Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system

Abstract

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m³, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.

Keywords: Litopenaeus vannamei; bacterioplankton community; biofloc technique; probiotics; rearing water; shrimp aquaculture.

Figure 1

Body weight of the reared Litopenaeus vannamei and physicochemical parameters of rearing water over 152 growth days in a biofloc aquaculture system. Curves show values of (A) body weight, (B) temperature of rearing water (upper curves) and air (lower curves), (C) alkalinity, (D) total ammonia nitrogen (TAN), (E) nitrite (NO₂-N), (F) nitrate (NO₃-N), (G) total suspended solids (TSS), (H) dissolved oxygen (DO), and (I) salinity in culture Tank-1 and -2.

Figure 2

Compositional variations of bacterioplankton community in rearing water. Principal coordinate analysis (PCoA) plots represent beta diversity variations based on Bray-Curtis (A) weighted UniFrac (B) distance metrics in rearing water samples collected across various culture stages from a commercial BFT-based aquaculture system. The designated sample IDs (TAS1 to TAS10) represent shrimp Litopenaeus vannamei culture stages in terms of their growth days 6, 20, 34, 48, 69, 83, 104, 118, 132, and 146, respectively, in culture Tank-1.

Figure 3

Bacterioplankton community dynamic in rearing water of a biofloc aquaculture system. Stacked bar plots depict the relative abundance of top bacterioplankton taxa at (A) phylum/class and (B) family levels during various culture stages. The proportions of dominant taxa are only shown. “Others” denotes cumulative relative abundances of remaining taxa. The indicated sample identifiers (TAS1 to TAS10) correspond to different shrimp culture stages in culture Tank-1 based on their growth days 6, 20, 34, 48, 69, 83, 104, 118, 132, and 146, respectively.

Figure 4

Temporal dynamics in bacterioplankton community composition of rearing water at the genus level. The hierarchically clustered heatmap shows the relative abundance of dominant (top 45) bacterioplankton genera in the rearing water during various culture stages. The color intensity in each cell represents the relative abundance of bacterial genera (listed to the left of the figure) at various shrimp culture stages (indicated at the bottom of the figure), according to the color scale at the right. The culture stages (TAS1 to TAS10) represented here denote shrimp Litopenaeus vannamei growth days 6, 20, 34, 48, 69, 83, 104, 118, 132, and 146, respectively.

Figure 5

Linear discriminant analysis (LDA) effect size (LEfSe) shows the most differentially abundant bacterioplankton groups as a histogram (A) and cladogram (B) in rearing water of a BFT-based aquaculture system during various culture stages. The relative proportion of the identified bacterioplankton taxa through LEfSe are represented as boxplots (C). Bacterioplankton groups that possess an LDA threshold > 3 are only represented. In the cladogram, each ring indicates a taxonomic level (e.g., center to outermost as phylum, class, order), while each circle indicates a bacterioplankton group. The taxonomic groups highlighted with different colors signify their enrichment in a particular culture stage.

Figure 6

Physicochemical parameters of rearing water responsible for bacterioplankton community changes. Canonical correspondence analysis (CCA) shows an association between the dominant bacterioplankton groups (at phylum/class level) and the physicochemical properties of rearing water. WT, water temperature; TAN, Total ammonia nitrogen; TSS, total suspended solid; VSS, volatile suspended solid. The culture stages (TAS1 to TAS10) represent shrimp Litopenaeus vannamei growth days 6, 20, 34, 48, 69, 83, 104, 118, 132, and 146, respectively.