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IntroductionTheobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized.MethodsHerein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri.ResultsOur data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements.DiscussionTo the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.

Cacao is an understory plant cultivated under full-sun monocultures to multi-strata agroforestry systems, where cocoa trees are planted together with fruit, timber, firewood, and leguminous trees, or grown within thinned native forests. Under agroforestry systems of cultivation, cacao is subjected to excess shade due to high density of shade trees, and overgrown or unmanaged pruning of shade trees. Cacao is tolerant to shade, and the maximum photosynthetic rate occurs around irradiance of 400 μmol m−2 s−1 but excess shade reduces the irradiance further which is detrimental to photosynthesis and growth functions. Intra-specific variation is known to exist in cacao for the required saturation irradiance. A greenhouse study was implemented with 58 cacao genotypes selected from four geographically diverse groups: (i) wild cacao from river basins of the Peruvian Amazon, (PWC), (ii) Peruvian farmers’ collection (PFC), (iii) Brazilian cacao collection (BCC) and (iv) national and international cacao collections (NIC). All the cacao genotypes were subjected to 50% and 80% shade where photosynthetic photon flux density (PPFD) was 1000 and 400 μmol m-2 ּs-1 respectively. Intra-specific variations were observed for growth, physiological and nutritional traits, and tolerance to shade. Cacao genotypes tolerant to shade were: UNG-77 and UGU-130 from PWC; ICT-2173, ICT-2142, ICT-2172, ICT-1506, ICT-1087, and ICT-2171 from the PFC; PH-21, CA-14, PH-990 and PH-144 from BCC; and ICS-1, ICS-39, UF-613 and POUND-12 from NIC. Genotypes that tolerate excess shade might be useful plant types to maintain productivity and sustainability in agroforestry systems of cacao management.

Endophytic fungi (EF) are microorganisms that live asymptomatically within plant tissues. They can confer benefits to the plant as inducers of resistance to pests and diseases, tolerance to abiotic factors, plant growth promoters and mycoparasites of pathogens. This study aimed to isolate, identify, and determine occurrence frequency of endophytic fungi in stems and leaves of blueberry plants collected from ten farms in Lima and Ica Region, Peru. Productive branches of 39 healthy plants were sampled. For the isolation of EF, 702 tissue sections were disinfected and transferred to Petri dishes with potato dextrose agar (PDA) medium, and reproductive structures were induced for identification. A total of 134 EF strains were isolated successfully. Nine genera were identified (Trichoderma, Aspergillus, Alternaria, Ulocladium, Cladosporium, Fusarium, Nigrospora, Lasiodiplodia and Stemphylium). EF occurrence frequency varied greatly between organs, being in leaves more frequent than the stems; likewise, the genera Alternaria and Cladosporium were the most frequent and with most colonized in plant tissues, while Aspergillus, Ulocladium and Lasiodiplodia were the least frequent. These strains could be useful to control plant diseases and, therefore, of great interest in sustainable agriculture.

Cacao (Theobroma cacao L.) is a tropical rainforest tree that is indigenous to the Amazon region of South America. The myriad of river basins present in the Upper Amazon are where the largest diversity of cacao populations is found. Although it is generally accepted that cacao was first cultivated in Mesoamerica, there is evidence for domestication in South America, the center of origin. “Piura Porcelana” is a traditional cacao variety from northern Peru that is cultivated for the gourmet chocolate market. The demand for fine-flavored cacao used in high-end chocolates and the corresponding premium prices paid for distinct cacao flavors provide economic incentives for the use and conservation of these traditional varieties. In the present study, we compared the genetic identity of Piura Porcelana cacao with 11 known cacao germplasm groups existing in the ex situ cacao genebanks, along with the living wild populations from the Santiago and Morona river valleys in northern Peru. The results of SNP analysis showed that Piura Porcelana shares the same general population membership with the “Nacional” cacao from Ecuador. However, Piura Porcelana significantly differed from Nacional (Fst = 0.185, P

Knowledge of genetic diversity in farmers’ selections is essential for planning on-farm conservation and rehabilitation. Using 15 microsatellite loci, we analyzed parentage and population structure in 220 farmer selections of cacao from the Huallaga valley in Peruvian Amazon. A high level of allele richness and heterozygosity were detected in these selections. Coordination analysis showed that these farmer selections are mainly comprised of hybrids derived from Trinitario and Upper Amazon Forastero germplasm. Bayesian clustering analysis assigned 54 selections as Trinitario and 166 as Upper Amazon Forastero hybrids. Parentage analysis identified 15 international clones as probable parents for 96 farmer selections, which corresponded to a fraction of the known hybrid families disseminated in this region in the late 1980s. Combined analysis of demographic and molecular data revealed a significant spatial autocorrelation (r = 0.235; P = 0.006) at short geographical distances (

In many tropical soils, excessive weath- ering of primary minerals confounded by intense agricultural production has resulted in the depletion of organic matter and plant available forms of phosphorus (P). Long-term growth of cover crops in tropical agroforestry systems have been shown to influence nutrient cycling, and soil organic matter pools. The objective of this experiment was to assess the affect of 2 years of cover-crop cultivation on organic matter accumulation and P bioavailability using Mehlich I and sequential fractionation methods. The experiment included six treatments in the understory of a cacao-plantain agroforestry system adjacent to lower montane tropical forests of the San Martin district of Eastern Peru. Cacao and plantain formed the primary canopy on otherwise abandoned agricultural land. The treatments consisted of four perennial leguminous cover crops (Arachis pintoi, Calopogonium mucunoides, Canavalia ensiformis, and Centrosema macrocarpum), a non-legume cover crop (Callisia repens), and a control treatment (no cover crop). After only 2 years of cultivation, results suggest that all cover crop species accessed residual P pools in 0-5 cm soil depths as indicated by a decrease in the 0.5 M HCl extractable P pools when compared to control. Additional use of residual P pools by A. pintoi and C. macrocarpum were indicated by significant reduction in the 6.0 M HCl extractable P pool. Relative to control, there was no treatment effect on soil organic matter content; however significant differences occurred between treatments. The C. ensiformis, C. mucunoides and C. repens treatments in 5-15 cm soil depths contained significantly more organic matter than the A. pintoi treatment. In 15-30 cm soil depths the C. ensiformis treatment contains significantly more organic matter than the A. pintoi treatment. Continued research should focus on monitoring the long-term effects of cover crop cultivation on the bioavailability of soil P pools in surface soil horizons, development of organic matter pools and the productivity of the agroforestry species.