Bacterial community characterization of water and intestine of the shrimp Litopenaeus stylirostris in a biofloc system

Abstract

Background: Biofloc technology (BFT), a rearing method with little or no water exchange, is gaining popularity in aquaculture. In the water column, such systems develop conglomerates of microbes, algae and protozoa, together with detritus and dead organic particles. The intensive microbial community presents in these systems can be used as a pond water quality treatment system, and the microbial protein can serve as a feed additive. The current problem with BFT is the difficulty of controlling its bacterial community composition for both optimal water quality and optimal shrimp health. The main objective of the present study was to investigate microbial diversity of samples obtained from different culture environments (Biofloc technology and clear seawater) as well as from the intestines of shrimp reared in both environments through high-throughput sequencing technology.

Results: Analyses of the bacterial community identified in water from BFT and "clear seawater" (CW) systems (control) containing the shrimp Litopenaeus stylirostris revealed large differences in the frequency distribution of operational taxonomic units (OTUs). Four out of the five most dominant bacterial communities were different in both culture methods. Bacteria found in great abundance in BFT have two principal characteristics: the need for an organic substrate or nitrogen sources to grow and the capacity to attach to surfaces and co-aggregate. A correlation was found between bacteria groups and physicochemical and biological parameters measured in rearing tanks. Moreover, rearing-water bacterial communities influenced the microbiota of shrimp. Indeed, the biofloc environment modified the shrimp intestine microbiota, as the low level (27 %) of similarity between intestinal bacterial communities from the two treatments.

Conclusion: This study provides the first information describing the complex biofloc microbial community, which can help to understand the environment-microbiota-host relationship in this rearing system.

Keywords: Bacterial communities; Biofloc; Clear sea water; Culture environment; Microbiota; Shrimp.

Fig. 1

Changes in relative abundance of the five main taxa over the course of rearing in BFT

Fig. 2

Evolution of NO₂ ⁻-N, NH₄ ⁺-N and Chlorophyll a concentrations over the course of rearing

Fig. 3

Venn diagram showing the unique and shared OTUs (3 % of distance level) in the different libraries: BFT and CW intestines, BFT and CW water

Fig. 4

Non-metric multidimensional scaling (MDS) plot using the Bray-Curtis coefficient of sequencing results associated with intestines and water samples from CW or BFT treatments after 35 days of rearing. Each point represents a sequencing profile from one sample