Beneficial microorganisms, including members of the Trichoderma genus, are known for their ability to promote plant growth and disease resistance, as well as being alternatives to synthetic inputs in agriculture. In this study, 111 Trichoderma strains were isolated from the rhizospheric soil of Florence Aurore, an ancient wheat variety that was cultivated in an organic farming system in Tunisia. A preliminary ITS analysis allowed us to cluster these 111 isolates into three main groups, T. harzianum (74 isolates), T. lixii (16 isolates) and T. sp. (21 isolates), represented by six different species. Their multi-locus analysis (tef1, translation elongation factor 1; rpb2, RNA polymerase B) identified three T. afroharzianum, one T. lixii, one T. atrobrunneum and one T. lentinulae species. These six new strains were selected to determine their suitability as plant growth promoters (PGP) and biocontrol agents (BCA) against Fusarium seedling blight disease (FSB) in wheat caused by Fusarium culmorum. All of the strains exhibited PGP abilities correlated to ammonia and indole-like compound production. In terms of biocontrol activity, all of the strains inhibited the development of F. culmorum in vitro, which is linked to the production of lytic enzymes, as well as diffusible and volatile organic compounds. An in planta assay was carried out on the seeds of a Tunisian modern wheat variety (Khiar) by coating them with Trichoderma. A significant increase in biomass was observed, which is associated with increased chlorophyll and nitrogen. An FSB bioprotective effect was confirmed for all strains (with Th01 being the most effective) by suppressing morbid symptoms in germinated seeds and seedlings, as well as by limiting F. culmorum aggressiveness on overall plant growth. Plant transcriptome analysis revealed that the isolates triggered several SA- and JA-dependent defense-encoding genes involved in F. culmorum resistance in the roots and leaves of three-week-old seedlings. This finding makes these strains very promising in promoting growth and controlling FSB disease in modern wheat varieties.

Faba bean ascochyta blight, caused by Ascochyta fabae Speg. (teleomorph: Didymella fabae Punith.), is one of the most devastating diseases of the crop. It can cause yield losses that reach 95% in conducive weather conditions. Surveys were carried out in five regions of Tunisia: Beja, Bizerte, Jendouba, Kef and Tunis-Cap Bon. A total of 513 fungal isolates were collected from 2011 to 2013. A molecular characterization was conducted to identify the mating type of each individual using a mating type specific PCR. Results revealed that the two mating types MAT1-2 and MAT1-1 coexisted in all surveyed regions. An imbalance in favor of MAT1-2 was observed particularly in Bizerte and Jendouba regions (sex ratio was 18:85 and 32:80, respectively). Moreover, morphological and pathogenic characterization of 122 isolates among the collection revealed a significant variability in conidia type (one celled or two celled conidia) frequency, in conidia mean size and in aggressiveness toward Badii faba bean cultivar (incubation period, IP; percentage necrotic leaf area, S; and area under disease progression curve, AUDPC). A principal component analysis (PCA) performed on morphologically studied parameters (frequency of conidia cell number and conidia mean size) identified three groups of isolates based on morphological traits: one celled (1C) and two celled (2C) conidia rates, one celled and two celled conidia length and width (1L, 1W, 2L and 2W, respectively). A second PCA using aggressiveness parameters (IP: Incubation period, S1, S4 and S9: percentage of necrotic leaf area respectively 5, 20 and 45 days after inoculation) identified three distinct pathogenic groups: poorly pathogenic AG1, moderately pathogenic AG2 and highly pathogenic AG3. Morphological and pathogenic groups and mating type data were used to conduct a multiple factorial correspondence analysis (MFCA) which revealed a correlation between the variables studied. Five groups were identified, each associated with a morphological and pathogenic trait and mating type. The most pathogenic group belonged to MAT1-2 suggesting that in locations where MAT1-2 is prevalent the epidemic risk is more important.