Intensive cage aquaculture suppresses microbial biomass and restructures functional potential in coastal ecosystems.

Coastal cage aquaculture represents a significant anthropogenic disturbance that profoundly alters marine ecosystems by influencing microbial biomass and species diversity, thereby altering crucial biogeochemical functionalities. Here, we evaluated the ecological footprint of intensive cage aquaculture in Hainan, China, by tracking both microbial standing stocks and community network dynamics. While aquaculture exerted only a marginal effect on bacterial richness, it significantly restructured community composition (adonis, P < 0.01). Unexpectedly, it triggered nearly an 85% reduction in total bacterial abundance, dropping from (1.63 ± 0.11) ×108 copies/L in the control area to (2.51 ± 0.25) ×107 copies/L within the aquaculture area. This net quantitative suppression was characterized by a severe depletion of core autotrophic taxa, nitrifiers, and even opportunistic fish pathogens, suggesting that chronic aquaculture-specific filters override conventional waste-stimulation dynamics. Consequently, predicted functional potentials underwent a profound recession, shifted away from critical photosynthesis and nitrogen cycling pathways (response ratio = -0.05 ∼ -2.72, P < 0.05) toward stress-driven organic pollutant degradation and anaerobic sulfur respiration (response ratio = 0.03 ∼ 7.94, P < 0.05). Network analysis further revealed that aquaculture induced severe topological fragmentation and a substantial loss of essential keystone taxa. Collectively, these findings indicate that the aquaculture area was characterized by lower total bacterial abundance, altered community structure, and shifts in predicted functional potential, supporting the use of combined microbial abundance and diversity metrics as complementary indicators in coastal environmental management.