Aquaculture is gaining importance for food security worldwide. Intensive aquaculture practices, however, often prioritize production over ecological and health concerns. To assess both ecological and health-related impacts of intensive open-cage finfish aquaculture we studied water quality, organic matter loading, and bacterioplankton communities (separated into free-living (FL) and particle-attached (PA) bacterial communities to account for different bacterial lifestyles) in Bolinao, northwestern Philippines. We sampled 5 stations along the Guiguiwanen Channel, covering a gradient from the entrance of the channel, without fish cages and a more pronounced influence of the open ocean, to the secluded interior, exploited by numerous fish cages. This data set includes the observed physico-chemical parameters in the water column, measured either in-situ with multiparamter probes (temperature, salinity, pH, oxygen concentrations) or determined in the laboratory after sample collection (inorganic nutrient concentrations, dissolved and particulate carbon and nitrogen content, transparent exopolymers, carbon and nitrogen stable isotope signatures, chlorophyll a concentration). The latter parameters are only available for discrete samples collected at 5m water depth.Intensive aquaculture led to a reduced pH (7.8), oxygen concentrations close to hypoxia, and two to five times elevated concentrations of inorganic nutrients. Tidal currents moved water with increased particulate OM loading from the interior of the channel to areas otherwise less affected by aquaculture. Carbon to nitrogen ratios of these particles suggested that they derived primarily from fish feed (C:N ratio 8). Together with full length 16S amplicon as well as shotgun metagenomic sequencing (for more details see ENA submission), our goal is to provide a holistic assessment of the effects of intensive open-cage aquaculture, identifying potential indicators for detrimental impacts on animal and human health to promote more sustainable management strategies of this rapidly growing industry.
