Browsing by Author "Guajardo-Leiva, Sergio"

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    Active Crossfire Between Cyanobacteria and Cyanophages in Phototrophic Mat Communities Within Hot Springs
    (2018) Guajardo-Leiva, Sergio; Pedros-Alio, Carlos; Salgado, Oscar; Pinto, Fabian; Diez, Beatriz
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    Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities
    (2021) Alarcón-Schumacher, Tomás ; Guajardo-Leiva, Sergio ; Martinez-Garcia, Manuel ; Díez, Beatriz; Bernstein, Hans C.
    The Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a "natural" laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment.
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    Elucidating Viral Communities During a Phytoplankton Bloom on the West Antarctic Peninsula
    (2019) Alarcon Schumacher, Tomas; Guajardo-Leiva, Sergio; Antón, Josefa; Diez Moreno, Beatriz
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    Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities
    (2022) Salgado Salgado, Oscar; Guajardo-Leiva, Sergio; Moya-Beltrán, Ana; Barbosa, Carla; Ridley, Christina; Tamayo-Leiva, Javier; Quatrini, Raquel; Mojica, Francisco; Díez, Beatriz
    The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42–80°C, pH 6–9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.
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    Seasonal and Spatially Distributed Viral Metagenomes from Comau Fjord (42°S), Patagonia
    (2023) Castro-Nallar, Eduardo; Berrios-Farias, Valentin; Diez, Beatriz; Guajardo-Leiva, Sergio
    Viruses are key players in marine environments, affecting food webs and biogeochemical cycles. We present 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42 degrees S), to understand viral-mediated processes in coastal and estuarine waters. These data represent a spatial (35-km transect, two depths) and seasonal (winter and fall) data set.
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    Unveiling Ecological and Genetic Novelty within Lytic and Lysogenic Viral Communities of Hot Spring Phototrophic Microbial Mats
    (2021) Guajardo-Leiva, Sergio ; Santos, Fernando ; Salgado, Oscar ; Regeard, Christophe ; Quillet, Laurent; Beatriz Díez; Chen, Wei-Hua
    Viruses exert diverse ecosystem impacts by controlling their host community through lytic predator-prey dynamics. However, the mechanisms by which lysogenic viruses influence their host-microbial community are less clear. In hot springs, lysogeny is considered an active lifestyle, yet it has not been systematically studied in all habitats, with phototrophic microbial mats (PMMs) being particularly not studied. We carried out viral metagenomics following in situ mitomycin C induction experiments in PMMs from Porcelana hot spring (Northern Patagonia, Chile). The compositional changes of viral communities at two different sites were analyzed at the genomic and gene levels. Furthermore, the presence of integrated prophage sequences in environmental metagenome-assembled genomes from published Porcelana PMM metagenomes was analyzed. Our results suggest that virus-specific replicative cycles (lytic and lysogenic) were associated with specific host taxa with different metabolic capacities. One of the most abundant lytic viral groups corresponded to cyanophages, which would infect the cyanobacteria Fischerella, the most active and dominant primary producer in thermophilic PMMs. Likewise, lysogenic viruses were related exclusively to chemoheterotrophic bacteria from the phyla Proteobacteria, Firmicutes, and Actinobacteria. These temperate viruses possess accessory genes to sense or control stress-related processes in their hosts, such as sporulation and biofilm formation. Taken together, these observations suggest a nexus between the ecological role of the host (metabolism) and the type of viral lifestyle in thermophilic PMMs. This has direct implications in viral ecology, where the lysogenic-lytic switch is determined by nutrient abundance and microbial density but also by the metabolism type that prevails in the host community.