Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the “blast”. Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches’ broom disease in the late 1980s. Today, most of the world’s cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.

The genusBeauveriais considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species. Species identification inBeauveriais difficult because of its structural simplicity and the lack of distinctive phenotypic variation. Therefore, the use of multi-locus sequence data is essential to establish robust species boundaries in addition to DNA-based species delimitation methods using genetic distance, coalescent, and genealogical concordance approaches (polyphasic approaches). In this regard, our study used multilocus phylogeny and five DNA-based methods to delimit species inBeauveriausing three molecular makers. These polyphasic analyses allowed for the delimitation of 20–28 species inBeauveria, confirming cryptic diversity in five species (i.e.B. amorpha,B. bassiana,B. diapheromeriphila, andB. pseudobassiana) and supporting the description ofB. peruviensisas a new taxon from northeastern Peru. The other five species were not evaluated as they did not have enough data (i.e.B. araneola,B. gryllotalpidicola,B. loeiensis,B. medogensis, andB. rudraprayagi). Our results demonstrate that the congruence among different methods in a polyphasic approach (e.g. genetic distance and coalescence methods) is more likely to show reliably supported species boundaries. Among the methods applied in this study, genetic distance, coalescent approaches, and multilocus phylogeny are crucial when establishing species boundaries inBeauveria.

The hyperdiverse genus Trichoderma is one of most useful groups of microbes for a number of human activities, and their accurate identification is crucial. The structural simplicity and lack of distinctive phenotypic variation in this group enable the use of DNA-based species delimitation methods in combination with phylogenies (and morphology when feasible) to establish well-supported boundaries among species. Our study employed a multilocus phylogeny and four DNA-based methods (automated barcode gap discovery [ABGD], statistical parsimony [SPN], generalized mixed Yule coalescent [GMYC], and Bayesian phylogenetics and phylogeography [BPP]) for four molecular markers (acl1, act, rpb2, and tef1) to delimit species of two lineages of Trichoderma. Although incongruence among these methods was observed in our analyses, the genetic distance (ABGD) and coalescence (BPP) methods and the multilocus phylogeny strongly supported and confirmed recognition of 108 and 39 different species in the Harzianum and Longibrachiatum lineages, including three new species associated with cacao farms in northern Peru, namely, T.awajun, sp. nov., T. jaklitschii, sp. nov., and T. peruvianum, sp. nov. Morphological distinctions between the new species and their close relatives are primarily related to growth rates, colony appearance, and size of phialides and conidia. This study confirmed that an integrative approach (DNA-based methods, multilocus phylogeny, and phenotype) is more likely to reliably verify supported species boundaries in Trichoderma.

Cadmium (Cd) contamination threatens cocoa farming in the province of Bagua in Amazonas, Peru. This study reports our assessment of Cd concentrations in cocoa farm soils, and in cocoa roots, leaves, testa, and cotyledon, thus evaluating the magnitude of the problem caused by Cd exposure. For our analysis, we sampled agricultural soil, cocoa roots, leaves and pods at 29 farms in the province of Bagua. Concentrations of Cd in each of the samples were measured and correlated with selected variables at each sampling site. Within our collection of samples, Cd levels showed great variability. In soil, Cd concentrations ranged between 1.02 and 3.54 mg kg⁻¹. Concentrations of this metal within cocoa trees measured from roots, leaves, testa, and cotyledon, Cd ranged from 0.49 mg kg⁻¹ to 2.53 mg kg⁻¹. The cocoa trees exhibited variable degrees of allocation Cd from the soil to their tissues and thus considerable variation among themselves. We found that Cd amounts in roots were up to five times more concentrated than Cd levels in the soils and 2.85 times [Cd] the amounts found in cotyledon. Soil pH is a key variable enabling the uptake of this metal. Most importantly, our evaluation determined that measurements from the majority of farms exceeded the maximum permissible limits established by Peruvian and European legislation.

The use of native Trichoderma strains has been proposed as a sustainable alternative to control cocoa diseases. The aim of this study was to assess indigenous Trichoderma strains from Bagua Province, Peru, with reference to their antagonistic characteristics in vitro and their potential for in vitro biocontrol against frosty pod rot (FPR) disease. A total of 199 strains were assessed for in vitro mycoparasitism, antibiosis, and potential antagonism. The effect of four strains was evaluated in vitro using epidemiological variables, yield, and efficacy at two sites (Copallín and La Peca). Significant differences (p < 0.05) were reported for all variables evaluated in vitro and in vitro. Mycoparasitism ranged from 32% to 100%, antibiosis from 33.36% to 57.92%, and potential antagonism from 42.36% to 78.64%. All strains were found to affect the in vitro-assessed parameters in addition to enhancing the productive yield. The efficiency ranged from 38.99% to 71.9% in Copallín, and 45.88% to 51.16% in La Peca. The CP24-6 strain showed the highest potential for biocontrol under field conditions when considering its effect on both sites.

The use of Trichoderma spp. constitutes a promising biotechnological strategy for sustainable agriculture, owing to its capacity to control phytopathogens and to produce bioactive secondary metabolites. This study, one of the first of its kind, addresses the absence of a comprehensive bibliometric assessment in this field. A systematic bibliometric analysis was conducted on 235 publications indexed in Scopus (2000–2025). Advanced tools such as VOSviewer and Bibliometrix were employed to track publication trends, identify key research themes, map collaborative networks, and assess the influence of leading authors and institutions. An exponential increase in scientific output was observed, peaking in 2023. Four principal research clusters were identified: antifungal activity, gene regulation, secondary metabolite production, and biosynthesis. India and China accounted for the highest publication volume, while Italy, represented by authors such as Francesco Vinale, accounted for the greatest scientific impact. International collaboration was extensive, particularly between Asia and Europe. The analysis indicates a progression from applied biocontrol studies to research focusing on molecular and genetic mechanisms, highlighting the need for multidisciplinary approaches that integrate biotechnology, agronomy, and microbial ecology. This bibliometric study provides an overview of Trichoderma secondary metabolites in agricultural biocontrol and outlines a research agenda emphasizing field validation, interdisciplinary collaboration, and the adoption of innovative technologies to bridge the gap between research and on-farm application in sustainable agriculture.