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Did you know that fungi, like mushrooms and molds, are super important for our planet? Fungi can form critical relationships with other organisms. For example, many plants rely on fungi to help them grow and thrive. However, fungi are not always friendly and sometimes they can hurt plants by causing disease. Did you also know that there are fungi in the ocean? While you might not be able to see these fungi when you go to the beach (because they can only be seen with a microscope), they are found everywhere in the ocean. Marine fungi are pretty cool, but we do not know a lot about them yet or what roles they play in the ocean. Scientists are starting to learn more about how marine fungi help the ocean and keep our planet healthy. This article will explore the amazing world of marine fungi! 

Abstract Drylands comprise 45% of Earth’s land area and contain ecologically critical soil surface communities known as biocrusts. Biocrusts are composed extremotolerant organisms including cyanobacteria, microfungi, algae, lichen, and bryophytes. Fungi in biocrusts help aggregate these communities and may form symbiotic relationships with nearby plants. Climate change threatens biocrusts, particularly moss biocrusts, but its effects on the biocrust mycobiome remain unknown. Here, we performed a culture-dependent and metabarcoding survey of the moss biocrust mycobiome across an aridity gradient to determine whether local climate influences fungal community composition. As the local aridity index increased, fungal communities exhibited greater homogeneity in beta diversity. At arid and hyper-arid sites, communities shifted toward more extremotolerant taxa. We identified a significant proportion of fungal reads and cultures from biocrusts that could not be classified.Rhodotorula mucilaginosaandR. paludigenawere significantly enriched following surface sterilization of healthy biocrust mosses. This aligns with their known roles as plant endophytes. We also observed septate endophyte colonization in the photosynthetic tissues of mosses from arid climates. Collectively, these results suggest that the biocrust mycobiome will undergo significant shifts in diversity due to climate change, favoring extremotolerant taxa as climate conditions intensify. The survey results also highlight taxa with the potential to serve as bioinoculants for enhancing biocrust resilience to climate change. These findings offer valuable insights into the potential impacts of climate change on drylands and provide crucial information for biocrust conservation. 

Summary Arbuscular mycorrhizal fungi (AMF) form beneficial associations with plants, and are thought to have been critical to the adaptation of the ancestor of terrestrial plants during the transition onto land. However, the ability of AMF to associate with aquatic plants is unclear. To address this, we used 65 publicly available genomes and transcriptomes (25 freshwater, 23 terrestrial and 17 marine plants) to interrogate the genomic potential to form AMF associations in aquatic plant lineages in the order Alismatales. We explored the presence or absence of homologs of 45 genes, with a a special focus on six critical genes including three that co-evolved with AMF associations (RAD1, STR1, STR2) and three necessary for intracellular symbiosis (SymRK, CCaMK/DMI3, CYCLOPS/IDP3). Our results indicate a pattern likely consistent with independent gene losses (or extreme divergence) of symbiosis genes across aquatic lineages suggesting a possible inability to form AMF associations. However, some of these conserved genes (i.e.,CCaMK/DMI3) are purported to function in other types of fungal symbioses, such as ectomycorrhizal symbiosis, and were observed here in a subset of aquatic lineages, including seagrasses. Overall, our findings highlight the complex evolutionary trajectories of symbiosis-related genes in aquatic plants, suggesting that while AMF associations may have been lost in certain lineages, others have genes that may allow them to form alternative fungal symbioses which may still play an underappreciated role in their ecology. 

Abstract 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 marinahave 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 withZ. marinaleaves. Our efforts resulted in the recovery of five eukaryotic MAGs, including a single fungal MAG in the order Loubulomycetales (65% BUSCO completeness), three MAGs representing diatoms in the family Bacillariaceae (93%, 70% and 31% BUSCO completeness) and a single MAG representing a haptophyte algae in the genusPrymnesium(40% BUSCO completeness). Whole-genome phylogenomic assessment of these MAGs suggests they all largely represent under sequenced, 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 previousZ. marinaamplicon survey results. Annotation of this MAG yielded 5,650 gene models of which 77% shared homology to current databases. With-in these gene models, we predicted 121 carbohydrate-active enzymes and 393 secreted proteins (103 cytoplasmic effectors, 30 apoplastic effectors). Exploration of orthologs between the Lobulomycetales MAG and existing Chytridiomycota genomes have revealed a landscape of high-copy gene families related to host recognition and interaction. Further machine learning analyses based on carbohydrate-active enzyme composition predict that this MAG is a symbiont. 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. 

Abstract Designing CRISPR single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we present ALLEGRO, a combinatorial optimization algorithm able to design minimal, yet highly effective sgRNA libraries targeting thousands of species. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting several genes of interest for over 2,000 species across the fungal kingdom. We experimentally validated the sgRNAs designed by ALLEGRO inKluyveromyces marxianus, Komagataella phaffii, andYarrowia lipolytica. In addition, we adopted a generalized Cas9-Ribonucleoprotein delivery system coupled with protoplast transformation to extend ALLEGRO’s sgRNA libraries to other untested fungal genomes, such asRhodotorula araucariae. Our experimental results, along with cross-validation, show that ALLEGRO enables efficient CRISPR genome editing, supporting the development of universal sgRNA libraries applicable to entire taxonomic groups. 

Abstract BackgroundSeagrasses are globally distributed marine flowering plants that play foundational roles in coastal environments as ecosystem engineers. While research efforts have explored various aspects of seagrass-associated microbial communities, including describing the diversity of bacteria, fungi and microbial eukaryotes, little is known about viral diversity in these communities. ResultsTo begin to address this, we leveraged metagenomic sequencing data to generate a catalog of bacterial metagenome-assembled genomes (MAGs) and phage genomes from the leaves of the seagrass,Zostera marina. We expanded the robustness of this viral catalog by incorporating publicly available metagenomic data from seagrass ecosystems. The final MAG set represents 85 high-quality draft and 62 medium-quality draft bacterial genomes. While the viral catalog represents 354 medium-quality, high-quality, and complete viral genomes. Predicted auxiliary metabolic genes in the final viral catalog had putative annotations largely related to carbon utilization, suggesting a possible role for phage in carbon cycling in seagrass ecosystems. ConclusionsThese genomic resources provide initial insight into bacterial-viral interactions in seagrass meadows and are a foundation on which to further explore these critical interkingdom interactions. These catalogs highlight a possible role for viruses in carbon cycling in seagrass beds which may have important implications for blue carbon management and climate change mitigation. 

Abstract Colletotrichumspp. have a complicated history of association with land plants. Perhaps most well-known as plant pathogens for the devastating effect they can have on agricultural crops, someColletotrichumspp. have been reported as beneficial plant endophytes. However, there have been only a handful of reports ofColletotrichumspp. isolated from aquatic plant hosts and their ecological role in the marine ecosystem is underexplored. To address this, we present the draft genome and annotation ofColletotrichumsp. CLE4, previously isolated from rhizome tissue from the seagrassZostera marina. This genome (48.03 Mbp in length) is highly complete (BUSCO ascomycota: 98.8%) and encodes 12,015 genes, of which 5.7% are carbohydrate-active enzymes (CAZymes) and 12.6% are predicted secreted proteins. Phylogenetic placement putsColletotrichumsp. CLE4 within theC. acutatumcomplex, closely related toC. godetiae. We found a 8.69% smaller genome size, 21.90% smaller gene count, and the absence of 591 conserved gene families inColletotrichumsp. CLE4 relative to other members of theC. acutatumcomplex, suggesting a streamlined genome possibly linked to its specialized ecological niche in the marine ecosystem. Machine learning analyses using CATAStrophy on CAZyme domains predict this isolate to be a hemibiotroph, such that it has a biotrophic phase where the plant is kept alive during optimal environmental conditions followed by a necrotrophic phase where the fungi actively serves a pathogen. While future work is still needed to definitively tease apart the lifestyle strategy ofColletotrichumsp. CLE4, this study provides foundational insight and a high-quality genomic resource for starting to understand the evolutionary trajectory and ecological adaptations of marine-plant associated fungi. 

ABSTRACT The fungal genusNeonectriacontains many phytopathogenic species currently impacting forests and fruit trees worldwide. Despite their importance, a majority ofNeonectriaspp. lack sufficient genomic resources to resolve suspected cryptic species. Here, we report draft genomes and assemblies forNeonectria magnoliaeNRRL 64651 andNeonectria puniceaNRRL 64653. 

Every fungal cell is encapsulated in a cell wall, essential for cell viability, morphogenesis, and pathogenesis. Most knowledge of the cell wall composition in fungi has focused on ascomycetes, especially human pathogens, but considerably less is known about early divergent fungal groups, such as species in the Zoopagomycota and Mucoromycota phyla. To shed light on evolutionary changes in the fungal cell wall, we studied the monosaccharide composition of the cell wall of 18 species including early diverging fungi and species in the Basidiomycota and Ascomycota phyla with a focus on those with pathogenic lifestyles and interactions with plants. Our data revealed that chitin is the most characteristic component of the fungal cell wall, and was found to be in a higher proportion in the early divergent groups. The Mucoromycota species possess few glucans, but instead have other monosaccharides such as fucose and glucuronic acid that are almost exclusively found in their cell walls. Additionally, we observed that hexoses (glucose, mannose and galactose) accumulate in much higher proportions in species belonging to Dikarya. Our data demonstrate a clear relationship between phylogenetic position and fungal cell wall carbohydrate composition and lay the foundation for a better understanding of their evolution and their role in plant interactions. 

A 30.28 Mb draft genome sequence was assembled and annotated for the melanized ascomycetous fungus Exophiala xenobiotica NRRL_64630 (Pezizomycotina; Chaetothyriales) isolated from La Brea Tar Pits, Los Angeles, California. Species identification was made by phylogenetic assessment of the Internal Transcribed Spacer. This is the first isolated fungal species from this historic space.