Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins

Goodfellow, Michael; Brown, Roselyn; Ahmed, Lina Qadir; Pathom-aree, Wasu; Bull, Alan T.; Jones, Amanda; Stach, James E. M.; Zucchi, Tiago Domingues; Zhang, Lixin; Wang, Jian

doi:10.1007/s10482-012-9831-y

Cited by 23 publications

(11 citation statements)

References 30 publications

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“…The description is as given for Verrucosispora fiedleri (Goodfellow et al, 2013 ). The type strain is MG-37 = NCIMB 14794 = NRRL-B-24892 = DSM 46741 = KACC 18210.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

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“…The description is as given for Verrucosispora fiedleri (Goodfellow et al, 2013 ). The type strain is MG-37 = NCIMB 14794 = NRRL-B-24892 = DSM 46741 = KACC 18210.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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“…The almost complete 16S rRNA gene sequence of strain 2603PH03 T (1475 nt, GenBank accession number HQ123438) was compared with sequences of representatives of the genus Verrucosispora. The 16S rRNA gene sequence similarities of strain 2603PH03 T with the type strains of V. gifthornensis , Verrucosispora andamanensis (Supong et al 2013 ), V. fiedleri (Goodfellow et al 2013 ), V. maris (Goodfellow et al 2012 ), Verrucosispora wenchangensis (Xie et al 2012 ), Verrucosispora sediminis (Dai et al 2010 ) , Verrucosispora lutea (Liao et al 2009 ) and Verrucosispora qiuiae (Xi et al 2012 ) were 99.4, 99.4, 99.4, 99.2, 99.1, 99.0 and 99.0%, respectively. Based on 16S rRNA gene sequence analysis, strain 2603PH03 T formed a phyletic line on the periphery of the 16S rRNA gene subclade comprised of the type strains of V. gifhornensis , V. fiedleri and V. maris , a relationship which was supported by all of the tree-making algorithms and by a 93% bootstrap value (Fig.…”

Section: Resultsmentioning

confidence: 99%

“… Strains 1 2603PH03 T ; 2 V. gifhornensis DSM 44337 T ; 3 V. maris AB18-032 T ; 4 V. fiedleri MG-37 T ; + positive; − negative PE phosphatidylethanolamine; DPG diphosphatidylglycerol; PIM phosphatidylinositol mannoside; PS phosphatidylserine; PI phosphatidylinositol; PG phosphatidyl glycerol; PL unidentified phospholipid a Data from Rheims et al ( 1998 ) b Data from Goodfellow et al ( 2013 ) c Data from Goodfellow et al ( 2012 ); all other phenotypic data were determined in this study …”

Section: Resultsmentioning

confidence: 99%

Verrucosispora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil

Xie

Bao

et al. 2017

Antonie van Leeuwenhoek

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An actinomycete strain, 2603PH03T, was isolated from a mangrove rhizosphere soil sample collected in Wenchang, China. Phylogenetic analysis of the 16S rRNA gene sequence of strain 2603PH03T indicated high similarity to Verrucosispora gifthornensis DSM 44337T (99.4%), Verrucosispora andamanensis (99.4%), Verrucosispora fiedleri MG-37T (99.4%) and Verrucosispora maris AB18-032T (99.4%). The cell wall was found to contain meso-diaminopimelic acid and glycine. The major menaquinones were identified as MK-9(H4), MK-9(H6) and MK-9(H8), with MK-9(H2), MK-10(H2), MK-9(H10) and MK-10(H6) as minor components. The characteristic whole cell sugars were found to be xylose and mannose. The phospholipid profile was found to contain phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylserine and an unidentified phospholipid. The DNA G+C content was determined to be 70.1 mol%. The results of physiological and biochemical tests and low DNA-DNA relatedness readily distinguished the isolate from the closely related species. On the basis of these phenotypic and genotypic data, strain 2603PH03T is concluded to represent a novel species of the genus Verrucosispora, for which the name Verrucosispora rhizosphaerae sp. nov. is proposed. The type strain is 2603PH03T (=CCTCC AA 2016023T = DSM 45673T).Electronic supplementary materialThe online version of this article (doi:10.1007/s10482-017-0933-4) contains supplementary material, which is available to authorized users.

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“…It has been debated for many years without consensus whether marine actinomycetes are actually native marine population or simply a wash off terrestrial microorganisms (Jensen et al, 1991;Takizawa et al, 1993). According to Goodfellow et al (2013), all six validly described Verrucosispora taxon members came from the marine environment indicating that they are true autochthonous marine community and denying the theory of land runoff microorganisms. However, the present Verrucosispora maris strain was of terrestrial origin and able to grow without the presence of salt content which contradicts the fact of an autochthonous marine bacteria while suggesting the possibility of salinity adaptation.…”

Section: Resultsmentioning

confidence: 99%

Taxonomic Diversity and Antimicrobial Activities of Actinomycetes from Manure Composts

Low

Mohamad

Abdullah

2015

Research J. of Microbiology

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Manure compost is a unique microenvironment which harbours potential new microorganisms that is able to produce a variety of anti-infective agents. However, the exploration of this ecosystem for actinomycetes and its bioactive secondary metabolites remained understudied. Therefore, this study aims to study the diversity of manure compost actinomycetes and to investigate their antimicrobial potential using conventional disc diffusion method and a modified resazurin microtiter based approach. A collection of 191 actinomycete isolates were recovered from 5 types of manure composts collected around Selangor, Malaysia. Utilizing a combination of micromorphological characteristics and 16S rRNA sequence analysis, the isolated actinomycetes were grouped into 12 genera within 9 families. Streptomyces spp. dominated the culture collection (79.1%) while the rest belonged to the non-Streptomyces group (20.9%), including an unusual isolate from the genus Verrucosispora. The evaluation of antimicrobial activities demonstrated that 21.5% of the isolates exhibited antagonistic effect against at least one of the test microorganisms with strong inhibition observed against fungal strains compared to pathogenic bacteria. A modified resazurin microtiter based assay was also developed and displayed higher sensitivity (40.0%) compared to the disc diffusion assay (26.0%). All ten actinomycete isolates which displayed narrow and broad spectrum effects also produce pigmented extracts. The results demonstrated that manure compost actinomycetes could be a promising source of novel bioactive agents and that the resazurin microtiter based assay is a more sensitive approach in screening antimicrobial properties of large numbers of microbial extracts.

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Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins

Cited by 23 publications

References 30 publications

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Verrucosispora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil

Taxonomic Diversity and Antimicrobial Activities of Actinomycetes from Manure Composts

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