Biology subjects

Avendano, R.

Publications and source records attributed to Avendano, R..

9 recordsLinked to original sources

bioRxiv2024

Engineering Intercellular Communication using M13 Phagemid and CRISPR-based Gene Regulation for Multicellular Computing in Escherichia coli

Engineering multicellular consortia, where information processing is distributed across specialized cell types, offers a promising strategy for implementing sophisticated biocomputing systems. However, a major challenge remains in establishing orthogonal intercellular communication, or "wires", within synthetic bacterial consortia. In this study, we address this bottleneck by integrating phagemid-mediated intercellular communication with CRISPR-based gene regulation for multicellular computing in synthetic E. coli consortia. We achieve intercellular communication by regulating the transfer of single guide RNAs (sgRNAs) encoded on M13 phagemids from sender to receiver cells. Once inside the receiver cells, the transferred sgRNAs mediate gene regulation via CRISPR interference. Leveraging this approach, we successfully constructed one-, two-, and four-input logic gates. Our work expands the toolkit for intercellular communication and paves the way for complex information processing in synthetic microbial consortia, with diverse potential applications, including biocomputing, biosensing, and biomanufacturing.

synthetic biology↗

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

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↗

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↗