Characterization of microbial communities in minimal-exchange, intensive aquaculture systems and the effects of suspended solids management

Minimal-exchange, intensive culture systems require little, if any, water exchange and have high animal stocking densities. Intensive nutrient inputs lead to an abundant community of microorganisms. These microbes are partially contained within suspended “biofloc” particles and contribute to water quality maintenance and provision of supplemental nutrition to the culture species. Optimal function of minimal-exchange, intensive systems is likely dependent on the structure of the microbial communities within them. This document offers a short review of microbial groups important for intensive marine aquaculture and descriptions of three methods for quantifying their abundance. The document also describes an experiment during which these methods were used to monitor the effects of partial biofloc removal on microbe abundance. The first method uses light microscopy, with the option of epifluorescence, along with a ranking system to enumerate the abundance of microbial taxa. The second method exclusively uses epifluorescence to illuminate chlorophyll and cyanobacteria pigments. Images are taken of each fluorescing group of pigments and processed using image analysis software to quantify the respective abundance of the two pigment types. Using the third method, changes in bacterial abundance were determined by gas chromatographic measurement of bacteria-specific fatty acids in solvent extracted water column lipids. Using these techniques, it was determined that removing solids from the culture water significantly (P ≤ 0.01) reduced the abundance of nematodes, rotifers, cyanobacteria, and bacteria. Understanding microbial composition and the effects that management protocols have on that composition may help system managers make better informed decisions.