title: Challenges in microbial ecology: building predictive understanding of community function and dynamics.
abstract: The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model-experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.
authors.affiliation: CUBE, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
authors.forename: Stefanie
authors.identifier: 0000-0003-0733-5666
authors.initials: S
authors.lastname: Widder
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
authors.forename: Rosalind J
authors.initials: RJ
authors.lastname: Allen
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.
authors.forename: Thomas
authors.initials: T
authors.lastname: Pfeiffer
authors.affiliation: School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Curtis
authors.affiliation: Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Carsten
authors.initials: C
authors.lastname: Wiuf
authors.affiliation: Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, UK.
authors.forename: William T
authors.initials: WT
authors.lastname: Sloan
authors.affiliation: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Otto X
authors.initials: OX
authors.lastname: Cordero
authors.affiliation: Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
authors.forename: Sam P
authors.identifier: 0000-0003-1892-9275
authors.initials: SP
authors.lastname: Brown
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, MA, USA.|Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Babak
authors.identifier: 0000-0003-1271-5196
authors.initials: B
authors.lastname: Momeni
authors.affiliation: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
authors.forename: Wenying
authors.initials: W
authors.lastname: Shou
authors.affiliation: Biomathematics and Statistics Scotland, Edinburgh, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Kettle
authors.affiliation: Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK.
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
authors.affiliation: Biology Department, San Diego State University, San Diego, CA, USA.
authors.forename: Andreas F
authors.initials: AF
authors.lastname: Haas
authors.affiliation: Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France.
authors.forename: Béatrice
authors.initials: B
authors.lastname: Laroche
authors.affiliation: School of Biosciences, University of Birmingham, Birmingham, UK.
authors.forename: Jan-Ulrich
authors.identifier: 0000-0002-2351-224X
authors.initials: JU
authors.lastname: Kreft
authors.affiliation: New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Rainey
authors.affiliation: Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel.
authors.forename: Shiri
authors.initials: S
authors.lastname: Freilich
authors.affiliation: Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schuster
authors.affiliation: INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Narbonne, France.
authors.forename: Kim
authors.initials: K
authors.lastname: Milferstedt
authors.affiliation: Department of Fundamental Microbiology, Université de Lausanne, Lausanne, Switzerland.
authors.forename: Jan R
authors.initials: JR
authors.lastname: van der Meer
authors.affiliation: School of Life Sciences, The University of Warwick, Coventry, UK.
authors.forename: Tobias
authors.initials: T
authors.lastname: Groβkopf
authors.affiliation: Department of Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands.
authors.forename: Jef
authors.initials: J
authors.lastname: Huisman
authors.affiliation: Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Science, University of Edinburgh, Edinburgh, UK.
authors.forename: Andrew
authors.initials: A
authors.lastname: Free
authors.affiliation: Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
authors.forename: Cristian
authors.initials: C
authors.lastname: Picioreanu
authors.affiliation: Warwick Medical School, University of Warwick, Coventry, UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Quince
authors.affiliation: Department of Mathematics, Temple University, Philadelphia, PA, USA.
authors.forename: Isaac
authors.initials: I
authors.lastname: Klapper
authors.affiliation: Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France.
authors.forename: Simon
authors.initials: S
authors.lastname: Labarthe
authors.affiliation: Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Barth F
authors.identifier: 0000-0003-4119-6292
authors.initials: BF
authors.lastname: Smets
authors.affiliation: Department of Systems Biology, Columbia University, New York, NY, USA.
authors.forename: Harris
authors.initials: H
authors.lastname: Wang
authors.affiliation: School of Life Sciences, The University of Warwick, Coventry, UK.
authors.forename: Orkun S
authors.identifier: 0000-0002-9504-3796
authors.initials: OS
authors.lastname: Soyer
mesh_terms: D000391:Air Microbiology; D000818:Animals; D017753:Ecosystem; D006801:Humans; D008962:Models, Theoretical; D012623:Seawater / Q000382:microbiology*; D012988:Soil Microbiology