Browsing by Author "Gaete, Alexis"

Now showing 1 - 9 of 9
  • No Thumbnail Available
    Item
    Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile
    (2022) Aguila-Torres, Patricia; Gonzalez, Mauricio; Maldonado, Jonathan E.; Miranda, Richard; Zhang, Liqing; Gonzalez-Stegmaier, Roxana; Rojas, Luis Antonio; Gaete, Alexis
    The presence of microplastics in oceans and coastlines has increased during recent years due anthropogenic activities and represents a serious environmental problem. The establishment and assembly of microbial communities in these microplastics, specifically located near aquaculture activities, is not well understood. In this study, we analyzed unique and core members of bacterial communities attached to microplastics collected from three coastal environments of the South Pacific, which represent low, medium and high anthropogenic activity derived from the aquaculture industry. Microplastics were analyzed with Fourier-transform infrared spectroscopy, scanning electron microscopy, and next-generation sequencing to assess the prevailing microplastics types, and to characterize microbial communities attached to them. We identified four main types of microplastics (polypropylene, polyethylene, nylon and polystyrene) and 3102 Operational Taxonomic Units (OTUs) at the sampled sites, which were dominated by the phylum Cyanobacteria, Bacteroidetes and Proteobacteria (mainly Alpha and Gammaproteobacteria). Similarity index analysis showed that bacterial communities in microplastics differed from those found in the surrounding seawaters, and also that they varied among locations, suggesting a role of the environment and level of anthropogenic activities on the plastisphere taxa. Despite this difference, 222 bacterial OTUs were shared among the three sites representing between 34 and 51% of OTUs of each sampled site, and thus constituted a core microbiome of microplastics. Comparison of the core microbiome with bacterial communities of the surrounding seawater suggested that the plastisphere constituted a selective habitat for diverse microbial communities. Computational predictions also provided evidence of significantly enriched functions in the core microbiome. Co-occurrence networks revealed that putative ecological interactions among microplastics OTUs was dominated by positive correlations. To the best of our knowledge, this is the first study that evaluated the composition of microbial communities found in microplastics from the Patagonia region of the Southern Pacific Ocean.
  • Thumbnail Image
    Item
    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
  • No Thumbnail Available
    Item
    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.
  • No Thumbnail Available
    Item
    Bioprospecting of Plant Growth-Promoting Traits of Pseudomonas sp. Strain C3 Isolated from the Atacama Desert: Molecular and Culture-Based Analysis
    (2022) Gaete, Alexis; Andreani-Gerard, Constanza; Maldonado, Jonathan E.; Munoz-Torres, Patricio A.; Sepulveda-Chavera, German F.; Gonzalez, Mauricio
    Soil microorganisms that inhabit extreme environments have unique metabolic capacities and/or physical structures that allow them to survive in oligotrophic conditions. The bioprospecting of unknown bacteria in the context of current advances in genome mining is fundamental for the discovery of natural products with novel properties or applications. In this study, the plant growth-promoting and biocontrol traits of a Pseudomonas isolated from soil associated with plants from the Atacama Desert were characterized by whole-genome sequencing and in vitro assays. A high-quality genome draft of Pseudomonas sp. isolate C3 was obtained. An automated biosynthetic gene cluster analysis using antiSMASH 6.0 revealed the presence of a cluster of genes for the biosynthesis, regulation, and transport of the metabolite 2,4-diacetylphloroglucinol, which showed a high protein sequence identity (>89%) with a validated orthologous gene cluster from another Pseudomonas. In addition, via an in vitro assay, the biocontrol activity of Pseudomonas sp. isolate C3 against Botrytis cinerea, Monilinia fructicola, Phytium sp., Alternaria sp., Geotrichum candidum, and Fusarium oxysporum was corroborated. Finally, through KofamKOALA, the presence of genes involved in different metabolic pathways of plant growth-promoting traits was identified, which was corroborated by in vitro assays. This study provides information obtained from genomic analyses and culture tools on a bacterial isolate from the Atacama Desert characterized by plant growth-promoting capacities and biocontrol activity.
  • Thumbnail Image
    Item
    DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species
    (2023) Kobayashi, Sanae; Maldonado, Jonathan E.; Gaete, Alexis; Araya, Ingrid; Aguado-Norese, Constanza; Cumplido, Nicolás; Díaz, Sebastián; Espinoza, Alonso; Fernández, Edelmira; Gajardo, Felipe; González-Ordenes, Felipe; Hauyon, Khantati; Maldonado, Piedad; Maldonado, Rodrigo; Pochet, Isabel; Riveros, Aníbal; Sandoval, Paula; Sepúlveda-González, Ailynne; Stuardo, Camila; Tapia-Reyes, Patricio; Thornton, Carolina; Undurraga, Soledad; Varas, Macarena; Valdivieso, Camilo; Gutiérrez Ilabaca, Rodrigo Antonio; Orellana, Ariel; Montecino, Martín; Maass, Alejandro; González, Mauricio; Allende, Miguel L.; Hodar, Christian; Irles, Paula
    Background Despite representing the largest fraction of animal life, the number of insect species whose genome has been sequenced is barely in the hundreds. The order Dermaptera (the earwigs) suffers from a lack of genomic information despite its unique position as one of the basally derived insect groups and its importance in agroecosystems. As part of a national educational and outreach program in genomics, a plan was formulated to engage the participation of high school students in a genome sequencing project. Students from twelve schools across Chile were instructed to capture earwig specimens in their geographical area, to identify them and to provide material for genome sequencing to be carried out by themselves in their schools. Results The school students collected specimens from two cosmopolitan earwig species: Euborellia annulipes (Fam. Anisolabididae) and Forficula auricularia (Fam. Forficulidae). Genomic DNA was extracted and, with the help of scientific teams that traveled to the schools, was sequenced using nanopore sequencers. The sequence data obtained for both species was assembled and annotated. We obtained genome sizes of 1.18 Gb (F. auricularia) and 0.94 Gb (E. annulipes) with the number of predicted protein coding genes being 31,800 and 40,000, respectively. Our analysis showed that we were able to capture a high percentage (≥ 93%) of conserved proteins indicating genomes that are useful for comparative and functional analysis. We were also able to characterize structural elements such as repetitive sequences and non-coding RNA genes. Finally, functional categories of genes that are overrepresented in each species suggest important differences in the process underlying the formation of germ cells, and modes of reproduction between them, features that are one of the distinguishing biological properties that characterize these two distant families of Dermaptera. Conclusions This work represents an unprecedented instance where the scientific and lay community have come together to collaborate in a genome sequencing project. The versatility and accessibility of nanopore sequencers was key to the success of the initiative. We were able to obtain full genome sequences of two important and widely distributed species of insects which had not been analyzed at this level previously. The data made available by the project should illuminate future studies on the Dermaptera.
  • No Thumbnail Available
    Item
    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.
  • Thumbnail Image
    Item
    Partners to survive: Hoffmannseggia doellii root‐associated microbiome at the Atacama Desert
    (2022) Maldonado, Jonathan E.; Gaete, Alexis; Mandakovic, Dinka; Aguado‐Norese, Constanza; Aguilar, Melissa; Gutiérrez Ilabaca, Rodrigo Antonio; González, Mauricio
  • Thumbnail Image
    Item
    Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert
    (2023) Mandakovic, Dinka; Aguado-Norese, Constanza; García-Jiménez, Beatriz; Hodar, Christian; Maldonado, Jonathan E.; Gaete, Alexis; Latorre, Mauricio; Wilkinson, Mark D.; Gutiérrez Ilabaca, Rodrigo Antonio; Cavieres, Lohengrin A.; Medina, Joaquín; Cambiazo, Verónica; Gonzalez, Mauricio
    Background Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400–4500 m a.s.l.) of the Talabre–Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities. Results Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT. Conclusions In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.
  • No Thumbnail Available
    Item
    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.