Browsing by Author "Maldonado, Jonathan E."

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    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.
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    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.
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    Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools
    (2022) Carrasco, Basilio; Arevalo, Barbara; Perez-Diaz, Ricardo; Rodriguez-Alvarez, Yohaily; Gebauer, Marlene; Maldonado, Jonathan E.; Garcia-Gonzales, Rolando; Chong-Perez, Borys; Pico-Mendoza, Jose; Meisel, Lee A.; Ming, Ray; Silva, Herman
    A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.
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    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.
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    Molecular and Phylogenomic Analysis of a Vancomycin Intermediate Resistance USA300LV Strain in Chile
    (2024) Nunez, Daniela; Jimenez, Pablo; Martin, Marcelo Cortez-San; Cortes, Carolina; Cardenas, Matias; Michelson, Sofia; Garay, Tamara; Vecchiola, Maggie; Cespedes, Alejandra; Maldonado, Jonathan E.; Vasquez-Martinez, Yesseny
    Antimicrobial resistance is a major global health problem, and, among Gram-positive bacteria, methicillin-resistant Staphylococcus aureus (MRSA) represents a serious threat. MRSA causes a wide range of infections, including bacteremia, which, due to the limited use of beta-lactams, is difficult to treat. This study aimed to analyze 51 MRSA isolates collected in 2018 from samples of patients with bacteremia from two hospitals of the Metropolitan Health Service of Santiago, Chile, both in their resistance profile and in the identification of virulence factors. In addition, genomic characterization was carried out by the WGS of an isolate that was shown to be the one of greatest concern (N degrees. 42) due to its intermediate resistance to vancomycin, multiple virulence factors and being classified as ST8 PVL-positive. In our study, most of the isolates turned out to be multidrug-resistant, but there are still therapeutic options, such as tetracycline, rifampicin, chloramphenicol and vancomycin, which are currently used for MRSA infections; however, 18% were PVL positive, which suggests greater virulence of these isolates. It was determined that isolate N degrees 42 is grouped within the USA300-LV strains (ST8, PVL+, COMER+); however, it has been suggested that, in Chile, a complete displacement of the PVL-negative ST5 clone has not occurred.
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    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
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    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.