Challenges in microbial ecology

building predictive understanding of community function and dynamics

Stefanie Widder, Rosalind J Allen, Thomas Pfeiffer, Thomas P Curtis, Carsten Wiuf, William T Sloan, Otto X Cordero, Sam P Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J Flint, Andreas F Haas, Béatrice Laroche, Jan-Ulrich Kreft, Paul B Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R van der Meer & 11 others Tobias Groszkopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F Smets, Harris Wang, Orkun S Soyer, Isaac Newton Institute Fellows

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180 Citations (Scopus)
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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.The ISME Journal advance online publication, 29 March 2016; doi:10.1038/ismej.2016.45.

Original languageEnglish
Pages (from-to)2557-2568
Number of pages12
JournalThe ISME Journal
Volume10
Issue number11
Early online date29 Mar 2016
DOIs
Publication statusPublished - Nov 2016

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microbial ecology
Ecology
microbial communities
microbial community
Atmosphere
Oceans and Seas
biogeochemical cycle
Ecosystem
community dynamics
Publications
ecosystem function
Theoretical Models
Soil
biogeochemical cycles
community composition
mathematical models
experiment
oceans
Research
atmosphere

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Widder, S., Allen, R. J., Pfeiffer, T., Curtis, T. P., Wiuf, C., Sloan, W. T., ... Isaac Newton Institute Fellows (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. The ISME Journal, 10(11), 2557-2568. https://doi.org/10.1038/ismej.2016.45

Challenges in microbial ecology : building predictive understanding of community function and dynamics. / Widder, Stefanie; Allen, Rosalind J; Pfeiffer, Thomas; Curtis, Thomas P; Wiuf, Carsten; Sloan, William T; Cordero, Otto X; Brown, Sam P; Momeni, Babak; Shou, Wenying; Kettle, Helen; Flint, Harry J; Haas, Andreas F; Laroche, Béatrice; Kreft, Jan-Ulrich; Rainey, Paul B; Freilich, Shiri; Schuster, Stefan; Milferstedt, Kim; van der Meer, Jan R; Groszkopf, Tobias; Huisman, Jef; Free, Andrew; Picioreanu, Cristian; Quince, Christopher; Klapper, Isaac; Labarthe, Simon; Smets, Barth F; Wang, Harris; Soyer, Orkun S; Isaac Newton Institute Fellows.

In: The ISME Journal, Vol. 10, No. 11, 11.2016, p. 2557-2568.

Research output: Contribution to journalArticle

Widder, S, Allen, RJ, Pfeiffer, T, Curtis, TP, Wiuf, C, Sloan, WT, Cordero, OX, Brown, SP, Momeni, B, Shou, W, Kettle, H, Flint, HJ, Haas, AF, Laroche, B, Kreft, J-U, Rainey, PB, Freilich, S, Schuster, S, Milferstedt, K, van der Meer, JR, Groszkopf, T, Huisman, J, Free, A, Picioreanu, C, Quince, C, Klapper, I, Labarthe, S, Smets, BF, Wang, H, Soyer, OS & Isaac Newton Institute Fellows 2016, 'Challenges in microbial ecology: building predictive understanding of community function and dynamics', The ISME Journal, vol. 10, no. 11, pp. 2557-2568. https://doi.org/10.1038/ismej.2016.45
Widder, Stefanie ; Allen, Rosalind J ; Pfeiffer, Thomas ; Curtis, Thomas P ; Wiuf, Carsten ; Sloan, William T ; Cordero, Otto X ; Brown, Sam P ; Momeni, Babak ; Shou, Wenying ; Kettle, Helen ; Flint, Harry J ; Haas, Andreas F ; Laroche, Béatrice ; Kreft, Jan-Ulrich ; Rainey, Paul B ; Freilich, Shiri ; Schuster, Stefan ; Milferstedt, Kim ; van der Meer, Jan R ; Groszkopf, Tobias ; Huisman, Jef ; Free, Andrew ; Picioreanu, Cristian ; Quince, Christopher ; Klapper, Isaac ; Labarthe, Simon ; Smets, Barth F ; Wang, Harris ; Soyer, Orkun S ; Isaac Newton Institute Fellows. / Challenges in microbial ecology : building predictive understanding of community function and dynamics. In: The ISME Journal. 2016 ; Vol. 10, No. 11. pp. 2557-2568.
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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.The ISME Journal advance online publication, 29 March 2016; doi:10.1038/ismej.2016.45.",
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AU - Widder, Stefanie

AU - Allen, Rosalind J

AU - Pfeiffer, Thomas

AU - Curtis, Thomas P

AU - Wiuf, Carsten

AU - Sloan, William T

AU - Cordero, Otto X

AU - Brown, Sam P

AU - Momeni, Babak

AU - Shou, Wenying

AU - Kettle, Helen

AU - Flint, Harry J

AU - Haas, Andreas F

AU - Laroche, Béatrice

AU - Kreft, Jan-Ulrich

AU - Rainey, Paul B

AU - Freilich, Shiri

AU - Schuster, Stefan

AU - Milferstedt, Kim

AU - van der Meer, Jan R

AU - Groszkopf, Tobias

AU - Huisman, Jef

AU - Free, Andrew

AU - Picioreanu, Cristian

AU - Quince, Christopher

AU - Klapper, Isaac

AU - Labarthe, Simon

AU - Smets, Barth F

AU - Wang, Harris

AU - Soyer, Orkun S

AU - Isaac Newton Institute Fellows

N1 - Acknowledgements We thank the Isaac Newton Institute of Mathematical Sciences for hosting the programme ‘Understanding microbial communities: structure, function dynamics’, which made this paper possible. This programme was partially funded by the Biotechnology and Biological Sciences Research Council and the US Army Research Office under grant number W911NF-14-1-0445. We thank all participants of the programme for inspiring discussions, and Aglika Gungova and Stela Ilieva for assistance with the figures.

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