Nematodes are the most diverse and abundant metazoans in soil. While free-living nematodes are involved in nutrient recycling through the influencing microbial communities, plant parasitic nematodes are a major threat to agriculture, causing enormous crop losses worldwide. Nematicides have been widely banned from use in nematode management due to their negative impact on the environment and on non-target organisms in the soil. Therefore, it is relevant to explore root metabolites as an eco-friendly and sustainable nematode management strategy to minimize plant parasitic nematode induced yield losses. This Ph.D. thesis aimed to elucidate the effects of plant secondary metabolites on root-associated soil nematode communities. To achieve this, we first optimized the method for studying soil nematodes using the metabarcoding approach. Further, we compiled the available information on the impact of root metabolites on soil nematodes in agriculture and used that knowledge as a backbone to study the effects of phytohormones and the secondary metabolites benzoxazinoids, glucosinolates, camalexin and flavonoids on soil nematodes communities. Finally, we also explored whether microorganisms play a role in host-nematode interactions.
While metabarcoding has revolutionized the understanding of soil ecology, application of this technique to decipher soil nematode communities is lagging, mainly due to the lack of a validated sequencing strategy and consensus on nematode metabarcoding primers. Hence, we tested four primer sets on a range of individual nematode species, mock communities, agricultural field soil, and roots with the aim to standardize nematode metabarcoding strategies for different sample types. We found the previously published Nemf/18Sr2b to be a suitable primer set, which was able to amplify and detect a broad taxonomic range of nematodes in all tested samples. The method developed in this part of the research was applied in the subsequent experiments.
Plant exudes diverse root metabolites during their growth and development. Several root secondary metabolites act as attractants or repellants, hatching stimulants/inhibitors, or nematicides depending on their chemical nature and plant parasitic nematode species. Some root metabolites trigger nematode parasitism genes and act as signaling molecules to plant parasitic nematodes, whereas other root metabolites suppress the expression of nematode defense genes as part of plant defense strategies.
Benzoxazinoids are important phytoanticipins present in plants that belong to several species of Poaceae and a few other dicot plants. Using maize as a model plant, we demonstrated that benzoxazinoids shows pronounced effect on soil nematodes in roots compared to rhizosphere. The abundance of the root lesion nematode Pratylenchus neglectus was depleted, whereas Pratylenchus crenatus was enriched in the parental maize line. Correlation analysis revealed that benzoxazinoids mostly negatively correlated with nematode taxa in roots, although a few positive correlations between benzoxazinoids and nematodes were also detected. Benzoxazinoids were negatively correlated with P. neglectus, while P. crenatus had a positive correlation, which indicates that benzoxazinoids are species-specific in their action.
Understanding of the impact of phytohormones and secondary metabolites on nematodes in the plant-soil systems is limited. To determine the impact of root metabolites on soil nematodes, we used Arabidopsis thaliana as a model plant. Our results clearly demonstrate that genetic disruptions in synthesis of phytohormones or secondary metabolic pathways affect soil nematode communities, especially the abundance of the sedentary endoparasitic nematode Meloidogyne hapla, which has an intimate relationship with the host plant. We also found that the microbiome of a flavonoid defective mutant negatively affected infectivity of Meloidogyne incognita to tomato roots, whereas the microbiome of the flavonoid and anthocyanin overproducing pap1-D showed increased susceptibility to the root-knot nematode. Further analysis revealed that microbial taxa were generally unaffected or depleted in pap1-D, while enriched in flavonoid defective mutants. Our results indicated that presence of specific microbes and their abundance determined by plant secondary metabolites might govern the outcome of host-nematode interactions. Therefore, exploitation of plant root metabolites and harnessing key members of root-rhizosphere microbiomes could serve as a basis for the development of eco-friendly nematode management strategies.