Metagenomic and Bioinformatics Analysis of Sebacina vermifera for Next-Generation Biofertilizer Development

Abstract

Background: Sebacina vermifera is a fungus that belongs to the Basidiomycota phylum (order Sebacinales). It has potential as a biofertilizer because it forms mutualistic relationships with many plant species, including orchids and other flowering plants. However, it is still not fully understood how this fungus plays a role in the soil/rhizosphere ecosystems where it occurs. Methods: To profile S. vermifera-associated microbial community structures in relation to the different agroecological zone types, a multi-platform metagenomic sequencing approach was employed using sequencing technology platforms such as PacBio long read, Illumina short Read and Oxford Nanopore. Data processing for these metagenomic sequence assemblies included multiple steps including quality control using Trimmomatic and fastp, metagenome assembly with MEGAHIT and SPAdes, taxonomic profiling with Kraken2 and MetaPhlAn4, and functional annotation through EggNOG-mapper, KEGG Orthology, and CAZy databases. Network and comparative genomic analyses were also performed to characterise potential microbial interactions, as well as unique gene content. Results: The results of metagenomic analyses showed that genes associated with phosphate solubilization (e.g., phytases, acid phosphatases), nitrogen fixation (e.g., nifH, nifD), production of siderophores, and the biosynthesis of indole-3-acetic acid were present. The association of S. vermifera with rhizosphere microbial networks increased the occurrence of interactions between nitrogen-fixing bacteria, arbuscular mycorrhizal fungi, and plant growth-promoting rhizobacteria. Unique effector proteins and secreted hydrolases were identified that were distinct from those of related fungal species. The field trials demonstrated a 34-42% increase in plant biomass, a 28% increase in phosphorus uptake, and a 19% decrease in applied chemical fertilizer. Conclusion: With its rich repertoire of functional genes and beneficial interactions with other microorganisms, Sebacina vermifera represents a potential new source of biofertilizers for use in agriculture. The use of this fungus will result in greater crop yields, less dependence on chemical fertilizers, and healthier soils, thereby supporting the development of sustainable and climate-resilient agricultural systems.