Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genusHypocrea/Trichoderma.Results: Here we report an analysis of the genome sequences of the two biocontrol speciesTrichoderma atroviride(teleomorphHypocrea atroviridis) andTrichoderma virens(formerlyGliocladium virens, teleomorphHypocrea virens), and a comparison withTrichoderma reesei(teleomorphHypocrea jecorina). These threeTrichodermaspecies display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative toT. reeseior other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows thatT. reeseiandT. virensare derived relative toT. atroviride. The mycoparasitism-specific genes thus arose in a commonTrichodermaancestor but were subsequently lost inT. reesei.Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

Trichoderma species are widely used in agriculture and industry as biopesticides and sources of enzymes, respectively. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Many strains produce elicitors and induce resistance in plants through colonization of roots. Seven species have now been sequenced. Comparison of a primarily saprophytic species with two mycoparasitic species has provided striking contrasts and has established that mycoparasitism is an ancestral trait of this genus. Among the interesting outcomes of genome comparison is the discovery of a vast repertoire of secondary metabolism pathways and of numerous small cysteine-rich secreted proteins. Genomics has also facilitated investigation of sexual crossing in Trichoderma reesei, suggesting the possibility of strain improvement through hybridization.

Rice brown spot (BS) is a chronic disease that affects millions of hectares of rice every growing season, grown by some of the most resource-poor farmers. Despite its widespread occurrence and impact, much still needs to be understood about BS. Reported yield losses in relative terms vary widely from 4 to 52 %. However, accurate, systematic estimates are lacking. BS is conventionally perceived as a secondary problem that reflects rice crops that experience physiological stresses, e.g. drought and poor soil fertility, rather than a true infectious disease. Much remains to be understood about the mechanisms leading to epidemics and crop losses. Quantitative and qualitative knowledge gaps exist in our understanding of the epidemiological processes, sources of resistance and biocontrol methods. In this review we identify several of these gaps, which if filled, could lead to a strong impact on the management of brown spot. We also use the architecture of a simulation model to position and prioritize these knowledge gaps, assess the epidemiological consequences of disease management options on BS monocyclic processes and explore the impact changing production situations on this important disease.

Background: In fungi, environmental pH is an important signal for development, and successful host colonization depends on homeostasis. Surprisingly, little is known regarding the role of pH in fungal-fungal interactions. Species of Trichoderma grow as soil saprobes but many are primarily mycotrophic, using other fungi as hosts. Therefore, Trichoderma spp. are studied for their potential in biocontrol of plant diseases. Particularly in alkaline soil, pH is a critical limiting factor for these biofungicides, whose optimal growth pH is 4–6. Gaining an understanding of pH adaptability is an important step in broadening the activity spectrum of these economically important fungi. Results: We studied the pH-responsive transcription factor PacC by gene knockout and by introduction of a constitutively active allele (pacC ^c ). ΔpacC mutants exhibited reduced growth at alkaline pH, while pacC ^c strains grew poorly at acidic pH. In plate confrontation assays ΔpacC mutants showed decreased ability to compete with the plant pathogens Rhizoctonia solani and Sclerotium rolfsii. The pacC ^c strain exhibited an overgrowth of R. solani that was comparable to the wild type, but was unable to overgrow S. rolfsii. To identify genes whose expression is dependent on pH and pacC, we designed oligonucleotide microarrays from the transcript models of the T. virens genome, and compared the transcriptomes of wild type and mutant cultures exposed to high or low pH. Transcript levels from several functional classes were dependent on pacC, on pH, or on both. Furthermore, the expression of a set of pacC-dependent genes was increased in the constitutively-active pacC ^c strain, and was pH-independent in some, but not all cases. Conclusions: PacC is important for biocontrol-related antagonism of other fungi by T. virens. As much as 5% of the transcriptome is pH-dependent, and of these genes, some 25% depend on pacC. Secondary metabolite biosynthesis and ion transport are among the relevant gene classes. We suggest that ΔpacC mutants may have lost their full biocontrol potential due to their inability to adapt to alkaline pH, to perceive ambient pH, or both. The results raise the novel possibility of genetically manipulating Trichoderma in order to improve adaptability and biocontrol at alkaline pH.

An adenylate-cyclase-encoding gene, tac1, of Trichoderma virens, a soil fungus used in the biocontrol of plant pathogens, has been cloned and sequenced. The tac1 ORF spanned 7032 bp, encoding a protein of 2153 aa, which shared an identity of 65 % with the adenylate cyclase of Colletotrichum lagenarium. Deletion of tac1, through double-crossover homologous recombination, lowered the intracellular cAMP levels to below the detection limit. The mutants showed only 5–6 % of the wild-type growth rate on agar, but grew normally in shake culture. The mutants did not sporulate in darkness, and the spores failed to germinate in water. In the confrontation assay, the mutants did not overgrow the test plant pathogens Sclerotium rolfsii, Rhizoctonia solani and Pythium sp. Against Pythium sp., the mutants produced a clear zone of inhibition in the confrontation assay. HPLC analysis and bioassay showed reduced secondary metabolite production in the mutants. Using suppression subtractive hybridization (SSH), the genes that were underexpressed in the mutants were identified. Based on an array of 53 SSH library clones, 11 clones were identified as strongly downregulated in the Δtac1 mutants; of these 11 clones, nine sequences were homologous to secondary metabolism-related gene sequences. Therefore, cAMP signalling positively regulates secondary metabolism in T. virens. This is believed to be the first direct genetic study on the role of cAMP signalling in a Trichoderma sp. Tac1 is also believed to be the first regulatory protein to be identified in T. virens that is involved in growth, germination, mycoparasitism and secondary metabolism.