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A more realistic model of microbial mobility and its effect on coexistence

Ward Quaghebeur (UGent) , Aisling Daly (UGent) , Jan Baetens (UGent) and Bernard De Baets (UGent)
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Abstract
Biodiversity is a key factor underpinning the stability and productivity of microbial ecosystems. However, the mechanisms that give rise to and maintain biodiversity in microbial communities are not yet fully understood. The individual-based model (IBM) developed by Reichenbach et al. [1] has been used extensively in literature to investigate biodiversity in microbial communities. It is based on a three-species intransitive competition structure, found in real microbial communities [2]. When interactions are localised on a lattice, bacteria arrange themselves in spatial structures, thereby maintaining coexistence. However, models are always an approximation of reality, and in this case a strict simplification of mobility was used. Therefore, we modified the original model in several significant ways to make it more realistic, and investigated the influence on the maintenance of coexistence. First, we constructed its lattice-free counterpart, allowing the bacteria to position themselves more realistically. We found that this approach allows maintenance of coexistence better than the lattice-based model. By having more spatial degrees of freedom, the spirals in the lattice-free model tend to be more robust, with small refuges able to survive, thereby maintaining coexistence. These findings agree with experimental results [2]. Second, we adapted the movement mechanism of the Reichenbach's IBM to mimic movement more realistically. We found similar qualitative dynamics, namely emerging spatial patterns and a jeopardising effect of mobility on coexistence. Finally, we incorporated substrate-dependent growth. We found that a higher substrate availability allows the system to support more individuals, thereby retrieving the macroscopic concept of carrying capacity, and also promoting the maintenance of coexistence. Furthermore, adding substrate dynamics to the model promotes the maintenance of coexistence by lowering the rate of reproduction. These adaptations made the model more representative of real microbial systems.
Keywords
KERMIT, coexistence, individual-based model, mobility, biodiversity

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Chicago
Quaghebeur, Ward, Aisling Daly, Jan Baetens, and Bernard De Baets. 2017. “A More Realistic Model of Microbial Mobility and Its Effect on Coexistence.” In Proceedings of the 2nd International MRM Conference .
APA
Quaghebeur, W., Daly, A., Baetens, J., & De Baets, B. (2017). A more realistic model of microbial mobility and its effect on coexistence. Proceedings of the 2nd international MRM conference . Presented at the 2nd international MRM conference .
Vancouver
1.
Quaghebeur W, Daly A, Baetens J, De Baets B. A more realistic model of microbial mobility and its effect on coexistence. Proceedings of the 2nd international MRM conference . 2017.
MLA
Quaghebeur, Ward, Aisling Daly, Jan Baetens, et al. “A More Realistic Model of Microbial Mobility and Its Effect on Coexistence.” Proceedings of the 2nd International MRM Conference . 2017. Print.
@inproceedings{8588355,
  abstract     = {Biodiversity is a key factor underpinning the stability and productivity of microbial ecosystems. However, the mechanisms that give rise to and maintain biodiversity in microbial communities are not yet fully understood. The individual-based model (IBM) developed by Reichenbach et al. [1] has been used extensively in literature to investigate biodiversity in microbial communities. It is based on a three-species intransitive competition structure, found in real microbial communities [2]. When interactions are localised on a lattice, bacteria arrange themselves in spatial structures, thereby maintaining coexistence. However, models are always an approximation of reality, and in this case a strict simplification of mobility was used. Therefore, we modified the original model in several significant ways to make it more realistic, and investigated the influence on the maintenance of coexistence. First, we constructed its lattice-free counterpart, allowing the bacteria to position themselves more realistically. We found that this approach allows maintenance of coexistence better than the lattice-based model. By having more spatial degrees of freedom, the spirals in the lattice-free model tend to be more robust, with small refuges able to survive, thereby maintaining coexistence. These findings agree with experimental results [2]. Second, we adapted the movement mechanism of the Reichenbach's IBM to mimic movement more realistically. We found similar qualitative dynamics, namely emerging spatial patterns and a jeopardising effect of mobility on coexistence. Finally, we incorporated substrate-dependent growth. We found that a higher substrate availability allows the system to support more individuals, thereby retrieving the macroscopic concept of carrying capacity, and also promoting the maintenance of coexistence. Furthermore, adding substrate dynamics to the model promotes the maintenance of coexistence by lowering the rate of reproduction. These adaptations made the model more representative of real microbial systems. },
  author       = {Quaghebeur, Ward and Daly, Aisling and Baetens, Jan and De Baets, Bernard},
  booktitle    = {Proceedings of the 2nd international MRM conference },
  keyword      = {KERMIT,coexistence,individual-based model,mobility,biodiversity},
  location     = {Ghent},
  title        = {A more realistic model of microbial mobility and its effect on coexistence},
  year         = {2017},
}