Digestive microbiota of shrimp Penaeus vannamei and oyster Crassostrea gigas co-cultured in integrated multi-trophic aquaculture system

A current practice of marine aquaculture is to integrate different trophic-level organisms to optimise nutrients uptake, improve water quality, and potentially increase economic income. Even though bacterial communities in the intestine of the Pacific white shrimp Penaeus vannamei and in the digestive gland of the Pacific oyster Crassostrea gigas have been studied, the effect of an integrated multi-trophic aquaculture (IMTA) system in the digestive microbiome of both species is unknown. In the present work, we examined the bacterial communities in the intestine of P. vannamei and digestive gland of C. gigas under monoculture and co-culture in IMTA conditions. The results revealed a higher final weight of shrimp in co-culture compared to monoculture (2.73 ± 0.07 g and 2.47 ± 0.13 g, respectively) (P < .1). The total sedimentable particles in water were significantly reduced in co-culture conditions compared to shrimp monoculture (P < .05). Analysis of oyster gut bacterial communities in co-culture with shrimp showed higher diversity compared to oyster from monoculture and shrimp treatments. We found that Proteobacteria is the most abundant phylum in all treatments, followed by Bacteroidetes and Actinobacteria. Higher abundance of Bacteroidetes and abundance variation in Alphaproteobacteria (Sphingomonodales and Rhodobacterales) of oyster from IMTA were attributed to consumption of shrimp waste and consequently reduction of suspended matter in the system. Moreover, shrimp intestine and oyster digestive gland in the co-culture system showed a lower relative abundance of Vibrionaceae compared to monoculture treatments. These results suggest that IMTA system impose digestive microbiome dynamics changes that could improve water management and shrimp productivity.