Elucidation of the Biosynthetic Pathway of Vitamin B Groups and Potential Secondary Metabolite Gene Clusters Via Genome Analysis of a Marine Bacterium Pseudoruegeria sp. M32A2M

Abstract

The symbiotic nature of the relationship between algae and marine bacteria is well-studied among the complex microbial interactions. The mutual profit between algae and bacteria occurs via nutrient and vitamin exchange. It is necessary to analyze the genome sequence of a bacterium to predict its symbiotic relationships. In this study, the genome of a marine bacterium, Pseudoruegeria sp. M32A2M, isolated from the southeastern isles (GeoJe-Do) of South Korea, was sequenced and analyzed. A draft genome (91 scaffolds) of 5.5 Mb with a DNA G+C content of 62.4% was obtained. In total, 5,101 features were identified from gene annotation, and 4,927 genes were assigned to functional proteins. We also identified transcription core proteins, RNA polymerase subunits, and sigma factors. In addition, full flagella-related gene clusters involving the flagellar body, motor, regulator, and other accessory compartments were detected even though the genus Pseudoruegeria is known to comprise non-motile bacteria. Examination of annotated KEGG pathways revealed that Pseudoruegeria sp. M32A2M has the metabolic pathways for all seven vitamin Bs, including thiamin (vitamin B1), biotin (vitamin B7), and cobalamin (vitamin B12), which are necessary for symbiosis with vitamin B auxotroph algae. We also identified gene clusters for seven secondary metabolites including ectoine, homoserine lactone, beta-lactone, terpene, lasso peptide, bacteriocin, and nonribosomal proteins.

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

“…Most importantly, P. coloniale is also a vitamin B 7 (biotin) auxotroph, lacking all four genes involved in the biosynthesis of this vitamin, and apparently the only biotin auxotroph currently known among Archaeplastida 82 (Supplementary Table 21). Many genomes of marine bacteria contain full sets of biotin biosynthesis genes 83,84 and these bacteria could be a source of biotin for P. coloniale. Genome compaction in these picoplanktonic eukaryotes may have facilitated evolution of such symbiotic interactions in an oligotrophic marine environment.…”

Compositional and Functional Microbiome Variation Between Tubes of an Intertidal Polychaete and Surrounding Marine Sediment

“…Similarly, Pseudoruegeria is associated with algae. Algae produces dissolved organic matter, oxygen, and sulfur, and the bacteria supplies the algae with the vitamins thiamin, biotin, and cobalamin (Cho et al, 2020). As mentioned before, tube tops contain plant material and algae, so it is not surprising genera associated with algae and sea grasses are enriched in tubes.…”

“…Bacteroidetes and Verrucomicrobia were associated with diatoms (Bruckner et al, 2008), and Latescibacteria are also associated with algae cells (Youssef et al, 2015). More specifically, Granulosicoccus have been isolated from seagrass (Kurilenko et al, 2010) and algae (Park et al, 2014), while Pseudoruegeria supplies algae with thiamin, biotin, and cobalamin (Cho et al, 2020), and Maribacter is found on the surface of macroalgae (Bakunina et al, 2012). Worms have been shown to collect algae and use it as building material to add structure to the tube tops (Berke et al, 2006;Berke, 2012) and may serve as a direct food supply for omnivorous worms (Magnum et al, 1968) or as an indirect food supply when the worm eats the algae-associated meiofuana (Bell and Coen, 1982).…”

Elucidation of the Algicidal Mechanism of the Marine Bacterium Pseudoruegeria sp. M32A2M Against the Harmful Alga Alexandrium catenella Based on Time-Course Transcriptome Analysis

“…•s −1 photons at 20 • C ± 1 • C. Pseudoruegeria sp. M32A2M was isolated from surface water of the South Sea in South Korea, where HABs of Alexandrium are frequently observed (Cho et al, 2020). Pseudoruegeria sp.…”