Metagenomic Bioprospecting of Bioremediation-Related Genes in Amazonian Aquatic Ecosystems.

Environmental monitoring of contaminated freshwater systems still lacks curated genomic resources tailored to bioremediation-oriented screening. In this study, we developed a curated catalogue of 546 genes from 80 microbial species associated with heavy-metal resistance, hydrocarbon degradation, detoxification and related functions and applied it to river metagenomes from four municipalities in Pará, Brazilian Amazon: Altamira, Bragança, Marabá and Paragominas. Functional annotation was performed using eggNOG-mapper and metagenomic reads were aligned against the curated catalogue with Bowtie2. Mercury- and copper-related genes were the most frequently represented functional categories across all river systems, a pattern that may reflect both sequence representation in the metagenomes and the unequal composition of the curated reference catalogue. Bragança showed the largest detected gene repertoire, whereas diversity, Jaccard, UpSet and Dunn-based analyses revealed marked spatial heterogeneity and sites of localized functional enrichment. Recurrently associated bacterial taxa included Acinetobacter, Enterobacter, Pseudomonas, Stenotrophomonas, Cupriavidus and Sphingopyxis. These findings indicate that the catalogue provides a targeted genomic reference for environmental screening and bioprospecting, although metagenomic detection represents functional potential rather than experimentally confirmed remediation activity.