First insights into the prokaryotic community structure of Lake Cote, Costa Rica: influence on nutrient cycling

This article is part of the Research Topic: Rising Stars in Aquatic Microbiology: 2022Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems

Evaluación de la capacidad de cepas de cianobacterias (Cyanophyta) en la remoción de agroquímicos utilizados en la industria piñera de Costa Rica

Tesis (licenciatura en biología con énfasis en biotecnología y biología molecular)UCR::Vicerrectoría de Docencia::Ciencias Básicas::Facultad de Ciencias::Escuela de Biologí

Análisis metagenómico de fuentes termales de Costa Rica: potencial fuente de enzimas hidrolíticas termoestables

En el presente estudio independiente de cultivo, se investigó a nivel taxonómico y funcional las comunidades microbianas de seis metagenomas de fuentes termales cercanas a la Cordillera de Tilarán, volcán Miravalles, volcán Rincón de la Vieja y zona sur, y datos de 13 metagenomas de fuentes termales del Parque Nacional Yellowstone, Nueva Zelanda y Chile. Se obtuvieron en total 229 Gbp de secuencias cortas obtenidas con la plataforma Illumina. Los resultados de la comparación del perfil taxonómico muestran que los tapetes microbianos de Chile y Costa Rica tienen 60% similitud, junto a las muestras de Nueva Zelanda que provienen de agua filtrada, siendo Proteobacteria, Firmicutes y en algunas muestras Cyanobacteria y Chloroflexi los filos más abundantes. Se creó una base de datos de potenciales enzimas hidrolíticas tales como peptidasas, amilasas, lipasas y esterasas, así como enzimas involucradas en la remoción de metales pesados y agroquímicos. La base de datos tiene más de 48 000 secuencias, muchas de las cuales podrían ser novedosas y objeto de estudios posteriores. La mayoría de las secuencias tienen un porcentaje de identidad entre el 70% y el 90% con las de microorganismos que toleran altas temperaturas, lo que sugiere que podrían tener funciones similares. Muchas de las enzimas encontradas dentro de estas categorías tienen una función housekeeping, por lo que son muy importantes para el mantenimiento de las funciones básicas de las células, sin embargo, podrían participar en los procesos de degradación e hidrólisis de herbicidas y diversos xenobióticos. En los MAGs obtenidos se encontraron genes que participan en el transporte, acumulación y oxidación-reducción de arsénico, cobre, plomo, hierro, aluminio y los herbicidas paraquat y atrazina, estos resultados sugieren la presencia de diversos mecanismos celulares, que les confieren a estos microorganismos resistencia/tolerancia a alta concentraciones de estos metales o por el contrario tienen mecanismos para poder obtenerlos cuando las concentraciones son muy bajas. Este estudio proporcionó un primer acercamiento diversidad funcional de los microorganismos que habitan estos sitios, las secuencias encontradas en este estudio podrían utilizarse para futuras investigaciones en el área de la biorremediación y la geomicrobiología.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM

Draft Genome Sequences of Two Cyanobacteria Leptolyngbya spp. Isolated from Microbial Mats in Miravalles Thermal Spring, Costa Rica

We report the draft genome sequences of Leptolyngbya sp. strain 7M and Leptolyngbya sp. strain 15MV, isolated from Miravalles Thermal Spring, Costa Rica. The thermophilic cyanobacteria exhibit unique diversity features that provide insight into the adaptation and evolution of phototrophic microorganisms in geothermal habitats.Universidad de Costa Rica/[801-C0054]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de Agronomí

Raoultella terrigena y Pectobacterium carotovorum en hortalizas en dos provincias de Costa Rica

Introduction. Soft rot in crops is caused by a group of bacteria capable of secreting enzymes that degrade pectin in the cell wall of the plants and causes significant economic losses in agriculture worldwide. In Costa Rica, there is few data available about the distribution, hosts, and genetic diversity of the causal agents of disease. Objective. To identify the presence of bacteria causing soft rot in vegetables located in Cartago and Alajuela using molecular and enzymatic analysis, and pathogenicity techniques. Materials and methods. The study was carried out between July and October 2017 in Cartago and Alajuela, Costa Rica. Plants with soft roth symptoms were collected: sweet chili (Capcicum annum), onion leaves and bulbs (Allium cepa), zucchini plants (Cucurbita pepo), tomato fruits (Solanum lycopersicum), and potato plants (Solanum tuberosum). Bacterial isolation was performed on a selective violet crystal and pectate (CVP) medium. Hypersensitive reaction (RH) tests were performed, the isolates were inoculated into sweet chili leaves and pathogenicity tests (Koch´s postulates) were carried out for the positive bacteria. The isolates were identified by the 16S RNA-Ribosomal gene. Results. Five bacteria with pectinolytic activity were isolated: Pt1-A, 6-M2, Ech2A, CfspA, and Cfsab. According to the pathogenicity analysis, CfspA, Cfsab, and Ech2A strains were causal agents of soft rot in chile. It was not possible to reproduce the symptoms in onion and potato. According to the molecular identification, CfspA and Cfsab strains were classified within the Pectobacterium carotovorum clade, while Ech2A was classified as Raoultella terrigena. Conclusion. Raoultella and Pectobacterium carotovorum were considered the causal agents of soft rotting of chili in the areas of Cartago and Alajuela respectivelyIntroducción. La pudrición blanda en los cultivos es causada por un grupo de bacterias capaces de secretar enzimas que degradan la pectina de la pared celular de las plantas y ocasionan pérdidas económicas importantes en la agricultura a nivel mundial. En Costa Rica existe poca información acerca de la distribución, hospederos y diversidad genética de los agentes causales de esta enfermedad. Objetivo. Identificar la presencia de bacterias causantes de pudrición blanda en hortalizas de la zona de Cartago y Alajuela con análisis moleculares, enzimáticos y técnicas de patogenicidad. Materiales y métodos. El estudio se llevó a cabo entre julio y octubre de 2017 en Cartago y Alajuela, Costa Rica. Se recolectaron plantas con síntomas de pudrición blanda en: chile dulce (Capcicum annum), hojas y bulbos de cebolla (Allium cepa), plantas de zucchini (Cucurbita pepo), frutos de tomate (Solanum lycopersicum) y plantas de papa (Solanum tuberosum). Se realizaron aislamientos bacterianos en un medio selectivo de cristal violeta y pectato (CVP). Se efectuaron ensayos de reacción hipersensible (RH), los aislamientos se inocularon en hojas de chile dulce y se llevaron a cabo pruebas de patogenicidad (postulados de Koch) para las bacterias positivas. Los aislamientos se identificaron molecularmente mediante el gen ARN-Ribosomal 16S. Resultados. Se aislaron cinco bacterias con actividad pectinolítica: Pt1-A, 6-M2, Ech2A, CfspA y Cfsab. Según el análisis de patogenicidad, las cepas CfspA, Cfsab y Ech2A fueron causantes de pudrición blanda en chile. No se logró reproducir los síntomas en cebolla y papa. De acuerdo con la identificación molecular, las cepas CfspA y Cfsab se clasificaron dentro del clado de Pectobacterium carotovorum, mientras que Ech2A se clasificó como Raoultella terrigena. Conclusión. Las bacterias Raoultella terrigena y Pectobacterium carotovorum se consideraron los agentes causales de pudrición blanda del chile en las zonas de Cartago y Alajuela, respectivamente

Tolerance and sorption of Bromacil and Paraquat by thermophilic cyanobacteria Leptolyngbya 7M from Costa Rican thermal springs

We studied the adsorption ability and tolerance of the thermophilic filamentous cyanobacteria Letolyngbya 7M towards Paraquat and Bromacil. Adsorption isotherms at pH = 7.0 showed an adsorption capacity of 24.4 mg/g and 66.8 mg/g, respectively, and a good fit to the Langmuir model (R2 = 0.97 and 0.99, respectively). To evaluate the effect of both herbicides on photosynthetic pigments and viability of cyanobacteria, cell autoflorescence and esterase activity was determined using flow cytometry. Autofluorescence was less sensitive to changes in cell viability, as it was only slightly reduced at high Paraquat and Bromacil concentrations. Herbicide effect on esterase activity is dose-dependent. Bromacil did not cause a significant effect on either chlorophyll a content or cell viability. This study demonstrates the potential of Leptolyngbya 7M to remove Paraquat and Bromacil herbicides from aqueous solution under laboratory conditions.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM

Calidad de ensilado y diversidad bacteriana de los silos inoculados con Listeria monocytogenes y Lacticaseibacillus paracasei_6714

Introduction: King grass (Cenchrus purpureus (Schumach.) Morrone, syn. Pennisetum purpuphoides) and pineapple peel (Ananas comosus) silages are food alternatives for livestock in conditions of feed shortage. Objective: To describe the dynamics of the microbiota present in king grass and pineapple silage during the fermentation process using next generation sequencing (NGS) and to evaluate the protective effect of Lacticaseibacillus paracasei_6714 as a silage inoculum against Listeria monocytogenes. Methods: We used an unrestricted randomized design to characterize the microbiota present in silages made from king grass harvested 70 days after regrowth and pineapple peel. We inoculated mixtures of grass and peel with L. paracasei_6714 or L. monocytogenes, or both, with a non-inoculated treatment as control. The nutritional and fermentative profile was evaluated after 30 days. After 15 and 30 days of fermentation, we used 16S rRNA analysis to determine the dynamics and diversity of the microbiota in the inoculated and control silages. Result: Dry matter content and digestibility did not differ significantly; however, there were differences in crude protein, pH and organic acids. We obtained 4432 amplicon sequence variants of Proteobacteria, Firmicutes, Bacterioidetes, Actinobacteria, Verrucomicrobia, Planctomycetes and Patescibacteria. The relative abundance of each phylum varied depending on the material and fermentation period. Phylum similarity was over 70 % (but not greater than 50 % with Bray-Curtis at the species level). Conclusion: These bacterial communities seem to have an important role during silage fermentation. Proper management of silage processing can reduce or eliminate pathogenic bacteria.Introducción: Los ensilajes del pasto king grass (Cenchrus purpureus (Schumach.) Morrone, syn. Pennisetum purpuphoides) y cáscaras de piña (Ananas comosus) son alternativas de alimento para ganado en condiciones de escasez alimentaria. Objetivo: Describir las dinámicas de la microbiota presente en los ensilajes de king grass y piña durante el pro ceso de fermentación usando secuenciación de próxima generación (NGS) y evaluar el efecto de protección de Lacticaseibacillus paracasei_6714 como inoculante de ensilaje ante Listeria monocytogenes. Métodos: Usamos un diseño aleatorio no restringido para caracterizar la microbiota presente en ensilajes de king Grass cosechados 70 días después de rebrote y de cáscaras de piña. Inoculamos mezclas de pasto y cáscara con L. paracasei_6714 o L. monocytogenes, o ambos, con un tratamiento control sin inocular. El perfil nutricional y de fermentación fue evaluado luego de 30 días. Después de 15 y 30 días de fermentación, usamos un análisis de para determinar la dinámicas y diversidad de la microbiota en los ensilajes inoculados y control. Resultado: Los contenidos de materia seca y digestibilidad, no difirieron significativamente; sin embargo, hubo diferencias en proteína cruda, pH y ácidos orgánicos. Obtuvimos 4 432 secuencias variantes de ampli con de Proteobacteria, Firmicutes, Bacterioidetes, Actinobacteria, Verrucomicrobia, Planctomycetes y de Patescibacteria. La abundancia relativa de cada filo vario dependiendo del material y periodo de fermentación. Similitudes de filo fueron mayores al 70 % (pero no mayor que 50 % con Bray-Curtis a nivel de especie). Conclusión: Estas comunidades bacterianas parecen cumplir un papel importante durante la fermentación del ensilaje. Un manejo apropiado del proceso de ensilaje puede reducir o eliminar baterías patogénicas.Universidad de Costa Rica/[735-B5-505]/UCR/Costa RicaUniversidad de Costa Rica/[735-B9-457]/UCR/Costa RicaUCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de ZootecniaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro Nacional de Ciencia y Tecnología de Alimentos (CITA)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA)UCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de Tecnología de AlimentosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigación en Nutrición Animal (CINA

Novel Cyanobacterial Diversity Found in Costa Rican Thermal Springs Associated with Rincon de la Vieja and Miravalles Volcanoes: A Polyphasic Approach

Central America is one of the most important biodiversity hot spots in the world, and Costa Rican microbial communities from thermal springs are the best characterized in the isthmus. Miravalles is an inactive quaternary stratovolcano, and the Rincón de la Vieja is a unique active volcano, in whose slopes diverse hydrothermal springs, such as Las Lilas, are located. These springs harbor extensive microbial mats, whose diversity has been studied. Based on their importance as primary producers, in this study we focused on cultured cyanobacterial diversity from two geothermal environments of northern Costa Rica. Several cultural, molecular and taxonomic techniques were employed to maximize the results of a polyphasic approach. Sample collection sites were physicochemically described, and strains were isolated and characterized by light and electron microscopy. Phylogenetic analysis was performed using 16S rRNA gene sequences and amplified ribosomal DNA restriction analysis (ARDRA). Fifty‐six phylotypes were isolated and classified into 21 morphotypes and identified in 14 genera, some of them might be new species within these genera. Furthermore, according to phylogenetic analysis, there are three possible new genera in our collection. Miravalles and Las Lilas thermal springs are reservoirs of novel phylogeographic lineages of phototrophic microorganisms. This study is the first report of strains that belong to the genera Gloeocapsa, Stanieria, Microseira, Klisinema and Oculatella isolated from thermal springs and growing at temperatures above 50°C. We also obtained isolates assigned to Synechococcus, Leptolyngbya spp., and Fischerella, which are considered typical strains in these environments.Volkswagen Foundation[I/78 136]//AlemaniaUniversidad de Costa Rica/[801-A3-516]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM

Valorization of cow manure: Unraveling bacterial community changes driven by vermicomposting and their impact on vermicompost tea production

Vermicomposting is utilized to valorize agricultural residues, including excess manure from dairy farms. The microbiome diversity of vermicompost contributes to its numerous beneficial characteristics. However, it remains unstudied whether teas derived from cow manure vermicompost, even with additives, preserve this microbiome. To respond that, we analyzed the dynamics of bacterial communities in the vermicomposting of precomposted dairy manure, and derived vermicompost teas with and without molasses, using 16S rRNA amplicon sequencing and bioinformatics. Communities of fresh and precomposted manure were dominated by rumen-dwelling and excreta bacteria from the Firmicutes and Bacteroidetes and shared a Bray–Curtis similarity of 71.0% at the genus-level. Precomposting resulted in a decline in the relative abundance of dominant genera, including coliforms. Vermicomposting enhanced diversity and led to a notable shift in the bacterial community composition, as indicated by an 87.0% dissimilarity at the genus-level seen between manure and vermicompost samples. Vermicompost predominantly comprised cellulolytic, nitrogen-fixing, and complex organic compound-degrading bacteria from the Proteobacteria and Bacteroidetes. Production of vermicompost tea did not significantly alter the diversity and bacterial composition of the tea, although pseudomonads and clostridia displayed higher relative abundances. Addition of molasses had a drastic impact, reducing diversity, abundance, and community structure, favoring the proliferation of Acinetobacter and Aeromonas, which collectively accounted for 78.0% of the sequences. In summary, vermicomposting significantly shifted the bacterial community of excreta. The tea retained the diversity and core community of the vermicompost, however, the addition of molasses negatively affected diversity and facilitated the growth of specific gamma-proteobacteriaUniversidad de Costa Rica/[733-A1-821]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigación en Nutrición Animal (CINA)UCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de ZootecniaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET)UCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de Agronomí

Valorization of cow manure: Unraveling bacterial community changes driven by vermicomposting and their impact on vermicompost tea production

Vermicomposting is utilized to valorize agricultural residues, including excess manure from dairy farms. The microbiome diversity of vermicompost contributes to its numerous beneficial characteristics. However, it remains unstudied whether teas derived from cow manure vermicompost, even with additives, preserve this microbiome. To respond that, we analyzed the dynamics of bacterial communities in the vermicomposting of precomposted dairy manure, and derived vermicompost teas with and without molasses, using 16S rRNA amplicon sequencing and bioinformatics. Communities of fresh and precomposted manure were dominated by rumen-dwelling and excreta bacteria from the Firmicutes and Bacteroidetes and shared a Bray-Curtis similarity of 71.0 % at the genus-level. Precomposting resulted in a decline in the relative abundance of dominant genera, including coliforms. Vermicomposting enhanced diversity and led to a notable shift in the bacterial community composition, as indicated by an 87.0 % dissimilarity at the genus-level seen between manure and vermicompost samples. Vermicompost predominantly comprised cellulolytic, nitrogen-fixing, and complex organic compound-degrading bacteria from the Proteobacteria and Bacteroidetes. Production of vermicompost tea did not significantly alter the diversity and bacterial composition of the tea, although pseudomonads and clostridia displayed higher relative abundances. Addition of molasses had a drastic impact, reducing diversity, abundance, and community structure, favoring the proliferation of Acinetobacter and Aeromonas, which collectively accounted for 78.0 % of the sequences. In summary, vermicomposting significantly shifted the bacterial community of excreta. The tea retained the diversity and core community of the vermicompost, however, the addition of molasses negatively affected diversity and facilitated the growth of specific gamma-proteobacteria.Universidad de Costa Rica/[733-A1-821]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA)UCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de AgronomíaUCR::Vicerrectoría de Docencia::Ciencias Agroalimentarias::Facultad de Ciencias Agroalimentarias::Escuela de ZootecniaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biodiversidad y Ecología Tropical (CIBET