Host-specific transcriptomic pattern of Trichoderma virens during interaction with maize or tomato roots

BACKGROUND: Members of the fungal genus Trichoderma directly antagonize soil-borne fungal pathogens, and an increasing number of species are studied for their potential in biocontrol of plant pathogens in agriculture. Some species also colonize plant roots, promoting systemic resistance. The Trichoderma-root interaction is hosted by a wide range of plant species, including monocots and dicots. RESULTS: To test the hypothesis that gene expression by the fungal partner in this beneficial interaction is modulated by the plant, Trichoderma virens was co-cultured with maize or tomato in a hydroponic system allowing interaction with the roots. The transcriptomes for T. virens alone were compared with fungus-inoculated tomato or maize roots by hybridization on microarrays of 11645 unique oligonucleotides designed from the predicted protein-coding gene models. Transcript levels of 210 genes were modulated by interaction with roots. Almost all were up-regulated. Glycoside hydrolases and transporters were highly represented among transcripts induced by co-culture with roots. Of the genes up-regulated on either or both host plants, 35 differed significantly in their expression levels between maize and tomato. Ten of these were expressed higher in the fungus in co-culture with tomato roots than with maize. Average transcript levels for these genes ranged from 1.9 fold higher on tomato than on maize to 60.9 fold for the most tomato-specific gene. The other 25 host-specific transcripts were expressed more strongly in co-culture with maize than with tomato. Average transcript levels for these genes were 2.5 to 196 fold higher on maize than on tomato. CONCLUSIONS: Based on the relevant role of Trichoderma virens as a biological control agent this study provides a better knowledge of its crosstalk with plants in a host-specific manner. The differentially expressed genes encode proteins belonging to several functional classes including enzymes, transporters and small secreted proteins. Among them, glycoside hydrolases and transporters are highlighted by their abundance and suggest an important factor in the metabolism of host cell walls during colonization of the outer root layers. Host-specific gene expression may contribute to the ability of T. virens to colonize the roots of a wide range of plant species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-014-1208-3) contains supplementary material, which is available to authorized users

Wheat fungal endophyte communities are inseparable from the host and influence plant development

ABSTRACTPlants harbor complex and highly diverse fungal endophyte communities (FECs), making it difficult to evaluate the functional role of individual taxa, subsets of the community, or the FEC as a whole. To reduce the complexity of this system, we aimed to produce fungi-null wheat (Triticum aestivum) plants. To this end, we treated seeds with heat and fungicides and generated plants from rescued embryos and callus tissue. A culture-based approach and reverse transcription PCR analysis were negative, indicating that all treatments produced plants apparently free of fungi. However, the analysis of DNA using digital droplet PCR and next-generation sequencing revealed that tissues from all treatments retained low levels but diversity-rich FECs. While the FECs varied in composition across treatments and tissues, they all included core taxa of the mycobiome. The reduced fungal biomass, along with the changes in FEC composition, negatively affected plant development, supporting a FEC contribution to proper plant development and fitness. Our discovery that a large part of the FEC cannot be separated from plants and can be transmitted through seeds and tissue culture calls for reevaluation of particular microbiome paradigms, such as core taxa concepts, transmission modes, and functional species.IMPORTANCEThe native microbiome in a given plant must be considered when evaluating the effect of a single taxon or synthetic community. The pre-existing microbiome can interact with artificially added microbial cargo, which affects the final outcome. Such issues can be at least partially solved by the use of endophyte-free plants, which provide a clean background that should be useful in determining the effect of a single taxon, taxa combinations, or the entire microbiome on plant performance. Previous reports regarded plants as endophyte-free or axenic by the lack of fungal growth on culture media or the generation of plants from tissue cultures. We showed here that while fungi could not be isolated from fungicide-treated or tissue culture-regenerated plants, nevertheless, all plants contained rich fungal endophyte communities; namely, it was impossible to create fungi-free wheat plants. Our results call for rethinking fundamental microbiome-related concepts, such as core taxa, transmission mode, and functional species

Transmission Mode and Assembly of Seed Fungal Endophyte Communities in Wheat and Wheat Wild Relatives

Seeds acquire fungal endophytes either from the environment or from their progenitors. These transmission modes are central in shaping the microbiome because they affect species composition and balance. We studied fungal endophyte communities (FECs) in three plant species: bread wheat (Triticum aestivum), wild emmer wheat (Triticum turgidum dicoccoides), and wild barley (Hordeum spontaneum). We conducted two experiments to test seed-to-seed transmission: (i) we compared FECs in stems and seeds collected from agricultural and natural habitats and (ii) we grew plants under greenhouse conditions to isolate the effect of vertical transmission on the plant FECs. The analysis of seed communities revealed differences in FEC composition and diversity among plant species; however, Alternaria infectoria dominated FECs in all plant species. In field-collected plants, the number of taxa in the seeds was less than half the number in stems, and close to 90% of the seed taxa were found in stems. The FECs from stems and seeds of greenhouse-grown plants were more diverse than the FECs of original seeds; they lacked a single dominant taxon, and the FECs in the new seeds had a similar richness and diversity to stem FECs, with only 40% overlap. The controlled-environment experiment confirmed vertical transmission of certain species but also showed that external infection of the seeds is the main source for specific taxa. Our results show that many taxa can reach the seeds internally, albeit in different abundance, that both infection sources affect seed FEC composition, and that external conditions affect the balance between FECs within the plant