Biology subjects

Chaverri, P.

Publications and source records attributed to Chaverri, P..

9 recordsLinked to original sources

bioRxiv2026

A novel pipeline for the rapid expansion of ecological trait databases using LLMs

This paper presents a novel workflow leveraging Large Language Models (LLMs) to rapidly extract trait data from fungal species descriptions, addressing a significant bottleneck in ecological research. We developed and evaluated an LLM pipeline to extract morphological trait data from arbuscular mycorrhizal fungi, comparing performance against a manually curated dataset (TraitAM). Results demonstrate the potential of LLMs for automated trait data acquisition, though accuracy varies by trait and model, with systematic biases observed. This framework offers a blueprint for building trait databases across diverse taxa and domains, significantly accelerating ecological research and conservation efforts.

ecology↗

bioRxiv2025

Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes

BackgroundEndohyphal microbiomes, comprising bacteria and viruses, significantly influence fungal phenotypes, host fitness, and ecological interactions. Endohyphal bacterial symbionts are known to affect fungal pathogenicity, secondary metabolite production, and adaptability, yet many aspects of their diversity and interactions remain uncertain. In contrast, endohyphal viruses, despite their widespread presence, are poorly understood in terms of their diversity, ecological roles, and evolutionary relationships with fungal hosts. These gaps highlight the need for integrative studies to explore the composition, diversity, host associations, and functional roles of both bacterial and viral communities in fungi. This study aimed to (1) characterize the diversity of endohyphal bacterial and viral communities within selected fungal endophytes using genomic and transcriptomic approaches, and (2) test for host specialization through phylogenetic signals and core microbial taxa. ResultsEndohyphal microbial communities from 19 fungal isolates from eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales) obtained from Fagus grandifolia leaves were characterized. Bacterial communities exhibited high diversity and significant phylogenetic signals, with core taxa such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales, shared across all fungal samples. Specific bacterial taxa displayed potential host specialization, including Moraxellales, Sphingomonadales, and Streptosporangiaceae for Amphisphaeriales fungal samples; Enterobacterales (e.g., Enterobacteraceae), Hyphomicrobiales (e.g., Rhizobiaceae), and Micrococcales for Glomerellales; and Cytophagales for Diaporthales. Viral communities were less diverse, with Bamfordvirae and Heunggongvirae (double-stranded DNA viruses) identified as core taxa in metagenomic data, while metatranscriptomic data revealed no core taxa. Surprisingly, only a few reads of double-stranded RNA mycoviruses were detected. ConclusionsThe findings suggest a level of host specialization in bacterial communities and a more complex, limited association for viral communities, with dsDNA dominating the endohyphal virome. This study enhances our understanding of fungal-microbe interactions and highlights the ecological and evolutionary dynamics of endohyphal microbiota. Future efforts to expand reference databases and investigate the functional roles of these microbial taxa will further elucidate their contributions to fungal biology, impacts on their plant hosts, and ecosystem processes.

ecology↗

bioRxiv2024

Reduced functional fungal communities in two species of sloths (Bradypus variegatus and Choloepus hoffmanni) suggest a link to slow digestion

Sloths, with their ruminant-like digestive systems, possess the slowest digestion among mammals due to their low metabolic rate, minimal food intake, and extremely low-energy diet. However, no comprehensive studies have characterized the sloths gut microbiota, including fungi, and their role in digestion. This study hypothesized that effective plant fiber-degrading fungi (e.g., Neocallimastigomycota) would be scarce in the sloths gut. The aim was to describe the gut microbiota of three-toed (Bradypus variegatus) and two-toed (Choloepus hoffmanni) sloths to understand their link to slow digestion. Microbial composition and functionality were analyzed using shotgun metagenomics, metatranscriptomics, fungal metabarcoding (ITS 1 and 2 nrDNA), and cellulose degradation analysis. Microbial communities were dominated by bacteria (92-97%), followed by viruses (1-7%). Fungi accounted for only 0.06-0.5% of metagenomic reads and 0.1% of transcripts. Functional analysis revealed minimal CAZy abundance (1.7-1.9% in metagenomes, 0.2% in metatranscriptomes), with no fungal CAZys or glycoside hydrolases detected. Neocallimastigomycota had negligible abundance in metagenomic data and was absent in metatranscriptomic or ITS metabarcoding data. Bradypus variegatus showed overall lower CAZy abundance and fungal presence compared to Choloepus hoffmanni. Lastly, cellulose degradation analyses revealed that only [~]5-35% of the intake was digested. This study highlights the unique microbial ecosystem in sloths guts, showing minimal presence of plant fiber-degrading anaerobic fungi and limited microbial CAZys, aligning with their slow digestion and low metabolic rate, thus enhancing our understanding of their digestive efficiency and metabolic adaptations.

microbiology↗

bioRxiv2024

Exploring biodiversity dynamics and taxonomy of Rubiaceae fungal endophytes in tropical regions

Fungal endophytes play a pivotal role in tropical forest dynamics, influencing plant fitness through growth stimulation, disease suppression, stress tolerance, and nutrient mobilization. This study investigates the effects of region, leaf developmental stage, and tissue type on endophyte communities in tropical plants. Young and mature leaves were collected from 47 Rubiaceae species, and sapwood from 23 species, in old-growth forests of Golfito and Guanacaste, Costa Rica. Fungal diversity and composition were assessed through metabarcoding of the ITS2 nrDNA region. Most identified ASVs belonged to the phylum Ascomycota. The orders Botryosphaeriales and Glomerellales significantly contributed to endophytic assemblages, without detection of host-specific communities. We observed significant differences in species richness across regions, confirming distinct compositions through beta diversity. No statistically significant variances were found between mature and juvenile leaf tissues. In contrast, leaves exhibited richer and more diverse assemblages than sapwood. As plants experienced diverse environments over time and space, our results may be influenced by changing structural and chemical properties through ontogeny. Given the potential impact of these fungi on agricultural and forest ecosystems, ongoing research is crucial to discern the roles of hosts, endophytes, and other ecological mechanisms in apparent colonization patterns.

ecology↗

bioRxiv2023

A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data

MicrobeMASST, a taxonomically-informed mass spectrometry (MS) search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging a curated database of >60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health.

microbiology↗

bioRxiv2023

Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma

Trichoderma is a cosmopolitan genus with diverse lifestyles and nutritional modes, including mycotrophy, saprophytism, and endophytism. Previous research has reported greater metabolic gene repertoires in endophytic fungal species compared to closely-related non-endophytes. However, the extent of this ecological trend and its underlying mechanisms are unclear. Some endophytic fungi may also be mycotrophs and have one or more mycoparasitism mechanisms. Mycotrophic endophytes are prominent in certain genera like Trichoderma, therefore, the mechanisms that enable these fungi to colonize both living plants and fungi may be the result of expanded metabolic gene repertoires. Our objective was to determine what, if any, genomic features are overrepresented in endophytic fungi genomes in order to undercover the genomic underpinning of the fungal endophytic lifestyle. Here we compared metabolic gene cluster and mycoparasitism gene diversity across a dataset of thirty-eight Trichoderma genomes representing the full breadth of environmental Trichodermas diverse lifestyles and nutritional modes. We generated four new Trichoderma endophyticum genomes to improve the sampling of endophytic isolates from this genus. As predicted, endophytic Trichoderma genomes contained, on average, more total biosynthetic and degradative gene clusters than non-endophytic isolates, suggesting that the ability to create/modify a diversity of metabolites potential is beneficial or necessary to the endophytic fungi. Still, once the phylogenetic signal was taken in consideration, no particular class of metabolic gene cluster was independently associated with the Trichoderma endophytic lifestyle. Several mycoparasitism genes, but no chitinase genes, were associated with endophytic Trichoderma genomes. Most genomic differences between Trichoderma lifestyles and nutritional modes are difficult to disentangle from phylogenetic divergences among species, suggesting that Trichoderma genomes maybe particularly well-equipped for lifestyle plasticity. We also consider the role of endophytism in diversifying secondary metabolism after identifying the horizontal transfer of the ergot alkaloid gene cluster to Trichoderma.

genomics↗

bioRxiv2023

Let there be nightlights: the ecological role of bioluminescence in a Costa Rican mushroom

Both marine and terrestrial organisms produce light enzymatically in a process called bioluminescence. Though the ecological role of light production is known for some species, such as fireflies and bacteria, the ecological role in mushroom-producing fungi remains relatively unexplored, particularly in Central America. Here, we discovered a bioluminescent mushroom in the high-elevation oak forests of Costa Rica. We developed mushroom models with Light-Emitting Diodes (LEDs) producing various colors: green, blue, red, and yellow. Over three consecutive evenings after sunset, we applied Tanglefoot invertebrate-trapping glue to both mushroom models and actual mushrooms, and collected the traps before sunrise, then identified the trapped invertebrates to Order. We found green LED traps attracted more invertebrates than non-lit control traps, suggesting that light functions to attract invertebrates. The majority of invertebrates attracted to the green lights were Dipteran flies, who would be capable of dispersing fungal spores. The higher-intensity green LEDs attracted more total invertebrates than the dimmer mushrooms, but the results were not significant. Though we predicted that the invertebrate assemblages attracted to green lights would be similar to the invertebrate assemblage attracted to actual mushrooms, the results were not significant. Similarly, the red, blue, and yellow LEDs attracted fewer invertebrates than the green LEDs, but the differences in community composition were not statistically significant. Our findings corroborate other similar studies in tropical regions that found bioluminescent mushrooms may attract invertebrates.

ecology↗

bioRxiv2022

Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica

Through nondestructive techniques, we studied the physicochemical characteristics and mycobiota of five key historic documents from Costa Rica, including the Independence Act of Costa Rica from 1821. We determined that for documents dated between 1500 and 1900 (i.e., the Cloudy Days Act, the Independence Act, and two documents from the Guatemalan Series from 1539 and 1549), the paper composition was cotton, whereas the 1991 replicate of the Political Constitution from 1949 was made of wood cellulose with an increased lignin content. We also determined that the ink employed in 1821 documents is ferrogallic, i.e., formed by iron sulfate salts in combination with gallic and tannic acids. In total, 22 fungal isolates were obtained: 15 from the wood-cellulose-based Political Constitution and seven from the other three cotton-based documents. These results suggest that cotton-based paper is the most resistant to microbial colonization. Molecular identifications using three DNA markers (i.e., ITS nrDNA, beta-tubulin, and translation elongation factor 1-alpha) classified the isolates in eight orders and ten genera. The most frequent genera were Cladosporium, Penicillium, and Purpureocillium. Of the isolates, 95% presented cellulolytic activity correlated to their ability to cause deterioration of the paper. This work increases the knowledge of the fungal diversity that inhabits historic documents and its relationship with paper composition and provides valuable information to develop strategies to conserve and restore these invaluable documents.

microbiology↗

bioRxiv2019

A missing link in mutualistic networks: symbiotic fungi in plant-animal interactions

We explored the hypothesis of an indirect mutualistic relationship (i.e., when the association between two species is modified by a third one) within a plant-animal seed dispersal network. Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits they may disperse not only the plants seeds, but also the endosymbiotic fungi within those fruits. We characterized fungal communities in fruits of Ficus colubrinae and in feces of Ectophylla alba to determine if passage through the digestive tract of the bats affected the total mycobiome. Results show a significant reduction, after passage through the gut, of fungi known to be plant pathogenic, while abundance of species known to have beneficial properties significantly increased. These findings suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they also promote the dispersal of potentially beneficial microbial symbionts while hindering those that can cause plant disease.

ecology↗