Biology subjects

Chavarria, M.

Publications and source records attributed to Chavarria, M..

13 recordsLinked to original sources

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↗

bioRxiv2022

Production of selenium nanoparticles occurs through an interconnected pathway of sulfur metabolism and oxidative stress response in Pseudomonas putida KT2440

The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulfur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to converting selenite into selenium. On the other hand, mutants affecting the activity of sulfite reductase reduced the bacterias ability to transform selenite. Other genes related to sulfur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformations. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria, and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.

microbiology↗

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↗

bioRxiv2022

Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths

Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. In addition, we isolated nine strains of Brevibacterium and Rothia able to produce substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales inhabiting sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem.

microbiology↗

bioRxiv2022

Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river

Rio Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study suggested that this color is not caused by dissolved chemical species, but by precipitation of lightscattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Rio Buenavista. We now present microbiological information on Rio Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Rio Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids with Quebrada Agria as the main contributor to the phenomenon, with Rio Buenavista acting as a secondary source of silica to the reaction. We also show how the sky-blue color of Rio Celeste arises from the tight interaction between chemical and biological processes. Sulfur-oxidizing bacteria generate an acidic environment in Quebrada Agria, which in turn cause dissolution and mobilization of aluminum and other metals, while in Rio Buenavista the growth of diatoms transforms dissolved silicon into colloidal biogenic forms. The local interaction between these two well-known biological activities gives rise to the unique Rio Celeste phenomenon, in what constitutes a textbook example of emergent behavior in environmental microbiology.

microbiology↗

bioRxiv2020

Rapid shift in microbial community structure in a neutral hydrothermal hot spring from Costa Rica

In this work, we characterize the geochemistry and microbial community of Bajo las Penas, a neutral (pH 6.5-7.4), hot spring (T = 62.0-68.0{degrees}C) located near Turrialba Volcano, Costa Rica. The microbiota at its two sources belongs mainly to the family Aquificae, comprising OTUs closely related to the genera Sulfurihydrogenibium, Thermosulfidibacter, Thermodesulfovibrio and Thermocrinis which is consistent with the presence of moderate levels of sulfate (243-284 mg/L) along the stream. We determined a dramatic shift in the microbial community just a few meters downstream of the sources of the hot spring (15-20 meters), with a change from sulfur related chemoautotrophic (e.g. Sulfurihydrogenibium and an OTU closely related to Thermodesulfovibrio) to chemoheterotrophic prokaryotes (e.g. Meiothermus, Nitrososphaera, Thermoflexus, Thermus). Thus, in this neutral hot spring, the first level of the trophic chain is associated with photosynthesis as well other anaerobic CO2 fixing bacteria. Then, thermotolerant chemoheterotrophic bacteria colonize the environment to degrade organic matter and use fermentative products from the first level of the trophic chain. Our data demonstrate how quickly the microbial community of an ecosystem can change in response to environmental variables and sheds light on the microbial ecology of less common circumneutral pH hot springs.

microbiology↗

bioRxiv2020

Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments

Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microbial communities to early planet life conditions such as high temperatures, high metal concentrations, and low pH. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in the Central Volcanic mountain range of Costa Rica. Both locations hold a very low pH (pH 1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO42- = 1170-2460 mg/L measured as S), but significant differences in their temperature (90.0-95.0{degrees}C in the seepages at Poas Volcano versus 19.1-26.6 {degrees}C in Agrio River) and in the abundance of elemental sulfur. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp., sulfur-oxidizing bacteria, represented more than half (58.4-78.4%) of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by the iron- and sulfur-oxidizing Leptospirillum (7.4-55.5%) and members of the archeal order Thermoplasmatales (16.0-58.2%). Both environments share some chemical characteristics and part of their microbiota, however the temperature and the presence of reduced sulfur are likely the main distinguishing feature ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.

microbiology↗

bioRxiv2020

C1 compounds shape the microbial community of an abandoned century-old oil exploration well.

The search for microorganisms that degrade hydrocarbons is highly relevant because it enables the bioremediation of these substances cheaply and without dangerous by-products. In this work, we studied the microbial communities of an exploratory oil well, abandoned a century ago, located in the Cahuita National Park of Costa Rica. Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including C2-dibenzothiophene, phenanthrene or anthracene, fluoranthene pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria (Methylobacillus (6.3-26.0 % of total reads) and Methylococcus (4.1-30.6 %)) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6 %), Hydrogenophaga (1.5-3.3 %) Rhodobacter (1.0-4.9 %) and Flavobacterium (1.1-6.5 %). We evidenced the presence of methane monooxygenase (MMO) activities, responsible for the first step in methane metabolism, by amplifying the pmo gene from environmental DNA. We also isolated a strain of Methylorubrum rhodesianum, which was capable of using methanol as its sole carbon source. This work represents a contribution to the understanding of the ecology of communities of microorganisms in environments with permanently high concentrations of methane and hydrocarbons, which also has biotechnological implications for the bioremediation of highly polluting petroleum components.

microbiology↗

bioRxiv2020

The putative phosphate transporter PitB (PP1373) is involved in tellurite uptake in Pseudomonas putida KT2440

Tellurium oxyanions are chemical species with great toxicity; their presence in the environment has increased because of mining industries and photovoltaic and electronic waste. Recovery strategies based on microorganisms for this metalloid are of interest, but further studies of the transport systems and enzymes responsible for implementing tellurium transformations are required because many mechanisms remain unknown. Here, we investigated the involvement in tellurite uptake of the putative phosphate transporter PitB (PP1373) in soil bacterium Pseudomonas putida KT2440. For this purpose, through a method based on the CRISPR/Cas9 system, we generated a strain deficient in pitB gene and characterized its phenotype on exposing it to varied concentrations of tellurite. Growth curves and Transmission Electronic Microscopy experiments of wild type and {Delta}pitB showed that both strains were able to internalize tellurite into the cytoplasm and reduce the oxyanion to black nano-sized and rod-shaped tellurium particles, however, {Delta}pitB strain showed an increased resistance to the tellurite toxic effects. At a concentration of 100 uM tellurite, where the biomass formation of wild type strain decreased by half, we observed a greater ability of {Delta}pitB to reduce this oxyanion with respect to wild type strain (~38% vs ~16%), which is related by the greater biomass production of {Delta}pitB and not by a greater consumption of tellurite per cell. The phenotype of the mutant was restored on over-expressing pitB in trans. In summary, our results indicate that PitB is one of several transporters responsible for tellurite uptake in P. putida KT2440.

microbiology↗

bioRxiv2020

Redox stress reshapes carbon fluxes of Pseudomonas putida for cytosolic glucose oxidation and NADPH generation

The soil bacterium and metabolic engineering platform Pseudomonas putida tolerates high levels of endogenous and exogenous oxidative stress, yet the ultimate reason of such property remains unknown. To shed light on this question, NADPH generation routes--the metabolic currency that fuels redox stress responses--were assessed when P. putida KT2440 was challenged with H2O2 as proxy of oxidative conditions. 13C-tracer experiments, metabolomics and flux analysis, together with inspection of physiological parameters and measurement of enzymatic activities, revealed a substantial flux reconfiguration under oxidative stress. In particular, periplasmic glucose processing was rerouted to cytoplasmic oxidation, and cyclic operation of the pentose phosphate pathway led to significant NADPH fluxes, exceeding biosynthetic demands by ~50%. This NADPH surplus, in turn, fuelled the glutathione system for H2O2 reduction. These properties not only contribute to the tolerance of P. putida to environmental stresses, but they also highlight the value of this host for harsh biotransformations.

microbiology↗

bioRxiv2019

Untapped microbial composition along a horizontal oxygen gradient in a Costa Rican volcanic influenced acid rock drainage system

Based on the analysis of 16S rRNA gene metabarcoding, here we report the shift in the microbial community structure along a horizontal oxygen gradient (0.40-6.06 mg L-1) in a volcanic influenced acid rock drainage (VARD) environment, known as San Cayetano (Cartago, Costa Rica; pH =2.94-3.06, sulfate ~0.87-1.19 g L-1, iron ~35-61 mg L-1). This VARD is dominated by microorganisms involved in the geochemical cycling of iron, sulfur and nitrogen; however, the identity of the species changes with the oxygen gradient along the river course. The anoxic spring of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium as well as sulfur-oxidizing bacteria (such as Acidithiobacillus or Sulfobacillus), which favor the process of dissolution of sulfide minerals and oxidation of H2S. In oxic conditions, aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferritrophicum, Ferrovum) and heterotrophic bacteria (Burkholderiaceae Betaproteobacterium, Trichococcus, Acidocella) were identified among others. Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD/AMD niches were also found throughout the entire ecosystem. This work describes the changes in bacterial diversity, and possible metabolic activities occurring along a horizontal oxygen gradient in a volcanic influenced acid rock drainage system.

microbiology↗

bioRxiv2019

Bocaparvovirus, Erythroparvovirus and Tetraparvovirus in New World Monkeys from Central America

Parvoviruses in the genera Bocaparvovirus (HBoV), Erythroparvovirus (B19) and Tetraparvovirus (PARV4) are the only autonomous parvoviruses known to be associated with human and non-human primates based on studies and clinical cases in humans worldwide and non-human primates in Asia and Africa. Here, the presence of these pathogenic agents was assessed by PCR in blood and feces from 55 howler monkeys, 112 white-face monkeys, 3 squirrel monkeys, and 127 spider monkeys in Costa Rica and El Salvador. Overall, 3.7% of the monkeys had HboV DNA, 0.67% had B19 DNA, and 14.1% had PARV4 DNA, representing the first detection of these viruses in New World monkeys. Sex was significantly associated with the presence of HBoV, males having risk up to nine times compared with females. Captivity was associated with increased prevalence for PARV4 and when all viruses were analyzed together. This work underscores the importance of future research aimed at understanding how these viruses behave in natural environments of the Neotropics, and what variables may favor their presence and transmission.

epidemiology↗