Genomic resources for soil protists to advance soil carbon sequestration and plant health

Overview

Soil protists are single-celled eukaryotes that play a critical yet underexplored role in shaping soil microbial communities through selective predation of bacteria. By regulating bacterial populations, protists influence carbon and nitrogen cycling, soil carbon sequestration, and ultimately plant health and productivity. Despite their importance, most soil protist groups lack published genomes, limiting the ability of researchers to identify the genetic mechanisms underlying protist-microbe-plant interactions.

This project addresses that gap by developing a curated genomic resource for soil protists. Preliminary greenhouse experiments have already demonstrated that certain protist-bacteria combinations consistently promote faster maize growth, confirming the feasibility of leveraging soil protists as beneficial agricultural inoculants. The genomic data produced through this effort will serve as a foundational resource for future mechanistic studies linking protist diversity and function to soil health and crop performance.

Technical specifications

Research approach:

• Selection of ten protist species from an existing maize-isolated culture collection, chosen for both superior plant health outcomes and broad representation of protist diversity
• Whole-genome sequencing using Oxford Nanopore MinION for long reads and Illumina NovaSeq 6000 for short reads
• Hybrid genome assembly using Unicycler software to produce high-quality contiguous genomes
• Gene annotation using EuGene and AUGUSTUS pipelines to identify functional genes

Existing capabilities:

• A culture collection of 103 protist isolates representing indigenous soil protist diversity from field-grown maize
• Validated greenhouse experimental system demonstrating positive plant-protist interactions
• Established protocols for isolating, culturing, and applying protists to potted maize plants

Anticipated outputs:

• Annotated reference genomes for ten ecologically and taxonomically diverse soil protist species
• A publicly relevant genomic resource enabling downstream functional and comparative genomic analyses

Technology readiness level

The project is currently at an early-to-mid stage of development. The research team has already validated the core biological premise through greenhouse experiments showing that specific protist-bacteria combinations enhance maize growth. The protist culture collection is established, and sequencing and bioinformatics pipelines have been selected. The next phase involves executing genome sequencing, hybrid assembly, and gene annotation. Upon completion, the resulting genomic resources will be available to support further research into soil protist ecology and the development of protist-based agricultural inoculants.