Advancing microbial sciences by individual-based modelling

作者: Ferdi L. Hellweger , Robert J. Clegg , James R. Clark , Caroline M. Plugge , Jan-Ulrich Kreft

DOI: 10.1038/NRMICRO.2016.62

关键词:

摘要: Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on findings such they help to explore competitive cooperative microbial interactions. Furthermore, describe IBMs provided insights into self-organized spatial patterns from biofilms oceans world, phage-CRISPR dynamics other emergent phenomena. Finally, discuss combining observations with advance our understanding at both population levels, leading new approach ecology (μIBE).

参考文章(93)
Mikkel Klausen, Anders Aaes-Jørgensen, Søren Molin, Tim Tolker-Nielsen, Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms Molecular Microbiology. ,vol. 50, pp. 61- 68 ,(2003) , 10.1046/J.1365-2958.2003.03677.X
S. Matsumoto, A. Terada, Y. Aoi, S. Tsuneda, E. Alpkvist, C. Picioreanu, M.C.M. van Loosdrecht, Experimental and simulation analysis of community structure of nitrifying bacteria in a membrane-aerated biofilm. Water Science and Technology. ,vol. 55, pp. 283- 290 ,(2007) , 10.2166/WST.2007.269
M. Heldal, D. J. Scanlan, S. Norland, F. Thingstad, N. H. Mann, Elemental composition of single cells of various strains of marine Prochlorococcus and Synechococcus using X‐ray microanalysis Limnology and Oceanography. ,vol. 48, pp. 1732- 1743 ,(2003) , 10.4319/LO.2003.48.5.1732
Matthew R. Evans, Volker Grimm, Karin Johst, Tarja Knuuttila, Rogier de Langhe, Catherine M. Lessells, Martina Merz, Maureen A. O’Malley, Steve H. Orzack, Michael Weisberg, Darren J. Wilkinson, Olaf Wolkenhauer, Tim G. Benton, Do simple models lead to generality in ecology? Trends in Ecology & Evolution. ,vol. 28, pp. 578- 583 ,(2013) , 10.1016/J.TREE.2013.05.022
D.J. Batstone, C. Picioreanu, M.C.M van Loosdrecht, Multidimensional modelling to investigate interspecies hydrogen transfer in anaerobic biofilms. Water Research. ,vol. 40, pp. 3099- 3108 ,(2006) , 10.1016/J.WATRES.2006.06.014
Volker Grimm, Uta Berger, Donald L. DeAngelis, J. Gary Polhill, Jarl Giske, Steven F. Railsback, The ODD protocol: A review and first update Ecological Modelling. ,vol. 221, pp. 2760- 2768 ,(2010) , 10.1016/J.ECOLMODEL.2010.08.019
Donald L. DeAngelis, Wolf M. Mooij, Individual-Based Modeling of Ecological and Evolutionary Processes Annual Review of Ecology, Evolution, and Systematics. ,vol. 36, pp. 147- 168 ,(2005) , 10.1146/ANNUREV.ECOLSYS.36.102003.152644
Dann Huh, Johan Paulsson, Non-genetic heterogeneity from stochastic partitioning at cell division Nature Genetics. ,vol. 43, pp. 95- 100 ,(2011) , 10.1038/NG.729