Publications by authors named "Alexis Gaete"

10 Publications

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Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities.

Front Plant Sci 2021 13;12:688533. Epub 2021 Jul 13.

Laboratorio de Genómica y Genética de Interacciones Biológicas (LG2IB), Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

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 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.
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http://dx.doi.org/10.3389/fpls.2021.688533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8313812PMC
July 2021

Isolation and Identification of Soil Bacteria from Extreme Environments of Chile and Their Plant Beneficial Characteristics.

Microorganisms 2020 Aug 10;8(8). Epub 2020 Aug 10.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, El Libano 5524, 7810000 Santiago, Chile.

The isolation of soil bacteria from extreme environments represents a major challenge, but also an opportunity to characterize the metabolic potential of soil bacteria that could promote the growth of plants inhabiting these harsh conditions. The aim of this study was to isolate and identify bacteria from two Chilean desert environments and characterize the beneficial traits for plants through a biochemical approach. By means of different culture strategies, we obtained 39 bacterial soil isolates from the Coppermine Peninsula (Antarctica) and 32 from Lejía Lake shore soil (Atacama Desert). The results obtained from the taxonomic classification and phylogenetic analysis based on 16S rDNA sequences indicated that the isolates belonged to four phyla (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes), and that the most represented genus at both sites was . Regarding biochemical characterization, all strains displayed in vitro PGP capabilities, but these were in different proportions that grouped them according to their site of origin. This study contributes with microbial isolates from natural extreme environments with biotechnological potentials in improving plant growth under cold stress.
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http://dx.doi.org/10.3390/microorganisms8081213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466141PMC
August 2020

Biochemical and Genomic Characterization of the Cypermethrin-Degrading and Biosurfactant-Producing Bacterial Strains Isolated from Marine Sediments of the Chilean Northern Patagonia.

Mar Drugs 2020 May 13;18(5). Epub 2020 May 13.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7810000, Chile.

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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http://dx.doi.org/10.3390/md18050252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281626PMC
May 2020

PCR-RFLP Detection and Genogroup Identification of in Field Samples.

Pathogens 2020 May 8;9(5). Epub 2020 May 8.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago 7830490, Chile.

, the causative agent of piscirickettsiosis, is genetically divided into two genomic groups, named after the reference strains as LF-89-like or EM-90-like. Phenotypic differences have been detected between the genogroups, including antibiotic susceptibilities, host specificities and pathogenicity. In this study, we aimed to develop a rapid, sensitive and cost-effective assay for the differentiation of the genogroups. Using an in silico analysis of the 16S rDNA digestion patterns, we have designed a genogroup-specific assay based on PCR-restriction fragment length polymorphism (RFLP). An experimental validation was carried out by comparing the restriction patterns of 13 strains and 57 field samples obtained from the tissues of dead or moribund fish. When the bacterial composition of a set of field samples, for which we detected mixtures of bacterial DNA, was analyzed by a high-throughput sequencing of the 16S rRNA gene amplicons, a diversity of taxa could be identified, including pathogenic and commensal bacteria. Despite the presence of mixtures of bacterial DNA, the characteristic digestion pattern of the genogroups could be detected in the field samples without the need of a microbiological culture and bacterial isolation.
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http://dx.doi.org/10.3390/pathogens9050358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281544PMC
May 2020

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment.

Sci Rep 2020 03 27;10(1):5560. Epub 2020 Mar 27.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

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 CO 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 (β-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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http://dx.doi.org/10.1038/s41598-020-62130-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7101325PMC
March 2020

Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability.

Front Bioeng Biotechnol 2019 5;7:10. Epub 2019 Feb 5.

Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

The Atacama Desert is a highly complex, extreme ecosystem which harbors microorganisms remarkable for their biotechnological potential. Here, a soil bacterial prospection was carried out in the high Altiplano region of the Atacama Desert (>3,800 m above sea level; m a.s.l.), where direct anthropogenic interference is minimal. We studied: (1) soil bacterial community composition using high-throughput sequencing of the 16S rRNA gene and (2) bacterial culturability, by using a soil extract medium (SEM) under a factorial design of three factors: temperature (15 and 30°C), nutrient content (high and low nutrient disposal) and oxygen availability (presence and absence). A total of 4,775 OTUs were identified and a total of 101 isolates were selected for 16S rRNA sequencing, 82 of them corresponded to unique or non-redundant sequences. To expand our view of the Altiplano landscape and to obtain a better representation of its microbiome, we complemented our Operational Taxonomic Units (OTUs) and isolate collection with data from other previous data from our group and obtained a merged set of OTUs and isolates that we used to perform our study. Taxonomic comparisons between culturable microbiota and metabarcoding data showed an overrepresentation of the phylum Firmicutes (44% of isolates vs. 2% of OTUs) and an underrepresentation of Proteobacteria (8% of isolates vs. 36% of OTUs). Within the Next Generation Sequencing (NGS) results, 33% of the OTUs were unknown up to genus, revealing an important proportion of putative new species in this environment. Biochemical characterization and analysis extracted from the literature indicated that an important number of our isolates had biotechnological potential. Also, by comparing our results with similar studies on other deserts, the Altiplano highland was most similar to a cold arid desert. In summary, our study contributes to expand the knowledge of soil bacterial communities in the Atacama Desert and complements the pipeline to isolate selective bacteria that could represent new potential biotechnological resources.
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http://dx.doi.org/10.3389/fbioe.2019.00010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371850PMC
February 2019

Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils.

Sci Rep 2019 01 31;9(1):1042. Epub 2019 Jan 31.

FONDAP Center for Genome Regulation, Santiago, Chile.

The rhizosphere is considered the primary place for soil microbiome differentiation and plays a key role in plant survival, especially for those subjected to environmental stress. Using high-throughput sequencing of the 16S rRNA gene, we analyzed and compared soil bacterial communities associated to four of the most abundant high altitude native plant species of the Chilean Andean grasslands. We examined three soil compartments: the rhizosphere (bacteria firmly attached to the roots), the rhizosphere-surrounding soil (bacteria loosely attached to the roots) and the bulk soil (plant-free soil). The rhizosphere microbiome was in all cases the least diverse, exposing that the bulk soil was a more complex environment. Taxonomic analysis revealed an abrupt change between the rhizosphere and the rest of the non-rhizospheric soils. Thus, while rhizobacterial communities were enriched in Proteobacteria (mainly Alphaproteobacteria), Actinobacteria (mostly Blastocatellia) dominated in bulk soils. Finally, we detected certain taxonomic rhizosphere signatures, which could be attributed to a particular genotype. Overall, our results indicate that the thin layer of soil surrounding the roots constitute a distinctive soil environment. This study contributes to expand the knowledge about soil bacterial communities in the Chilean highlands and takes the first step to understand the processes that might lead to the rhizosphere differentiation in that area.
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http://dx.doi.org/10.1038/s41598-018-37776-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355873PMC
January 2019

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert.

Extremophiles 2018 Jul 23;22(4):665-673. Epub 2018 Apr 23.

Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano, 5524, Santiago, Chile.

As a consequence of the severe climatic change affecting our entire world, many lakes in the Andes Cordillera are likely to disappear within a few decades. One of these lakes is Lejía Lake, located in the central Atacama Desert. The objectives of this study were: (1) to characterize the bacterial community from Lejía Lake shore soil (LLS) using 16S rRNA sequencing and (2) to test a culture-based approach using a soil extract medium (SEM) to recover soil bacteria. This extreme ecosystem was dominated by three phyla: Bacteroidetes, Proteobacteria, and Firmicutes with 29.2, 28.2 and 28.1% of the relative abundance, respectively. Using SEM, we recovered 7.4% of the operational taxonomic units from LLS, all of which belonged to the same three dominant phyla from LLS (6.9% of Bacteroidetes, 77.6% of Proteobacteria, and 15.3% of Firmicutes). In addition, we used SEM to recover isolates from LLS and supplemented the culture medium with increasing salt concentrations to isolate microbial representatives of salt tolerance (Halomonas spp.). The results of this study complement the list of microbial taxa diversity from the Atacama Desert and assess a pipeline to isolate selective bacteria that could represent useful elements for biotechnological approaches.
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http://dx.doi.org/10.1007/s00792-018-1027-6DOI Listing
July 2018

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

Sci Rep 2018 04 12;8(1):5875. Epub 2018 Apr 12.

Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.

Understanding the factors that modulate bacterial community assembly in natural soils is a longstanding challenge in microbial community ecology. In this work, we compared two microbial co-occurrence networks representing bacterial soil communities from two different sections of a pH, temperature and humidity gradient occurring along a western slope of the Andes in the Atacama Desert. In doing so, a topological graph alignment of co-occurrence networks was used to determine the impact of a shift in environmental variables on OTUs taxonomic composition and their relationships. We observed that a fraction of association patterns identified in the co-occurrence networks are persistent despite large environmental variation. This apparent resilience seems to be due to: (1) a proportion of OTUs that persist across the gradient and maintain similar association patterns within the community and (2) bacterial community ecological rearrangements, where an important fraction of the OTUs come to fill the ecological roles of other OTUs in the other network. Actually, potential functional features suggest a fundamental role of persistent OTUs along the soil gradient involving nitrogen fixation. Our results allow identifying factors that induce changes in microbial assemblage configuration, altering specific bacterial soil functions and interactions within the microbial communities in natural environments.
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http://dx.doi.org/10.1038/s41598-018-23931-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5897386PMC
April 2018

Analysis of Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.

Front Microbiol 2017 11;8:2462. Epub 2017 Dec 11.

Mathomics, Center for Mathematical Modeling, Universidad de Chile, Santiago, Chile.

is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on has grown in the last couple of years but many aspects of the pathogen's biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.
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http://dx.doi.org/10.3389/fmicb.2017.02462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5732189PMC
December 2017
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