High-throughput amplicon sequencing of fungi and microbial eukaryotes associated with the seagrass Halophila stipulacea (Forssk.) Asch. from Al-Leith mangroves, Saudi Arabia

This is the first high-throughput amplicon sequencing study of mycobiome associated with leaves of the seagrass Halophila stipulacea. Five leaf samples were collected from the Al-Leith mangroves along the Red Sea coast of Saudi Arabia. Total DNA was extracted from 250 mg of each sample, and the first 300 bp (contains D1-D2 variable regions) of the LSU rDNA amplicon was sequenced with the Illumina MiSeq (bTEFAP). A total of 928,626 reads were obtained from the five samples. The sequence reads belonged to Metazoa (48.1% of the total reads), Viridiplantae (41.1%), Eukaryota (8.8%), Fungi (1.96%), Bacteria (0.09%), and Archaea (0.0001%). Fungi represented between 1.1% and 5.8% of the total reads in the five samples. A total of 18,279 reads (representing 1.96% of the total reads) were recorded from the 5 samples representing 296 molecular species (OTUs) that belong to 13 fungal phyla. At the phylum level, Basidiomycota dominated the community (37.2–51.6%) in three samples, while Neocallimastigomycota (37.5%) and Mucoromycota (42.1%) dominated the community in the fourth and the fifth samples, respectively. High diversity of OTUs (28 molecular species) were recorded from the monokaryotic subkingdom with five unknown basal lineages that are not aligning with any known taxa. Total number of sequence reads of microbial eukaryote organisms (Stramenopiles) from the five samples ranged between 0.16 of total reads in the fifth sample (AL-Hs05) to 2.9% in the first one (AL-Hs01). Majority of the microbial eukaryote reads (93.6%) belong to the phylum Oomycota, followed by Opisthokonts (Fungi/Metazoa group) representing 6.4% of microbial eukaryote reads. Monokaryon phyla (i.e., Chytridiomycota, Mucoromycota, and Neocallimastigomycota) and microbial eukaryotes occupied a major portion of the sequence reads followed by Basidiomycota and Ascomycota. Our results support the findings that the majority of fungi and microbial eukaryotes communities are so far unknown with seven deep branching lineages remain to be cultivated.