Rubinisphaera margarita sp. nov., a novel planctomycete isolated from marine sediments collected in the Portuguese north coast

Abstract

The phylum Planctomycetota is constituted by bacteria with unique features that are well adapted to a vast range of habitats. Here, we describe a novel planctomycete isolated from marine sediments collected on a beach in Matosinhos (Portugal) using an iChip-based culturing technique. Strain ICM_H10T forms beige-coloured colonies in modified M14 medium and its cells are spherical to ovoid in shape, stalked, rosette-forming and showing motility in a phase of the life cycle. Transmission electron microscopy observations showed a typical planctomycetal cell plan and cell division by budding. This strain requires salt for growth and grows in the range of 2.0–5.0 % (w/v) NaCl, from 20 to 37 °C, within a pH of 6.0–9.0 and is able to use diverse nitrogen and carbon sources. It is heterotrophic, aerobic and capable of microaerobic growth. This strain has a genome size of approximately 6.0 Mb and a G+C content of 58.1 mol%. A 16S rRNA gene-based phylogenetic analysis supports the association of strain ICM_H10T to the phylum Planctomycetota and the family Planctomycetaceae , as it shares only 96.8 and 96.4% similarity to its closest relatives Rubinisphaera italica Pan54T and Rubinisphaera brasiliensis IFAM 1448T, respectively. Other phylogenetic markers also support the separation of this strain into a novel species. Morphological, physiological and genomic comparisons between strain ICM_H10T and its closest relatives strongly suggest that ICM_H10T represents a new species of the genus Rubinisphaera , for which we propose the name Rubinisphaera margarita sp. nov., with ICM_H10T (=CECT 30326T=LMG 32234T) as type strain.

Aeoliella straminimaris sp. nov., a novel member of the phylum Planctomycetota with an unusual filamentous structure

“…In this work, diverse macroalgae, water and sediments were sampled and different isolation techniques applied. The higher number of isolates and planctomycetal phylogenetic diversity (including 2 other putative novel taxa from family Pirellulaceae ) was obtained from sediments using an iChip-based approach, which was also successfully applied for the isolation of a novel Rubinisphaera species in a previous study conducted on the Portuguese north coast [31, 66]. Strain ICT_H6.2 T was isolated from mud-like sediments collected from the Tagus river estuary using this technique.…”

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

“…The assays for the evaluation of the pH range for growth, the salinity tolerance, and the carbon and nitrogen sources were performed in triplicates in a 96-well plate format using liquid cultures. For each tested condition, a pre-inoculum of strain ICT_E10.1 T was diluted in the proportion of 1:10 in the respective medium for a final volume of 100 µL culture per well, and results were recorded by measuring the culture turbidity (optical density (OD) at 600 nm) before and after 14 days incubation at 25 • C. The pH values tested ranged from 4.0 to 11.0 and the tolerance to NaCl was from 0 to 10 % (w/v) (media formulated as described previously [36]). The carbon sources assayed (0.1% w/v) included N-acetylglucosamine (NAG), cellobiose, galactose, glucose, xylose, carrageenan, mannitol, fructose, lactose, dextran and arabinose, and the nitrogen sources tested (0.1% w/v) were NAG, serine, alanine, cystine, tyrosine, tryptophan, phenylalanine, valine, arginine, lysine, histidine, sodium nitrite, sodium nitrate, glutamine, asparagine, urea, ammonium sulfate, and casamino acids.…”

“…The carbon sources assayed (0.1% w/v) included N-acetylglucosamine (NAG), cellobiose, galactose, glucose, xylose, carrageenan, mannitol, fructose, lactose, dextran and arabinose, and the nitrogen sources tested (0.1% w/v) were NAG, serine, alanine, cystine, tyrosine, tryptophan, phenylalanine, valine, arginine, lysine, histidine, sodium nitrite, sodium nitrate, glutamine, asparagine, urea, ammonium sulfate, and casamino acids. All these media were prepared as previously described [36]. The catalase test consisted of reacting a colony of strain ICT_E10.1 T with a drop of hydrogen peroxide, which lead to the formation of bubbles and indicated the presence of the enzyme.…”

“…Recently, we applied a novel culturing technique on samples collected in two regions of Portugal (north coast and Tagus river estuary) that allowed the isolation of planctomycetes from different taxa, including novel species [26,29,36]. In this polyphasic study, we formally describe a novel isolate from the genus Stieleria [52,56] previously isolated from the Tagus estuary, strain ICT_E10.1 T .…”

Uncovering the biotechnological capacity of marine and brackish water Planctomycetota

“…The vast majority of estimated bacterial diversity is still uncultured in laboratory (Barer and Harwood 1999;Rinke, et al 2013), which heavily restricts what could be screened for biotechnological purposes. Nonetheless, recent cultivation efforts from diverse research groups have allowed to bring into axenic culture many strains (including novel species) from underexplored and evolutionarily deep-branching groups such as the Planctomycetota (Almeida, et al 2022, Gaurav, et al 2021, Kaushik, et al 2020, Kulichevskaya, et al 2020a, Kulichevskaya, et al 2022, Kulichevskaya, et al 2020b, Kumar, et al 2020a, Kumar, et al 2020b, Kumar, et al 2021a, Vitorino, et al 2020, Vitorino et al 2021b, Vitorino, et al 2022b, Vitorino, et al 2022c, Vitorino, et al 2022d. The bacterial phylum Planctomycetes (now renamed Planctomycetota (Oren and Garrity 2021)) belongs to the super phylum Planctomycetota-Chlamydiota-Verrucomicrobiota (PVC) (Rivas-Marín and Devos 2018;Wagner and Horn 2006).…”