Trichoderma atroviride is a strong necrotrophic mycoparasite antagonizing and feeding on a broad range of fungal phytopathogens. It further beneficially acts on plants by enhancing growth in root and shoot and inducing systemic resistance. Volatile organic compounds (VOCs) are playing a major role in all those processes. Light is an important modulator of secondary metabolite biosynthesis, but its influence has often been neglected in research on fungal volatiles. To date, T. atroviride IMI 206040 and T. atroviride P1 are among the most frequently studied T. atroviride strains and hence are used as model organisms to study mycoparasitism and photoconidiation. However, there are no studies available, which systematically and comparatively analyzed putative differences between these strains regarding their light-dependent behavior and VOC biosynthesis. We therefore explored the influence of light on conidiation and the mycoparasitic interaction as well as the light-dependent production of VOCs in both strains. Our data show that in contrast to T. atroviride IMI 206040 conidiation in strain P1 is independent of light. Furthermore, significant strain- and light-dependent differences in the production of several VOCs between the two strains became evident, indicating that T. atroviride P1 could be a better candidate for plant protection than IMI 206040.

Background: Reverse transcription quantitative real-time PCR (RT-qPCR) is a well-established method for analysing gene expression. Most RT-qPCR experiments in the field of microbiology aim for the detection of transcriptional changes by relative quantification, which means the comparison of the expression level of a specific gene between different samples by the application of a calibration condition and internal reference genes. Due to the numerous data processing procedures and factors that can influence the final result, relative expression analysis and interpretation of RT-qPCR data are still not trivial and often necessitate the use of multiple separate software packages capable of performing specific functions. Results: Here we present qRAT, a stand-alone desktop application based on R that automatically processes raw output data from any qPCR machine using well-established and state-of-the-art statistical and graphical techniques. The ability of qRAT to analyse RT-qPCR data was evaluated using two example datasets generated in our laboratory. The tool successfully completed the procedure in both cases, returning the expected results. The current implementation includes functionalities for parsing, filtering, normalizing and visualisation of relative RT-qPCR data, like the determination of the relative quantity and the fold change of differentially expressed genes as well as the correction of inter-plate variation for multiple-plate experiments. Conclusion: qRAT provides a comprehensive, straightforward, and easy-to-use solution for the relative quantification of RT-qPCR data that requires no programming knowledge or additional software installation. All application features are available for free and without requiring a login or registration.

Mycoparasitic fungi, fungi preying on other fungal species, are prolific producers of volatile and non-volatile secondary metabolites. Several secondary metabolites are produced during mycoparasitism to weaken the host and support attack and parasitism. Further, evidence accumulated that some secondary metabolites also act as communication molecules. Besides their antagonistic activity, several fungal mycoparasites exhibit beneficial effects on plants and some of their secondary metabolites have plant growth-promoting and defense stimulating activities. As many secondary metabolism-associated gene clusters remain silent under standard laboratory conditions, the full variety as well as the underlying biosynthetic pathways employed by fungal mycoparasites for secondary metabolite production still await clarification. Nonetheless, the variety of currently known secondary metabolites and their range of activities is impressive already and they exhibit a great potential for agriculture, pharmacology and other industrial applications.