Fungal diversity in healthy and cladode-thickened Opuntia ficus-indica under drought and rainfall conditions: A metagenomic approach

Abstract

Plants from the Cactaceae family can survive under extreme environmental conditions due to their Crassulacean Acid Metabolism (CAM). However, Opuntia ficus-indica, an economically important species of this family, is affected by various pests and diseases, with cladode thickening being one of the most frequent problems. Although some studies have linked this disorder to phytoplasmas and viruses, its etiology remains uncertain. Therefore, exploring other microorganisms that may act as pathogenic agents or serve as indicators of plant health could provide further insight into this disease. The objective of this study was to describe the composition, diversity, and phylogenetic relationships of fungal communities in different compartments of thickened and healthy O. ficus-indica plants, through ITS2 region sequencing during the rainy and dry seasons. Thickened and healthy O. ficus-indica plants were collected during the rainy and dry seasons in San Miguel Atlamajac, Temascalapa, State of Mexico. Samples from five plant compartments (soil, rhizosphere, root tissue, phyllosphere, and cladode tissue) were analyzed using metagenomics to identify, through the ITS2 region, the fungal communities present in each condition (plant health status and season). Data were processed with the Mothur pipeline to evaluate the fungal diversity and taxonomic composition. Alpha diversity varied across compartments, with soil and rhizosphere harboring the richest and most diverse fungal communities, reflecting the structural heterogeneity that characterizes these environments, whereas cladode tissue showed the lowest diversity values. Fungal communities in the phyllosphere and root tissue were shaped mainly by plant thickening conditions, while cladode tissue, rhizosphere, and soil communities were strongly influenced by seasonal variation. Fungal community composition differed between thickened and healthy plants across all sampled compartments: thickened plants were consistently associated with members of the order Pleosporales, while healthy plants showed a higher relative abundance of Plectosphaerellaceae (order Glomerellales) in belowground compartments, with no clear predominance of a specific fungal group in aerial compartments. Despite these compositional differences, no specific taxon could be directly linked to the etiology of the thickening disorder.