Flagellimonas algicida sp. Nov.: A Novel Broad-Spectrum Algicidal Bacterium Targeting Harmful Algal Bloom Species and Genomic Insights into Its Secondary Metabolites

A novel Gram-negative bacterium, designated strain SN16T, was isolated from a harmful algal bloom (HAB). Strain SN16T exhibited potent, broad-spectrum algicidal activity against the colony-forming alga Phaeocystis globosa and eight other HAB-causing species, highlighting its potential as a promising candidate for the biological control of HABs. A phylogenetic analysis of 16S rRNA gene sequences placed strain SN16T within the genus Flagellimonas. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain SN16T and its relatives were 75.4–91.4% and 19.3–44.0%, respectively. These values fall below the established thresholds for species delineation, confirming that SN16T represents a novel species. A chemotaxonomic analysis revealed its dominant cellular fatty acids to be iso-C15:0 and iso-C15:1 G. The major polar lipid was phosphatidylethanolamine, and the primary respiratory quinone was menaquinone-6. Genome mining identified 11 biosynthetic gene clusters (BGCs), including those encoding for terpenes, ribosomal peptide synthetases, and non-ribosomal peptide synthetases. By integrating BGC analysis with the observed algicidal activities, we predicted that pentalenolactone and xiamycin analogues are the likely causative compounds. Based on this polyphasic evidence, strain SN16T is proposed as a novel species of the genus Flagellimonas, named Flagellimonas algicida sp. nov. This is the first report of Flagellimonas species exhibiting broad-spectrum algicidal activity, including activity against the colonial form of P. globosa—a key ecological challenge in HAB mitigation.