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Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil

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Abstract

Mangroves are ecosystems located at land–sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.

Data availability

Raw sequencing data (16S rRNA gene, ITS2, and metagenomic) and metagenome-assembled genomes are available through the European Nucleotide Archive (ENA) under BioProject ID PRJEB72453. Source data are provided with this paper. Additional data generated in this study are provided in the Supplementary Information/Source Data file. Source data are provided with this paper.

Code availability

Custom scripts for processing, analysis, and visualization of shotgun metagenomic data are available at https://github.com/mariafpv/LignoMangrove-MAGs and at Zenodo: https://doi.org/10.5281/zenodo.18651101131. Code for the structural and physicochemical characterization of putative PETases is available at https://github.com/Robaina/Mangrove-PETases and at Zenodo: https://doi.org/10.5281/zenodo.18656903132.

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Acknowledgements

We thank the Faculty of Sciences at the Universidad de los Andes (Colombia) for financial and administrative support. DNA samples for sequencing were exported under ANLA permit number 2784. Computational analyses were partially conducted using the ExaCore—IT Core Facility at the Vice Presidency for Research and Creation, Universidad de los Andes. This study was partially funded by the FAPA project (PR.3.2018.5287) awarded to D.J.J. at the Department of Biological Sciences, Universidad de los Andes, and by baseline resources (BAS/1/1096-01-01) provided by A.S.R. at KAUST. A.V. received funding from the Dutch Research Council (grant VI.Veni.212.029). O.T. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project Number 391977956–SFB 1357 Microplastics, subproject C03 at Bayreuth University. We thank Josh L. Espinoza for assistance with metagenomic analyses. O.T. thanks Prof. Birte Höcker for her supervision. We are also grateful to Intikhab Alam at KAUST for M5 motif predictions.

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Author notes

  1. These authors contributed equally: María Fernanda Peña-Valencia, Diego Javier Jiménez.

Authors and Affiliations

  1. Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia

    María Fernanda Peña-Valencia, Felipe Sierra & Alejandro Reyes

  2. NewAtlantis Labs, Inc., Wilmington, DE, USA

    Semidán Robaina-Estévez & Jay Gutiérrez

  3. Department of Natural Sciences, The University of Maryland Eastern Shore, Princess Anne, MD, USA

    Gordon F. Custer

  4. Department of Biochemistry, University of Bayreuth, Bayreuth, Germany

    Onur Turak

  5. Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil

    Lucas William Mendes

  6. Chemical and Biological Studies Group, Basic Sciences Faculty, Universidad Tecnológica de Bolívar, Cartagena de Indias, Colombia

    Carolina Rubiano-Labrador

  7. Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Hoorn, The Netherlands

    Annika Vaksmaa

  8. Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA

    Francisco Dini-Andreote

  9. One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA

    Francisco Dini-Andreote

  10. Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia

    Alexandre Soares Rosado & Diego Javier Jiménez

Authors

  1. María Fernanda Peña-Valencia
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  2. Semidán Robaina-Estévez
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Contributions

M.F.P.V.: Metagenomic analyses, statistical analyses, manuscript revision, and figure design. S.R.E.: Development of gene catalogs, screening of PET-active enzymes, protein characterization, and writing. G.F.C.: Amplicon sequencing analysis, statistical analyses, and writing. O.T.: Protein analyses and writing. F.S.: Sampling, microcosm setup, and computational analyses. L.W.M.: Co-occurrence analysis and writing. C.R.L.: Sampling, experimental design, and microcosm setup. J.G.: Development of gene catalogs, screening of PET-active enzymes, protein characterization, and writing. A.V.: Funding acquisition and writing/revision of the final draft. F.D.A.: Advising, computational analyses, and writing/revision of the final draft. A.S.R.: Funding acquisition, coordination, and writing/revision of the final draft. A.R.: Advising, funding acquisition, computational analyses, coordination, and writing/revision of the final draft. D.J.J.: Sampling, experimental design, microcosm setup, conceptualization, figure design, funding acquisition, project coordination, and writing of the first and final drafts of the manuscript.

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Alexandre Soares Rosado, Alejandro Reyes or Diego Javier Jiménez.

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Peña-Valencia, M.F., Robaina-Estévez, S., Custer, G.F. et al. Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.
Nat Commun (2026). https://doi.org/10.1038/s41467-026-71548-z

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