The biocontrol agent Pythium oligandrum, which is a member of the phylum Oomycota, can control diseases caused by a taxonomically wide range of plant pathogens, including fungi, bacteria, and oomycetes. However, whether P. oligandrum could control diseases caused by plant root-knot nematodes (RKNs) was unknown. We investigated a recently isolated P. oligandrum strain GAQ1, and the P. oligandrum strain CBS530.74, for the control of an RKN Meloidogyne incognita infection of tomato (Solanum lycopersicum L.). Initially, P. oligandrum culture filtrates were found to be lethal to M. incognita second-stage juveniles (J2s) with up to 84% mortality 24 h after treatment compared to 14% in the control group. Consistent with the lethality to M. incognita J2s, tomato roots treated with P. oligandrum culture filtrates reduced their attraction of nematodes, and the number of nematodes penetrating the roots was reduced by up to 78%. In a greenhouse pot trial, the P. oligandrum GAQ1 inoculation of tomato plants significantly reduced the gall number by 58% in plants infected with M. incognita. Notably, the P. oligandrum GAQ1 mycelial treatment significantly increased tomato plant height (by 36%), weight (by 27%), and root weight (by 48%). A transcriptome analysis of tomato seedling roots inoculated with the P. oligandrum GAQ1 strain identified ~2500 differentially expressed genes. The enriched GO terms and annotations in the up-regulated genes suggested a modulation of the plant hormone-signaling and defense-related pathways in response to P. oligandrum. In conclusion, our results support that P. oligandrum GAQ1 can serve as a potential biocontrol agent for M. incognita control in tomato. Multiple mechanisms appear to contribute to the biocontrol effect, including the direct inhibition of M. incognita, the potential priming of tomato plant defenses, and plant growth promotion.

The regulation of plant biomass degradation by fungi is critical to the carbon cycle, and applications in bioproducts and biocontrol. Trichoderma harzianum is an important plant biomass degrader, enzyme producer, and biocontrol agent, but few putative major transcriptional regulators have been deleted in this species. The T. harzianum ortholog of the transcriptional activator XYR1/XlnR/XLR-1 was deleted, and the mutant strains were analyzed through growth profiling, enzymatic activities, and transcriptomics on cellulose. From plate cultures, the Δxyr1 mutant had reduced growth on D-xylose, xylan, and cellulose, and from shake-flask cultures with cellulose, the Δxyr1 mutant had ~90% lower β-glucosidase activity, and no detectable β-xylosidase or cellulase activity. The comparison of the transcriptomes from 18 h shake-flask cultures on D-fructose, without a carbon source, and cellulose, showed major effects of XYR1 deletion whereby the Δxyr1 mutant on cellulose was transcriptionally most similar to the cultures without a carbon source. The cellulose induced 43 plant biomass-degrading CAZymes including xylanases as well as cellulases, and most of these had massively lower expression in the Δxyr1 mutant. The expression of a subset of carbon catabolic enzymes, other transcription factors, and sugar transporters was also lower in the Δxyr1 mutant on cellulose. In summary, T. harzianum XYR1 is the master regulator of cellulases and xylanases, as well as regulating carbon catabolic enzymes.

The potential of Trichoderma nordicum (Hypocreales, Ascomycota), a recently described species, for antagonism and use in the biocontrol of oomycete-caused plant diseases is unknown. Trichoderma is a well-known genus for containing microbial antagonists and biocontrol agents. The T. nordicum in this study was isolated from decomposing wood, and rpb2 and tef1 barcode sequencing demonstrated that the isolates were a match to the reference T. nordicum and T. nigricans strains. Since T. nordicum was described before T. nigricans, the isolates were assigned to T. nordicum, although taxonomic uncertainty between these species requires future clarification. In dual-culture confrontation assays, T. nordicum overgrew five economically important oomycete plant pathogens (Phytophthora capsici, P. sojae, Pythium aphanidermatum, P. myriotylum, and Globisporangium ultimum). The inability to recover viable P. aphanidermatum and P. capsici from the parts of the plate overgrown by T. nordicum, coupled with protease and endo-cellulase activities, correlates with T. nordicum having antagonistic abilities. Inoculation with T. nordicum preventively reduced the levels of cucumber seedling damping-off caused by P. aphanidermatum by up to 70%. The T. nordicum biocontrol effects against pepper blight caused by P. capsici were greater than 80%, compared to an autoclaved T. nordicum spore control. T. nordicum could also significantly promote the growth of pepper, with plant weight increased by up to 40%, compared to an autoclaved-spore control. In contrast, T. nordicum could not be used to control Pythium soft rot of ginger caused by P. myriotylum, even though P. myriotylum was overgrown by T. nordicum, suggesting host- or pathosystem-specific factors influence biocontrol efficacy. In summary, T. nordicum is a promising biocontrol agent for use in the control of pepper blight caused by P. capsici, and also has potential for use in the control of other oomycete-caused plant diseases in vegetable production systems.