Examinando por Autor "Ugalde, J.A."

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    Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation
    (Frontiers Media, 2018-08) Plominsky, A.M.; Henríquez-Castillo, C.; Delherbe, N.; Podell, S.; Ramirez-Flandes, S.; Ugalde, J.A.; Santibañez, J.F.; van den Engh, G.; Hanselmann, K.; Ulloa, O.; De la Iglesia, R.; Allen, E.E.; Trefault, N.
    Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (> 30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them. © 2018 Plominsky, Henríquez-Castillo, Delherbe, Podell, Ramirez-Flandes, Ugalde, Santibañez, van den Engh, Hanselmann, Ulloa, De la Iglesia, Allen and Trefault.
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    Draft Genome Sequence of Blautia luti DSM 14534T, Isolated from Human Stool
    (American Society for Microbiology, 2020-05) Ortiz, R.L.; Melis-Arcos, F.; Covarrubias, P.C.; Ugalde, J.A.; Apte, Z.S.; Pérez-Donoso, J.; Cárdenas, J.P.; Almonacid, D.E.
    Here, we report the draft sequence of Blautia luti strain DSM 14534T, originally isolated from human feces. This draft contains 74 contigs, comprising 3,718,760 bp with a GC content of 42.87%. The annotated draft contains 3,338 coding sequences (CDSs) and 110 RNA genes. © 2020 Ortiz et al.
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    Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations
    (Nature Publishing Group, 2017-12) Millán-Aguinãga, N.; Chavarria, K.L.; Ugalde, J.A.; Letzel, A.-C.; Rouse, G.W.; Jensen, P.R.
    Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.