Open Access

ARTICLE

Genomic and Functional Characterization of Thermophilic Paenibacillus sp. VCA1: A Biocontrol Agent Isolated from El Chichón Volcano Crater Lake

Nancy Abril Martínez-López¹, Betsy Anaid Peña-Ocaña², Rodolfo García-Contreras³, Toshinari Maeda⁴, Reiner Rincón-Rosales¹, Federico Antonio Gutiérrez-Miceli¹, Víctor Manuel Ruíz-Valdiviezo^1,*

1 Laboratorio de Biología Molecular, Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana km 1080, Tuxtla Gutiérrez, Chiapas, CP 29050, México
2 Departamento de Bioquímica, Instituto Nacional de Cardiología, Juan Badiano #1, Colonia Sección XVI, Tlalpan, Mexico City, CP 14080, México
3 Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, CP 04510, México
4 Department of Biological Functions Engineering, Kyushu Institute of Technology, 2-4 Wakamatsu-ku, Kita-kushu, 808-0196, Japan

* Corresponding Author: Víctor Manuel Ruíz-Valdiviezo. Email:

(This article belongs to the Special Issue: Advances in Enhancing Grain Yield: From Molecular Mechanisms to Sustainable Agriculture)

Phyton-International Journal of Experimental Botany 2025, 94(9), 2729-2743. https://doi.org/10.32604/phyton.2025.068176

Received 22 May 2025; Accepted 12 August 2025; Issue published 30 September 2025

Abstract

Species of the genus Paenibacillus, especially those from extreme environments that have been reported, are known for producing bioactive compounds with agricultural and biotechnological applications. In this study, we investigated the genomic and biochemical potential of Paenibacillus sp. VCA1 strain isolated from a thermophilic environment. Taxonomic identification was performed using whole genome similarity analysis, TETRA four-nucleotide frequency of occurrence analysis, ANI average nucleotide identity analysis, and gene distance analysis using digital DNA-DNA hybridization (dDDH). Functional analysis of the strain VCA1 was performed by detecting genes, enzymes, and genome subsystems involved in biocontrol and plant growth promotion, which was carried out using the RAST (Rapid Annotation using Subsystem Technology), the seed server and antiSAMSH (antibiotics & Secondary Metabolite Analysis Shell). Genetic analyses showed the existence of 11 fatty acid and isoprenoid production genes, 56 motility and chemotaxis genes, 29 N-acetylglucosamine genes, and five siderophore genes. Finally, the antifungal and emulsifying activities demonstrated that strain VCA1 has activity against Fusarium oxysporum strain 45ta using integrated genomic and experimental validation, and the antifungal properties of the Paenibacillus sp. VCA1 has suggested potential use as a biocontrol agent against phytopathogenic fungi, and its continuous study can have beneficial applications in sustainable agriculture and biotechnology.

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Supplementary Material

Supplementary Material File

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