Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches

Hourfane Sohaib; Morgan Fays; Abderrezzak Khatib; John Rivière; Noureddine El Aouad; Nicolas Desoignies

doi:10.3389/fmicb.2024.1310395

Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches

Front Microbiol. 2024 Mar 25:15:1310395. doi: 10.3389/fmicb.2024.1310395. eCollection 2024.

Authors

Hourfane Sohaib¹, Morgan Fays², Abderrezzak Khatib¹, John Rivière³, Noureddine El Aouad¹, Nicolas Desoignies^{2

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Affiliations

¹ Laboratory of Life and Health Sciences, Faculty of Medicine and Pharmacy of Tangier, University Abdelmalek Essaâdi, Tetouan, Morocco.
² Phytopathology, Microbial and Molecular Farming Lab, Centre D'Etudes et Recherche Appliquée-Haute Ecole Provinciale du Hainaut Condorcet, Ath, Belgium.
³ Laboratory of Biotechnology and Applied Biology, Haute Ecole Provinciale de Hainaut-Condorcet, Ath, Hainaut, Belgium.
⁴ University of Liege - Gembloux Agro-Bio Tech, TERRA - Teaching and Research Center, Plant Sciences Axis, Gembloux, Belgium.

Abstract

Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.

Keywords: Argania spinosa; NGS; PCR; bacteria; diversity; endophytes; fungus; seed.

Grants and funding

The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This study was financially supported by the Government of Belgium through the “Académie de Recherche et d’Enseignement Supérieur (ARES)” at the “Haute École Provinciale de Hainaut-Condorcet (HEPH-C).”