Metagenomic Characterization of Biofloc Microbial Communities for Enhanced Nutrient Recycling and Fish Health

Abstract

Biofloc Technology (BFT) represents a paradigm shift in sustainable aquaculture, operating through zero-water-exchange systems where dense microbial aggregates perform continuous in situ bioremediation of toxic nitrogenous wastes while providing supplemental nutrition to cultured species. This review synthesizes current metagenomic insights into the structural architecture, functional metabolic capacities, and host-immunomodulatory mechanics of biofloc-associated bacterial communities. High-throughput sequencing methodologies, particularly whole-genome shotgun metagenomics, have revolutionized our understanding of floc microbiomes by enabling species-level taxonomic resolution, reconstruction of Metagenome-Assembled Genomes (MAGs), and direct quantification of biogeochemical functional genes. Metagenomic profiling consistently identifies Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as core phyla, with community succession dynamically regulated by carbon-to-nitrogen (C/N) ratio manipulation, dissolved oxygen gradients, and total suspended solids. Functional gene analysis reveals interconnected nitrogen transformation pathways heterotrophic assimilation (amoA), nitrification (nxrA), denitrification (narG, nirK/S, nosZ), anaerobic ammonium oxidation (hzsA/B), and dissimilatory nitrate reduction to ammonium (nrfA) operating concurrently within spatially structured biofloc microenvironments. Concurrently, phosphorus (ppk, phoD) and sulfur (sox multienzyme) cycling pathways maintain broader system stoichiometry. Critically, biofloc microbiomes enhance host immunity through quorum quenching enzymes (AHL-lactonases) that suppress pathogen virulence, continuous probiotic provisioning, and immunostimulation via microbe-associated molecular patterns. Despite these benefits, challenges persist including high biological oxygen demand, total suspended solids management, and the potential for bioflocs to harbor latent opportunistic pathogens and antibiotic resistance genes. Future integration of metatranscriptomics, metabolomics, and machine learning with portable sequencing platforms promises real-time, predictive microbiome management, optimizing system stability, reducing energy consumption, and advancing BFT as a cornerstone of sustainable aquaculture intensification.