Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation

Abstract

Two actinobacterial strains, ADI 127-17^T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17^T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17^T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17^T (= DSM 46855^T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17^T = DSM 46855^T = CECT 9355^T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092^T and A. hoggarensis DSM 45943^T to unravel unique genome features and biosynthetic potential of the new isolates.

Keywords: Actinoalloteichus; Actinobacteria; Chemotaxonomy; Comparative genomics; Marine sponges; New species; Secondary metabolite biosynthesis gene clusters.

Fig. 1

Molecular phylogenetic analysis of Actinoalloteichus spp and related actinobacteria using 16S rRNA gene sequences by Maximum Likelihood method. The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura-Nei model (Tamura and Nei 1993). The tree with the highest log likelihood (−3981.4891) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 12 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1358 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 (Kumar et al. 2016)

Fig. 2

Cryo-scanning electron micrograph of the aerial mycelium of Actinoalloteichus spp. DSM 46855^T and DSM 46856. The strains were grown on 7 days on ISP2 medium (in half-strength artificial sea water) and then imaged. For each strain, aerial hyphae and spores are shown at three magnifications. Bar 2 µm

Fig. 3

Graphical maps of the chromosomes of a A. fjordicus DSM 46855^T and b A. fjordicus DSM 46856. From the outside to the center: Genes on forward strand (colour by COG categories), genes on reverse strand (color by COG categories—see Table 3), RNA genes (tRNAs green, rRNAs red, other RNAs black), G+C content, G+C skew