Wladimir Mardones

@ibio.cl

Young Researcher
Integrative Biology Institute

Wladimir Mardones


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https://researchid.co/wladimirmardones

EDUCATION

Ph.D. in Molecular Bioscience

RESEARCH, TEACHING, or OTHER INTERESTS

Biochemistry, Genetics and Molecular Biology, Ecology, Evolution, Behavior and Systematics, Biotechnology
14

Scopus Publications

Scopus Publications

  • Exploiting Sexual Reproduction and Mass-Mating to Expand Phenotypic Diversity in Saccharomyces cerevisiae for Bioethanol Fermentation
    Ignacio Guarda, Catalina Ardiles, Sebastián Dehnhardt-Amengual, Isidora Achiardi-Letelier, Wladimir Mardones
    Fermentation, 2026
    Sexual reproduction in yeasts is a fundamental biological process that promotes genetic recombination and phenotypic diversification, enabling adaptation to fluctuating and stressful environments. Sporulation and subsequent mating generate novel allele combinations that enhance evolutionary potential; however, many domesticated industrial strains exhibit reduced sporulation capacity, limiting their use in breeding programs and constraining the generation of new diversity. This represents one of the major bottlenecks for improving yeast performance in industrial fermentations, particularly under the harsh conditions characteristic of bioethanol production. In this study, we exploited meiotic recombination and mass-mating strategies to expand genetic and phenotypic diversity in S. cerevisiae. By mass-mating haploid spores derived from genetically distinct parental strains, we generated highly heterogeneous hybrid populations in a single step, overcoming the limitations imposed by conventional breeding approaches, such as micromanipulation. These populations were subsequently screened to identify strains with enhanced fermentative performance and increased tolerance to industrial stressor media associated with bioethanol production. Our results demonstrate that sexual reproduction combined with mass-mating represents an efficient strategy to unlock hidden genetic potential and generate superior industrial yeast phenotypes. This work highlights the value of utilizing the natural reproductive biology of S. cerevisiae to accelerate strain improvement and develop robust yeasts adapted to challenging fermentation environments.
  • OmniBio: an easy-to-use web app for kinetic growth parameter calculation from microplate reader data
    Sebastian Dehnhardt-Amengual, Catalina Ardiles, Ignacio Guarda, Isidora Achiardi-Letelier, Luis F Larrondo, et al.
    Bioinformatics Advances, 2026
    OmniBio is a user-friendly web application designed to streamline the analysis of microbial growth curves from microplate reader data, eliminating the need for coding skills or cumbersome file preprocessing. Built in R, using the gcplyr package and Shiny framework, OmniBio supports data outputs from most commercial plate readers (i.e. Gen5 and iControl software), handling multiple sheets within a single file. Users can upload raw data along with experimental metadata to the platform, compute kinetic parameters such as maximum growth rate, lag time, ODmax, and area under the curve, and promptly visualize the results in real-time. The app produces plots for each parameter and a global heatmap analysis for comparing microbial performance across strains and culture media. Importantly, all the primary and processed data can be readily downloaded in a summarized Excel report. In contrast to existing tools, OmniBio optimizes the analysis process by automating repetitive computations and offering an intuitive, step-by-step workflow that does not require bioinformatics training. OmniBio is freely accessible at https://sdehnhardt.shinyapps.io/OmniBio_beta2/, and can be modified from open-source code on GitHub (https://github.com/sidehnhardt/OmniBio). The tool enables researchers to conduct high-throughput kinetic analysis in an efficient and user-friendly manner, optimizing both time and resource utilization.
  • Native oleaginous yeasts Rhodotorula mucilaginosa and Solicoccozyma gelidoterrea: a sustainable biotechnological alternative for lipid production with potential application in diets for farmed fish
    Paola Díaz-Navarrete, Luis Marileo, Hugo Madrid, Wladimir Mardones, David Correa Galeote, et al.
    Frontiers in Fungal Biology, 2026
    Introduction The rapid global expansion of aquaculture has intensified the demand for sustainable and alternative lipid sources for fish feed formulations, driving interest in microbial platforms with specialized metabolic capabilities. Among these, oleaginous yeasts have emerged as promising candidates due to their ability to accumulate substantial intracellular lipid reserves and to modulate fatty acid composition in response to environmental and nutritional cues. Methods In this study, the lipid production potential and physiological responses of two native yeast strains isolated from volcanic soils of southern Chile were investigated. The strains were identified by ITS sequencing as Solicoccozyma gelidoterrea (7C) and Rhodotorula mucilaginosa (Rho 6S). Growth kinetics, substrate utilization, and lipid accumulation were systematically evaluated under different carbon sources, carbon-to-nitrogen (C/N) ratios, and temperature regimes (7–25 °C). Response surface methodology was applied to determine the combined effects of nutritional and thermal factors on biomass production and lipid yield, while fatty acid composition was analyzed to elucidate lipid remodeling strategies. Results and Discussion R. mucilaginosa exhibited pronounced metabolic versatility, characterized by higher maximum specific growth rates on alternative carbon sources such as xylose, sucrose, and raffinose. Under optimal conditions (25 °C and C/N 20), this strain achieved a lipid content of 30% and a biomass concentration of 2.54 g/L. In contrast, S. gelidoterrea displayed a distinct physiological profile associated with cold adaptation, reaching optimal lipid accumulation at 7 °C and C/N 20, with 26.6% lipid content and 2.11 g/L biomass. Increasing the C/N ratio to 90 significantly constrained lipid accumulation in both strains, highlighting the central role of nitrogen availability in regulating yeast lipid metabolism. Fatty acid profiling revealed clear species-specific lipid remodeling patterns: R. mucilaginosa produced a nutritionally favorable lipid profile enriched in mono and polyunsaturated fatty acids, reflected by high MUFA/SAFA and PUFA/SAFA ratios. In contrast, S. gelidoterrea exhibited a distinctive lipid profile dominated by monounsaturated fatty acids, particularly oleic acid, under nitrogen limited and low temperature conditions, and demonstrated the capacity to synthesize long chain polyunsaturated fatty acids under stress conditions, suggesting the activation of adaptive and stress responsive lipid metabolic pathways. Conclusion This study provides the first evidence of lipid accumulation and fatty acid composition in S. gelidoterrea and puts into evidence contrasting lipid metabolic strategies among native oleaginous yeasts. Collectively, these findings contribute to a deeper understanding of fungal lipid physiology and environmental adaptation and support the potential of native yeast strains as sustainable lipid sources for functional foods and aquaculture nutrition.
  • Experimental evolution and hybridization enhance the fermentative capacity of wild Saccharomyces eubayanus strains
    Franco Vega-Macaya, Pablo Villarreal, Tomas A Peña, Valentina Abarca, Agustín A Cofré, et al.
    FEMS Yeast Research, 2025
    Lager beer is traditionally fermented using Saccharomyces pastorianus. However, the limited availability of lager yeast strains restricts the potential range of beer profiles. Recently, Saccharomyces eubayanus strains showed the potential to impart novel aromas to beer, with slower fermentation rates than commercial strains. Here, we applied experimental evolution to nine S. eubayanus strains using three different selective conditions to generate improved strains to fermentative environments. We observed environment-dependent fitness changes across strains, with ethanol-enriched media resulting in the greatest fitness improvement. We identified subtelomeric genomic changes in a deficient fermentative strain underlying the greatest fitness improvement. Gene expression analysis and genome sequencing identified genes associated with oxidative stress, amino acid metabolism, sterol biosynthesis, and vacuole morphology underlying differences between evolved and the ancestral strain, revealing the cellular processes underlying fermentation improvement. A hybridization strategy between two evolved strains allowed us to expand the phenotypic space of the F2 segregants, obtaining strains with a 13.7% greater fermentative capacity relative to the best evolved parental strains. Our study highlights the potential of integrating experimental evolution and hybridization to enhance the fermentation capacity of wild yeast strains, offering strengthened solutions for industrial applications and highlighting the potential of Patagonian S. eubayanus in brewing.
  • Addition of Saccharomyces eubayanus to SCOBY fermentations modulates the chemical and volatile compound profiles in kombucha
    Camila A. Venegas, Luis A. Saona, Kamila Urbina, Pablo Quintrel, Tomás A. Peña, et al.
    Food Microbiology, 2023
  • Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions
    Wladimir Mardones, Carlos A. Villarroel, Valentina Abarca, Kamila Urbina, Tomás A. Peña, et al.
    Microbial Biotechnology, 2022
    SummaryAlthough the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then, we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (6 months) and compared them with propagated controls exposed solely to glucose. Propagated populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time‐course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all propagated lines, including SNPs, aneuploidies, INDELs and translocations. In addition, the different propagated populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic off‐flavours and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in ‘fast motion’ in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.
  • Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates
    Wladimir Mardones, Carlos A. Villarroel, Kristoffer Krogerus, Sebastian M. Tapia, Kamila Urbina, et al.
    Microbial Biotechnology, 2020
    SummaryThe utilization of S. eubayanus has recently become a topic of interest due to the novel organoleptic properties imparted to beer. However, the utilization of S. eubayanus in brewing requires the comprehension of the mechanisms that underlie fermentative differences generated from its natural genetic variability. Here, we evaluated fermentation performance and volatile compound production in ten genetically distinct S. eubayanus strains in a brewing fermentative context. The evaluated strains showed a broad phenotypic spectrum, some of them exhibiting a high fermentation capacity and high levels of volatile esters and/or higher alcohols. Subsequently, we obtained molecular profiles by generating ‘end‐to‐end’ genome assemblies, as well as metabolome and transcriptome profiling of two Patagonian isolates exhibiting significant differences in beer aroma profiles. These strains showed clear differences in concentrations of intracellular metabolites, including amino acids, such as valine, leucine and isoleucine, likely impacting the production of 2‐methylpropanol and 3‐methylbutanol. These differences in the production of volatile compounds are attributed to gene expression variation, where the most profound differentiation is attributed to genes involved in assimilatory sulfate reduction, which in turn validates phenotypic differences in H2S production. This study lays a solid foundation for future research to improve fermentation performance and select strains for new lager styles based on aroma and metabolic profiles.
  • Fungal diversity analysis of grape musts from central valley-chile and characterization of potential new starter cultures
    Dinka Mandakovic, Rodrigo Pulgar, Jonathan Maldonado, Wladimir Mardones, Mauricio González, et al.
    Microorganisms, 2020
    Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential capacities to become starters during fermentation. By using internal transcribed spacer (ITS) amplicon sequencing, we identified the taxonomic structure of the yeast community in unfermented and fermented musts of a typical Vitis vinifera L. var. Sauvignon blanc from the Central Valley of Chile throughout two consecutive seasons of production. Unsurprisingly, Saccharomyces represented the most abundant fungal genus in unfermented and fermented musts, mainly due to the contribution of S. uvarum (42.7%) and S. cerevisiae (80%). Unfermented musts were highly variable between seasons and showed higher values of fungal diversity than fermented musts. Since microbial physiological characterization is primarily achieved in culture, we isolated nine species belonging to six genera of fungi from the unfermented must samples. All isolates were characterized for their potential capacities to be used as new starters in wine. Remarkably, only Metschnikowia pulcherrima could co-exist with a commercial Saccharomyces cerevisiae strain under fermentative conditions, representing a feasible candidate strain for wine production.
  • Corncob and sugar beet pulp induce specific sets of lignocellulolytic enzymes in Penicillium purpurogenum
    Wladimir Mardones, Eduardo Callegari, Jaime Eyzaguirre
    Mycology, 2019
    Penicillium purpurogenum is a filamentous fungus, which grows on a variety of natural carbon sources and secretes a large number of enzymes involved in cellulose, hemicelluloses and pectin biodegradation. The purpose of this work has been to identify potential lignocellulolytic enzymes and to compare the secreted enzymes produced when the fungus is grown on sugar beet pulp (rich in cellulose and pectin) and corn cob (rich in cellulose and xylan). Culture supernatants were subjected to two-dimensional nano-liquid chromatography/tandem mass spectrometry. Using MASCOT and a genome-derived protein database, the proteins present in the supernatant were identified. The putative function in the degradation of the polysaccharides was determined using dbCAN software. The results show that there is a good correlation between the polysaccharide composition of the carbon sources and the function of the secreted enzymes: both cultures are rich in cellulases, while sugar beet pulp induces pectinases and corncob, xylanases. The eventual biochemical characterisation of these enzymes will be of value for a better understanding of the biodegradation process performed by the fungus and increase the availability of enzymes for biotechnological methods associated with this process.
  • The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes
    Wladimir Mardones, Alex Di Genova, María Paz Cortés, Dante Travisany, Alejandro Maass, et al.
    Mycology, 2018
    The high lignocellulolytic activity displayed by the soft-rot fungus P. purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and CEGMA analysis reveals that our assembly covers most if not all all protein-coding genes. RNASeq was performed and 93.1% of the reads aligned within the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.
  • Genomics Perspectives on Metabolism, Survival Strategies, and Biotechnological Applications of Brettanomyces bruxellensis LAMAP2480
    Liliana Godoy, Evelyn Silva-Moreno, Wladimir Mardones, Darwin Guzman, Francisco A. Cubillos, et al.
    Journal of Molecular Microbiology and Biotechnology, 2017
  • Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization
    Wladimir Mardones, Eduardo Callegari, Jaime Eyzaguirre
    Fungal Biology, 2015
  • Characterization of a recombinant α-glucuronidase from Aspergillus fumigatus
    Lorena Rosa, María Cristina Ravanal, Wladimir Mardones, Jaime Eyzaguirre
    Fungal Biology, 2013
  • Differential expression of genes from Penicillium purpurogenum when grown on sugar beet pulp and glucose as carbon sources
    Carolina Klagges, Wladimir Mardones, Jaime Eyzaguirre
    Mycology, 2012

Publications

• Vega-Macaya, F., Villarreal, P., Peña, T. A., Abarca, V., Cofré, A, Oporto, C. I., Mardones, W., Nespolo, R. F. and Cubillos, F. A. (2025). Experimental Evolution and Hybridization Enhance the Fermentative Capacity of Wild Saccharomyces eubayanus Strains. FEMS Yeast Research.
• Venegas, C., Saona, L. A., Urbina, K., Quintrel, P., Peña, T. A., Mardones, W. and Cubillos, F. A. (2023). Addition of Saccharomyces eubayanus to SCOBY fermentations modulates the chemical and volatile compound profiles in kombucha. Food Microbiol. 116(104357).
• Mardones, W., C. A. Villarroel, V. Abarca, K. Urbina, T. A. Pena, J. Molinet, R. F. Nespolo and F. A. Cubillos (2022). "Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing Microb Biotechnol 15(3): 967-984.
• Mardones, W., C. A. Villarroel, K. Krogerus, S. M. Tapia, K. Urbina, C. I. Oporto, S. O'Donnell, R. Minebois, R. Nespolo, G. Fischer, A. Querol, B. Gibson and F. A. Cubillos (2020). "Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus Microb Biotechnol 13(4): 1012-1025.
• Mandakovic, D., Pulgar, R., Maldonado, J., Mardones, W., Gonzalez, M., Cubillos, F. A. and Cambiazo, V (2020). "Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Microorganisms 8(6).
• Mardones, W., E. Callegari and J. Eyzaguirre (2