Academic Journal
Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes.
| Τίτλος: | Nanopore Long-Read Metagenomics Reveals Pollution-Driven Antibiotic Resistance and Xenobiotic Degradation in Urban Beach Microbiomes. |
|---|---|
| Συγγραφείς: | de Oliveira AFB; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., Carneiro BS; Instituto Evandro Chagas, Ananindeua, Pará, Brazil., de Carvalho JB; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., de Oliveira AR; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., da Costa da Silva AL; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., de Oliveira Veras AA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., Baraúna RA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil., das Graças DA; Laboratório de Engenharia Biológica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil. |
| Πηγή: | Environmental microbiology reports [Environ Microbiol Rep] 2026 Aug; Vol. 18 (4), pp. e70396. |
| Τύπος έκδοσης: | Journal Article |
| Γλώσσα: | English |
| Στοιχεία περιοδικού: | Publisher: Society for Applied Microbiology and Blackwell Pub Country of Publication: United States NLM ID: 101499207 Publication Model: Print Cited Medium: Internet ISSN: 1758-2229 (Electronic) Linking ISSN: 17582229 NLM ISO Abbreviation: Environ Microbiol Rep Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: [Hoboken, N.J.] : Society for Applied Microbiology and Blackwell Pub., c2009- |
| Ιατρικοί όροι (MeSH): | Microbiota*/genetics , Bacteria*/genetics , Bacteria*/classification , Bacteria*/isolation & purification , Bacteria*/metabolism , Bacteria*/drug effects , Xenobiotics*/metabolism , Metagenomics* , Bathing Beaches* , Drug Resistance, Bacterial* , Drug Resistance, Microbial*, Brazil ; Biodiversity ; Phylogeny ; Biodegradation, Environmental ; Cities |
| Περίληψη: | Coastal ecosystems are vital for biodiversity but are increasingly threatened by urbanisation and pollution, which significantly alter local microbial communities. This study assessed bacterial diversity and functional profiles in urban and island beaches in Belém, Brazil. Urban beaches showed significantly higher microbial diversity and evenness, alongside functional plasticity due to pollutant input, while island beaches hosted more specialised and stable communities. Taxonomic analysis revealed the significant enrichment of opportunistic genera such as Comamonas, Clostridium and Paenibacillus in urban areas, and the massive dominance of Prochlorococcus and Candidatus Pelagibacter in island sites. Furthermore, shotgun metagenomics identified a robust genomic potential for xenobiotic degradation and antibiotic resistance in urban microbiomes, whereas island microbiomes were significantly enriched in genes for energy production and biosynthesis. These results underscore the ecological divergence between anthropogenically impacted and natural coastal environments, highlighting the importance of microbiome monitoring for sustainable coastal management. (© 2026 The Author(s). Environmental Microbiology Reports published by John Wiley & Sons Ltd.) |
| References: | Alanzi, A. R. 2024. “Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.” Journal of Microbiology and Biotechnology 35: e2407064. https://doi.org/10.4014/jmb.2407.07064. Albuquerque, U. P., P. H. S. Gonçalves, W. S. Ferreira Júnior, et al. 2018. “Humans as Niche Constructors: Revisiting the Concept of Chronic Anthropogenic Disturbances in Ecology.” Perspectives in Ecology and Conservation 16: 1–11. Antonelli, P., S. Grizard, F. H. Tran, et al. 2024. “Bioaccumulation of Polycyclic Aromatic Hydrocarbons and Microbiota Dynamics Across Developmental Stages of the Asian Tiger Mosquito, Aedes albopictus Exposed to Urban Pollutants.” Ecotoxicology and Environmental Safety 286: 117214. Behrendt, U., P. Schumann, M. Stieglmeier, et al. 2010. “Characterization of Heterotrophic Nitrifying Bacteria With Respiratory Ammonification and Denitrification Activity – Description of Paenibacillus uliginis sp. nov., an Inhabitant of Fen Peat Soil and Paenibacillus purispatii sp. nov., Isolated From a Spacecraft Assembly Clean Room.” Systematic and Applied Microbiology 33: 328–336. Braz, V. S., K. Melchior, and C. G. Moreira. 2020. “Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium.” Frontiers in Cellular and Infection Microbiology 10: 548492. Buchfink, B., K. Reuter, and H.‐G. Drost. 2021. “Sensitive Protein Alignments at Tree‐Of‐Life Scale Using DIAMOND.” Nature Methods 18: 366–368. Callahan, B. J., K. Sankaran, J. A. Fukuyama, P. J. McMurdie, and S. P. Holmes. 2016. “Bioconductor Workflow for Microbiome Data Analysis: From Raw Reads to Community Analyses.” F1000Research 5: 1492. Cantalapiedra, C. P., A. Hernández‐Plaza, I. Letunic, P. Bork, and J. Huerta‐Cepas. 2021. “eggNOG‐Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.” Molecular Biology and Evolution 38: 5825–5829. https://doi.org/10.1093/molbev/msab293. Carini, P., L. Steindler, S. Beszteri, and S. J. Giovannoni. 2012. “Nutrient Requirements for Growth of the Extreme Oligotroph “Candidatus Pelagibacter ubique” HTCC1062 on a Defined Medium.” ISME Journal 7: 592–602. Chrairi, M., S. Barrijal, A. Castellano‐Hinojosa, et al. 2024. “Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait.” Water 16: 3202. Danecek, P., J. K. Bonfield, J. Liddle, et al. 2021. “Twelve Years of SAMtools and BCFtools.” GigaScience 10: giab008. Dang, H., T. Li, M. Chen, and G. Huang. 2008. “Cross‐Ocean Distribution of Rhodobacterales Bacteria as Primary Surface Colonizers in Temperate Coastal Marine Waters.” Applied and Environmental Microbiology 74: 52–60. De Coster, W., S. D'Hert, D. T. Schultz, M. Cruts, and C. Van Broeckhoven. 2018. “NanoPack: Visualizing and Processing Long‐Read Sequencing Data.” Bioinformatics 34: 2666–2669. Eltokhy, M. A., B. T. Saad, W. N. Eltayeb, I. S. Yahia, K. M. Aboshanab, and E. Ashour. 2021. “Exploring the Nature of the Antimicrobial Metabolites Produced by Paenibacillus ehimensis Soil Isolate MZ921932 Using a Metagenomic Nanopore Sequencing Coupled With LC‐Mass Analysis.” Antibiotics (Basel, Switzerland) 11: 12. Filippidou, S., T. Wunderlin, T. Junier, et al. 2016. “A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore‐Forming Firmicutes.” Frontiers in Microbiology 7: 1707. Finn, D. R. 2024. “A Metagenomic Alpha‐Diversity Index for Microbial Functional Biodiversity.” FEMS Microbiology Ecology 100: fiae019. Galperin, M. Y. 2016. Genome Diversity of Spore‐Forming Firmicutes, 1–18. ASM Press. Garg, A. P., and A. Ateeq. 2025. “Microbial Communities in Changing Climate: Challenges and Opportunities.” In Microorganisms for Sustainability, vol 56, 57–78. Springer. Ge, H., C. Li, C. Huang, L. Zhao, B. Cong, and S. Liu. 2024. “Bacterial Community Composition and Metabolic Characteristics of Three Representative Marine Areas in Northern China.” Marine Environmental Research 204: 106892. Huerta‐Cepas, J., D. Szklarczyk, D. Heller, et al. 2018. “eggNOG 5.0: A Hierarchical, Functionally and Phylogenetically Annotated Orthology Resource Based on 5090 Organisms and 2502 Viruses.” Nucleic Acids Research 47: D309–D314. Jiang, T., S. Sun, Y. Chen, et al. 2021. “Microbial Diversity Characteristics and the Influence of Environmental Factors in a Large Drinking‐Water Source.” Science of the Total Environment 769: 144698. Katoh, K., and D. M. Standley. 2013. “MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability.” Molecular Biology and Evolution 30: 772–780. Kolmogorov, M., D. M. Bickhart, B. Behsaz, et al. 2020. “metaFlye: Scalable Long‐Read Metagenome Assembly Using Repeat Graphs.” Nature Methods 17: 1103–1110. Li, D., C.‐M. Liu, R. Luo, K. Sadakane, and T.‐W. Lam. 2015. “MEGAHIT: An Ultra‐Fast Single‐Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph.” Bioinformatics 31: 1674–1676. Li, H. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34: 3094–3100. Liang, J., G. Mao, X. Yin, et al. 2020. “Identification and Quantification of Bacterial Genomes Carrying Antibiotic Resistance Genes and Virulence Factor Genes for Aquatic Microbiological Risk Assessment.” Water Research 168: 115160. Liang, S., H. Li, H. Wu, B. Yan, and A. Song. 2023. “Microorganisms in Coastal Wetland Sediments: A Review on Microbial Community Structure, Functional Gene, and Environmental Potential.” Frontiers in Microbiology 14: 1163896. Lin, Q., L. Li, J. M. Adams, et al. 2021. “Nutrient Resource Availability Mediates Niche Differentiation and Temporal Co‐Occurrence of Soil Bacterial Communities.” Applied Soil Ecology 163: 103965. Liu, H., B. Zhao, M. Jin, et al. 2024. “Anthropogenic‐Induced Ecological Risks on Marine Ecosystems Indicated by Characterizing Emerging Pollutants in Pearl River Estuary, China.” Science of the Total Environment 926: 172030. https://doi.org/10.1016/j.scitotenv.2024.172030. Liu, Y.‐X., Y. Qin, T. Chen, et al. 2020. “A Practical Guide to Amplicon and Metagenomic Analysis of Microbiome Data.” Protein & Cell 12: 315–330. Lu, J., F. P. Breitwieser, P. Thielen, and S. L. Salzberg. 2017. “Bracken: Estimating Species Abundance in Metagenomics Data.” PeerJ Computer Science 3: e104. McMurdie, P. J., and S. Holmes. 2013. “phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.” PLoS One 8: e61217. Miglani, R., N. Parveen, A. Kumar, et al. 2022. “Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach.” Metabolites 12: 818. Mo, L., A. Zanella, A. Squartini, et al. 2024. “Anthropogenic vs. Natural Habitats: Higher Microbial Biodiversity Pays the Trade‐Off of Lower Connectivity.” Microbiological Research 282: 127651. Oksanen, J. 2024. Vegan: An R Package for Community Ecologists. GitHub. Plantinga, A. M., and M. C. Wu. 2021. “Beta Diversity and Distance‐Based Analysis of Microbiome Data.” In Frontiers in Probability and the Statistical Sciences, 101–127. Springer. Price, M. N., P. S. Dehal, and A. P. Arkin. 2010. “FastTree 2 – Approximately Maximum‐Likelihood Trees for Large Alignments.” PLoS One 5: e9490. Ryan, M. P., L. Sevjahova, R. Gorman, and S. White. 2022. “The Emergence of the Genus Comamonas as Important Opportunistic Pathogens.” Pathogens 11: 1032. Santos, M. I. S., É. C. T. A. Brandão, E. Santos, et al. 2021. “Pendimethalin Biodegradation by Soil Strains of Burkholderia sp. and Methylobacterium radiotolerans.” Anais da Academia Brasileira de Ciências 93: e20210924. Sanz‐Montero, M. E., Ó. Cabestrero, and M. Sánchez‐Román. 2019. “Microbial Mg‐Rich Carbonates in an Extreme Alkaline Lake (Las Eras, Central Spain).” Frontiers in Microbiology 10: 148. Sayers, E. W., J. Beck, E. E. Bolton, et al. 2020. “Database Resources of the National Center for Biotechnology Information.” Nucleic Acids Research 49: D10–D17. Sharpe, G., L. Zhao, M. G. Meyer, et al. 2023. “Synechococcus Nitrogen Gene Loss in Iron‐Limited Ocean Regions.” ISME Communications 3: 1–11. https://doi.org/10.1038/s43705‐023‐00314‐9. Simon, E., K. Guseva, S. Darcy, et al. 2024. “Distinct Microbial Communities Are Linked to Organic Matter Properties in Millimetre‐Sized Soil Agregates.” ISME Journal 18: wrae156. Singh, A., M. K. Dwivedi, H. Yadav, and Garima. 2022. Potential of Microbes for Degradation of Xenobiotics: With Special Focus on Petroleum Hydrocarbons, 95–118. Elsevier eBooks. Steinegger, M., and J. Söding. 2017. “MMseqs2 Enables Sensitive Protein Sequence Searching for the Analysis of Massive Data Sets.” Nature Biotechnology 35: 1026–1028. Tavares, M., M. Kozak, A. Balola, and I. Sá‐Correia. 2020. “Burkholderia cepacia Complex Bacteria: A Feared Contamination Risk in Water‐Based Pharmaceutical Preparations.” Clinical Microbiology Reviews 33: e00139‐19. Wood, D. E., J. Lu, and B. Langmead. 2019. “Improved Metagenomic Analysis With Kraken 2.” Genome Biology 20: 257. Xie, G., C. Sun, W. Luo, Y. Gong, and X. Tang. 2024. “Distinct Ecological Niches and Community Dynamics: Understanding Free‐Living and Particle‐Attached Bacterial Communities in an Oligotrophic Deep Lake.” Applied and Environmental Microbiology 90: e0071424. Zhang, H., N. Jiang, S. Zhang, et al. 2024. “Soil Bacterial Community Composition Is Altered More by Soil Nutrient Availability Than pH Following Long‐Term Nutrient Addition in a Temperate Steppe.” Frontiers in Microbiology 15: 1455891. Zhao, C., X. He, X. Dan, et al. 2022. “Soil Dissolved Organic Matters Mediate Bacterial Taxa to Enhance Nitrification Rates Under Wheat Cultivation.” Science of the Total Environment 828: 154418. Zhi, M., Y. Zhao, X. Zeng, et al. 2023. “Filamentous Cyanobacteria and Hydrophobic Protein in Extracellular Polymeric Substances Facilitate Algae—Bacteria Aggregation During Partial Nitrification.” International Journal of Biological Macromolecules 251: 126379. |
| Grant Information: | 445350/2024-5 Conselho Nacional de Desenvolvimento Científico e Tecnológico |
| Substance Nomenclature: | 0 (Xenobiotics) |
| Entry Date(s): | Date Created: 20260810 Date Completed: 20260810 Latest Revision: 20260818 |
| Update Code: | 20260818 |
| PubMed Central ID: | PMC13456970 |
| DOI: | 10.1111/1758-2229.70396 |
| PMID: | 42575708 |
| Βάση Δεδομένων: | MEDLINE |
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