Genomic and ecological factors shaping specialism and generalism across an entire subphylum.

Journal

bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187

Informations de publication

Date de publication:
08 Sep 2023
Historique:
pubmed: 10 7 2023
medline: 10 7 2023
entrez: 10 7 2023
Statut: epublish

Résumé

Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,049 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.

Identifiants

DOI: 10.1101/2023.06.19.545611 PMID: 37425695 PMC: PMC10327049
pubmed: 37425695
doi: 10.1101/2023.06.19.545611
pmc: PMC10327049
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NIAID NIH HHS
ID : R01 AI153356
Pays : United States
Organisme : NIAID NIH HHS
ID : R56 AI146096
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM007133
Pays : United States
Organisme : NHGRI NIH HHS
ID : T32 HG002760
Pays : United States

Déclaration de conflit d'intérêts

Competing interests: JLS is a scientific adviser for WittGen Biotechnologies and an adviser for ForensisGroup, Inc. AR is a scientific consultant for LifeMine Therapeutics, Inc. The other authors declare no other competing interests.

Auteurs

Dana A Opulente (DA)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Biology Department Villanova University, Villanova, PA 19085, USA.

Abigail Leavitt LaBella (A)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223.

Marie-Claire Harrison (MC)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.

John F Wolters (JF)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Chao Liu (C)

College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China.

Yonglin Li (Y)

Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.

Jacek Kominek (J)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA.

Jacob L Steenwyk (JL)

Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.

Hayley R Stoneman (HR)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Jenna VanDenAvond (J)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Caroline R Miller (CR)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Quinn K Langdon (QK)

Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Margarida Silva (M)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Carla Gonçalves (C)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA; Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of WisconsinMadison, Madison, WI 53726, USA.

Emily J Ubbelohde (EJ)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Yuanning Li (Y)

Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.

Kelly V Buh (KV)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Martin Jarzyna (M)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Graduate Program in Neuroscience and Department of Biology, Washington University School of Medicine, St. Louis, MO 63130, USA.

Max A B Haase (MAB)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA.

Carlos A Rosa (CA)

Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.

Neža Čadež (N)

Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

Diego Libkind (D)

Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina.

Jeremy H DeVirgilio (JH)

Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA.

Amanda Beth Hulfachor (A)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Cletus P Kurtzman (CP)

Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA.

José Paulo Sampaio (JP)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Paula Gonçalves (P)

UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.

Xiaofan Zhou (X)

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.

Xing-Xing Shen (XX)

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China.

Marizeth Groenewald (M)

Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The Netherlands.

Antonis Rokas (A)

Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.

Chris Todd Hittinger (CT)

Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.

Classifications MeSH