Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts
Dana A. Opulente, Abigail L. LaBella, Marie‐Claire Harrison, John F. Wolters, Chao Liu, Yonglin Li, Jacek Kominek, Jacob L. Steenwyk, Hayley R Stoneman, Jenna VanDenAvond, Caroline R. Miller, Quinn K. Langdon, Margarida Silva, Carla Gonçalves, Emily J. Ubbelohde, Yuanning Li, Kelly V. Buh, Martin Jarzyna, Max A. B. Haase, Carlos A. Rosa, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P. Kurtzman, José Paulo Sampaio, Paula Gonçalves, Xiaofan Zhou, Xing‐Xing Shen, Marizeth Groenewald, Antonis Rokas, Chris Todd Hittinger
Abstract
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. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.