Bacterial Isolates from Estuarine Filter Feeders Reflect Anthropogenic and Environmental Impacts: From Halophilic Adaptations to Last-Resort Antibiotic Resistance

Invertebrate marine filter feeders serve as important indicators of ecosystem health, reflecting both local environmental conditions and anthropogenic impacts through their associated gut microbiome communities. In this study, we isolated and screened bacterial strains from the gut tissues of Perna viridis (mussel) and Styela pacifica (tunicate) in an aquaculture-impacted estuary in DaPeng Bay, Shenzhen. Our findings revealed a diverse microbiome consisting of taxa from Pseudomonadota, Bacillota, and Actinomycetota, including those implicated in plastic and hydrocarbon degradation, suggesting local pollution and run-off pressures. The study also identified multiple Multi-Antibiotic-Resistant Bacteria (MARBs) expressing resistance to last-resort antibiotics such as polymyxins, likely due to exposure to aquaculture-related antibiotic runoff. Additionally, we screened a bacteriophage capable of lysing a MARB strain, highlighting the potential of bacteriophage therapy as an alternative in combating antibiotic resistance. The presence of typically free-floating or soil-associating genera within host tissues suggests ecological plasticity facilitated by the estuarine conditions at the sampling site. These findings underscore the role of the gut microbiota of filter feeders as detectors of environmental runoff, antibiotic resistance, and biotechnological innovation, as well as emphasize the need for sustainable aquaculture practices, pollution regulation, and further research into phage-related treatments.