Illumina and PacBio insights into the metataxonomic enrichment of fish pond sediment microbiota via Candida albicans co-culture

As complex ecological systems, fish pond sediments host diverse microbial communities adapted to low-oxygen and chemically heterogeneous conditions, which foster unique metabolic pathways and the production of specialized secondary metabolites. Many of these compounds display antimicrobial, antifungal, or anticancer properties with biotechnological relevance. Sediments also accumulate organic matter and natural substrates that shape selective pressures, further enhancing microbial biochemical diversity. Consequently, fish pond sediments are increasingly recognized as promising reservoirs of novel bioactive compounds, though other environments may likewise offer valuable microbial sources. This study aimed to isolate and describe sediment microbiota using the enrichment co-culture technique with Candida albicans at two concentrations and compare the information provided by the Illumina and PacBio sequencing platforms. The experiment confirmed the presence of a rich microbiota in the sediments, with a selective role of C. albicans. Most microorganisms represented Proteobacteria, and up 90% of the relative bacterial richness constituted the "Other" group, indicating high diversity and the presence of rare or yet unidentified microorganisms. Actinobacteriota, Myxococcota, Nitrosomonadaceae, Gallionellaceae, and rare taxa (e.g., Sideroxydans, Gemmatimonas) were highly abundant in the taxonomic composition of the sediment microbiota. These findings were confirmed by both sequencing techniques. In addition, the Illumina technology demonstrated greater sensitivity to rare microorganisms, while the PacBio platform allowed deeper phylogenetic analysis enabling species detection. The presence of Pseudomonas sp. , Streptomyces sp., Streptococcus sp., and Anaeromyxobacter sp., potential candidates for producing antimicrobial substances, was additionally confirmed.