The root‐knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four “host races” had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4‐gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro‐economic challenges.

Antibiosis is the mechanism by which certain microorganisms respond to the presence of others, secreting compounds or metabolites capable of inhibiting or impeding their development. The crude extract of Trichoderma contains a mixture of secondary compounds, which may show antibiotic effect, and has been used for the prospect of this fungus for biological control and other industrial purposes. Faced with the increasing demand of agriculture for ecologically compatible alternatives for the management of diseases, this work aimed to investigate the spectrum of action of Non-Volatile Metabolites (NVMs) of Trichoderma isolates against different plant pathogenic fungi. The antagonistic potential of NVMs was evaluated through the incorporation method of the filtered liquid extract in PDA medium. The assays showed that all the NVMs produced inhibited the fungus Sclerotinia sclerotiorum similarly. On the other hand, strains CEN1245 and CEN1274, both belonging to the species Trichoderma brevicompactum, showed broad spectrum against Sclerotium rolfsii, Colletotrichum gloesporioides, Verticillium dahliae, Fusarium oxysporum and Cylindrocladium sp. The present study describes isolates producing non-volatile metabolites with broad spectrum of antifungal action, as well as pathogen-specific. The Trichoderma spp. NVMs obtained from different soil samples cultivated with vegetables, cassava and maize were efficient in inhibiting plant pathogenic fungi belonging to other patossystems, such as forest or fruit, which could increase their potential application in biological control of plant diseases. In addition, these antagonistic fungi should be studied in greater depth for the identification of bioactive molecules of industrial interest or in commercial formulations of products for biological control of plant pathogens.

Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. Paired culture tests showed that all isolates exhibited some antagonism, with a maximum of 77% mycelial inhibition and complete inhibition of sclerotia production. Two isolates were found to be the most promising biocontrol agents, considering both antagonistic parameters (CEN1253 - T. koningiopsis and CEN1265 - T. brevicompactum). Five different species were identified: T. harzianum (23), T. spirale (9), T. koningiopsis (8), T. brevicompactum (7) and T. asperellum (2). These isolates are stored in the Embrapa Fungi Collection for Biological Control and the information obtained in the experiments will be incorporated into the database of biological assets within the genetic resources information system (Allele) and be made available for further studies.

The objective of this study was to characterize isolates of biovar 2 of Ralstonia solanacearum pathogenic to eucalyptus "urograndis" hybrid by means of biochemical tests, as well as evaluation of host range and identification by PCR with primers for species, biovar and phylotype. Carbohydrate utilization assays revealed that the eucalyptus isolates belong to phenotype Tropical of biovar 2 (2T). From artificial inoculations it was possible to reproduce symptoms or recover the bacterium from: eucalyptus, potato, tomato, eggplant, datura, geranium, turnip, mustard, nasturtium, beetroot, sunflower, bean, French marigold, horseradish tree, and cashew. The PCR assays confirmed that the isolates belong to biovar 2, phylotype II of the bacterium. The confirmation of new biovar naturally infecting eucalyptus indicates that R. solanacearum easily adapts to new hosts.

Soil microorganisms present a great diversity, involving taxonomically distinct groups that play a role in the decomposition of organic matter, nutrient cycling, soil aggregation, among others. In this diversity, the fungi of the genus Trichoderma have been successful plant pathogen biocontrol agents, as plant growth promoters and as inducers of plant resistance to diseases. In addition, they are important in the sustainability of natural ecosystems. Aiming to verify the population density of Trichoderma fungi in natural environments and agroecosystems, in Cerrado area, samples of soils and roots from native vegetation and agroecological production system were collected in the Federal District, Brazil. The collection points were randomly selected, and each soil or root sample was individually wrapped. The soil adhered to the roots was removed for evaluations. Serial sample dilutions and number of Colony Forming Units (CFUs) of Trichoderma isolates were performed. The results showed that the number of CFU varied depending on the plant and location evaluated. The replacement of native vegetation by organic farming systems did not result in a significant reduction in this number.