Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances

Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)

8 Pág.Synthetic biology aims to develop novel biological systems and increase their reproducibility using engineering principles such as standardization and modularization. It is important that these systems can be represented and shared in a standard way to ensure they can be easily understood, reproduced, and utilized by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterization. Previously, this standard has only been used to represent designs in systems where the same design is implemented in every cell; however, there is also much interest in multicellular systems, in which designs involve a mixture of different types of cells with differing genotype and phenotype. Here, we show how the SBOL standard can be used to represent multicellular systems, and, hence, how researchers can better share designs with the community and reliably document intended system functionality.This work was supported in part by NSF Expeditions in Computing Program Award No. 1522074 as part of the Living Computing Project and by the Defense Advanced Research Projects Agency under Contract No. W911NF-17-2-0098. The views, opinions, and/or findings expressed are of the author(s) and should not be interpreted as representing official views or policies of the Department of Defense or the U.S. Government. A.G.-M. was supported by the SynBio3D project of the UK Engineering and Physical Sciences Research Council (No.EP/R019002/1) and the European CSA on biological standardization BIOROBOOST (EU Grant No. 820699)Peer reviewe

Engineering microbial-induced carbonate precipitation via meso-scale simulations

The engineering of bacterial activity for material production is subject of increasing interest from the scientific community. An important example is controlling microbially induced calcium carbonate precipitation to repair cracks in concrete. For example, by combining experimental research with macroscale modelling, the Resilient Materials for life (RM4L) project has identified a wide array of bacterial strand that can induce biomineralization in concrete. However, there is a range of scale between the micrometre and the millimetre, where the self-organisation of minerals and bacterial activities during biomineralization is not understood. Insights into the processes taking place at those length scales could provide new tools to select the most promising bacterial strands, better targeting future experimental efforts and thus reducing deployment time and cost for the new technology. This contribution will outline a new approach combine existing expertise from the RM4L network (on characterization of bacterial metabolism and engineering modelling and testing of self-healing concrete) with new mesoscale simulations of bacteria-mineral coevolution at Newcastle University. Key barriers for this undertaking will be addressed, and methodologies and first results from mesoscale modelling will be presented

Diversity and metabolic energy in bacteria

Why are some groups of bacteria more diverse than others? We hypothesize that the metabolic energy available to a bacterial functional group (a biogeochemical group or ‘guild’) has a role in such a group’s taxonomic diversity. We tested this hypothesis by looking at the metacommunity diversity of functional groups in multiple biomes. We observed a positive correlation between estimates of a functional group’s diversity and their metabolic energy yield. Moreover, the slope of that relationship was similar in all biomes. These findings could imply the existence of a universal mechanism controlling the diversity of all functional groups in all biomes in the same way. We consider a variety of possible explanations from the classical (environmental variation) to the ‘non-Darwinian’ (a drift barrier effect). Unfortunately, these explanations are not mutually exclusive, and a deeper understanding of the ultimate cause(s) of bacterial diversity will require us to determine if and how the key parameters in population genetics (effective population size, mutation rate, and selective gradients) vary between functional groups and with environmental conditions: this is a difficult task.</p

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.

We present NUFEB (Newcastle University Frontiers in Engineering Biology), a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems, with particular emphasis on biofilms. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (107 individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEB's functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate

Summary of the model.

<p>A representative volume is chosen from the large-scale biological system and this representative volume is the computational domain. A generic individual based model can predict the growth and emergent properties of biofilms and flocs in a range of large-scale biological systems.</p

Biofilm deformation and detachment at .

<p>(a) time, T^** = 0; (b) T^** = 8000; (c) T^** = 20000; (d) T^** = 70000; (e) T^** = 130000. Streamer formation and detachment is evident at the later stages of the deformation.</p

Biofilm growth when nutrients are supplied from the bottom substratum instead of the top wall.

<p>The same <i>δ</i>, <i>κ</i>, and <i>β</i> values as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181965#pone.0181965.g004" target="_blank">Fig 4(B)</a> are used for this simulation. The biofilm surface is flat in this case when compared with <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0181965#pone.0181965.g004" target="_blank">Fig 4(B)</a> where the nutrient is supplied from the top.</p

NUFEB-1.0

official release of the NUFEB softwar