Biology subjects

Belda, I.

Publications and source records attributed to Belda, I..

8 recordsLinked to original sources

bioRxiv2025

Contrasting evolutionary forces of specialization and admixture underlie the genomic and phenotypic diversity of Yarrowia lipolytica

Microbial diversity emerges from evolutionary processes that shape genomic and phenotypic traits in response to complex environmental pressures. Deciphering these dynamics is key to understanding microbial ecology and advancing biotechnological applications. Here, we use the yeast Yarrowia lipolytica to study genomic signatures of adaptation across a broad range of environments and to illustrate how population-level data can inform targeted bioprospecting for industrial traits. Whole-genome and phenotypic analyses of 126 isolates from natural and anthropogenic environments reveal a complex population structure in this species, shaped by both niche specialization and admixture events. Structured lineages exhibit ecological filtering, reduced genetic diversity, and distinct gene content, consistent with adaptation to substrates like dairy, hydrocarbons, or industrial substrates. In contrast, admixed populations display greater genetic diversity and broader phenotypic capacity, including enhanced stress tolerance and metabolic flexibility. Genome plasticity, reflected in pangenome and CNV variation, aligns with ecological origin, while trait assays link phenotypic divergence to underlying genetic variation. For instance, better growth performance on acetate, an ecological and industrially relevant trait, is associated with hydrocarbon-adapted strains and likely linked to variation in regulatory regions of acetate metabolism genes. Together, our results reflect how divergent evolutionary trajectories--ranging from ecological specialization to genomic plasticity through admixture-- underpin the species ecological success and provide a framework for harnessing its natural diversity in microbial bioprospecting.

evolutionary biology↗

bioRxiv2024

Community successional patterns and inter-kingdom interactions during granular biofilm development

Aerobic granular sludge is a compact and efficient biofilm process used for wastewater treatment which has received much attention and is currently being implemented worldwide. The microbial associations and their ecological implications occurring during granule development, especially those involving inter-kingdom interactions, are poorly understood. In this work, we monitored the prokaryote and eukaryote community composition and structure during the granulation of activated sludge for 343 days in a sequencing batch reactor (SBR), and investigated the influence of abiotic and biotic factors on the granule development. Sludge granulation was accomplished with low-wash out dynamics at long settling times, allowing for the microbial communities to adapt to the SBR environmental conditions. The sludge granulation and associated changes in microbial community structure could be divided into three stages: floccular, intermediate, and granular. The eukaryotic and prokaryotic communities showed parallel successional dynamics, with three main sub-communities identified for each kingdom, dominating in each stage of sludge granulation. Although inter-kingdom interactions were shown to affect community succession during the whole experiment, during granule development random factors like the availability of settlement sites or drift acquired increasing importance. The prokaryotic community was more affected by deterministic factors, including reactor conditions, while the eukaryotic community was to a larger extent shaped by biotic interactions (including inter-kingdom interactions) and stochasticity.

microbiology↗

bioRxiv2023

Multi-omics framework to reveal the molecular determinants of fermentation performance in wine yeast populations

BackgroundConnecting the composition and function of industrial microbiomes is a major aspiration in microbial biotechnology. Here, we address this question in wine fermentation, a model system where the diversity and functioning of fermenting yeast species is determinant of the flavor and quality of the resulting wines. ResultsFirst, we surveyed yeast communities associated with grape musts collected across wine appellations, revealing the importance of environmental (i.e., biogeography) and anthropic factors (i.e., farming system) in shaping community composition and structure. Then, we assayed the fermenting yeast communities in synthetic grape must under common winemaking conditions. The dominating yeast species defines the fermentation performance and metabolite profile of the resulting wines, and it is determined by the initial fungal community composition rather than the imposed fermentation conditions. Yeast dominance also had a more pronounced impact on wine meta-transcriptome than fermentation conditions. We unveiled yeast-specific transcriptomic profiles, leveraging different molecular functioning strategies in wine fermentation environments. We further studied the orthologs responsible for metabolite production, revealing modules associated with the dominance of specific yeast species. This emphasizes the unique contributions of yeast species to wine flavor, here summarized in an array of orthologs that defines the individual contribution of yeast species to wine ecosystem functioning. ConclusionsOur study bridges the gap between yeast community composition and wine metabolite production, providing insights to harness diverse yeast functionalities with the final aim to producing tailored high-quality wines.

microbiology↗

bioRxiv2022

Predictability of the community-function landscape in wine yeast ecosystems

Predictively linking taxonomic composition and quantitative ecosystem functions is a major aspiration in microbial ecology, which must be resolved if we wish to engineer microbial consortia. Here, we have addressed this open question for an ecological function of major biotechnological relevance: alcoholic fermentation in wine yeast communities. By exhaustively phenotyping an extensive collection of naturally occurring wine yeast strains, we find that most enologically-relevant traits exhibit a strong phylogenetic signal, indicating that the most relevant functions in wine yeast communities can be predicted from taxonomy. Further, we demonstrate that the quantitative contributions of individual wine yeast strains to the community function followed simple quantitative rules. These regularities can be integrated to quantitatively predict the function of newly assembled consortia. Besides addressing a fundamental open question in functional ecology, our results and methodologies provide a blueprint for rationally managing microbial processes of biotechnological relevance.

microbiology↗

bioRxiv2021

Soil Microbial Composition and Structure Allow Assessment of Biological Product Effectiveness and Crop Yield Prediction

Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk and rhizosphere soils microbial composition and structure to evaluate the effect of a Bacillus amyloliquefaciens strain QST713 inoculant on potatoes, and to explore its relationship with crop yield. We implemented NGS and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points -from planting to harvest -from three different geographical regions in the United States. In addition to variety, phenological stage of the potato plant and geography being important factors defining the microbiome composition and structure, the microbial inoculant applied as a treatment also had a significant effect. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Specific taxonomic groups, and most interestingly the structure of the fungal and bacterial communities (measured using co-occurrence and co-exclusion networks), changed after inoculation. Additionally, using information about the application of the microbial inoculant and considering microbiome composition and structure data we were able to train a Random Forest model to estimate if a bulk or rhizosphere soil sample came from a low or high yield block with relatively high accuracy, concluding that the structure of fungal communities is a better estimator of potato yield than the structure of bacterial communities. IMPORTANCEThe manuscripts results reinforce the notion that each crop variety on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed specific taxonomic groups and, most interestingly, the structure of local fungal and bacterial networks in bulk and rhizosphere soil. The data obtained, coming from in-field assays performed in three different geographical locations, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables -especially those related to microbial community structure- with a higher predictive power than the variety and geography of the block. The methods described here can be replicated to fit new models predicting yield in any other crop, and to evaluate the effect of any Ag-input product in the composition and structure of the soil microbiome.

microbiology↗

bioRxiv2020

Microbial map of the world's vineyards:Applying the concept of microbial terroir on a global scale

The specific microbial biodiversity linked to a particular vineyard location is reported to be a crucial aspect, in conjunction with edaphic, climatic and human factors, in the concept of wine terroir. These biogeographical patterns are known as microbial terroirs. This study applied an HTS amplicon library approach in order to conduct a global survey of vineyards soil microbial communities. In all, soil samples from 200 vineyards on four continents were analysed in an attempt to establish the basis for the development of a vineyard soil microbiome map to represent microbial wine terroirs on a global scale. This study established links between vineyard locations and microbial biodiversity on different scales: between continents and countries, and between different wine regions within the same country. Geography had a strong effect on the composition of microbial communities on a global scale, which was also maintained on a country scale. Furthermore, a predictive model was developed, based on random forest analyses, to discriminate between microbial patterns in order to identify the geographical source of the samples with reasonable precision. Finally this study is the first to describe the microbial community of new and northern wine-producing regions, such as Denmark, that could be of great interest for viticulture adaptation in a context of climate change.

microbiology↗

bioRxiv2020

New insights into the paradoxical distribution of IRC7 in Saccharomyces cerevisiae and its associated phenotypic and genomic landscapes

Biotic and abiotic factors of wine fermentations have led to the accumulation of numerous genomic hallmarks of domestication in Saccharomyces cerevisiae wine strains. Here we have studied the paradoxical distribution of a dominant allele of IRC7 in wine yeast strains. This gene encodes a cysteine-S-{beta}-lyase and presents two alleles: a wild full-length allele (IRC7F) and a mutated one (IRC7S), harboring a 38bp-deletion. Interestingly, IRC7S-coding for a less active enzyme-appears in the great majority of wine strains. Studying its global distribution among phylogenetic clades, we observed that IRC7S allele is dominant just in wine strains, having a moderate presence in other domesticated clades (Beer, Bread and Wine-PDM), but being completely absent in wild clades, appearing as a new hallmark of domestication. To explain this paradoxical distribution, we performed an IRC7-rooted phenotypic-wide survey, demonstrating that IRC7S-homozygous (HS) wine strains have both fitness (lower lag phases and higher growth rates) and competitive (killer toxin resistance, pseudohyphal growth) advantages. Hence, we performed a genome-wide survey across domesticated clades, finding a set of mutations that are conserved among wine strains and potentially associated to IRC7S allele, which can help to explain the outstanding phenotype of HS strains and their dominant distribution in wines. Originality-Significance StatementS. cerevisiae is one of the best studied microbes due to its industrial importance and its use as a eukaryotic model organism. S. cerevisiae is also an interesting model for studying the effects of domestication in yeast genomic, phenotype and ecology. The study of how wild S. cerevisiae strains evolved into a greatly adapted domesticated strains and changed its lifestyle drastically is still of great interest. In the case of wine populations, strains have accumulated numerous hallmarks of domestication in their genome, related with their great phenotypic adaptation to this environment. Here, we report a new hallmark of domestication in wine strains; the IRC7 deleted allele (IRC7S) and present the first insights about its unexpected global distribution among phylogenetic clades, understanding the genomic context and the phenotypic implications of this allele in wine strains.

microbiology↗

bioRxiv2020

Emergent properties in microbiome networks reveal the anthropogenic disturbance of farming practices in vineyard soil fungal communities

Agro-ecosystems are human-managed natural systems, and therefore are subject to generalized ecological rules. A deeper understanding of the factors impacting on the biotic component of ecosystem stability is needed for promoting the sustainability and productivity of global agriculture. Here we propose a method to determine ecological emergent properties through the inference of network properties in local microbial communities, and to use them as biomarkers of the anthropogenic impact of different farming practices on vineyard soil ecosystem functioning. In a dataset of 350 vineyard soil samples from USA and Spain we observed that fungal communities ranged from random to small-world network arrangements with differential levels of niche specialization. Some of the network properties studied were strongly correlated, defining patterns of ecological emergent properties that are influenced by the intensification level of the crop management. Low-intervention practices (from organic to biodynamic approaches) promoted densely clustered networks, describing an equilibrium state based on mixed (generalist-collaborative) communities. Contrary, in conventionally managed vineyards, we observed highly modular (niche-specialized) low clustered communities, supported by a higher degree of selection (more co-exclusion proportion). We also found that, although geographic factors can explain the different fungal community arrangements in both countries, the relationship between network properties in local fungal communities better capture the impact of farming practices regardless of the location. Thus, we hypothesize that local network properties can be globally used to evaluate the effect of ecosystem disturbances in crops, but also in when evaluating the effect of clinical interventions or to compare microbiomes of healthy vs. disturbed conditions.

ecology↗