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Galiano-Murillo F, Salas-Lara V, Echandi C, Brenes-Guillén L, Uribe-Lorío L. Draft genomes of two phylotype I and II Ralstonia solanacearum species complex (RSSC) isolates causing bacterial wilt in tomato plants from Costa Rica. Microbiol Resour Announc 2024; 13:e0104223. [PMID: 38294216 DOI: 10.1128/mra.01042-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024] Open
Abstract
Bacteria from RSSC hold agricultural significance as they are the causal agents of bacterial wilt. Here, we report the draft genomes of two bacteria extracted from vascular tissues of infected tomato plants. Isolate RALF-MA was classified as Ralstonia pseudosolanacearum (phylotype I) and RALSA-MA as Ralstonia solanacearum (phylotype II).
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Affiliation(s)
- Fiorella Galiano-Murillo
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Vidal Salas-Lara
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Echandi
- Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Agronomía, Universidad de Costa Rica, San José, Costa Rica
| | - Laura Brenes-Guillén
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Lorena Uribe-Lorío
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
- Escuela de Agronomía, Universidad de Costa Rica, San José, Costa Rica
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Barboza N, Brenes-Guillén L, Uribe L, WingChing-Jones R. Silage quality and bacterial diversity of silages inoculated with Listeria monocytogenes and Lacticaseibacillus paracasei_6714. REV BIOL TROP 2023. [DOI: 10.15517/rev.biol.trop..v71i1.50692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
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.
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Brenes-Guillén L, Vidaurre-Barahona D, Avilés-Vargas L, Castro-Gutierrez V, Gómez-Ramírez E, González-Sánchez K, Mora-López M, Umaña-Villalobos G, Uribe-Lorío L, Hassard F. First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling. Front Microbiol 2022; 13:941897. [PMID: 36262328 PMCID: PMC9574093 DOI: 10.3389/fmicb.2022.941897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Prokaryotic 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.
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Affiliation(s)
- Laura Brenes-Guillén
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | | | - Lidia Avilés-Vargas
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | | | - Eddy Gómez-Ramírez
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Kaylen González-Sánchez
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Marielos Mora-López
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Gerardo Umaña-Villalobos
- Research Center in Sciences of the Sea and Limnology, University of Costa Rica, San José, Costa Rica
| | - Lorena Uribe-Lorío
- Cellular and Molecular Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Francis Hassard
- Cranfield Water Science Institute, Cranfield University, Cranfield, United Kingdom
- Institute for Nanotechnology and Water Sustainability, University of South Africa, Johannesburg, South Africa
- *Correspondence: Francis Hassard,
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Brenes-Guillén L, Vidaurre-Barahona D, Morales S, Mora-López M, Sittenfeld A, Uribe-Lorío L. Novel Cyanobacterial Diversity Found in Costa Rican Thermal Springs Associated with Rincon de la Vieja and Miravalles Volcanoes: A Polyphasic Approach. J Phycol 2021; 57:183-198. [PMID: 33000870 DOI: 10.1111/jpy.13077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- Laura Brenes-Guillén
- Molecular and Biology Research Center, University of Costa Rica, San José, Costa Rica
| | | | - Saylen Morales
- Molecular and Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Marielos Mora-López
- Molecular and Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Ana Sittenfeld
- Molecular and Biology Research Center, University of Costa Rica, San José, Costa Rica
| | - Lorena Uribe-Lorío
- Molecular and Biology Research Center, University of Costa Rica, San José, Costa Rica
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Brenes-Guillén L, Fuentes-Schweizer P, García-Piñeres A, Uribe-Lorío L. Tolerance and sorption of Bromacil and Paraquat by thermophilic cyanobacteria Leptolyngbya 7M from Costa Rican thermal springs. J Contam Hydrol 2019; 226:103539. [PMID: 31408829 DOI: 10.1016/j.jconhyd.2019.103539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/18/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Laura Brenes-Guillén
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Costa Rica.
| | - Paola Fuentes-Schweizer
- Centro de Investigación en Electroquímica y Energía Química, Universidad de Costa Rica, Costa Rica; Escuela de Química, Universidad de Costa Rica, Costa Rica
| | - Alfonso García-Piñeres
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Costa Rica; Escuela de Química, Universidad de Costa Rica, Costa Rica
| | - Lorena Uribe-Lorío
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Costa Rica
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Uribe-Lorío L, Brenes-Guillén L, Hernández-Ascencio W, Mora-Amador R, González G, Ramírez-Umaña CJ, Díez B, Pedrós-Alió C. The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica. Microbiologyopen 2019; 8:e893. [PMID: 31271524 PMCID: PMC6813449 DOI: 10.1002/mbo3.893] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 11/27/2022] Open
Abstract
We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.
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Affiliation(s)
- Lorena Uribe-Lorío
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Laura Brenes-Guillén
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Walter Hernández-Ascencio
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, Ciudad Universitaria Rodrigo Facio, San José, Costa Rica
| | - Raúl Mora-Amador
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | - Gino González
- Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa Rica
| | | | - Beatriz Díez
- Departamento de Microbiología y Genética, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Pedrós-Alió
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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Brenes-Guillén L. Kary Mullis: padre de la técnica de la reacción en cadena de la polimerasa (PCR). REV BIOL TROP 2019. [DOI: 10.15517/rbt.v0i3.36951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brenes-Guillén L. Microbioma de la Tierra: análisis de datos a gran escala. REV BIOL TROP 2019. [DOI: 10.15517/rbt.v0i2.36583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brenes-Guillén L. Tara Oceans: explorando el microbioma del océano. REV BIOL TROP 2019. [DOI: 10.15517/rbt.v0i2.36220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Brenes-Guillén L. Ensamblaje y anotación de genomas microbianos. REV BIOL TROP 2019. [DOI: 10.15517/rbt.v0i2.35899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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