Nitrogen Modulation of Endophytic Microbiome in Nematode-Parasitized Tomato

To reveal the association between RKN parasitism and the variation in endophytic nitrogen-fixing bacteria, seedlings of tomato cultivar cv Xinzhongshu No.4 were planted in Meloidogyne sp.-parasitized soils by supplying different nitrogen sources, in pot experiments carried out from June to August 2020. The soil used was collected from a nursery field with a 3-year nematode parasitism history. In total, 11 different inorganic or organic nitrogen compounds and two biofertilizers were selected for testing (Additional Table S9). Nitrogen sources were separately applied to each plot at 300 mg N/Kg soil after tomato seeding (keeping 5 tomato plants per pot out of 8–10 seeds sowed). The two biofertilizers were fresh chicken manure (fermented) and commercial chicken manure-based biofertilizer. Each nitrogen amendment treatment was performed with three replicates. Pot-planted tomato plants in soil without nematode parasitism history were used as positive control, using tomato plants in soil with nematode parasitism history but no nitrogen supplementation as negative control. At 55 days after seeding, tomato plants were harvested for the evaluation of RKN parasitism, quantifying the attack severity using the number of galls per plant [22 (link), 49 (link)]. Subsequently, root and/or gall samples were separately collected from healthy or nematode-parasitized tomato plants, as described above. Together, 57 samples (45 root, and 12 gall samples) were collected from healthy and nematode-parasitized tomato plants, including healthy control, parasitized control, and plants treated with 13 different nitrogen sources (Additional Table S9). Furthermore, community analysis for the effect of nitrogen supplement on root endophytic microbiota was performed, following the procedure described above.