Towards a molecular toolkit to assess biological health of soil

Sugarcane farmers are becoming increasingly aware of the importance of soil health. However, there are limited tools by which the health of soils can be measured. Nematodes are known to be an excellent indicator of soil health, but their identification and enumeration is laborious and requires the expertise of a diminishing pool of trained scientists. Molecular methods are being used to detect specific nematode targets and estimate their numbers, but in the sugar industry this work has focused on two key pests: root-lesion nematode (Pratylenchus zeae) and root knot nematode (Meloidogyne spp.). However, such methods are not useful against the huge range of free-living nematodes that are present in sugarcane soils and are arguably more informative with regards to soil health. Advances in DNA sequencing technology have facilitated the development of metabarcoding tools which can effectively identify as well as enumerate soil micro-organisms such as bacteria and fungi. We describe how we aim to apply this technology to the identification and enumeration of soil nematodes, and how the molecular tests that are developed could be used by farmers to assess the effectiveness or otherwise of soil health interventions. Key words Soil health, nematodes, metabarcoding