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Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery

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Abstract

Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka–Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.

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Data Availability

The crude sequence dataset is available through NCBI accession number PRJNA673517. The pipeline for the bioinformatics data process is included in Supplementary File SF1. The samples analyzed may be available upon request after a share transfer agreement. The datasets generated during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

This work was funded by El Colegio de la Frontera Sur (Project #5103711808) and by Consejo Estatal de Investigación Científica y Desarrollo Tecnológico del Estado de Campeche (COESICYDET). AABL thanks Consejo Nacional de Ciencia y Tecnología (CONACYT) for its Master’s scholarship number 624546.

Funding

Consejo Estatal de Investigación Científica y Desarrollo Tecnológico de Campeche (COESICYDET), Research Grant YPR 2015-2018. El Colegio de la Frontera Sur, Research Grant 5103711808. AABL Consejo Nacional de Ciencia y Tecnología, Scholarship Grant 624546.

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  1. Department of Sustainability Sciences, El Colegio de la Frontera Sur Unidad Campeche, Av. Rancho Polígono 2-A Col. Ciudad Industrial, Lerma, CP 24500, Campeche, Campeche, México

    Angel A. Becerra-Lucio, Natalia Y. Labrín-Sotomayor, Patricia A. Becerra-Lucio, Flor I. Trujillo-Elisea & Yuri J. Peña-Ramírez

  2. Agrobiologia School, Universidad Michoacana de San Nicolás de Hidalgo, CP 6017, Uruapan, Michoacán, México

    Ana T. Chávez-Bárcenas

  3. Department of Biodiversity Conservation, El Colegio de la Frontera Sur Unidad Chetumal, Av. Centenario km 5.5, CP 77014, Chetumal, Quintana Roo, México

    Salima Machkour-M’Rabet

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Contributions

All authors contributed to the study conception and design. Material preparation and data collection and analysis were performed by all authors. The first draft of the manuscript was written by Yuri Jorge Peña-Ramírez, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Yuri J. Peña-Ramírez.

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This work received approval from the “Comité de Ética para la Investigación” from El Colegio de la Frontera Sur in April 2017. Samples were collected after approval from SEMARNAT according to “Permiso de colecta de material biológico para investigación científica” SGPA/DGGFS/712/2062/17 granted to the authors.

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Becerra-Lucio, A.A., Labrín-Sotomayor, N.Y., Becerra-Lucio, P.A. et al. Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery. Curr Microbiol 78, 3417–3429 (2021). https://doi.org/10.1007/s00284-021-02603-9

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