Metagenomic Bioprospecting of Bioremediation-Related Genes in Amazonian Aquatic Ecosystems.
- 1Laboratory of Bioinformatics and Genomics of Microorganisms, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.
- 2Laboratory of Simulation and Computational Biology, High Performance Computing Center, Federal University of Pará, Belém, Brazil.
- 3Santo Domingo Institute of Technology, Santo Domingo, Dominican Republic.
Abstract
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.
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BibTeX
@article{anjos2026metagenomic,
title = {{Metagenomic Bioprospecting of Bioremediation-Related Genes in Amazonian Aquatic Ecosystems.}},
author = {Thais Mayara Castro Dos Anjos and Daralyns Borges Macedo and Victor Benedito Costa Ferreira and Carlos Willian Dias Dantas and Edian Franklin Franco de Los Santos and Oscar Victor Cardenas-Alegria and Rommel Thiago Jucá Ramos},
journal = {Environmental microbiology reports},
year = {2026},
month = oct,
doi = {10.1111/1758-2229.70435},
url = {https://europepmc.org/article/MED/42906596},
note = {CC BY},
}
RIS
TY - JOUR
TI - Metagenomic Bioprospecting of Bioremediation-Related Genes in Amazonian Aquatic Ecosystems.
AU - Thais Mayara Castro Dos Anjos
AU - Daralyns Borges Macedo
AU - Victor Benedito Costa Ferreira
AU - Carlos Willian Dias Dantas
AU - Edian Franklin Franco de Los Santos
AU - Oscar Victor Cardenas-Alegria
AU - Rommel Thiago Jucá Ramos
PY - 2026
DA - 2026/10/01
JO - Environmental microbiology reports
DO - 10.1111/1758-2229.70435
UR - https://europepmc.org/article/MED/42906596
AB - 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.
SN - 1758-2229
ER -