Metagenomic analysis of composition, function and cycling processes of microbial community in water, sediment and effluent of Litopenaeus vannamei farming environments under different culture modes

Abstract

With the increasing production of farmed Litopenaeus vannamei, the discharge of culture sewage and the accumulation of deleterious substances (nitrite, ammonia, sulfide…) in ponds have been more severe, especially at the mid-late farming stage, severely inhibiting the sustainability of aquaculture. Considering vital roles of microorganisms in cycling processes, we thereupon comprehensively investigated microbiotas in water, sediment and effluent of L. vannamei ponds under different culture modes by 16S rRNA gene and metagenome sequencing. Results revealed that microbial communities in water, sediment and effluent of white shrimp ponds were diverse and had active metabolism. Genes related to quorum sensing were abundant. Furthermore, we uncovered carbon fixation, such as CBB, WL and 3-HP; N, S, P cycling except nitrification and sulfide oxidation were active in shrimp farming environments at mid-late farming stage. Remarkably, each gene encoding key enzyme involved in cycling processes was assigned to specific taxa, such as Rhodobacteraceae, Rubrivivax and so on. Interestingly, many functional taxa (Vibrio, Aeromonas) were also potential pathogens to shrimp and microbiotas' structure along with function were correlated with environmental factors, reminding us of regulating variations of environmental factors during the shrimp farming period. Meanwhile, water, sediment and effluent under different culture modes had different microbial diversity and characteristics. Notably, we called for urgent management of direct discharge of aquaculture sewage including numerous genes related to human diseases, which is vital to public health. Briefly, this was the first study analyzing microbiotas' structure, function, ecology cycling in different L. vannamei culture surroundings and their correlation with environmental factors, advancing our knowledge for aquaculture ecosystems and providing preliminary data for probiotics screening and cycling regulation in the future.