A Combination of Metabolomics and Machine Learning Results in the Identification of a New Cyst Nematode Hatching Factor

Abstract

Potato Cyst Nematodes (PCNs) are an economically important pest for potato growers. A crucial event in the life cycle of the nematode is hatching, after which the juvenile will move toward the host root and infect it. The hatching of PCNs is induced by known and unknown compounds in the root exudates of host plant species, called hatching factors (HFs, induce hatching independently), such as solanoeclepin A (solA), or hatching stimulants (HSs, enhance hatching activity of HFs). Unraveling the identity of unknown HSs and HFs and their natural variation is important for the selection of cultivars that produce low amounts of HFs and HSs, thus contributing to more sustainable agriculture. In this study, we used a new approach aimed at the identification of new HFs and HSs for PCNs in potato. Hereto, root exudates of a series of different potato cultivars were analyzed for their PCN hatch-inducing activity and their solA content. The exudates were also analyzed using untargeted metabolomics, and subsequently the data were integrated using machine learning, specifically random forest feature selection, and Pearson’s correlation testing. As expected, solA highly correlates with hatching. Furthermore, this resulted in the discovery of a number of metabolite features present in the root exudate that correlate with hatching and solA content, and one of these is a compound of m/z 526.18 that predicts hatching even better than solA with both data methods. This compound’s involvement in hatch stimulation was confirmed by the fractionation of three representative root exudates and hatching assays with the resulting fractions. Moreover, the compound shares mass fragmentation similarity with solA, and we therefore assume it has a similar structure. With this work, we show that potato likely produces a solA analogue, and we contribute to unraveling the hatch-inducing cocktail exuded by plant roots.

Solanoeclepin B, a hatching factor for potato cyst nematode

“…The detection of SEA has been reported in soil-grown or hydroponically grown tomato and potato plants in open environments ( 17 , 18 ) . The absence of SEA in the sterile tomato hairy roots medium led us to hypothesize that biotic agents present in unsterilized soil and hydroponic solution are involved in the formation of SEA.…”

“…( 18 ) conducted a metabolomic analysis of root exudates from 51 cultivars of soil-grown potato plants and predicted a compound giving m/z 526.18 as a HF, and its presence was correlated with both the presence of SEA and HS activity. They assumed that the compound has a similar structure to SEA based solely on their mass fragmentation similarity and named it “solanoeclepin B (solB)” ( 18 ). We believe that the compound giving m/z 526.18 is not identical to our structurally determined SEB because the determined m/z is different, i.e., the molecular formula is different.…”

“…Devine and Jones (32) conducted hatching assay-guided purification of HFs and reported the existence of nine HFs for PCNs with a molecular weight of 530.5 Da, but their chemical structures were not determined. Recently, Vlaar et al (18) conducted a metabolomic analysis of root exudates from 51 cultivars of soil-grown potato plants and predicted a compound giving m/z 526.18 as a HF, and its presence was correlated with both the presence of SEA and HS activity. They assumed that the compound has a similar structure to SEA based solely on their mass fragmentation similarity and named it "solanoeclepin B (solB)" (18).…”

“…Recently, Vlaar et al (18) conducted a metabolomic analysis of root exudates from 51 cultivars of soil-grown potato plants and predicted a compound giving m/z 526.18 as a HF, and its presence was correlated with both the presence of SEA and HS activity. They assumed that the compound has a similar structure to SEA based solely on their mass fragmentation similarity and named it "solanoeclepin B (solB)" (18). We believe that the compound giving m/z 526.18 is not identical to our structurally determined SEB because the determined m/z is different, i.e., the molecular formula is different.…”

“…More recently, SEA was identified in the root exudate from several Solanaceae plants, such as tomato, in addition to potato (16,17). In contrast, studies of hydroponically grown tomatoes and soil-grown potatoes have shown that SEA alone cannot explain all the hatch-stimulating (HS) activity for PCN (16,(18)(19)(20). Thus, there are many unclear aspects of HFs.…”