A rule-based approach to the modelling of bacterial ecosystems

Vlachos, C.; Paton, Ray; Saunders, J. R.

doi:10.1016/j.biosystems.2005.06.017

Cited by 22 publications

(12 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Different organism types were assigned attributes with complementary functional mechanisms (e.g., secreted versus cell-associated polymer hydrolases). Similarly, since each individual cell could be associated with its own physiological state [22,26,27,42,52], individual-based modeling enabled representation of population diversity with respect to physiological state in response to the local microenvironment.…”

Section: Introductionmentioning

confidence: 99%

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

et al. 2011

View full text Add to dashboard Cite

We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the organisms in the community shared the soluble carbon product and grew together. Although pore geometry affected the kinetics of cellulose degradation, the patterns observed for the bacterial community dynamics in the 6-20 μm-sized micro-pores were relevant to the dynamics in the more complex 111-μm-sized porous soil aggregates, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied. As shown with examples in this study, various functional niches of the bacterial communities can be investigated using complex predictive mathematical models where the role of key environmental aspects such as the heterogeneous three-dimensional structure, functional niches of the community members, and environmental biochemical processes are directly connected to microbial metabolism and maintenance in an integrated model.

show abstract

Section: Introductionmentioning

confidence: 99%

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

et al. 2011

View full text Add to dashboard Cite

show abstract

“…Therefore, in this study, a virtual computer-based system designed to study the evolution of a community of ribozyme-like agents is presented. The system is based on rules in a similar manner to some of the earlier computing systems that have treated the evolution of bacterial populations (Vlachos et al 2006;Gregory et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Dynamics of a Laterally Evolving Community of Ribozyme-Like Agents as Studied with a Rule-Based Computing System

Jalasvuori

Bamford

2009

Orig Life Evol Biosph

View full text Add to dashboard Cite

The very early forms of life probably comprised ribozyme-like agents that were able to catalyze reactions and serve as templates for their own replication. The early evolution has also been suggested to occur mainly horizontally between proto-cells or inorganic compartments rather than vertically from parent cell to their dividing siblings. In order to study the evolutionary dynamics of such a community a rule-based computing system entitled as PrimordialEvo was developed. The system simulates a three dimensional matrix of compartments in which replicators, resource collectors and various other actors thrive. Horizontal movement between compartments may be due to genetically induced vesicle formation or random drift. Analysis of the simulation experiments suggests that active sharing of innovations between compartments is important for the overall reproductive success of life. The capability of natural selection to favor genes in the system was also tested, and, for example, the frequency of anti-parasites was observed to increase when parasites were allowed to emerge.

show abstract

“…Agent-based Models or Individual-based Models (IbMs), in which individuals interact dynamically with each other as structural elements in the model world, exemplify this view of simulation modelling [2]. This type of modelling has become the sine qua non for understanding complex systems and has been used successfully in microbiology [3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

INDISIM-YEAST: an individual-based simulator on a website for experimenting and investigating diverse dynamics of yeast populations in liquid media

Gisbert

Cañadas

2008

J Ind Microbiol Biotechnol

View full text Add to dashboard Cite

Simulation modelling can be used to capture and mimic real-world microbial systems that, unlike the real-world, can then be experimented upon as a new kind of experimental milieu. Individual-based models, in which individuals interact dynamically with each other as structural elements in the model world, exemplify this view of simulation modelling. These models are more difficult to analyze, understand and communicate than traditional analytical models. It is good practice to provide executable versions that perform simulation results. INDISIM-YEAST, developed to deal with yeast populations in liquid media, models the evolution of a set of yeasts by setting up rules of behavior for each individual cell according to its own biological regulations and characteristics. The aim of this work is to develop and present a website from which INDISIM-YEAST is accessible, and how to carry out yeast simulations to further the skills associated with the use of this individual-based simulator. A good and useful way to analyze this yeast simulator is to experiment and explore the manner in which it reacts to changes in parameter values, initial conditions or assumptions. The application results in a very versatile program that could be used in controlled simulation experiments via the Internet.

show abstract

A rule-based approach to the modelling of bacterial ecosystems

Cited by 22 publications

References 20 publications

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

Modeling Microbial Dynamics in Heterogeneous Environments: Growth on Soil Carbon Sources

Dynamics of a Laterally Evolving Community of Ribozyme-Like Agents as Studied with a Rule-Based Computing System

INDISIM-YEAST: an individual-based simulator on a website for experimenting and investigating diverse dynamics of yeast populations in liquid media

Contact Info

Product

Resources

About