Complete genome sequence of a novel Winogradskyella species isolated from deep-sea sponge reveals a β-propeller phytase.

Microbial phytases are crucial to organic phosphorus mineralization in marine phosphorus cycle, however, phytases from deep-sea bacteria remain poorly characterized. Here, we isolated and cultured a phytate-hydrolyzing Winogradskyella sp. 266wxhm from sponge Hymeniacidon sp. collected at a depth of 2435 m in the South Atlantic Ocean. The strain 266wxhm showed the highest similarity of 16S rRNA gene with Winogradskyella poriferorum UST030701-295ᵀ (96.61%), and the average nucleotide identity (ANI) was 76.90% with W. poriferorum UST030701-295ᵀ. These results suggest that strain 266wxhm represents a novel species of Winogradskyella. Whole-genome sequencing revealed a single circular chromosome of 3.96 Mb with a GC content of 33.33%, containing 3572 genes, including 3512 CDSs. Genes targeting phosphate uptake and regulation, organic phosphorus turnover, polyphosphate metabolism, and phosphonate-associated metabolism were identified. Notably, A.266wxhm_GM001357 was identified and annotated as a gene encoding 3-phytase (K01083/EC 3.1.3.8), containing conserved residues associated with Ca2+ coordination and structural stabilization, and belonged to the β-propeller phytase family. Finally, recombinant expression assays of A.266wxhm_GM001357 confirmed the phytase activity. This study provides microbial evidence for phytate-derived phosphorus mineralization in the deep sea.