Bacterias cultivables resistentes a oxitetraciclina durante el proceso de vermicompostaje de excretas bovinas

Introducción: A nivel mundial se han detectado bacterias con genes de resistencia al antibiótico oxitetraciclina en estiércol de vacas lecheras, sin embargo, es una práctica común utilizar este estiércol como fertilizante. El vermicompostaje puede reducir el problema, pero este tema no ha sido evaluado en Costa Rica. Objetivo: Analizar la presencia de bacterias resistentes a la oxitetraciclina durante el vermicompostaje en una finca lechera costarricense. Métodos: A partir de estiércol fresco, precompostado, lombricomposta, y tés de composta con y sin melaza y tés de composta con y sin melaza, inoculamos caldos suplementados con oxitetraciclina. Extrajimos el ADN de estos cultivos líquidos y secuenciamos en masa el amplicón ribosómico 16S. Resultados: Clasificamos 105 292 secuencias en 58 variantes de secuencia de amplicón de caldos suplementados con oxitetraciclina, la mayoría identificadas como Proteobacteria, Bacteroidetes y Firmicutes. El estiércol fresco tuvo más bacterias resistentes (32), seguido de los “tés” sin y con melaza. El precompostaje y el vermicompostaje disminuyeron la cantidad y variedad de bacterias resistentes. Sin embargo, la preparación de los tés provocó la multiplicación de géneros bacterianos reconocidos por su capacidad de acumular determinantes de resistencia. Conclusión: El precompostaje y el vermicompostaje disminuyeron el número y tipo de bacterias resistentes.

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

Caracterización del hábitat de nematodos entomopatógenos aislados de fincas bananeras de la Región del Caribe Costarricense

Vidaurre Barahona, D. (2016). Caracterización del hábitat de nematodos entomopatógenos aislados de fincas bananeras de la Región del Caribe Costarricense. [Tesis de Licenciatura]. Universidad Nacional, Heredia, C.R.Dentro de la producción agrícola de Costa Rica, el banano es uno de los cultivos más importantes en lo que respecta a producción y exportaciones; por lo tanto, es necesario la aplicación de agroquímicos para controlar el efecto de plagas en la plantación, tal como el escarabajo Cosmopolites sordidus. Debido a los efectos perjudiciales del uso de pesticidas en la salud humana y ambiental, y la resistencia en los organismos plaga, se han investigado otras alternativas que complementen el efecto de los agroquímicos y a su vez, sean amigables con el ambiente. Los nematodos entomopatógenos de los géneros Heterorhabditis y Steinernema han sido foco de estudio en el campo de control biológico debido a que presentan una relación simbiótica con bacterias de los géneros Photorhabdus y Xenorhabdus, respectivamente, y ambos conforman un complejo capaz de eliminar insectos hospederos en 48 horas. El objetivo de este trabajo fue deteminar la presencia de nematodos entomopatógenos (NEP) de los géneros Heterorhabditis y Steinernema en muestras de suelo tomadas en fincas bananeras del Caribe costarricense y caracterizar el hábitat. Se seleccionaron puntos de muestreo dentro de las plantaciones y zonas aledañas y se realizaron análisis químicos, físicos y microbiológicos (pH, acidez, materia orgánica, Ca, K, Mg, P, Fe, Cu, Zn, Mn, textura, biomasa y respiración microbiana) del suelo. Los resultados demostraron que las variables relacionadas con presencia de nematodos entomopatógenos corresponden a materia orgánica, biomasa de carbono y respiración microbiana. Se encontró que 38,4% de las muestras fueron positivas con respecto a la presencia de NEP, de las cuales el 95% correspondía al género Steinernema, y el 5% restante, a Heterorhabditis. No fueron evidentes diferencias estadísticas entre los hábitats de muestreo seleccionados, por lo tanto se determinó que las tres variables mencionadas anteriormente presentan influencia en lo que respecta la presencia de nematodos entomopatógenos y valores altos de las mismas, indican condiciones favorables para su persistencia.Within Costa Rica's agricultural production, bananas are one of the most important crops in terms of production and exports; therefore, the application of agrochemicals is necessary to control the effect of pests in the plantation, such as the Cosmopolites sordidus beetle. Due to the detrimental effects of the use of pesticides on human and environmental health, and the resistance in pest organisms, other alternatives have been investigated that complement the effect of agrochemicals and, in turn, are friendly to the environment. Entomopathogenic nematodes of the genera Heterorhabditis and Steinernema have been the focus of study in the field of biological control because they present a symbiotic relationship with bacteria of the genera Photorhabdus and Xenorhabdus, respectively, and both form a complex capable of eliminating host insects in 48 hours. The objective of this work was to determine the presence of entomopathogenic nematodes (NEP) of the genera Heterorhabditis and Steinernema in soil samples taken from banana farms in the Costa Rican Caribbean and to characterize the habitat. Sampling points were selected within the plantations and surrounding areas and chemical, physical and microbiological analyzes were carried out (pH, acidity, organic matter, Ca, K, Mg, P, Fe, Cu, Zn, Mn, texture, biomass and respiration). microbial) from the soil. The results showed that the variables related to the presence of entomopathogenic nematodes correspond to organic matter, carbon biomass and microbial respiration. It was found that 38.4% of the samples were positive regarding the presence of NEP, of which 95% corresponded to the genus Steinernema, and the remaining 5% to Heterorhabditis. There were no evident statistical differences between the selected sampling habitats, therefore it was determined that the three variables mentioned above have an influence regarding the presence of entomopathogenic nematodes and high values ​​of the same, indicate favorable conditions for their persistence.Universidad Nacional, Costa RicaEscuela de Ciencias Biológica

Erwinia billingiae causes bacterial Canker of Mango (Mangifera indica) in Costa Rica

Introduction. In Costa Rica, bacterial canker of mango has caused economic losses in most of the productive areas since the mid-1980s. The causal agents have been identified only by phenotypic methods such as Erwinia mangifera and E. herbicola. Objective. To confirm, using a molecular and phenotypic approach, the species of the Enterobacteriaceae the cause bacterial canker of mango in Costa Rica. Material and methods. Fruits, branches, and trunks with symptoms were collected in different orchards in the Alajuela province. Bacterial isolation was performed, and pathogenicity was evaluated by inoculating fruits and trunks of the Tommy Atkins variety. The positive isolates for the pathogenic test were re-inoculated, isolated, and identified in order to fulfill Koch’s postulates. The CIBCMMg-115 positive isolate that caused symptoms was analyzed by complete biochemical characterization and molecular identification by phylogenetic analyses of 16S rRNA and the atpD, gyrB, infB, and rpoB housekeeping genes. Results. According to the data obtained from the biochemical and molecular analysis, the CIBCM-Mg-115 strain was identified as Erwinia billingiae. Conclusion. E. billingiae corresponds to one of the causal agents of bacterial canker on mango (M. indica) trees in Costa Rica.Introducción. El cáncer del mango ha ocasionado pérdidas económicas en áreas productivas en Costa Rica desde mediados de los 80. Los agentes causales han sido caracterizados solamente por métodos fenotípicos como Erwinia mangifera y E. herbicola. Objetivo. Confirmar, utilizando un enfoque molecular y fenotípico las especies de enterobacterias causantes del cáncer bacterial del mango en Costa Rica. Materiales y métodos. Se tomaron frutas, ramas y troncos con síntomas en diferentes huertos de la provincia de Alajuela. Se realizó un aislamiento bacteriano y se evaluó la patogenicidad mediante la inoculación de frutos y troncos de la variedad Tommy Atkins Los aislamientos positivos para la prueba de patogenicidad fueron re-inoculados, aislados e identificados para cumplir con los postulados de Koch. El aislado positivo CIBCM-Mg-115 que causó los síntomas fue analizado mediante la caracterización bioquímica completa y la identificación molecular mediante análisis filogenéticos del ARNr 16S y los genes de mantenimiento atpD, gyrB, infB y rpoB. Resultados. De acuerdo con los datos obtenidos a partir de los análisis bioquímicos y moleculares se identificó a la cepa CIBCM-Mg-115 como Erwinia billingiae. Conclusión. E. billingiae corresponde a uno de los agentes causales del cáncer bacteriano del mango (M. indica) en Costa Rica

Edaphic factors and entomopathogenic nematodes in a neotropical banana agroecosystem

Introduction: In Costa Rica the banana is one of the most important crops in terms of production and exports; the application of pesticides is hence necessary to control the effect of pests on the plantation, such as the Cosmopolites sordidus black weevil. Because of the harmful effects of pesticides on human and environmental health, and the possibility that pests become resistant to these substances, alternatives compatible with the environment, as potential biological controllers, have been investigated to complement the effect of agrochemicals. The entomopathogenic nematodes (EPN) of genera Heterorhabditis and Steinernema have become a focus of study in the field of biological control because of their symbiotic relation with bacteria of genera Photorhabdus and Xenorhabdus, which are a complex capable of eliminating host insects in hours. Objective: The objective was to determine the presence of EPN of genera Heterorhabditis and Steinernema in soil samples taken from banana plantations in the Caribbean region of Costa Rica, and to characterize their habitat. Methods: Sampling points were selected within the plantations and surrounding areas; physicochemical and microbiological analyses were undertaken (pH, acidity, organic matter, Ca, K, Mg, P, Fe, Cu, Zn, Mn, texture, biomass and microbial respiration of the soil, EPN isolation). Variables were analyzed statistically to determine differences between them, in sampling sites, and samples with presence and absence of EPN. A principal-component analysis (PCA) was undertaken using the variables of greater influence in both categories to find their combinations that would explain their presence according to habitat conditions. A discriminant analysis was undertaken to determine the efficiency of the variables selected in the diagnosis of nematode occurrence. Results: The variables related to the presence of EPN were shown to correspond to organic matter, carbon biomass and microbial respiration. Of the samples 38.4 % were found to be positive with respect to the presence of EPN, of which 95 % correspond to genus Steinernema and the remaining 5 % to Heterorhabditis. According to the quadratic discriminant equation, from 81.2 % of the samples without nematodes, six belong to the group with their presence, whereas for those with EPN, 55.0 % (nine of 20) belong to the absence group. Conclusions: No statistical difference was found between the selected sampling habitats (P = 0.4296); the three variables mentioned above were thus determined have an influence on the presence of EPN; their large values indicate favorable conditions for their persistence.UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA

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

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

Biogas Production and Microbial Communities of Mesophilic and Thermophilic Anaerobic Co-Digestion of Animal Manures and Food Wastes in Costa Rica

Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina represented the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion

Biogas production and microbial communities of mesophilic and thermophilic anaerobic co-digestion of animal manures and food wastes in Costa Rica

Biomass generated from agricultural operations in Costa Rica represents an untapped renewable resource for bioenergy generation. This study investigated the effects of two temperatures and three mixture ratios of manures and food wastes on biogas production and microbial community structure. Increasing the amount of fruit and restaurant wastes in the feed mixture significantly enhanced the productivity of the systems (16% increase in the mesophilic systems and 41% in the thermophilic). The methane content of biogas was also favored at higher temperatures. Beta diversity analysis, based on high-throughput sequencing of 16S rRNA gene, showed that microbial communities of the thermophilic digestions were more similar to each other than the mesophilic digestions. Species richness of the thermophilic digestions was significantly greater than the corresponding mesophilic digestions (F = 40.08, p = 0.003). The mesophilic digesters were dominated by Firmicutes and Bacteroidetes while in thermophilic digesters, the phyla Firmicutes and Chloroflexi accounted for up to 90% of all sequences. Methanosarcina was the key methanogen and was more abundant in thermophilic digestions. These results demonstrate that increasing digestion temperature and adding food wastes can alleviate the negative impact of low C:N ratios on anaerobic digestion.Universidad de Costa Rica/[733-A1-821]/UCR/Costa RicaUniversidad de Michigan/[]/UMICH/Estados UnidosUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Centro de Investigaciones Agronómicas (CIA)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 Básicas::Centro de Investigación en Electroquímica y Energía Química (CELEQ