Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

Reiter, Taylor; Montpetit, Rachel; Runnebaum, Ron C.; Brown, Calvin; Montpetit, Ben

doi:10.1128/mbio.02345-21

“…Like PCA, diffusion maps identify a new set of variables that describe the data in a coordinate system that follows the manifolds. Recent papers demonstrate that the application of diffusion maps to ecological data (22; 23; 24) yields new variables that can be interpreted as composite functional strategies. The diffusion map thus relates to the fundamental ecological niche space in a system (22; 25).…”

Section: Introductionmentioning

confidence: 99%

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Massing

¹

,

Fahimipour

²

,

Bunse

³

et al. 2022

Preprint

0

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Progress in molecular methods has enabled the monitoring of bacterial populations in time. Nevertheless, understanding community dynamics and its links with ecosystem functioning remains challenging due to the tremendous diversity of microorganisms. Conceptual frameworks that make sense of time-series of taxonomically-rich bacterial communities, regarding their potential ecological function, are needed. A key concept for organizing ecological functions is the niche, the set of strategies that enable a population to persist and define its impacts on the surroundings. Here we present a framework based on manifold learning, to organize genomic information into potentially occupied bacterial metabolic niches over time. We apply the method to re-construct the dynamics of putatively occupied metabolic niches using a long-term bacterial time-series from the Baltic Sea, the Linnaeus Microbial Observatory (LMO). The results reveal a relatively low-dimensional space of occupied metabolic niches comprising groups of taxa with similar functional capabilities. Time patterns of occupied niches were strongly driven by seasonality. Some metabolic niches were dominated by one bacterial taxon whereas others were occupied by multiple taxa, and this depended on season. These results illustrate the power of manifold learning approaches to advance our understanding of the links between community composition and functioning in microbial systems.

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Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Massing

¹

,

Fahimipour

²

,

Bunse

³

et al. 2023

mSystems

2

0

View full text Add to dashboard Cite

Progress in molecular methods has enabled the monitoring of bacterial populations in time. Nevertheless, understanding community dynamics and its links with ecosystem functioning remains challenging due to the tremendous diversity of microorganisms. Conceptual frameworks that make sense of time-series of taxonomically-rich bacterial communities, regarding their potential ecological function, are needed. A key concept for organizing ecological functions is the niche, the set of strategies that enable a population to persist and define its impacts on the surroundings. Here we present a framework based on manifold learning, to organize genomic information into potentially occupied bacterial metabolic niches over time. Manifold learning tries to uncover low-dimensional data structures in high-dimensional datasets, that can be used to describe the data in reduced dimensions. We apply the method to re-construct the dynamics of putatively occupied metabolic niches using a long-term bacterial time-series from the Baltic Sea, the Linnaeus Microbial Observatory (LMO). The results reveal a relatively low-dimensional space of occupied metabolic niches comprising groups of taxa with similar functional capabilities. Time patterns of occupied niches were strongly driven by seasonality. Some metabolic niches were dominated by one bacterial taxon whereas others were occupied by multiple taxa, depending on season. These results illustrate the power of manifold learning approaches to advance our understanding of the links between community composition and functioning in microbial systems. IMPORTANCE The increase in data availability of bacterial communities highlights the need for conceptual frameworks to advance our understanding of these complex and diverse communities alongside the production of such data. To understand the dynamics of these tremendously diverse communities, we need tools to identify overarching strategies and describe their role and function in the ecosystem in a comprehensive way. Here, we show that a manifold learning approach can coarse grain bacterial communities in terms of their metabolic strategies and that we can thereby quantitatively organize genomic information in terms of potentially occupied niches over time. This approach therefore advances our understanding of how fluctuations in bacterial abundances and species composition can relate to ecosystem functions and it can facilitate the analysis, monitoring and future predictions of the development of microbial communities.

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Use of commercial or indigenous yeast impacts the S. cerevisiae transcriptome during wine fermentation

Whiteley,

Rieckh,

Diggle

et al. 2024

Microbiol Spectr

0

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Grapes have been cultivated for wine production for millennia. Wine production involves a complex biochemical process where sugars in grapes must be converted into alcohol and other compounds by microbial fermentation, primarily by the yeast Saccharomyces cerevisiae . Commercially available S. cerevisiae strains are often used in winemaking, but indigenous (native) strains are gaining attention for their potential to contribute unique flavors. Recent advancements in high-throughput DNA sequencing have revolutionized our understanding of microbial communities during wine fermentation. Indeed, transcriptomic analysis of S. cerevisiae during wine fermentation has revealed a core gene expression program and provided insights into how this yeast adapts to fermentation conditions. Here, we assessed how the age of vines impacts the grape fungal microbiome and used transcriptomics to characterize microbial functions in grape must be fermented with commercial and native S. cerevisiae . We discovered that ~130-year-old Zinfandel vines harbor higher fungal loads on their grapes compared to 20-year-old Zinfandel vines, but fungal diversity is similar. Additionally, a comparison of inoculated and uninoculated fermentations showed distinct fungal dynamics, with uninoculated fermentations harboring the yeasts Metschnikowia and Pichia . Transcriptomic analysis revealed significant differences in gene expression between fermentations inoculated and not inoculated with a commercial S. cerevisiae strain. Genes related to metabolism, stress response, and cell adhesion were differentially expressed, indicating varied functionality of S. cerevisiae in these fermentations. These findings provide insights into S. cerevisiae function during fermentation and highlight the potential for indigenous yeast to contribute to wine diversity. IMPORTANCE Understanding microbial functions during wine fermentation, particularly the role of Saccharomyces cerevisiae , is crucial for enhancing wine quality. While commercially available S. cerevisiae strains are commonly used, indigenous strains can offer unique flavors, potentially reflecting vineyard terroir. By leveraging high-throughput DNA sequencing and transcriptomic analysis, we explored the impact of vine age on the grape mycobiome and characterized microbial functions during grape fermentation. Our findings revealed that older vines harbor higher fungal loads, but fungal diversity remains similar across vine ages. Additionally, uninoculated fermentations exhibited diverse fungal dynamics, including the beneficial wine yeasts Metschnikowia and Pichia. Transcriptomic analysis uncovered significant differences in S. cerevisiae gene expression between inoculated and uninoculated fermentations, highlighting the potential of indigenous yeast to enhance wine diversity and inform winemaking practices.

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Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps

Cited by 3 publications

References 65 publications

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Use of commercial or indigenous yeast impacts the S. cerevisiae transcriptome during wine fermentation

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