Arable - Are chitin amendments to soil a means to control potato cyst nematodes?

Summary:
Plant parasitic nematodes cause an estimated $80 billion of annual damage to global agriculture and threaten food security in many regions. The potato cyst nematode (PCN) is a plant parasitic nematode that infects solanaceous species and causes significant damage, primarily to potato crops. In the UK alone, PCN causes more than £31 million in damage annually. Historically, PCN has been managed by using nematicides. However, due to potential environmental concerns, these chemicals have become tightly regulated. Currently there is only one granular nematicide left on the UK market and this has an uncertain future with an upcoming regulation review in 2024. Scotland is a large producer and exporter of seed potatoes. Current regulations state that if PCN has been detected in a field, that field can no longer be used for seed potato production. PCN is spreading in seed growing areas and recent predictions suggest that without improved PCN management tools this industry will collapse by 2050.
Chitin is an abundant biomolecule which is found in insects, fungi and shellfish. Chitin is also present in PCN eggshells where it protects the developing juvenile by providing the eggshell with rigidity and tensile strength. Chitinous soil amendments have previously been proposed for control of plant parasitic nematodes. Addition of chitin to soils may help select for chitin-degrading microbial populations, naturally raising the prevalence of these organisms in that environment. The microbes may subsequently use sources of chitin already present in the soil, such as PCN eggshells, as an energy source, allowing the suppression of PCN numbers to a level where they are no longer a threat to the potato crop.
We currently do not know if chitinous soil amendments are suitable for Scottish growing conditions or the impact they have on beneficial, chitin-containing, soil organisms. In this work we will investigate whether chitinous soil amendments control PCN in UK soils and how this control is achieved. Soil samples from field plots treated either with or without chitinous soil amendments will be collected. These samples will be used to identify the presence of different fungal, bacterial and free-living nematode populations and to quantify PCN numbers and chitin degrading activity. Comparing treated and untreated samples will allow understanding of changes in PCN populations, which microorganisms are responsible and if there is a negative impact on wider soil biodiversity. Testing in a controlled greenhouse environment will confirm whether the chitin within the soil amendment has a positive effect towards reducing PCN populations through eggshell degradation and will confirm which microorganisms are responsible.
The project outcomes will include identifying differences in microbial and nematode populations in field samples treated with or without a chitin-rich soil amendment. Analysis of the increased presence of chitinase, the enzyme responsible for chitin degradation, in soil samples will confirm the pathway utilised to degrade PCN eggshells. Additionally, structural investigation of PCN eggshells will validate whether eggshells are degraded sufficiently to prevent PCN hatching. Populations of potentially beneficial free-living nematodes will be identified in treated and untreated samples to survey for potential wider nematocidal effects of chitin-based soil amendments.

Technical Summary:
Chitin-containing soil amendments have been proposed as tools for control of soil-borne pathogens, including plant-parasitic nematodes such as potato cyst nematodes (PCN), but information on the efficacy of these products and their mode of action is lacking. We will use a combination of field and controlled environment trials to examine the impact of these amendments on PCN viability and populations of microbial agents that may provide the control of PCN. We will characterise the prokaryotic and eukaryotic communities in field and controlled environment soils using next generation sequencing of 16SrRNA, 18SrRNA and ITS amplicon libraries. We will quantify the abundance and range of chitin degraders in response to soil amendments using quantitative PCR on the chiA gene. To address the concern that chitin-containing soil amendments could impact beneficial free-living nematodes, we will characterise these nematode communities through a combination of metagenetic analysis and visual identification. Viability assays will be used to quantify the degradation of PCN eggs. We will employ a range of univariate and multivariate statistical techniques to test the links between microbial community structure, chitinase levels and PCN numbers. These experiments will address the overarching hypothesis that the addition of chitin-containing soil amendments will increase the selection for specific chitin degraders and increase levels of chitinase production which will lead to a breakdown of PCN eggshells and an increase in PCN mortality. The alpha diversity of fungi and free-living nematodes will not be reduced by the increase in chitinase production.