Light-regulated interactions between Phaeobacter sp. and Ulva ohnoi (Chlorophyta): Effects on microbiome dynamics, metabolome composition, and tropodithietic acid production

Ulva spp. are economically important macroalgae with various industrial applications, including as biofiltration agents for fish effluents in integrated multi-trophic aquaculture recirculating systems (IMTA-RAS). Recent works have proposed inoculating U. ohnoi with the probiotic bacterium Phaeobacter sp. strain 4UAC3 to tackle fish pathogens such as Vibrio spp. in IMTA-RAS. However, the disappearance of Phaeobacter sp. 4UAC3 upon inoculation of U. ohnoi under a regular photoperiod presents significant challenges. This study aimed to investigate how different light regimes impact the relationship between the U. ohnoi holobiont and Phaeobacter sp., focusing on how the colonization of Phaeobacter sp. strain 4UAC3 on U. ohnoi surfaces affects the alga's microbiome and metabolome dynamics. We also sought to validate the presence of tropodithietic acid (TDA), which can act as a probiotic. The study revealed the critical role of light in shaping microbial interactions between Phaeobacter sp. and U. ohnoi : The light regime significantly altered the microbial community structure, metabolite production, and physiological responses of both the bacterium and the alga. Phaeobacter sp. strain 4UAC3 thrived in darkness, modulating the microbiome and the exo - and endo -metabolomes of U. ohnoi . TDA was only identified under dark conditions and released into the algal chemosphere, while Phaeobacter antimicrobial properties were most pronounced in close association with the alga. These findings underline the importance of environmental factors, such as light regime, in driving microbial and molecular dynamics in marine holobionts. In addition, our results have direct implications for the application of U. ohnoi and Phaeobacter sp. in aquaculture, providing valuable insights for future research and practical applications in the field. The diagram depicts the chemical reactions occurring within the Ulva holobiont and its chemosphere during periods of darkness (respiration in mitochondria) and exposure to light (photosynthesis in chloroplasts). Different light regimes promote distinct microbial assemblages and to a lesser extent, different endo - and exo -metabolites within the Ulva holobiont. The figure was created by BioRender.com . Qui Minet, Z. (2025) https://BioRender.com/q56i179 . • Light regimes affect microbial and molecular interactions between Phaeobacter sp. strain 4UAC3 and U. ohnoi . • Phaeobacter sp. strain 4UAC3 vanished under a regular photoperiod but endured the 14-day trial in darkness with Ulva . • Phaeobacter sp. strain 4UAC3 exhibited enhanced growth when inoculated with spent media from Ulva maintained in darkness. • Phaeobacter sp. strain 4UAC3 influenced the microbial and molecular diversity of the holobiont. • Antibacterial tropodithietic acid was identified in Phaeobacter sp. strain 4UAC3 during dark conditions.