Cultivation mode of Saccharina japonica impacts planktonic and epiphytic microbiomes

To mitigate aquaculture environmental issues, certain animal species are usually co-cultured with economically important seaweeds. However, there is little information on how co-cultivation impacts the planktonic and epiphytic microbiomes despite their important roles in nutrient cycling and seaweed health. In the present study conducted in Ailian Bay, a typical intensive mariculture area in China, the epiphytic microbiomes on Saccharina japonica and the surrounding planktonic microbiomes were assessed using cultivation-dependent and -independent techniques. The microbiomes, along with environmental parameters, were compared among different cultivation modes. Four environmental parameters (i.e., seawater temperature, salinity, specific conductance, and dissolved oxygen) were significantly different between kelp mono-culture and kelp–abalone co-culture modes, with a significant increase in temperature and a significant decrease in dissolved oxygen in the co-culture region. There were different alpha and beta diversity patterns regarding the two cultivation modes for fungal vs. bacterial communities, in both planktonic and epiphytic communities. The co-culture mode may help to maintain the planktonic bacterial diversity and ecological functions to make them comparable to the no-culture region. This involved restoring alpha diversity, decreasing the number of differentially abundant predicted pathways, and maintaining the relative abundances of predicted pathways (such as nitrate reduction, fermentation, aerobic chemoheterotrophy, and chemoheterotrophy). Although there were fewer cultured microbes on the distal part of co-cultured compared to mono-cultured kelp, potentially pathogenic and harmful microbial pathways were significantly enriched in co-cultured kelp, indicating potential disease risks for kelp. These findings expand our knowledge of planktonic and epiphytic microbiomes under different kelp cultivation modes. Further investigation not only of nutrient cycling but also kelp disease risks in the co-culture mode is required in order to improve the co-culture mode.