Endophytes are known to play important roles in plant’s health and productivity. In this study, we investigated the root microbiome of tomato in association with infection by root knot nematodes. Our objectives were to observe the effects and response of the bacterial endophytes before nematode attacks and to reveal the functional attributes of microbes in plant health and nematode pathogenesis. Community analysis of root-associated microbiomes in healthy and nematode-infected tomatoes indicated that nematode infections were associated with variation and differentiation of the endophyte and rhizosphere bacterial populations in plant roots. The community of the resident endophytes in tomato root was significantly affected by nemato-pathogenesis. Remarkably, some bacterial groups in the nematode feeding structure, the root gall, were specifically enriched, suggesting an association with nematode pathogenesis. Function-based metagenomic analysis indicated that the enriched bacterial populations in root gall harbored abundant genes related to degradation of plant polysaccharides, carbohydrate and protein metabolism and biological nitrogen fixation. Our data indicated that some of the previously assumed beneficial endophytes or bacterial associates with nematode might be involved in nematode infections of the tomato roots.

The genus Trichoderma is comprised of many common fungi species that are distributed worldwide across many ecosystems. Trichoderma species are well-known producers of secondary metabolites with a variety of biological activities. Their potential use as biocontrol agents has been known for many years. Several reviews about metabolites from Trichoderma have been published. These reviews are based on their structural type, biological activity, or fungal origin. In this review, we summarize the secondary metabolites per Trichoderma species and elaborate on approximately 390 non-volatile compounds from 20 known species and various unidentified species.