Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors

• We explore the diversity of microorganism communities in aquaculture.
• Microbial diversity was higher for sediment samples than that for water samples.
• AN and TN contents had the greatest influence on bacterial communities.
• Appropriate environmental factors and probiotics to reduce disease in aquaculture

In present study, we explored the diversity of microorganism communities in aquaculture and the relationship between potential pathogenic microorganisms and aquacultural environments in water and sediment samples from Litopenaeus vannamei culture ponds at stock breeding farms at Chenghu Lake, Kunshan City, China. Bacteria in the samples were analyzed by sequencing of the 16S rRNA gene through Roche 454 and Illumina miseq sequencing platforms. 31 phyla, 66 classes, 90 orders, 213 families and 697 bacterial genera were detected in samples collected at 6 time points; 6 bacterial genera were found in all samples. Microbial richness and diversity indexes were significantly higher for sediment samples than that for water samples. Bacterial phyla with more than 10% abundance were Proteobacteria, Cyanobacteria/Chloroplast, Actinobacteria and Bacteroidetes in water samples, and Proteobacteria, Cyanobacteria/Chloroplast, Firmicutes, Acidobacteria, Chloroflexi and Bacteroidetes in sediment samples, but the dominant microbes changed seasonally. The composition and abundance of the dominant microbes showed no substantially correlation between water and sediment samples collected at the same time. Canonical correspondence analysis (CCA) or redundancy analysis (RDA) was used for ordination to address the relationship between microbial communities and environmental factors, the results showed that ammonia nitrogen (AN) and total nitrogen (TN) contents in water had the greatest influence on bacterial communities. Abundance of the pathogenic bacterial genera Pseudomonas and Aeromonas but not the probiotic bacterial genus Bacillus correlated negatively with AN, chemical oxygen demand (COD) and TN, and positively with pH value and water temperature (WT). Abundance of the pathogenic bacterial genus Flavobacterium and probiotic bacterial genus Bdellovibrio correlated positively with pH, TN, and COD, and negatively with WT and AN. These findings provided novel information about improving microflora in aquaculture environments and inhibiting pathogens to reduce L. vannamei disease by regulating environmental factors, however for practical applications more research of comprehensively functional relationship among the variables is further needed.Statement of relevanceThis paper provides the extremely relevant to the development of commercial aquaculture. Our findings provided novel information about improving microflora in aquaculture environments and inhibiting pathogens to reduce L. vannamei disease by regulating environmental factors. Thus it is beneficial to improve commercial aquaculture.