Browsing by Author "Diez, Beatriz"

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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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    Adaptation strategies of giant viruses to low-temperature marine ecosystems
    (2024) Buscaglia, Marianne; Iriarte, Jose Luis; Schulz, Frederik; Diez, Beatriz
    Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses ( Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenomeassembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10 degrees C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.
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    Antarctic Polyester Hydrolases Degrade Aliphatic and Aromatic Polyesters at Moderate Temperatures
    (2022) Blazquez-Sanchez, Paula; Engelberger, Felipe; Cifuentes-Anticevic, Jeronimo; Sonnendecker, Christian; Grinen, Aransa; Reyes, Javiera; Diez, Beatriz; Guixe, Victoria; Richter, P. Konstantin; Zimmermann, Wolfgang; Ramirez-Sarmiento, Cesar A.
    Polyethylene terephthalate (PET) is one of the most widely used synthetic plastics in the packaging industry, and consequently has become one of the main components of plastic waste found in the environment. However, several microorganisms have been described to encode enzymes that catalyze the depolymerization of PET. While most known PET hydrolases are thermophilic and require reaction temperatures between 60 degrees C and 70 degrees C for an efficient hydrolysis of PET, a partial hydrolysis of amorphous PET at lower temperatures by the polyester hydrolase IsPETase from the mesophilic bacterium Ideonella sakaiensis has also been reported. We show that polyester hydrolases from the Antarctic bacteria Moraxella sp. strain TA144 (Mors1) and Oleispira antarctica RB-8 (OaCut) were able to hydrolyze the aliphatic polyester polycaprolactone as well as the aromatic polyester PET at a reaction temperature of 25 degrees C. Mors1 caused a weight loss of amorphous PET films and thus constitutes a PET-degrading psychrophilic enzyme. Comparative modeling of Mors1 showed that the amino acid composition of its active site resembled both thermophilic and mesophilic PET hydrolases. Lastly, bioinformatic analysis of Antarctic metagenomic samples demonstrated that members of the Moraxellaceae family carry candidate genes coding for further potential psychrophilic PET hydrolases.
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    Diversity and functionality of soil prokaryotic communities in antarctic volcanic soils: insights from penguin-influenced environments
    (2024) Segura, Diego; Jordaan, Karen; Diez, Beatriz; Tamayo-Leiva, Javier; Doetterl, Sebastian; Wasner, Daniel; Cifuentes-Anticevic, Jeronimo; Casanova-Katny, Angelica
    In the nutrient-limited Antarctic terrestrial habitat, penguins transfer a significant amount of nutrients from the marine to the terrestrial ecosystem through their depositions (i.e., guano). This guano influences soil physicochemical properties, leading to the formation of ornithogenic soil rich in nutrients and organic matter. We hypothesize that soil prokaryotic communities will be strongly influenced by the contribution of nitrogenous nutrients from penguin rookeries, maintaining the influence over long distances. The objective was to establish how the soil prokaryotic diversity and community structure change with distance from a penguin colony, which provides large amounts of guano and nitrogenous compounds, and to study the effects of these nutrients on the functional role of these communities. Methods include volcanic soil sampling along a 1200 m transect from the penguin active rookery and the characterization of soil nutrient content and soil prokaryotic communities using 16S rRNA high-throughput amplicon sequencing. In contrast to our hypothesis, the results showed that the impact of guano from the penguin colony was restricted to the first 300 m. Probably because the penguin rookery was sheltered, strong wind and wind direction did not affect the transport of nutrients from the penguin rookery. Areas close to the penguin rookery were dominated by Proteobacteria and Bacteroidetes, while areas situated further away were dominated by Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and Planctomycetes. Beta diversity analysis among the soil prokaryotic communities revealed a high degree of community heterogeneity, strongly associated with N compound characteristics (NH4, NO3, and %N), C, and pH. Inferences from N metabolism genes suggest a high potential of the microbial community for dissimilatory nitrate reduction genes (DNRA) to ammonium, assimilatory nitrate reduction (ANR), and denitrification. Although it is assumed that the nitrogenous compounds of the penguin colonies reach long distances and affect the prokaryotic community, this effect can vary with wind directions or the morphology of the site, reducing the impact of the guano over long distances, as our results indicate. On the other hand, functional predictions give some clues about the main actors in nitrogen cycling, through processes like dissimilatory nitrate reduction, assimilatory nitrate reduction, and denitrification.
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    Engineering the catalytic activity of an Antarctic PET-degrading enzyme by loop exchange
    (2023) Blazquez-Sanchez, Paula; Vargas, Jhon A.; Furtado, Adriano A.; Grinen, Aransa; Leonardo, Diego A.; Sculaccio, Susana A.; Pereira, Humberto D'Muniz; Sonnendecker, Christian; Zimmermann, Wolfgang; Diez, Beatriz; Garratt, Richard C.; Ramirez-Sarmiento, Cesar A.
    Several hydrolases have been described to degrade polyethylene terephthalate (PET) at moderate temperatures ranging from 25 degrees C to 40 degrees C. These mesophilic PET hydrolases (PETases) are less efficient in degrading this plastic polymer than their thermophilic homologs and have, therefore, been the subject of many protein engineering campaigns. However, enhancing their enzymatic activity through rational design or directed evolution poses a formidable challenge due to the need for exploring a large number of mutations. Additionally, evaluating the improvements in both activity and stability requires screening numerous variants, either individually or using high-throughput screening methods. Here, we utilize instead the design of chimeras as a protein engineering strategy to increase the activity and stability of Mors1, an Antarctic PETase active at 25 degrees C. First, we obtained the crystal structure of Mors1 at 1.6 A resolution, which we used as a scaffold for structure- and sequence-based chimeric design. Then, we designed a Mors1 chimera via loop exchange of a highly divergent active site loop from the thermophilic leaf-branch compost cutinase (LCC) into the equivalent region in Mors1. After restitution of an active site disulfide bond into this chimera, the enzyme exhibited a shift in optimal temperature for activity to 45 degrees C and an increase in fivefold in PET hydrolysis when compared with wild-type Mors1 at 25 degrees C. Our results serve as a proof of concept of the utility of chimeric design to further improve the activity and stability of PETases active at moderate temperatures.