Varvara D. Salova

Two novel verrucomicrobial strains, RX08ᵀ and T20Ac3, were isolated from a boreal fen in northern European Russia and alpine meadow soil in the North Caucasus, respectively. Both strains were Gram-stain-negative, aerobic, non-motile rods growing at 15–30°C (optimum 25°C) and pH 6.5–8.5. A reversible light-dependent transition from yellow to pink pigmentation was observed in both strains during growth on solid and in liquid media. Phylogenetic analysis placed the isolates within the recently established genus Neoluteolibacter, with Neoluteolibacter rhizosphaerae GHJ8T representing the closest described relative (98.4% 16S rRNA gene sequence similarity). The complete genome of strain RX08ᵀ comprised a single 6.34 Mb chromosome with a G+C content of 62.0 mol% and 5,106 predicted protein-coding genes. Genome analysis revealed a complete C30 carotenoid biosynthesis pathway, while HPLC demonstrated that pigmentation change was accompanied by the accumulation of glycosylated diapocarotenoid derivatives, consistent with the observed pigmentation shift. Both strains utilized a wide range of sugars and polysaccharides, including chitin and inulin, as growth substrates. Consistent with these phenotypic characteristics, the genome encoded multiple glycoside hydrolases, including a distinct GH18 chitinase and four GH32 fructanases, suggesting adaptation to the degradation of structurally distinct environmental polysaccharides. Comparative phylogenomic analyses and overall genome relatedness indices supported the classification of strains RX08ᵀ and T20Ac3 as representing a novel species, for which the name Neoluteolibacter xanthoroseus sp. nov. is proposed. The type strain is RX08ᵀ (= LMG 34154ᵀ = KCTC 102489ᵀ).

The bacterial phylum Verrucomicrobiota accommodates free-living and symbiotic microorganisms, which inhabit a wide range of environments and specialize in polysaccharide degradation. Due to difficulties in cultivation, much of the currently available knowledge about these bacteria originated from cultivation-independent studies. A phylogenetic clade defined by the free-living bacterium from oilsands tailings pond, Oleiharenicola alkalitolerans, and the symbiont of the tunicate Lissoclinum sp., Candidatus Didemniditutus mandelae, is a poorly studied verrucomicrobial group. This clade includes two dozen methagenome-assembled genomes (MAGs) retrieved from aquatic and soil habitats all over the world. A new member of this clade, strain Vm1, was isolated from a methane-fed laboratory bioreactor with a Methylococcus-dominated methane-oxidizing consortium and characterized in this study. Strain Vm1 was represented by ultra-small, motile cocci with a mean diameter of 0.4 µm that grew in oxic and micro-oxic conditions at temperatures between 20 and 42 °C. Stable development of strain Vm1 in a co-culture with Methylococcus was due to the ability to utilize organic acids excreted by the methanotroph and its exopolysaccharides. The finished genome of strain Vm1 was 4.8 Mb in size and contained about 4200 predicted protein-coding sequences, including a wide repertoire of CAZyme-encoding genes. Among these CAZymes, two proteins presumably responsible for xylan and arabinan degradation, were encoded in several MAGs of Vm1-related free-living verrucomicrobia, thus offering an insight into the reasons behind wide distribution of these bacteria in the environment. Apparently, many representatives of the Oleiharenicola–Candidatus Didemniditutus clade may occur in nature in trophic associations with methanotrophic bacteria, thus participating in the cycling of methane-derived carbon.

Microorganisms associated with algae and able to utilize complex substrates (e.g., plant heteropolysaccharides) may be important producers of hydrolytic enzymes. The microbial communities of the red algae Corallina sp. and Phyllophora sp. sampled in the Kandalaksha Gulf basin of the White Sea were analyzed using high-throughput sequencing of the V4-variable region of the 16S rRNA gene. The dominant phyla in microbiomes of both samples were Pseudomonadota and Bacteroidota (GTDB classification, https://gtdb.ecogenomic.org/). For the Corallina sp. sample, dominance of the Vibrio, Agarivorans, and Photobacterium genera was shown, while Granulosicoccus and Aliivibrio dominated in the Phyllophora sp. sample. The analyzed red macroalgae with associated microbiota were used as an inocula to obtain microbial enrichment cultures growing on β-1,4-xylan or β-1,3-glucan (curdlan). It was shown that, similar to environmental samples Pseudomonadota and Bacteroidota phyla representatives were prevalent in all enrichment cultures. However, unlike the environmental samples, in the enrichment cultures the dominant genera were Marinomonas, Reinekea, Polaribacter, and Pseudoalteromonas. The latter, as well as the representatives of Vibrio sp., were isolated in pure cultures for which the xylanolytic activity was shown.

Microbial Communities Associated with the White Sea Red Algae as a Source of Xylanolytic Microorganisms Микробные сообщества, ассоциированные с красными водорослями белого моря, как источник ксиланолитических микроорганизмов