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Individual-based modelling of invasion in bioaugmented sand filter communities

Aisling Daly (UGent) , Jan Baetens (UGent) , Johanna Vandermaesen, Nico Boon (UGent) , Dirk Springael and Bernard De Baets (UGent)
(2018) PROCESSES. 6(1).
Author
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Abstract
Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synthesizing these effects into a competition structure for our model. Pairwise competition outcomes are determined based on interaction effects in terms of functionality. We also consider non-deterministic competition, where winning probabilities are assigned based on the relative intrinsic competitiveness of each strain. Our model is able to reproduce the key qualitative dynamics observed in in vitro experiments with similar synthetic sand filter communities. Simulation outcomes can be explained based on the underlying competition structures and the resulting spatial dynamics. Our results highlight the importance of community diversity and in particular evenness in stabilizing the community dynamics, allowing us to study the establishment and development of these communities, and thereby illustrate the potential of the individual-based modelling approach for addressing microbial ecological theories related to synthetic communities.
Keywords
individual-based model, invasion, bioaugmentation, engineered community, MICROBIAL-GROWTH, METABOLITE 2, 6-DICHLOROBENZAMIDE, HERBICIDE DICHLOBENIL, ECOSYSTEMS, INTRANSITIVITY, BIODIVERSITY, POPULATIONS, COEXISTENCE, REGRESSION, DIVERSITY

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Citation

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MLA
Daly, Aisling, et al. “Individual-Based Modelling of Invasion in Bioaugmented Sand Filter Communities.” PROCESSES, vol. 6, no. 1, 2018, doi:10.3390/pr6010002.
APA
Daly, A., Baetens, J., Vandermaesen, J., Boon, N., Springael, D., & De Baets, B. (2018). Individual-based modelling of invasion in bioaugmented sand filter communities. PROCESSES, 6(1). https://doi.org/10.3390/pr6010002
Chicago author-date
Daly, Aisling, Jan Baetens, Johanna Vandermaesen, Nico Boon, Dirk Springael, and Bernard De Baets. 2018. “Individual-Based Modelling of Invasion in Bioaugmented Sand Filter Communities.” PROCESSES 6 (1). https://doi.org/10.3390/pr6010002.
Chicago author-date (all authors)
Daly, Aisling, Jan Baetens, Johanna Vandermaesen, Nico Boon, Dirk Springael, and Bernard De Baets. 2018. “Individual-Based Modelling of Invasion in Bioaugmented Sand Filter Communities.” PROCESSES 6 (1). doi:10.3390/pr6010002.
Vancouver
1.
Daly A, Baetens J, Vandermaesen J, Boon N, Springael D, De Baets B. Individual-based modelling of invasion in bioaugmented sand filter communities. PROCESSES. 2018;6(1).
IEEE
[1]
A. Daly, J. Baetens, J. Vandermaesen, N. Boon, D. Springael, and B. De Baets, “Individual-based modelling of invasion in bioaugmented sand filter communities,” PROCESSES, vol. 6, no. 1, 2018.
@article{8553494,
  abstract     = {{Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synthesizing these effects into a competition structure for our model. Pairwise competition outcomes are determined based on interaction effects in terms of functionality. We also consider non-deterministic competition, where winning probabilities are assigned based on the relative intrinsic competitiveness of each strain. Our model is able to reproduce the key qualitative dynamics observed in in vitro experiments with similar synthetic sand filter communities. Simulation outcomes can be explained based on the underlying competition structures and the resulting spatial dynamics. Our results highlight the importance of community diversity and in particular evenness in stabilizing the community dynamics, allowing us to study the establishment and development of these communities, and thereby illustrate the potential of the individual-based modelling approach for addressing microbial ecological theories related to synthetic communities.}},
  articleno    = {{2}},
  author       = {{Daly, Aisling and Baetens, Jan and Vandermaesen, Johanna and Boon, Nico and Springael, Dirk and De Baets, Bernard}},
  issn         = {{2227-9717}},
  journal      = {{PROCESSES}},
  keywords     = {{individual-based model,invasion,bioaugmentation,engineered community,MICROBIAL-GROWTH,METABOLITE 2,6-DICHLOROBENZAMIDE,HERBICIDE DICHLOBENIL,ECOSYSTEMS,INTRANSITIVITY,BIODIVERSITY,POPULATIONS,COEXISTENCE,REGRESSION,DIVERSITY}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{21}},
  title        = {{Individual-based modelling of invasion in bioaugmented sand filter communities}},
  url          = {{http://doi.org/10.3390/pr6010002}},
  volume       = {{6}},
  year         = {{2018}},
}
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