Novel viruses of the family Partitiviridae discovered in Saccharomyces cerevisiae.

It has been 49 years since the last discovery of a new virus family in the model yeast Saccharomyces cerevisiae. A large-scale screen to determine the diversity of double-stranded RNA (dsRNA) viruses in S. cerevisiae has identified multiple novel viruses from the family Partitiviridae that have been previously shown to infect plants, fungi, protozoans, and insects. Most S. cerevisiae partitiviruses (ScPVs) are associated with strains of yeasts isolated from coffee and cacao beans. The presence of partitiviruses was confirmed by sequencing the viral dsRNAs and purifying and visualizing isometric, non-enveloped viral particles. ScPVs have a typical bipartite genome encoding an RNA-dependent RNA polymerase (RdRP) and a coat protein (CP). Phylogenetic analysis of ScPVs identified three species of ScPV, which are most closely related to viruses of the genus Cryspovirus from the mammalian pathogenic protozoan Cryptosporidium parvum. Molecular modeling of the ScPV RdRP revealed a conserved tertiary structure and catalytic site organization when compared to the RdRPs of the Picornaviridae. The ScPV CP is the smallest so far identified in the Partitiviridae and has structural homology with the CP of other partitiviruses but likely lacks a protrusion domain that is a conspicuous feature of other partitivirus particles. ScPVs were stably maintained during laboratory growth and were successfully transferred to haploid progeny after sporulation, which provides future opportunities to study partitivirus-host interactions using the powerful genetic tools available for the model organism S. cerevisiae.

Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events.

In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.

Uncovering the Yeast Communities in Fungus-Growing Ant Colonies.

Yeast-insect interactions are compelling models to study the evolution, ecology, and diversification of yeasts. Fungus-growing (attine) ants are prominent insects in the Neotropics that evolved an ancient fungiculture of basidiomycete fungi over 55-65 million years, supplying an environment for a hidden yeast diversity. Here we assessed the yeast diversity in the attine ant environment by thoroughly sampling fungus gardens across four out of five ant fungiculture systems: Acromyrmex coronatus and Mycetomoellerius tucumanus standing for leaf-cutting and higher-attine fungicultures, respectively; Apterostigma sp., Mycetophylax sp., and Mycocepurus goeldii as ants from the lower-attine fungiculture. Among the fungus gardens of all fungus-growing ants examined, we found taxonomically unique and diverse microbial yeast communities across the different fungicultures. Ascomycete yeasts were the core taxa in fungus garden samples, with Saccharomycetales as the most frequent order. The genera Aureobasidium, Candida, Papiliotrema, Starmerella, and Sugiyamaella had the highest incidence in fungus gardens. Despite the expected similarity within the same fungiculture system, colonies of the same ant species differed in community structure. Among Saccharomycotina yeasts, few were distinguishable as killer yeasts, with a classical inhibition pattern for the killer phenotype, differing from earlier observations in this environment, which should be further investigated. Yeast mycobiome in fungus gardens is distinct between colonies of the same fungiculture and each ant colony harbors a distinguished and unique yeast community. Fungus gardens of attine ants are emergent environments to study the diversity and ecology of yeasts associated with insects.

Yeasts in the attine ant-fungus mutualism: Diversity, functional roles, and putative biotechnological applications.

Insects interact with a wide variety of yeasts, often providing a suitable substrate for their growth. Some yeast-insect interactions are tractable models for understanding the relationships between the symbionts. Attine ants are prominent insects in the Neotropics and have performed an ancient fungiculture of mutualistic basidiomycete fungi for more than 55-65 million years. Yeasts gain access to this sophisticated mutualism, prompting diversity, ecological, and biotechnological studies in this environment. We review half a century research in this field, surveying for recurrent yeast taxa and their putative ecological roles in this environment. We found that previous studies mainly covered the yeast diversity from a small fraction of attine ants, being Saccharomycetales, Tremellales, and Trichosporonales as the most frequent yeast or yeast-like orders found. Apiotrichum, Aureobasidium, Candida, Cutaneotrichosporon, Debaryomyces, Meyerozyma, Papiliotrema, Rhodotorula, Trichomonascus, and Trichosporon are the most frequent recovered genera. On the other hand, studies of yeasts' ecological roles on attine ant-fungus mutualism only tapped the tip of the iceberg. Previous established hypotheses in the literature cover the production of lignocellulosic enzymes, chemical detoxification, and fungus garden protection. Some of these roles have parallels in biotechnological processes. In conclusion, the attine ant environment has a hidden potential for studying yeast biodiversity, ecology, and biotechnology, which has been particularly unexplored considering the vast diversity of fungus-growing ants.

The experience of teaching introductory programming skills to bioscientists in Brazil.

Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners. Here, we describe the conception, organization, and implementation of the Brazilian Python Workshop for Biological Data. This workshop has been organized by graduate and undergraduate students and supported, mostly in administrative matters, by experienced faculty members since 2017. The workshop was conceived for teaching bioscientists, mainly students in Brazil, on how to program in a biological context. The goal of this article was to share our experience with the 2020 edition of the workshop in its virtual format due to the Coronavirus Disease 2019 (COVID-19) pandemic and to compare and contrast this year's experience with the previous in-person editions. We described a hands-on and live coding workshop model for teaching introductory Python programming. We also highlighted the adaptations made from in-person to online format in 2020, the participants' assessment of learning progression, and general workshop management. Lastly, we provided a summary and reflections from our personal experiences from the workshops of the last 4 years. Our takeaways included the benefits of the learning from learners' feedback (LLF) that allowed us to improve the workshop in real time, in the short, and likely in the long term. We concluded that the Brazilian Python Workshop for Biological Data is a highly effective workshop model for teaching a programming language that allows bioscientists to go beyond an initial exploration of programming skills for data analysis in the medium to long term.

Soluble Compounds of Filamentous Fungi Harm the Symbiotic Fungus of Leafcutter Ants.

Chemical compounds are key to understand symbiotic interactions. In the leafcutter ant-microbe symbiosis a plethora of filamentous fungi continuously gain access the ant colonies through plant substrate collected by workers. Many filamentous fungi are considered transient in attine ant colonies, however, their real ecological role in this environment still remains unclear. A possible role of these microorganisms is the antagonism towards Leucoagaricus gongylophorus, the mutualistic fungus that serve as food for several leafcutter ant species. Here, we showed the antagonism of filamentous fungi isolated from different sources, and the negative impacts of their metabolites on the growth of the ant-fungal cultivar. Our results demonstrate that the chemical compounds produced by filamentous fungi can harm the mutualistic fungus of leafcutter ants.

Metabolomics Reveals a 26-Membered Macrolactone Produced by Endophytic Colletotrichum spp. from Alcatrazes Island, Brazil.

Comparative metabolomics analysis of nonphytotoxic endophytic Colletotrichum spp. isolated from Anthurium alcatrazense endemic to Alcatrazes island (Brazil) and phytopathogenic Colletotrichum spp. isolated from the mainland of Brazil revealed significant differences in chemical composition. Examination of endophytic Colletotrichum spp. from Alcatrazes island led to the discovery of a 26-member macrolactone, colletotrichumolide (1), containing a phosphatidyl choline side chain. Further examination of the phytopathogenic strains from the mainland identified a family of phytopathogenic metabolites not present in the nonpathogenic island-derived strains, suggesting that geographical isolation could influence the secondary metabolism of fungal strains.

Climate Change Influences Basidiome Emergence of Leaf-Cutting Ant Cultivars.

Maintaining symbiosis homeostasis is essential for mutualistic partners. Leaf-cutting ants evolved a long-term symbiotic mutualism with fungal cultivars for nourishment while using vertical asexual transmission across generations. Despite the ants' efforts to suppress fungal sexual reproduction, scattered occurrences of cultivar basidiomes have been reported. Here, we review the literature for basidiome occurrences and associated climate data. We hypothesized that more basidiome events could be expected in scenarios with an increase in temperature and precipitation. Our field observations and climate data analyses indeed suggest that Acromyrmex coronatus colonies are prone to basidiome occurrences in warmer and wetter seasons. Even though our study partly depended on historical records, occurrences have increased, correlating with climate change. A nest architecture with low (or even the lack of) insulation might be the cause of this phenomenon. The nature of basidiome occurrences in the A. coronatus-fungus mutualism can be useful to elucidate how resilient mutualistic symbioses are in light of climate change scenarios.

Fungi inhabiting attine ant colonies: reassessment of the genus Escovopsis and description of Luteomyces and Sympodiorosea gens. nov.

Escovopsis is a diverse group of fungi, which are considered specialized parasites of the fungal cultivars of fungus-growing ants. The lack of a suitable taxonomic framework and phylogenetic inconsistencies have long hampered Escovopsis research. The aim of this study is to reassess the genus Escovopsis using a taxonomic approach and a comprehensive multilocus phylogenetic analysis, in order to set the basis of the genus systematics and the stage for future Escovopsis research. Our results support the separation of Escovopsis into three distinct genera. In light of this, we redefine Escovopsis as a monophyletic clade whose main feature is to form terminal vesicles on conidiophores. Consequently, E. kreiselii and E. trichodermoides were recombined into two new genera, Sympodiorosea and Luteomyces, as S. kreiselii and L. trichodermoides, respectively. This study expands our understanding of the systematics of Escovopsis and related genera, thereby facilitating future research on the evolutionary history, taxonomic diversity, and ecological roles of these inhabitants of the attine ant colonies.