Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts

Science, Journal Year: 2024, Volume and Issue: 384(6694)

Published: April 25, 2024

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to broad (generalists). Two general paradigms have been proposed explain this variation: (i) trade-offs between performance efficiency and breadth (ii) the joint influence of extrinsic (environmental) intrinsic (genomic) factors. We assembled genomic, metabolic, data nearly all known species ancient fungal subphylum Saccharomycotina (1154 yeast strains 1051 species), grown 24 different environmental conditions, examine evolution. found that large differences carbon utilization traits yeasts stem genes encoding specific metabolic pathways, but we limited evidence for trade-offs. These comprehensive argue factors shape microbes.

Language: Английский

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Machine learning enables identification of an alternative yeast galactose utilization pathway

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(18)

Published: April 26, 2024

How genomic differences contribute to phenotypic is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources conditions 1,154 strains from 1,049 fungal species (nearly all known) the yeast subphylum Saccharomycotina provide powerful, yet complex, dataset for addressing this question. We used random forest algorithm trained these genomic, metabolic, environmental data predict several carbon with high accuracy. Known structural genes involved assimilation presence/absence other were important features contributing prediction By further examining galactose, we found that it can be predicted accuracy either (92.2%) or (82.6%) but not environment (65.6%). Prediction was even higher (93.3%) when combined data. After

Language: Английский

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The rate of glucose metabolism sets the cell morphology across yeast strains and species

Current Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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Microbial Community Structure and Causal Analysis. in Sediments of Shallow Eutrophic Freshwater Lakes. Under Heavy Metal Compound Pollution

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 487, P. 137135 - 137135

Published: Jan. 7, 2025

Language: Английский

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Ancient origin and high diversity of zymocin-like killer toxins in the budding yeast subphylum

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(7)

Published: Feb. 10, 2025

Zymocin is a well-characterized killer toxin secreted by some strains of the yeast Kluyveromyces lactis . It acts cleaving specific tRNA in sensitive recipient cells. encoded plasmid or virus-like element (VLE), which linear DNA molecule located cytosol. We hypothesized that tRNA-cleaving similar to zymocin may have caused three parallel changes nuclear genetic code occurred during evolution, codon CUG became translated as Ser Ala instead Leu. However, zymocin-like toxins are rare — both among species, and within species —and only four this type previously been discovered. Here, we identified 45 genes Saccharomycotina, budding subphylum, using bioinformatics strategy, verified many them toxic Saccharomyces cerevisiae when expressed. Some on cytosolic VLEs, whereas others VLE-derived integrated into genome. The extraordinarily diverse sequence show evidence positive selection. Toxin were found five taxonomic orders yeasts, including two reassigned codons, indicating VLEs parasites for at least 300 My their existence predates changes.

Language: Английский

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Celebrating the fifth edition of the International Symposium on Fungal Stress – ISFUS, a decade after its 2014 debut

Fungal Biology, Journal Year: 2025, Volume and Issue: unknown, P. 101590 - 101590

Published: May 1, 2025

Language: Английский

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Diverse signatures of convergent evolution in cactus-associated yeasts

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(9), P. e3002832 - e3002832

Published: Sept. 23, 2024

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset genomic data from 1,049 yeast species subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) explore signatures convergent evolution cactophilic yeasts, specialists associated with cacti. We inferred association yeasts cacti arose independently approximately 17 times. Using machine learning-based approach, further found cactophily can be predicted 76% accuracy both functional data. The most informative feature for predicting was thermotolerance, which likely altered evolutionary rates genes impacting cell envelope several lineages. also identified horizontal gene transfer duplication events plant wall-degrading enzymes clades, suggesting putatively adaptive disparate molecular mechanisms. Notably, multiple their close relatives been reported as emerging human opportunistic pathogens, lifestyle-and perhaps more generally favoring thermotolerance-might preadapt cause disease. This work underscores potential multifaceted approach involving high-throughput shed light onto adaptation highlights how wild environments could facilitate transition pathogenicity.

Language: Английский

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Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating Baijiu fermentation through multi-omics analysis

Food Microbiology, Journal Year: 2024, Volume and Issue: 125, P. 104655 - 104655

Published: Oct. 9, 2024

Language: Английский

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Effects of soil water on fungal community composition along elevational gradients on the northern slope of the Central Kunlun Mountains

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 8, 2025

Soil fungi are essential to ecosystem processes, yet their elevational distribution patterns and the ecological mechanisms shaping communities remain poorly understood actively debated, particularly in arid regions. Here, we investigated diversity underlying soil fungal along an gradient (1,707-3,548 m) on northern slope of Central Kunlun Mountains northwest China. Results indicated that dominant phyla identified across seven gradients were Basidiomycota Ascomycota, displaying a unimodal pattern U-shaped relative abundance, respectively. saprotroph nectar/tap functional groups (>1.0%). Along gradients, α-diversity demonstrated generally decreasing trend, whereas β-diversity showed contrasting increasing trend. Among environmental variables, altitude climate (mean annual precipitation, MAP; mean temperature, MAT) strongest predictors for α-diversity. Partial least squares path modeling (PLSPM) analysis revealed water content (Wat) was most influential factor driving α-diversity, while vegetation coverage (Veg) emerged as primary determinant community composition. The influence Wat shifted from indirect direct elevation increased, transitioning lower elevations (≤2,448 higher (≥2,746 m). Similarly, impact Veg composition exhibited comparable pattern. null model homogeneous selection dispersal limitation dominated assembly at than 2,448 m 2,746 m, Variations processes may be linked changes key factors elevation-dependent manner. These findings can enhance our ability predict responses change ecosystems Mountain.

Language: Английский

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Whole‐Genome Sequencing and Phenotyping Reveal Specific Adaptations of Lachancea thermotolerans to the Winemaking Environment

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 6, 2025

ABSTRACT Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans , related fermentation and one current trends wine technology research, has undergone anthropisation process, leading notable genomic phenomic differentiation. Using whole‐genome sequencing, 145 L. strains, we identified six well‐defined groups primarily delineated by their ecological origin exhibiting high levels genetic diversity. Anthropised strains showed lower diversity due pressure imposed winemaking environment. Strong evidence adaptation through modification gene content was also found. Differences genes involved assimilation alternative carbon nitrogen sources, such MAL31 DAL5 genes, which confer greater fitness environment, were observed. Additionally, found that phenotypic traits considered domestication hallmarks are present anthropised strains. Among these, increased presence ethanol sulphites, non‐fermentable residual fructose under fermentative conditions highlight. We hypothesise lactic acid production Saccharomyces‐Lachancea lineage is signature linked winemaking, resulting from loss respiratory chain complex I evolutionary preference for over respiration, even oxygen. Overall, results this work provide valuable insight into process demonstrate how environments give rise similar adaptations different species.

Language: Английский

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