Genomic Characterization and Functional Description of Beauveria bassiana Isolates from Latin America.

Beauveria bassiana is an entomopathogenic fungus used in agriculture as a biological controller worldwide. Despite being a well-studied organism, there are no genomic studies of B. bassiana isolates from Central American and Caribbean countries. This work characterized the functional potential of eight Neotropical isolates and provided an overview of their genomic characteristics, targeting genes associated with pathogenicity, the production of secondary metabolites, and the identification of CAZYmes as tools for future biotechnological applications. In addition, a comparison between these isolates and reference genomes was performed. Differences were observed according to geographical location and the lineages of the B. bassiana complex to which each isolate belonged.

Draft Genome Sequences of Eight Isolates of Beauveria bassiana of Neotropical Origin.

Beauveria bassiana, a well-known entomopathogenic fungus, has a worldwide distribution; however, genomes of isolates from the Neotropical region are scarce. Here, we report the draft genome sequences of eight B. bassiana isolates from Costa Rica, Puerto Rico, and Honduras.

Identification and phylogenetic analysis of a collection of Beauveria spp. Isolates from Central America and Puerto Rico.

The genus Beauveria comprises economically important entomopathogenic fungi, widely used for biological control in agriculture. Interest in these organisms in Costa Rica prompted surveys and establishment of collections in the past two decades. However, there was neither a formal identification nor a characterization of the isolates. With that purpose, the morphology and genetic variation by microsatellites and partial sequencing of Bloc, TEF-1α and RPB2 regions were studied for 32 isolates of Beauveria, which included 26 from Costa Rica, five from Puerto Rico and one from Honduras. The isolates were identified as B. bassiana (29) and B. caledonica (3). Ninety-three percent of B. bassiana isolates belonged to a monophyletic group of African and Neotropical isolates. A total of 105 alleles were recorded with 11 SSR markers, and the results suggested high diversity within the collection. Mantel tests showed low association between geographic origin and the variation among isolates.

A Combined Metagenomics and Metatranscriptomics Approach to Unravel Costa Rican Cocoa Box Fermentation Processes Reveals Yet Unreported Microbial Species and Functionalities.

Cocoa fermentation is the first step in the post-harvest processing chain of cocoa and is important for the removal of the cocoa pulp surrounding the beans and the development of flavor and color precursors. In the present study, metagenomic and metatranscriptomic sequencing were applied to Costa Rican cocoa fermentation processes to unravel the microbial diversity and assess the function and transcription of their genes, thereby increasing the knowledge of this spontaneous fermentation process. Among 97 genera found in these fermentation processes, the major ones were Acetobacter, Komagataeibacter, Limosilactobacillus, Liquorilactobacillus, Lactiplantibacillus, Leuconostoc, Paucilactobacillus, Hanseniaspora, and Saccharomyces. The most prominent species were Limosilactobacillus fermentum, Liquorilactobacillus cacaonum, and Lactiplantibacillus plantarum among the LAB, Acetobacter pasteurianus and Acetobacter ghanensis among the AAB, and Hanseniaspora opuntiae and Saccharomyces cerevisiae among the yeasts. Consumption of glucose, fructose, and citric acid, and the production of ethanol, lactic acid, acetic acid, and mannitol were linked to the major species through metagenomic binning and the application of metatranscriptomic sequencing. By using this approach, it was also found that Lacp. plantarum consumed mannitol and oxidized lactic acid, that A. pasteurianus degraded oxalate, and that species such as Cellvibrio sp., Pectobacterium spp., and Paucilactobacillus vaccinostercus could contribute to pectin degradation. The data generated and results presented in this study could enhance the ability to select and develop appropriate starter cultures to steer the cocoa fermentation process toward a desired course.

Inoculation and co-inoculation of two monosporic fungi onto surface-sterile blackberry fruits for quantification experiments.

Trichoderma is used as a biocontrol agent against different plant pathogens in different crops. In Costa Rica, Trichoderma isolates from blackberry fruits (Rubus adenotrichos Schltdl.) have shown antagonism in laboratory and field trials against Botrytis cinerea. Quantifying fungal antagonistic activity directly on target organs or target tissues is of interest to estimate the performance of biocontrol agents. However, this is difficult due to the lack of visual manifestations of fungal structures. As part of a larger study to quantify antagonistic activity by quantitative PCR, we detail here a method to isolate and purify each fungus and then inoculate or co-inoculate them onto surface-sterilized blackberry fruits. • A procedure to co-inoculate the surfaces of blackberry fruits with monosporic fungal suspensions for molecular analyses is described. • The protocol described herein was implemented for subsequent qPCR analysis.

A multiplex qPCR TaqMan-assay to detect fungal antagonism between Trichoderma atroviride (Hypocreaceae) and Botrytis cinerea (Sclerotiniaceae) in blackberry fruits using a de novo tef1-α- and an IGS-sequence based probes.

The aim of this study was to design a Trichoderma atroviride-specific qPCR oligo set, evaluate its specificity, and standardize a methodology that quantifies antagonism against Botrytis cinerea in blackberry fruits (Rubus adenotrichos Schltdl.). Primers and probe were designed based on the nuclear translation elongation factor 1-alpha (tef1-α) of T. atroviride. A commercial IGS-based oligo set was used to quantify B. cinerea. The specificity of the designed oligo set, along with ITS-based oligo sets, was assessed using other Trichoderma species and B. cinerea. Multiplex qPCR assays were performed using DNA from B. cinerea, T. atroviride, and blackberries inoculated with these fungi. Assays with the tef1-α oligo set showed high sensitivity and reproducibility. In inoculated fruits, T. atroviride and B. cinerea were quantified simultaneously, including in symptomless tissues. This work standardized a qPCR methodology that specifically targets a T. atroviride isolate. This newly-designed qPCR oligo set could be useful in future biological control programs.