Browsing by Author "Maldonado, Jonathan "

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    Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils
    (2019) Fernandez-Gomez, Beatriz; Maldonado, Jonathan; Mandakovic, Dinka; Gaete, Alexis; Gutiérrez Ilabaca, Rodrigo Antonio; Maass, Alejandro; Cambiazo, Verónica; González, Mauricio
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    Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia
    (2020) Aguila-Torres, Patricia; Maldonado, Jonathan; Gaete, Alexis; Figueroa, Jaime; Gonzalez, Alex; Miranda, Richard; Gonzalez-Stegmaier, Roxana; Martin, Carolina; Gonzalez, Mauricio
    Pesticides cause severe environmental damage to marine ecosystems. In the last ten years, cypermethrin has been extensively used as an antiparasitic pesticide in the salmon farming industry located in Northern Patagonia. The objective of this study was the biochemical and genomic characterization of cypermethrin-degrading and biosurfactant-producing bacterial strains isolated from cypermethrin-contaminated marine sediment samples collected in southern Chile (MS). Eleven strains were isolated by cypermethrin enrichment culture techniques and were identified by 16S rDNA gene sequencing analyses. The highest growth rate on cypermethrin was observed in four isolates (MS13, MS15a, MS16, and MS19) that also exhibited high levels of biosurfactant production. Genome sequence analyses of these isolates revealed the presence of genes encoding components of bacterial secondary metabolism, and the enzymes esterase, pyrethroid hydrolase, and laccase, which have been associated with different biodegradation pathways of cypermethrin. These novel cypermethrin-degrading and biosurfactant-producing bacterial isolates have a biotechnological potential for biodegradation of cypermethrin-contaminated marine sediments, and their genomes contribute to the understanding of microbial lifestyles in these extreme environments.
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    Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling
    (2018) Carrasco Gálvez, Basilio Alejandro; González, Máximo; Gebauer H., Marlene; García González, Rolando; Maldonado, Jonathan; Silva, Hernan
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    De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina)
    (2016) González, Máximo; Maldonado, Jonathan; Salazar, Erika; Silva, Herman; Carrasco Gálvez, Basilio Alejandro
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    Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures
    (2020) Mandakovic, Dinka; Pulgar, Rodrigo; Maldonado, Jonathan; Mardones, Wladimir; Gonzalez, Mauricio; Cubillos, Francisco A.; Cambiazo, Veronica
    Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential capacities to become starters during fermentation. By using internal transcribed spacer (ITS) amplicon sequencing, we identified the taxonomic structure of the yeast community in unfermented and fermented musts of a typicalVitis viniferaL. var. Sauvignon blanc from the Central Valley of Chile throughout two consecutive seasons of production. Unsurprisingly,Saccharomycesrepresented the most abundant fungal genus in unfermented and fermented musts, mainly due to the contribution ofS. uvarum(42.7%) andS. cerevisiae(80%). Unfermented musts were highly variable between seasons and showed higher values of fungal diversity than fermented musts. Since microbial physiological characterization is primarily achieved in culture, we isolated nine species belonging to six genera of fungi from the unfermented must samples. All isolates were characterized for their potential capacities to be used as new starters in wine. Remarkably, onlyMetschnikowia pulcherrimacould co-exist with a commercialSaccharomyces cerevisiaestrain under fermentative conditions, representing a feasible candidate strain for wine production.
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    Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
    (2020) Mandakovic, Dinka; Cintolesi, Angela; Maldonado, Jonathan; Mendoza, Sebastian N.; Aite, Meziane; Gaete, Alexis; Saitua, Francisco; Allende, Miguel; Cambiazo, Veronica; Siegel, Anne; Maass, Alejandro; Gonzalez, Mauricio; Latorre, Mauricio
    The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (beta -carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.
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    Plant ecological genomics at the limits of life in the Atacama Desert
    (2021) Eshel, Gil; Araus, Viviana; Undurraga, Soledad; Soto, Daniela C.; Moraga, Carol; Montecinos, Alejandro; Moyano, Tomas; Maldonado, Jonathan; Diaz, Francisca P.; Varala, Kranthi; Nelson, Chase W.; Contreras-Lopez, Orlando; Pal-Gabor, Henrietta; Kraiser, Tatiana; Carrasco-Puga, Gabriela; Nilo-Poyanco, Ricardo; Zegar, Charles M.; Orellana, Ariel; Montecino, Martin; Maass, Alejandro; Allende, Miguel L.; DeSalle, Robert; Stevenson, Dennis W.; Gonzalez, Mauricio; Latorre, Claudio; Coruzzi, Gloria M.; Gutierrez, Rodrigo A.
    The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Leji = a transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growthpromoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codonbased methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an Arabidopsis ortholog, we uncovered functional evidence linking them to plant resilience. As some Atacama plants are closely related to staple crops, these candidate PSGs are a "genetic goldmine" to engineer crop resilience to face climate change.
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    Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
    (2018) Mandakovic, Dinka ; Rojas, Claudia; Maldonado, Jonathan ; Latorre, Mauricio ; Travisany, Dante ; Delage, Erwan ; Bihouée, Audrey ; Díaz, Francisca P. ; Latorre, Claudio ; Navarrete, Sergio A.
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    Taxonomy and diversity of bacterial communities associated with marine sediments from Chilean salmonid farms
    (2021) Miranda, Richard M.; Aguila-Torres, Patricia; Aranda, Carlos P.; Maldonado, Jonathan; Casado, Alin
    A marine sediment survey beneath four salmon farms in southern Chile was conducted. 16S rRNA pyrosequencing-based analysis was used to study the taxonomy and diversity of bacterial communities in sediments. Samples were taken under farm cages (study site) and reference (control) sites at different seasons and productive periods. Families associated with phyla Proteobacteria and Bacteroidetes were the most abundant, representing on average 50.7% of the total bacterial community. Flavobacteriaceae was the single family observed in all samples and also the most abundant. Bacterial diversity and richness indices (Chao1, Shannon and PD) at the study sites during productive periods showed a broader range of values than those measured in control or resting stage samples. Also, a very low number of shared families (2/54), compared with those taken at control (13/31) and resting stages (13/45), was observed. Bray-Curtis clustering of libraries resulted in two main clades, one mainly represented by samples of the study site and productive states, dominated by Sulfurovum with low values for bacterial diversity and richness indices and a community structure related to sulphidic sediments, while the other clades, mainly composed by control and resting samples, resulted dominated by Flavobacteriaceae and exhibited higher values of diversity and richness.
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    Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities
    (2021) Gaete, Alexis; Pulgar, Rodrigo; Hodar, Christian; Maldonado, Jonathan; Pavez, Leonardo; Zamorano, Denisse; Pastenes, Claudio; Gonzalez, Mauricio; Franck, Nicolas; Mandakovic, Dinka
    Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible Solanum lycopersicum cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.