Upwelling intensity structures free-living and particle-associated bacterial communities in an eastern boundary upwelling system

Eastern Boundary Upwelling Systems (EBUS) are among the most productive oceanic regions, driven by the upwelling of cold, nutrient-rich, and low-oxygen waters. These systems are increasingly affected by climate change, with intensified upwelling activity in frequency, strength, and duration, potentially reshaping microbial communities and their ecosystem functions. Furthermore, upwelling activity is not only subject to long-term climate change but also responds to natural variability across multiple scales, from intra-seasonal to decadal, which also modulates the timing and characteristics of upwelling events. Despite their ecological relevance, bacterial communities in upwelling zones remain poorly characterized. Here, we aimed to determine how upwelling intensity shapes bacterial community structure and predicted their functional potential in Tongoy Bay, a key coastal upwelling area in the southeastern Pacific, using high-throughput 16S rDNA sequencing from monthly seawater samples collected over one year at 9 m depth. Community composition was evaluated across physicochemical gradients and bacterial lifestyles (free-living - FL vs. particle-associated - PA). Marked compositional and functional differences were observed between both fractions: FL communities were dominated by stable core taxa such as Alphaproteobacteria and Gammaproteobacteria across conditions, whereas PA communities showed stronger temporal variability and responded more dynamically to upwelling intensity, with enrichment of the NS5 marine group, Psychrobacter, and Bdellovibrionaceae during intense events. Functionally, PA fractions exhibited higher relative abundances of pathways linked to carbon degradation (aerobic and anaerobic chemoheterotrophy, fermentation) and sulfur cycling. In contrast, FL fractions were enriched in photoautotrophy and nitrification-related functions, reflecting niche specialization. Differential abundance analysis using LEfSe identified taxa differentially enriched along the upwelling gradient: intense upwelling favored NS5 marine group, Psychrobacter, and the families Bdellovibrionaceae and Moraxellaceae; moderate upwelling was associated with Nitrosococcales, Methylophagaceae, and Jannaschia cystaugens; and relaxation periods favored Actinobacteriota, Nocardioidaceae, and Alcanivoraceae. Potential pathogens such as Vibrio kanaloae, V. crassostreae, and V. pectinicida were detected during intense upwelling. These findings underscore the ecological importance of lifestyle-specific bacterial shifts under upwelling variability and highlight the role of bacteria in biogeochemical cycling, pollutant degradation, and ecosystem resilience in productive coastal systems under changing climatic conditions.