Understanding the parasitic variability of the northern root knot nematode (Meloidogyne hapla) through multidisciplinary approaches of soil biome and environment

Managing Meloidogyne hapla remains challenging due to the ban of broad-spectrum nematicides, lack of resistant crops and its broad host range. It also has parasitic variability (PV) where populations (pop) are morphologically and genetically similar but vary in pathogenicity and reproductive potential. Although PV in M. hapla appears to have some relationship to soil types, what soil conditions favor its PV and/or its distribution are unknown. The goal of my research was to understand the soil conditions where M. hapla PVexist by quantifying the biophysicochemical (BPC) conditions from the ecosystem down to microbiome level. I designed observational and experimental approaches and tested four objectives. First, was to evaluate the association between soil conditions and M. hapla distribution at the ecosystem level. My hypothesis was that the presence of M. hapla will be associated with degraded soil conditions. I selected 15 (6 muck and 9 mineral soil)agricultural fields with adjacent natural vegetation in southwest, northwest and eastern regions of the lower peninsula of Michigan as study sites. I collected a total of 75 (5 per field)georeferenced soil samples from agricultural fields and equal number from adjacent natural vegetation soils, quantified the soil food web (SFW) conditions using the Ferris SFW model, and screened for M. hapla presence or absence. The fields were described either as disturbed, degraded (worst-case) or maturing (best-case). Meloidogyne hapla was present in 3 mineral (2, 8 and 13) and 6 muck (4, 5, 6, 10, 14 15) agricultural fields with degraded and/or disturbed soil conditions and absent from maturing soils, partially supporting the hypothesis.Degraded soils had low nitrogen content in both soil groups. The second objective was to isolate and culture the 9 M. hapla populations to test a hypothesis that PV is related to specific SFW conditions. I found three categories of reproductive potential: the highest (Pop 13), medium (Pop 8), both from degraded mineral soils, and lowest from disturbed mineral (Pop 2) and disturbed (Pops 4, 6 and 10) and degraded (Pops 5, 14 and 15) muck soils. Thus, the hypothesis was not supported. The third objective, was to determine relationships between microbial community structure and M. hapla distribution. My working hypotheses were that there is a relationship among microbiome, soil health and M. hapla occurrence. Microbial community structure in the fields was determined from sub-samples of the same samples where the nematodes were isolated. I used 16S (bacteria) and ITS (fungi) rDNA analysis and characterized the microbial composition, core- and indicator-microbes co-existing with M. hapla pop in the field soils and soil conditions relative to the Ferris SFW model description. The results showed that bacterial and fungal community abundance and composition varied by soil group, SFW conditions and/or M. hapla occurrence. I found that a core of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) were found variably, 25 bacterial OTUs associated with presence or absence of M. hapla, and 1,065 OTUs were associated SFW conditions. All three hypotheses were supported. The final objective was to determine the relationship between PV and the microbes associated with M. hapla pop. I compared bacteria present in M. hapla pop isolated from the field and greenhouse cultures. The hypothesis was that either presence and/or absence of specific bacteria are associated with M. hapla population. Population 8 shared more bacteria with the lowest reproductive potential pop than Population 13. Presence of several bacteria was unique to Population 8 as was the absence of other bacteria to Pop 13 in either field or greenhouse nematodes. Therefore, the hypothesis was supported. My research findings provide a foundation for: a) testing the relationship between M. hapla PV and the BPC conditions and b) designing soil health-based management strategies.