The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings

Simple Summary Salinity has a negative impact on crop production, yet this impact can be effectively mitigated using environmentally friendly plant growth-promoting microorganisms, which may naturally exist within the native microflora. Environmental conditions and the specific host plant control the presence and abundance of such microorganisms. As a first step toward the isolation of plant growth-promoting fungi, epiphytic mycobiomes associated with the salt-tolerant ‘Umsila’ and salt-susceptible ‘Zabad’ date palm cultivars when grown under saline and normal growth conditions were identified using internal transcribed spacer (ITS) rRNA sequences and next-generation sequencing (NGS) technology. A bioinformatic analysis revealed an apparent effect of salinity and the plant’s genotype on the fungal community structure. However, plant genotypes had no significant impact when grown under normal conditions. While the operational taxonomic units (OTUs) were annotated to Acremonium, Acrocalymma, Agaricus, Aspergillus, Clonostachys, Fusarium, Penicillium, and Remersonia, only a limited number of OTUs from the Fusarium and Aspergillus genera exhibit significant differential accumulation in response to salinity stress in date palms. The identified OTUs hold potential for advancing sustainable agricultural practices, as they could be further investigated as promising candidates for developing biofertilizers. Abstract Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, ‘Zabad’, and the tolerant cultivar, ‘Umsila’. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.