Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments

Abstract

The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1^T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1^T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1^T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1^T into the genus Stieleria with Stieleria neptunia Enr13^T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1^T as the type of strain (=CECT 30514^T= DSM 113784^T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.

Keywords: Alcochete; Planctomycetota; bioactivity screenings; biosynthetic gene clusters; carbohydrate-active enzymes; iChip; novel taxa; organic extraction; transmission electron microscopy.

Figure 1

Phylogeny of strain ICT_E10.1^T through the analysis of the 16S rRNA gene sequence. The maximum-likelihood tree evidences the proximity of strain ICT_E10.1^T to the genus Stieleria within the family Pirellulaceae of the bacterial phylum Planctomycetota. GenBank sequence identifiers of other type strains are shown in parentheses. One thousand bootstraps were applied, and the respective values given at the nodes (in %). Branches of the other families in the class Planctomycetia collapsed at the family level. Three strains from the phylum Verrucomicrobiota were utilized as outgroups.

Figure 2

Genome-based tree (MLS) consolidating the affiliation of strain ICT_E10.1^T to the family Pirellulaceae in the genus Stieleria but as a separate species. Other genomes utilized in this tree were retrieved from NCBI and the GenBank tags given in parenthesis. Members belonging to other families in class Planctomycetia collapsed at the family level. The bootstrap used in this tree was 1000 and the respective percentages shown at the nodes (in %). Three Streptomyces spp. (phylum Actinomycetota) were used as outgroups.

Figure 3

Ecological summary of ICT_E10.1^T-related metagenomes and other isolated strains with proximity to the genus Stieleria. The 16S rRNA gene sequence-based tree was constructed with MEGA X as described previously. Metagenomic 16S rRNA gene sequences were retrieved from the SILVA SSU database (release 138.1 from 27 August 2020) and sequences from isolated strains retrieved from the NCBI database (GenBank accession numbers are given in parentheses).

Figure 4

Phenotypic characterization of strain ICT_E10.1^T while in exponential phase. Photographies of strain ICT_E10.1^T in modified M14 medium (a) show its pink coloration and in bright field microscopy images (b–d) cells appear spherical to ovoid in shape and cluster in aggregates (b) or small chains (c). Budding is the division mode (d).

Figure 5

Micrographs from transmission electron microscopy observations showing the cell plan of strain ICT_E10.1^T in aggregated (a) and individual cells (b,c). A strong extracellular material is seen connecting the cells (a). F: fimbriae, H: holdfast, CMI: cytoplasmatic membrane invaginations, CM: cytoplasmatic membrane, OM: outer membrane.

Figure 6

Distribution of number and structural types of BGCs putatively found in strain ICT_E10.1^T and in its closest relatives S. maiorica Mal15^T, S. neptunia Enr13^T and S. varia Pla52n^T for comparison, evidencing the content differences between strains. The genome size of each strain was additionally added above each bar.

Figure 7

Boxplot diagram showing the percentage of growth of S. aureus (a) and E. coli (b) when exposed to ICT_E10.1^T extract, considering the three biologically replicated assays. The solvent control corresponds to DMSO (2% v/v final concentration in the assay), the positive control of ampicillin (4 mg/mL final concentration in the assay), and the growth control of the target bacteria without exposure to treatments. The planctomycete extract consistently inhibited the growth of S. aureus in the three assays (a). In contrast, very low bioactivity was observed against E. coli (b).