Three novel marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading polysaccharides

Abstract

Bacteroidota is a group of marine polysaccharide degraders, which play a crucial role in the carbon cycle in the marine ecosystem. In this study, three novel gliding strains, designated as SS9-22T, W9P-11T, and SW1-E11T, isolated from algae and decaying wood were proposed to represent three novel species of the genus Fulvivirga. We identified a large number of genes encoding for carbohydrate-active enzymes, which potentially participate in polysaccharide degradation, based on whole genome sequencing. The 16S rRNA sequence similarities among them were 94.4–97.2%, and against existing species in the genus Fulvivirga 93.1–99.8%. The complete genomes of strains SS9-22T, W9P-11T, and SW1-E11T comprised one circular chromosome with size of 6.98, 6.52, and 6.39 Mb, respectively; the GC contents were 41.9%, 39.0%, and 38.1%, respectively. The average nucleotide identity and the digital DNA-DNA hybridization values with members in the genus Fulvivirga including the isolates were in a range of 68.9–85.4% and 17.1–29.7%, respectively, which are low for the proposal of novel species. Genomic mining in three genomes identified hundreds of carbohydrate-active enzymes (CAZymes) covering up to 93 CAZyme families and 58–70 CAZyme gene clusters, exceeding the numbers of genes present in the other species of the genus Fulvivirga. Polysaccharide-degrading activities were found, highlighting that the three strains are rich sources of CAZymes of polysaccharide degraders for biotechnological applications. The phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of three novel species in the genus Fulvivirga, for which the names Fulvivirga ulvae sp. nov. (SS9-22T = KCTC 82072T = GDMCC 1.2804T), Fulvivirga ligni sp. nov. (W9P-11T = KCTC 72992T = GDMCC 1.2803T), and Fulvivirga maritima sp. nov. (SW1-E11T = KCTC 72832T = GDMCC 1.2802T) are proposed.

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov

“…The plates were kept in a 20 °C incubator for seven days and observed using a stereoscopic microscope (ZEISS Stemi 508). The gliding colonies were transferred onto rich media of marine agar (MA, BD) and modified VY/2 agar media [MVY; 60% (v/v) seawater, 5 g/L baker's yeast (Sigma), and 25 mg/L vitamin B12] [19]. The colonies were further purified and preserved at -80 °C in 20% glycerol.…”

“…The number of CAZymes in the family Marivirgaceae (53-152 CAZymes) closely resembled that of neighboring families within the phylum Bacteroidota, including Reichenbachiellaceae (79-216 CAZymes) [49], Fulvivirgaceae (55-264 CAZymes) [19], and Flavobacteriaceae Zobellia sp (257-315 CAZymes) [64,65]. The presence of high numbers of CAZymes in bacteria offers insights into their ecological roles, adaptability, and potential applications across various biotechnological processes [66].…”

Halocynthiibacter laminarini gen. nov., sp. nov. and Halocynthiibacter xylanolyticus sp. nov., marine anaerobic laminarin and xylan degraders in the phylum Bacteroidota

“…For isolation, a low nutrient solid medium prepared by sixty percent strength seawater (collected from the sampling site) solidi ed with 1.5% agar (BD) was used. After autoclaving the medium, 50 mg/L cycloheximide (Aldrich Sigma) was added to the agar medium [19]. All the steps for bacterial isolation were performed in an anaerobic chamber (Coy Lab Products, USA; N 2 : H 2 : CO 2 = 94.5%:1.5%:5%).…”

“…To date, members of the class Flavobacteriia are found to be abundant in the macroalgal phycosphere microbiome and in microalgal blooms and are well documented for macro-and microalgal polysaccharide degradation [14,15]. Several studies have meanwhile demonstrated the ability of members of the class Cytophagia to degrade polysaccharides [16,17] and predicted potential polysaccharide degradation [18], although there are fewer available literature sources of marine Cytophagia bacteria degrading polysaccharides [19]. On the other hand, members of the class Bacteroidia are mostly anaerobes and have been well studied for polysaccharide degradation in the mammalian gut microbiota [20].…”

“…Several isolation methods have been applied to isolate members of the family Prolixibacteraceae, including enrichment [22], a dilution technique [38], and nitrogen-free medium cultivation [39]. In this study, we used another strategy to isolate novel bacteria by using a low nutrient isolation medium, which was prepared from 60% strength seawater (at the collection site) with 1.5% agar (BD) and a piece of lter paper placed on the surface of the agar as the sample carrier [19]. We isolated two novel bacteria from a sea squirt under anaerobic conditions.…”