Nematodes constitute a very abundant and diverse group of microfaunal organisms that provide various ecosystem services. They play an important role in the soil food web, contribute to soil structure and function, are involved in nutrient cycling and decomposition, and act as biological control agents. However, plant-parasitic nematodes (PPN) inhabit tropical, temperate and cool climates and infect more than 3,000 plant species of economic interest, including staple crops, vegetables and ornamental plants. PPNs result in yield losses that can amount to billions of dollars. Traditionally, nematicides have been used to manage PPN, but their harmful environmental effects have prompted the search for alternative methods, such as crop rotation and resistant crop varieties. Effective implementation of these strategies requires a deeper understanding of PPN taxonomy and biology, as most plant resistance genes target only specific PPN species.

This research proposal aims to improve the accurate and efficient identification of plant-parasitic nematodes to manage them effectively and minimize unnecessary agrochemical use. Nematodes from different parts of the world will be investigated, and new species will be described as needed. Each nematode population will be studied both morphologically and molecularly. Previously described morphospecies will be linked to  informative sequences, including D2-D3 of 28S, 18S rRNA gene, COI gene of mtDNA, and NAD5 for root-knot nematodes. Additionally, new informative barcodes will be introduced. To ensure an unequivocal link between morphological information and new DNA barcodes, morphological vouchers will be prepared prior to DNA extraction. Where possible, topotype material will also be collected to secure a link with type material.

However, our previous research has shown that developing a universal barcode for nematodes, comparable to COI in most other animals, is challenging, if not impossible. Therefore, we will also explore the most efficient methods to move from short barcodes and use parts of nuclear and/or mitochondrial genomes to improve diagnostic resolution and eliminate the need for primer-based barcodes for identification.

The obtained molecular barcodes will also form the basis for a next-generation DNA-based metabarcoding approach, enabling high-throughput species identification. This approach will be crucial for assessing community structures from bulk samples or even environmental DNA samples, allowing the identification of both beneficial and detrimental organisms in a single analysis.

Deliverables:

• Provide a comprehensive description of nematode biodiversity based on the combined acquisition of molecular, morphological, biogeographical, ecological, and parasitic data, with a special focus on global agricultural considerations.
• Link morphologically identified species to the most informative and efficient molecular barcodes, creating a comprehensive taxonomic reference database.
• Comprehensively describe newly discovered plant-parasitic nematodes.
• Use the information obtained to optimize the DNA-metabarcoding approach for identifying (plant-parasitic) nematodes from bulk samples.
• Developing a method to move from the traditionally used short barcodes to incorporating genomic information for nematode characterisation and identification.