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

Opulente, Dana A.; LaBella, Abigail Leavitt; Harrison, Marie-Claire; Wolters, John F.; Liu, Chao; Li, Yonglin; Kominek, Jacek; Steenwyk, Jacob L.; Stoneman, Hayley R.; VanDenAvond, Jenna; Miller, Caroline R.; Langdon, Quinn K.; Silva, Margarida; Gonçalves, Carla; Ubbelohde, Emily J.; Li, Yuanning; Buh, Kelly V.; Jarzyna, Martin; Haase, Max A. B.; Rosa, Carlos A.; ČCadež, Neža; Libkind, Diego; DeVirgilio, Jeremy H.; Hulfachor, Amanda Beth; Kurtzman, Cletus P.; Sampaio, José Paulo; Gonçalves, Paula; Zhou, Xiaofan; Shen, Xing-Xing; Groenewald, Marizeth; Rokas, Antonis; Hittinger, Chris Todd

doi:10.1126/science.adj4503

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

Journal Article · 26 April 2024 · Science

DOI: https://doi.org/10.1126/science.adj4503 · OSTI ID:2406610

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University of Wisconsin–Madison, WI (United States); Villanova University, PA (United States); Vanderbilt University Department of Biological Sciences and Evolutionary Studies Initiative
Vanderbilt University, Nashville, TN (United States); University of North Carolina at Charlotte, Kannapolis, NC (United States)
Vanderbilt University, Nashville, TN (United States)
University of Wisconsin–Madison, WI (United States)
Zhejiang University, Hangzhou (China)
South China Agricultural University, Guangzhou (China)
University of Wisconsin–Madison, WI (United States); LifeMine Therapeutics, Inc., Cambridge, MA (United States)
Vanderbilt University, Nashville, TN (United States); University of California, Berkeley, CA (United States)
University of Wisconsin–Madison, WI (United States); University of Colorado Anschutz Medical Campus, Aurora, CO (United States)
Universidade NOVA de Lisboa, Caparica (Portugal)
University of Wisconsin–Madison, WI (United States); Vanderbilt University, Nashville, TN (United States); Universidade NOVA de Lisboa, Caparica (Portugal)
Vanderbilt University, Nashville, TN (United States); Shandong University, Qingdao (China); Qingdao Marine Science and Technology Center (China)
University of Wisconsin–Madison, WI (United States); Washington University School of Medicine, St. Louis, MO (United States)
University of Wisconsin–Madison, WI (United States); NYU Langone Health, New York, NY (United States); Max Planck Institute of Molecular Physiology, Dortmund (Germany)
Universidade Federal de Minas Gerais (Brazil)
University of Ljubljana (Slovenia)
Universidad Nacional del Comahue (Argentina)
US Department of Agriculture, Peoria, IL (United States)
Vanderbilt University, Nashville, TN (United States); South China Agricultural University, Guangzhou (China)
Vanderbilt University, Nashville, TN (United States); Zhejiang University, Hangzhou (China)
Westerdijk Fungal Biodiversity Institute (Netherlands)

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

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Research Organization:: Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); National Institutes of Health (NIH), National Institute of Allergy and Infectious Diseases (NIAID); National Key R&D Program of China; National Science Foundation for Distinguished Young Scholars of Zhejiang Province; Fundamental Research Funds for the Central Universities; Slovenian Research Agency; Fundação para a Ciência e a Tecnologia

Grant/Contract Number:: SC0018409

OSTI ID:: 2406610

Journal Information:: Science, Journal Name: Science Journal Issue: 6694 Vol. 384; ISSN 0036-8075

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: English

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