Aquaculture in Lake Titicaca plays a crucial role in local economies; however, the expansion of rainbow trout Oncorhynchus mykiss farming in floating cages has raised concerns about its environmental impact, particularly on microbial diversity as key bioindicators of ecosystem health. In this sense, we looked to characterize the spatio-temporal variation of bacterial communities in five farming areas of the basin of Lake Titicaca (Puno, Perú) during the rainy and dry seasons, between 2018 and 2019, using DNA metabarcoding of the V3–V4 region of the 16S rRNA gene. A total of 1.4 million raw reads were obtained through Illumina MiSeq sequencing. After quality control in QIIME2 program, sequences were processed by adapter trimming, removal of low-quality regions, and chimera detection using the DADA2 algorithm, which corrected sequencing errors and generated amplicon sequence variants (ASVs).
In total, 875 high-confidence ASVs were identified. Taxonomic assignment revealed dominance of the phyla Bacteroidota, Acidobacteriota, Cyanobacteria, Verrucomicrobiota, Actinobacteriota, and Proteobacteria, as well as exclusive taxa in certain localities, with Arapa, Lagunillas, and Yunguyo showing the highest number of unique records. Alpha-diversity indices (Shannon, Simpson, and Faith’s PD) indicated higher richness and a more even distribution in Ichu and Lagunillas, and Cachipucara with the lowest values, possibly reflecting anthropogenic pressures. Beta-diversity analyses (PCoA and UPGMA) revealed a clear separation of bacterial communities by season and hydrological connectivity, showing a consistent clustering of samples between rainy and dry periods. Functional prediction with FAPROTAX program indicated that chemoheterotrophy, aerobic chemoheterotrophy, and phototrophy were the predominant processes, while fermentation and nitrate reduction were associated with localities showing signs of eutrophication.
Overall, we concluded that bacterial communities in Lake Titicaca respond significantly to spatial and seasonal dynamics, reflecting the influence of aquaculture and environmental factors. DNA metabarcoding approach provided high-resolution insights into the structure and potential functions of the microbiota, establishing itself as a valuable tool for environmental monitoring and the sustainable management of aquaculture in high Andean ecosystem