Verrucosispora andamanensis sp. nov., isolated from a marine sponge

Supong, Khomsan; Suriyachadkun, Chanwit; Suwanborirux, Khanit; Pittayakhajonwut, Pattama; Thawai, Chitti

doi:10.1099/ijs.0.050906-0

Cited by 20 publications

(10 citation statements)

References 44 publications

(44 reference statements)

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“…The description is as given for Verrucosispora andamanensis (Supong et al, 2013 ). The type strain is SP03-05 = BCC 45620 = NBRC 109075 = DSM 46721.…”

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 andamanensis (Supong et al, 2013 ). The type strain is SP03-05 = BCC 45620 = NBRC 109075 = DSM 46721.…”

Section: Discussionmentioning

confidence: 99%

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

et al. 2018

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“…In the List of Prokaryotic names with Standing in the Nomenclature (http://www.bacterio.net), 14 novel species of 10 genera of actinomycetes from marine sponges are cited, at the time of writing, including Actinoalloteichus hymeniacidonis (Zhang et al, 2006), Actinokineospora spheciospongiae (Kämpfer et al, 2015), Marmoricola aquaticus (de Menezes et al, 2015), Micromonospora yangpuensis (Zhang et al, 2012), Mycobacterium poriferae (Padgitt & Moshier, 1987), Rubrobacter aplysinae (Kämpfer et al, 2014), Saccharopolyspora cebuensis (Pimentel-Elardo et al, 2008), Streptomyces axinellae (Pimentel-Elardo et al, 2009), Streptomyces spongiae (Khan et al, 2011), Streptomyces tateyamensis, Streptomyces marinus, Streptomyces haliclonae (Khan et al, 2010), Tsukamurella spongiae (Olson et al, 2007) and Verrucosispora andamanensis (Supong et al, 2013). Therefore, marine sponges are a good habitat for novel species of actinomycete.…”

mentioning

confidence: 99%

Streptomyces spongiicola sp. nov., an actinomycete derived from marine sponge

Huang

Zhou

Huang

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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A novel actinomycete (strain HNM0071 T ) was isolated from an unidentified marine sponge collected from the coast of Sanya City, PR China and its taxonomic position was investigated.The major menaquinones were MK-9 (H 6 ) (65.6 %), MK-9 (H 4 ) (23.8 %) and MK-9 (H 8 ) (10.6 %). The predominant fatty acids were anteiso-C 15 : 0 (25.5 %), iso-C 16 : 0 (19.5 %) and iso-C 15 : 0 (15.4 %). The predominant phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, four unidentified phospholipids were found. The G+C content of the genomic DNA was 69.8 mol%. Based on 16S rRNA gene sequence analysis, strain HNM0071 T was most closely related to Streptomyces wuyuanensis

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“…We next tried more specialized media typically used to culture organisms such as Verrucosispora spp. (39)(40)(41). Here we found that AMM and ISP-2 (Figure 1C and 1D) media were much better suited for rapid biomass accumulation, as evidenced by the 3-5 day increase in optical density for AMM, and for ISP-2 after the 6-day time point.…”

Section: Cultivation and Domestication Of A Novel Isolate Of The Verrucosispora Genusmentioning

confidence: 50%

Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

Kennedy

Atkinson

Tomlinson

et al. 2021

Preprint

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The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental hole in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic decay through the pseudogenization of amino acids metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

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Verrucosispora andamanensis sp. nov., isolated from a marine sponge

Cited by 20 publications

References 44 publications

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

Streptomyces spongiicola sp. nov., an actinomycete derived from marine sponge

Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

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