2024) that are important components of ecosystems and are widely used in biotechnology, especially pharmaceuticals. Phylogenetic analysis of the family Micromonosporaceae (based on the 16S rRNA gene sequence) allowed us to group members of different genera into separate clades; however, the genus Actinoplanes was divided into three separate clades. Such phylogenetic heterogeneity could be due to the limitations of 16S rRNA gene analysis. In response to this heterogeneity, genomic phylogeny was performed. Phylogenomic reconstruction based on 324 single-copy orthologous genes allowed us to divide the genus Actinoplanes first into four clades and then, based on average nucleotide identity analysis, into five clades. Finally, chemotaxonomic analysis of each clade confirmed each clade’s distinctiveness and the necessity to reclassify the genus Actinoplanes. The obtained data allowed us to divide the genus Actinoplanes into five genera: Actinoplanes, Paractinoplanes, Winogradskya, Symbioplanes and Amorphoplanes.

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“…The description is the same as for A. rishiriensis [58]. Phylogenetic and chemotaxonomic analysis strongly supported the placement of this species in the genus Paractinoplanes .…”

Section: Description Of Paractinoplanes Rishiriensis Comb Novmentioning

confidence: 70%

Phylogenomic analyses of the genus Actinoplanes: description of four novel genera

Roman,

Fedorenko,

Gromyko

2024

International Journal of Systematic and Evolutionary Microbiology

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“…rishiriensis was separated by Yamamura et al . by the hydration–recentrifugation method [56]. This method was improved on the basis of dehydration–rehydration method, which greatly improved the bacteriological yield of migratory Actinoplanes and effectively reduced the interference of Streptomyces .…”

Section: Resultsmentioning

confidence: 99%

“…Mazza et al also selectively isolated a large number of migratory Actinoplanes and their related genera using the rehydrationcentrifugation method [55]. A. rishiriensis was separated by Yamamura et al by the hydration-recentrifugation method [56]. This method was improved on the basis of dehydration-rehydration method, which greatly improved the bacteriological yield of migratory Actinoplanes and effectively reduced the interference of Streptomyces.…”

Section: A Brasiliensis Dsm 43805 Tmentioning

confidence: 99%

Three novel Actinoplanes species isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ

Ding

Liu

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

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Three novel actinomycete strains, designated TRM66264-DLMT, TRM88002T and TRM88003T, were isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ. The 16S rRNA gene sequence and phylogenetic analyses of three strains indicated that they belonged to the genus Actinoplanes . The phylogenetically closest strains of TRM66264-DLMT, TRM88002T and TRM88003T were Actinoplanes bogorensis LIPI11-2-Ac043T (98.4 %), Actinoplanes abujensis A4029T (98.0 %) and Actinoplanes ferrugineus IFO15555T (98.1 %), respectively. The major polar lipids of strains TRM66264-DLMT and TRM88002T were phosphatidylethanolamine and disphosphatidylglycerol, while strain TRM88003T only had phosphatidylethanolamine. The predominant menaquinones of strain TRM66264-DLMT were identified as MK-9(H4) and MK-9 (H6). Strains TRM88002T and TRM88003T had MK-9(H4). The cell-wall peptidoglycan of three strains contained meso-diaminopimelic acid. The whole-cell sugars of strain TRM66264-DLMT were identified as arabinose, glucose, galactose and xylose. Strains TRM88002T and TRM88003T mainly had arabinose and glucose. The DNA G+C content of strains TRM66264-DLMT, TRM88002T and TRM88003T were 70.48, 70.46 and 70.64 mol%, respectively. Genotypic and phenotypic analysis confirmed that all three strains sre new members of the genus Acinoplanes. Therefore, it is proposed that strains TRM66264-DLMT, TRM88002T and TRM88003T represent three novel species of the genus Actinoplanes , for which the names Actinoplanes polyasparticus sp. nov. (type strain TRM66264-DLMT=CCTCC AA 2021015T=LMG 32389T), Actinoplanes hotanensis sp. nov. (type strain TRM88002T=CCTCC AA 2021036T=LMG 32621T) and Actinoplanes aksuensis sp. nov. (type strain TRM88003T=CCTCC AA 2021037 T=LMG 32622T) are proposed.

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“…Actinoplanes 38 , Micromonospora 39 , and Streptomyces 39 , followed by a gamma-radiationresistant genus Geodermatophilus 40 (Figures 2D and 2E). The two fungal phyla Ascomycota and Mucoromycota are key drivers of the arable soil decomposition process 41,42 ; The Nitrospirae and archaeal Thaumarchaeota participate in nitrogen cycles 43,44 .…”

Section: Desert Microbiome Dynamics Indicate That the Soil Ecological...mentioning

confidence: 99%

Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration

Chen,

Yuan,

Jiang

et al. 2023

Preprint

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SummaryEcological restoration of degraded lands is essential to human sustainability. Yet, an in-depth community, functional, and evolutionary microbial perspective of long-term restoration of damaged ecosystems is lacking. Herein, we comprehensively assessed the impact of long-term (up to 17 years) restoration of Tengger Desert, China, by multi-omic profiling of 1,910 topsoil samples. The soil biophysiochemical properties, especially soil hydraulics, microbiome stability, and functional diversity, significantly improved during restoration. The soil microbiome transitioned from an extreme oligotrophic and autotrophic community to a diverse copiotrophic ecosystem. The soil microbiota, including fungi, could mediate the soil physicochemical changes through metabolites. Importantly, the systematic rewiring of nutrient cycles featured the multi-domain preference of an efficient carbon fixation strategy in the extreme desert environment. Finally, the microbiome was evolving via positive selections of genes of biogeochemical cycles, resistance, and motility. In summary, we present a comprehensive community, functional, biogeochemical, and evolutionary landscape of the soil microbiome during the long-term restoration of desert environments. We highlight the crucial microbial role in restoration from soil hydraulic and biogeochemical perspectives, offering promising field applications.HighlightsThe desert soil microbiome transformed from simple oligotrophic to a diverse, stable, and nutrient-rich ecosystem with expanded functional diversity.Restoration led to systematically rewired biogeochemical cycles, which are highly efficient in carbon fixation in the desert environment.The microbiome was evolving via positive selections of genes involved in biogeochemical cycles and environmental adaptations.Microbes and metabolites could facilitate desert restoration from hydraulic and biogeochemical aspects, offering promising field applications.

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Actinoplanes rishiriensis sp. nov., a novel motile actinomycete isolated by rehydration and centrifugation method

Cited by 12 publications

References 35 publications

Phylogenomic analyses of the genus Actinoplanes: description of four novel genera

Phylogenomic analyses of the genus Actinoplanes: description of four novel genera

Three novel Actinoplanes species isolated by using polyaspartic acid as a water-retaining agent for the enrichment in situ

Progressive community, biogeochemical and evolutionary remodeling of the soil microbiome underpins long-term desert ecosystem restoration

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