Inferring the functional properties of bacterial communities in shrimp-culture bioflocs produced with amaranth and wheat seeds as fouler promoters

Abstract The aim of this work was to study the functional properties of bacterial communities in shrimp-culture bioflocs produced with amaranth (BFT_Amaranth) and wheat (BFT_Wheat) as biofloc promoters. No significant differences between treatments were recorded for physical and chemical parameters of water. A total of 22 phyla were detected in the biofloc samples, but the taxonomic structure was based on four principal phyla (Planctomycetes, Proteobacteria, Bacteroidetes, and Firmicutes). Most of the predicted KEGG pathways of bacterial communities contained in both bioflocs were associated with metabolism (50–53%), genetic information processing (19–21%), environmental information processing (12–15%), cellular processes and signaling (4–6%), organismal systems (1–2%) and other (3–5%). Both, the taxonomic and functional profiles of the two bioflocs were different at the beginning of the trial, but similar at the end of it, suggesting that the micro-environmental conditions of the culture units shaped the microbiota of biofloc regardless the type of seed used. Evidence of methane (RuMP and Serine pathways) and nitrogen (via N fixation, denitrification, nitrification, and detoxification) metabolism was detected in both BFT_Amaranth and BFT_Wheat, regardless of the sampling date. Carbon dioxide fixation was also detected, including photosynthetic pathways such as the Calvin cycle; however, other carbon dioxide fixation pathways including the reductive citric acid cycle, dicarboxylate-hydroxybutyrate cycle, 3-hydroxypropionate-bicycle and the Wood-Ljungdahl pathway were detected in both bioflocs. These results represent a first insight into the functions exerted by bioflocs in aquacultural systems, and suggest that nitrogenous and carbonaceous compounds can be simultaneously processed through diverse pathways by bacteria thriving in bioflocs.