Verrucosispora sediminis sp. nov., a cyclodipeptide-producing actinomycete from deep-sea sediment

Abstract

An actinomycete, designated MS426 T , the culture broth of which showed potent antimicrobial activity, was isolated from a deep-sea sediment sample of the South China Sea. An almostcomplete sequence of the 16S rRNA gene of strain MS426 T was determined and aligned with those of representatives of the family Micromonosporaceae available in public databases. Phylogenetic trees were inferred by using three algorithms. Strain MS426 T formed a branch adjacent to Verrucosispora lutea YIM 013 T in a distinct cluster occupied only by strains of the genus Verrucosispora. Strain MS426 T was distinguishable from the type strains of the two described Verrucosispora species by using a combination of chemical and morphological markers and by DNA-DNA relatedness. On the basis of these genotypic and phenotypic differences, the novel antimicrobial strain with pharmaceutical potential represents a novel species, for which the name Verrucosispora sediminis sp. nov. is proposed. The type strain is MS426 T (5CGMCC 4.3550 T 5JCM 15670 T ).The exploration of microbial diversity in marine environments has become one of the most popular research areas now that the ocean has been recognized as a microbiological 'rainforest'. Novel microbes and their associated bioactive compounds have been isolated (Demain & Zhang, 2005). Since the description of the marine genus Salinispora and its bioactive secondary metabolites, marine actinomycetes, especially members of the family Micromonosporaceae, have received attention from both taxonomists and chemists (Maldonado et al., 2005;Laatsch, 2006;Lam, 2006;Knight et al., 2003;Zhang et al., 2005). The discovery of abyssomicin, an inhibitor of p-aminobenzoic acid biosynthesis, in the marine strain AB-18-032 of the genus Verrucosispora has led to this genus receiving special attention (Riedlinger et al., 2004).The genus Verrucosispora was established by Rheims et al. (1998) and, to date, only two species have been described, namely Verrucosispora gifhornensis (Rheims et al., 1998) and Verrucosispora lutea (Liao et al., 2009). The genus Verrucosispora is characterized by branching hyphae that form a well-developed septate mycelium, absent or sparse aerial mycelium, non-motile, singly borne spores with smooth, warty or hairy surfaces, the presence of 16S rRNA gene signature nucleotides specific to the family Micromonosporaceae, a unique nucleotide signature (59-CAAUUCGGUUG-39) between positions 1132 and 1143 (Escherichia coli numbering), DNA G+C content of 69.3-70.0 mol%, peptidoglycan of type A1c (directly crosslinked, presence of glycine, alanine, glutamic acid and meso-diaminopimelic acid in the peptide side-chain), lack of arabinose in whole-cell sugars, a polar lipid composition 3These authors contributed equally to this work.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MS426 T is EU870859.A scanning electron micrograph of strain MS426 T is available as supplementary material with the online version of this paper. The main interest of our joint research project is t...

Description of Verrucosispora qiuiae sp. nov., isolated from mangrove swamp sediment, and emended description of the genus Verrucosispora

“…All physiological data and fatty acid data for V. lutea YIM 013 T were obtained in this study. Spore morphological characteristics and other chemotaxonomic data for recognized species are from previous studies (Rheims et al, 1998;Liao et al, 2009;Dai et al, 2010). +, Positive; W, weakly positive; 2, negative.…”

“…At the time of writing, this genus comprised three species with validly published names, Verrucosispora gifhornensis, Verrucosispora lutea and Verrucosispora sediminis, with type strains isolated from peat bog, mangrove sediment and deep-sea sediment, respectively (Rheims et al, 1998;Liao et al, 2009;Dai et al, 2010). Marine environments seem to be a good source of both novel species of this genus and unique natural products.…”

“…According to the revised 16S rRNA gene sequence similarity threshold range of 98.7-99 % (Stackebrandt & Ebers, 2006), and a recent study that showed that, between Verrucosispora type strains, even 16S rRNA gene sequence similarity as high as 99.1 % corresponded to a low DNA-DNA relatedness of less than 60 % (Dai et al, 2010), hybridizations between strain RtIII47 T and the other two Verrucosispora type strains were not performed. Based on the unique 16S rRNA gene sequence, the low gyrB gene sequence similarities and the level of Table 1.…”

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

“…Ampicillin ( Determined by spectrophotometric method (Dai et al 2010); e. Determined by a modified fluorimetric microwell plate method (Xi et al 2012); f. Determined by using melting profiles in microplates (Xie et al 2012) …”

“…The taxon currently encompass six species, Verrucosispora gifhornensis (Rheims et al 1998), the type species, Verrucosispora lutea (Liao et al 2009), Verrucosispora maris (Goodfellow et al 2012), Verrucosispora qiuiae (Xi et al 2012), Verrucosispora sediminis (Dai et al 2010) and Verrucosispora wenchangensis (Xie et al 2012), the single members of which can be separated using a combination of genotypic and phenotypic procedures (Goodfellow et al 2012;Xi et al 2012;Xie et al 2012). The type strains of these species were isolated from a peat bog (V. gifhornensis), mangrove soils (V. lutea, V. qiuiae and V. wenchangensis) and deep-sea sediments (V. maris and V. sediminis).…”