Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associated with the seagrass, Zostera marina, have revealed an abundance of potentially novel chytrids. In this study, we employed deep metagenomic sequencing to extract metagenome-assembled genomes (MAGs) from these chytrids and other microbial eukaryotes associated with Z. marina leaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Lobulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte alga in the genus Prymnesium (40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent undersequenced and possibly novel eukaryotic lineages. Of particular interest, the chytrid MAG was placed within the order Lobulomycetales, consistent with the identity of the dominant chytrid from previous Z. marina amplicon survey results. Annotation of this MAG yielded 5,650 gene models, of which 77% shared homology with current databases. Within these gene models, we predicted 121 carbohydrate-active enzymes (CAZymes) and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes has revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on CAZyme composition classified this MAG’s CAZyme profile as most consistent with a symbiotic lifestyle. Overall, these five eukaryotic MAGs represent substantial genomic novelty and valuable community resources, contributing to a deeper understanding of the roles of fungi and other microbial eukaryotes in the larger seagrass ecosystem.