Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
[['Soil hosts the greatest diversity and abundance of microbial life in all of the biosphere , with over 109 cells per gram of soil [1] expressing thousands to millions of different operational taxonomic units in small volumes [2 , 3] .', 'Nonetheless , considering the vast surface area per volume of a typical soil , bacterial cells are sparsely distributed within the soil matrix , covering less than 1% of the total available soil surface [4 , 5] .', 'This highly non-uniform distribution is further reinforced by localized resource distribution giving rise to microbial hotspots , such as in soil aggregates , the rhizosphere , biopores or the detritusphere [6] .', 'These hotspots are important for large-scale biogeochemical cycles of carbon and nitrogen and for the emission of greenhouse gases [6–9] .', 'Improved prediction of soil ecological functioning mediated by bacterial processes requires better understanding of how these bacterial hotspots function and their response to dynamic conditions and integrated influence on large-scale processes .', 'In addition to its inherent complexity , soil opacity limits direct visualization of bacterial distribution within soil [10 , 11] .', 'Although the use of soil thin sections and artificial micrometric pore networks offers insights into spatial quantification of bacterial distributions and self-organization [12 , 13] , the simultaneous acquisition of the dynamic chemical landscape is not yet resolvable .', 'Mechanistic models are capable of bridging some of the experimental gaps and facilitate systematic studies of the interplay of physical , chemical and biological factors and their spatiotemporal interactions .', 'Individual-based models ( IBM ) have gained in popularity owing to their local scale and cell-level representation of interactions , which offer a useful platform for prediction of emergent spatial patterns and population abundances arising from microscale interactions .', 'IBMs have been used to investigate a range of questions in microbial ecology such as altruism in biofilms [14] , the influence of metabolic switching on biofilm structure [15] , bacterial coexistence due to hydration dynamics [16] , bacterial spatial organization in soil aggregates [17] , and the dynamics of bacterial community diversity in desert soils [18] .', 'A common feature of IBM models is the estimation of individual bacterial growth rates and nutrient consumption based on simple growth kinetics ( e . g . Monod kinetics ) with empirically prescribed stoichiometric parameters .', 'A flexible approach to calculating bacterial cell response to local conditions and potential switching of metabolic strategies became available with the solution of metabolic networks that make no prior assumptions about growth rates [19] .', 'New approaches using spatiotemporal metabolic modeling with genome-scale metabolic networks enable quantification of cell growth rates , and the associated uptake of nutrients and excretion of intermediate ( by-product ) metabolites .', 'Such approaches have been used to create biofilm models through an extension of Matlab with NetLogo named MatNet [20] , a population-based model of trophically interacting bacterial communities [21] , an extension of the MatNet approach to include multispecies communities [22] , as well as to investigate bacterial intra-colony nutrient heterogeneities [23] .', 'Common to these modeling approaches is their ability to describe trophic dependencies of microbial species that automatically adapt to spatially and temporally varying nutrient conditions .', 'However , all of the above-mentioned spatiotemporal metabolic models employ basic and unresolved representations of the physical microbial habitats that are considerably simpler than conditions in soil .', 'To realistically simulate bacterial life in complex and partially saturated habitats , such as those found in soil , a description of the physical ( pore spaces and surfaces ) and characteristics of the aqueous habitats with the resulting diffusion fields is essential [5] .', 'In this study , we developed and tested a new type of spatiotemporal metabolic model that assigns metabolic networks to individual agents capable of chemotactic motion within spatially resolved soil habitats .', 'The physical domain is comprised of angular pore networks representing soil pores .', 'The hydration conditions are imposed by a prescribed matric potential that interacts with the physical domain and results in aqueous phase configurations similar to those expected in soil ( with dual occupancy of the liquid and gas phases in angular pores ) .', 'The matric potential is a component of the total soil water potential attributed to capillary and adsorptive forces between water and the soil solid matrix , with values ranging from 0 for saturated soil to large negative as the soil dries ( often expressed as negative pressure ) .', 'The physical domain including the water phase serve as a backbone for numerical diffusion of nutrients and intermediate metabolites , with explicit account of diffusive bottlenecks for oxygen when pores are saturated or for nutrient diffusion in unsaturated soil , whilst maintaining connectivity of the aqueous phase throughout the simulated domain .', 'Finally , bacterial cells are represented as individual agents with the ability to autonomously move and disperse , intercept nutrients and grow at rates determined by local ( often spatially variable ) nutrient conditions owing to the integration of metabolic networks .', 'The model is compared to predictions obtained from a previously published population-based spatiotemporal metabolic network [21] and to bacterial spatial segregation observations from experimental data and simulation results from a previous IBM [13] .', 'Additionally , the model was used to mimic experiments of glucose perfusion in soil aggregates [24] and strategically to highlight the influence of pore size distributions under wet and dry conditions with contrasting results–a primary distinction between IndiMeSH and other spatiotemporal metabolic network models .'], ['A pseudo two-dimensional pore network composed of interlinked pores connected by nodes forming a lattice defines the spatial component of the model .', 'The coordination number expresses the number of pores connected to each node within the lattice ( e . g . 4 for a chessboard , 6 for a honeycomb ) .', 'Each pore has an angular cross-sectional area represented by either isosceles triangles [17] or rectangles ( when used to represent microfluidic networks [13] ) .', 'Angular pores were selected due to their ability to simultaneously have liquid and gas phases under unsaturated conditions , an attribute not possible within cylindrical pores [26] .', 'Different pore sizes are included by varying the inscribed circle radius of each individual pore ( for example taken from a lognormal distribution to represent soil pores [17] ) .', 'The geometry of the triangle was determined by varying the central angle of the isosceles triangle .', 'For rectangular pores , the width and height can be defined for each individual pore ( more detail is provided in [17] and [13] ) .', 'A visual representation of parameters determining pore geometry is provided in S1 Fig . An important aspect of the model is its ability to represent different hydration conditions using the energy state of water or the matric potential .', 'The matric potential determines the aqueous phase configuration ( amount retained in the pores and connectivity ) , hence it also shapes the nutrient diffusional landscape and constrains bacterial dispersal ranges .', 'The water-filled cross-sectional area in each pore is calculated from the matric potential and geometrical considerations [27] as shown in Eq', '1 . Here Aw is the water filled cross-sectional area ( m2 ) , At the total cross-section area of the pore ( m2 ) , Ψ the matric potential ( Pa ) , σ the water surface tension ( Nm-1 ) and γi the angle i within the corner of the angular pore .', 'Pores are considered unsaturated whenever an air phase is present , specifically , when a continuous connection of unsaturated pores is available from a liquid-air interface at the boundary to the pore under consideration .', 'We note that the water-filled cross-sectional area of a pore defines available pathways for nutrient diffusion and for the calculation of total nutrient storage in each pore ( depending on pore size , length , and local nutrient concentration ) .', 'An important parameter of the aqueous phase in each pore is the effective water film thickness defined as the diameter of the largest sphere fully inscribed between the liquid-air interface and the pore wall [28] and calculated using Eq', '2 . Here , WFT is the water film thickness defined as the smallest radius of an inscribed circle between the liquid-air interface and the pore wall ( m ) , Ψ the matric potential ( Pa ) , σ the water surface tension ( Nm-1 ) and γi the angle within the corner under consideration of the angular pore .', 'The water film thickness affects the speed and range of bacterial motility , as further described below .', 'Of particular importance is the fact that different angular pore geometries ( e . g . , pores with obtuse angles ) may retain water films that are too thin to support bacterial flagellated motion , hence , disconnect this bond from other parts of the network in terms of cell dispersion [29] .', 'Despite considerable simplifications compared to natural pore networks , this formulation of physical pore network architecture and associated water configurations retains the salient features of the soil aqueous phase , such as continuity of liquid pathways for nutrient diffusion and cell dispersion and dual occupancy of the liquid and gas phases within angular pores .', 'Diffusive fluxes of dissolved substrates within the aqueous phase are described by Fick’s law and are evaluated between nodes subject to mass balance at the nodes , as given by:', 'Vw∂C∂t=AwD∂2C∂x2−R', '( 3 )', 'where C is the substrate concentration ( M ) , D the diffusion coefficient in water ( m2s-1 ) , Aw the liquid cross-sectional area ( m2 ) , Vw the volume of water attributed to the node ( m3 ) , x the spatial coordinate along pores ( m ) , and R a sink term ( mols-1 ) attributed to the combined consumption of individual bacterial cells .', 'The volume at each node is calculated using Eq 4 where Vw the volume of water attributed to the node ( m3 ) , Aw the liquid cross-sectional area of connected pore j ( m2 ) , Lj the length of the connected pore j ( m ) and d the degree of the node .', 'Liquid films of pores sharing the same node are assumed to be continuous .', 'Neglecting bacterial consumption , which is calculated separately using FBA , Eq 1 is solved numerically using an implicit scheme .', 'Nutrient sources are represented by fixed concentration boundaries ( e . g . calculated maximum saturation for oxygen using Henry’s law ) .', 'Consumption and production of nutrients is calculated as the sum of contributions from individual bacterial cells and subtracted from the local nutrient content before calculation of diffusion .', 'Bacteria are represented as individual agents capable of dispersing ( by motility when the aqueous film thickness permits ) within the pore network , intercepting nutrients and growing according to locally available nutrient conditions .', 'Bacterial cells respond locally and independently with no knowledge of global system properties such as concentration fields or bacterial density even at the nearest pore .', 'Thus , global phenomena such as exponential population growth , spatial organization of bacterial species or diffusion fields due to bacterial consumption are emergent properties based on the local interactions of individual agents with their immediate chemical and physical surroundings .', 'Bacterial cells divide when they reach a prescribed mass at division; they may be removed from the simulation if they deplete internal energy and reach a critical biomass [30] .', 'We evaluated the proposed IndiMeSH framework by comparing it to a population-based metabolic model ( COMETS ) [21] and to experimental data [13] , and used it to mimic experiments of glucose perfusion in soil aggregates [24] to evaluate the potential of IndiMeSH to predict dynamic shifts in the total abundance of a bacterial community due to boundary condition perturbations .', 'In addition , simulations with contrasting hydration conditions and varying pore size distributions were created to highlight the capability of IndiMeSH to simulate bacterial life in soil .', 'A list of all user defined parameters can be found in S2 Table in the supplementary material .'], ['The performances of genome-scale metabolic networks ( GEM ) and their reduced-scale networks ( rGEM ) were compared using flux variability analysis in varying environmental conditions .', 'Table 2 summarizes the median percentage and standard deviation of common reactions that differ to varying degrees in their maximum or minimum flux between the GEM and rGEM models for all environmental conditions .', 'Overall , the performance of the reduced-scale model was very similar to the genome-scale models , with approximately 85% of all reactions within the models having minimal flux and maximal flux differences of less than 1 mmol/gDW/h .', 'In addition , the standard deviations were small for most metabolic network comparisons , with the exception of the E . coli metabolic networks .', 'S4 Fig in the supplementary material relates the comparison of the metabolic networks to environmental conditions to elucidate potential biases due to specific combinations of nutrient uptake rates .', 'The metabolic networks of E . coli perform differently at the combination of high lactose , low methionine and medium to high oxygen uptakes .', '- The aim of comparing COMETS with IndiMeSH was to verify IndiMeSH ability to predict bacterial community trophic interactions in the absence of prior assumptions regarding nutrient uptake ( in contrast with Monod kinetic models ) .', 'Fig 2 shows the final ratio of E . coli and S . enterica after 48 h of simulated growth , including the experimental results and model simulations from the original COMETS publication [21] .', 'Both inoculation ratios ( 99:1 and 1:99 as E . coli:S . enterica inoculated at 100 randomly chosen nodes ) were included , demonstrating the metabolic interdependence of the two species and the convergence of the system to the same stable community composition .', 'No significant difference was found between IndiMeSH simulations and both COMETS experimental and simulation results ( p value of 0 . 66 and 0 . 33 , respectively , two-tailed t-test ) .', 'Additional simulations were performed to ensure that the motility algorithm of IndiMeSH and changing to super agents resulted in similar biomass dispersion characteristics as in the diffusion algorithm used in COMETS .', 'S3 Fig in the supplementary material shows the biomass dispersion for the COMETS algorithm and IndiMeSH run-and-tumble algorithm , both with and without super agents .', 'To evaluate the ability of IndiMeSH predict the spatial organization of a bacterial community in pore networks due to nutrient cross-gradients ( where different metabolism is required ) , we compared IndiMeSH predictions with previously published experimental data [13] .', 'Fig 3 depicts the resulting spatial distribution of P . putida ( further termed aerobes ) and P . veronii/P .', 'stutzeri ( further termed facultative anaerobes ) along the shortest path from the central to the peripheral ports of the physical and simulated pore networks ( details of the physical domain and chemical boundary conditions are described in the methods and shown in S2 Fig of the supplementary material ) .', 'The aerobes proliferate closer to the periphery than the facultative anaerobes , with a small subpopulation of facultative anaerobes residing at the oxygen-rich peripheral ports .', 'The magnitude of the populations of both species is captured well both at the central and peripheral ports , although the location of aerobes is predicted to be in closer proximity to the peripheral port than observed experimentally .', 'For the facultative anaerobes , the simulations capture both the central population utilizing anaerobic metabolism ( fermentation ) as well as the peripheral sub-population using aerobic respiration .', 'We evaluated the capability of IndiMeSH to predict the shift in total bacterial population size due to perturbations in boundary conditions in the form of glucose perfusion into soil aggregates previously under certain steady ecological state .', 'Simulations were set up to mimic experiments performed on 2 mm soil aggregates where the bacterial community was first grown into steady state for 7 days after which glucose was added at high concentrations to observe the short-term impact on the function and the spatial distribution of soil bacteria and fungi [24] .', 'Fig 4 depicts the pore network employed for the simulation congruent to the reported pore size distribution in the experiment ( Fig 4A ) , the resulting diffusional scheme of the pore network calculated using Millington-Quirk equation ( Fig 4B ) as well as the total temporal response of the community during the pre-incubation and dynamic response to the addition of a glucose pulse ( Fig 4C ) .', 'Due to the unsaturated conditions ( expressed by a matric potential of -10 kPa ) , the diffusion of nutrients confined to the aqueous phase was severely limited whereas oxygen in the gas phase was able to penetrate the pore network rapidly .', 'The primary mode of growth was thus aerobic respiration within all regions of the pore network .', 'During the pre-incubation period , the bacterial population grew into steady state dictated by the carrying capacity of the supplied carbon .', 'Glucose addition after 7 days triggered a secondary rapid growth phase until a maximum is reached after approximately 8 days into the simulation .', 'The population then starts to decline due to the lack of carbon availability , tending towards the previously established population size due to the system carrying capacity .', 'Glucose perfusion does not have a homogeneous effect on the population concerning space .', 'The relative increase in population size of the outer aggregate faction ( peeling off 1 mm of the aggregate conceptually ) compared to the inner faction is 2 . 5 to 1 . 1 , respectively .', 'This is similar to the observation made within the experiments where they reported a total increase in cell number of 1 . 6 and 1 . 3 for the outer and inner faction , respectively .', 'Within the simulation this is mostly due to the availability of carbon at the periphery which otherwise is intercepted by the population closer to the center of the aggregate .', 'Thus , the initial spatial distribution of the community was disrupted by the change in carbon availability , creating a more heterogeneous distribution of the population .', 'Finally , we created simulations with two contrasting hydration conditions in three different pore networks to highlight the capability of IndiMeSH to capture and predict the shift in metabolic activity due to the interplay of soil physics , aqueous configuration and bacterial metabolism .', 'Pore size distributions resembling different soils are shown in Fig 5A with the related soil water characteristic curves shown in Fig 5B .', 'A matric potential of -1 kPa and -10 kPa , was applied to simulate wet and dry conditions , respectively , with profound consequences for the hydration conditions for each network as indicated by the green lines in Fig 5B .', 'The degree of saturation in turn dictates the relative diffusion of gaseous and aqueous nutrients as shown in Fig 5C .', 'In dry conditions , aqueous nutrients are restricted in their diffusive capability due to thin water films whilst gaseous nutrient diffusion ( e . g . oxygen ) is facilitated .', 'Due to the constant flux boundary conditions , bacterial populations reach similar magnitudes in wet conditions as shown in Fig 5D .', 'Under dry conditions , diffusion of substrate in the large pore network is restricted more profoundly compared to the small pore networks , which results in a lower total carrying capacity .', 'A main difference between the saturated and unsaturated simulation also lies in the metabolic activity of the population .', 'Due to the penetration of oxygen deep into the aggregate for all pore sizes under dry conditions , the sole mode of growth is via aerobic respiration as shown in the consumption pattern for the small sized pore domain in Fig 5E .', 'Under wet conditions , the additional consumption of nitrate indicates the use of denitrification pathways .', 'Under these conditions , overflow metabolism occurs at the center due to an imbalance in electron donor and acceptor ratio resulting in the production of acetate , which is consumed at the periphery using aerobic respiration as shown in Fig 5F .'], ['The IndiMeSH model has been developed to capture the multifaceted bacterial metabolism of individual-based agents inhabiting a complex habitat such as soil .', 'The use of adaptive metabolic networks enables a life-like transition between aerobic and anaerobic conditions compared to empirical and arbitrary kinetic models .', 'Additionally , FBA predicts uptake and secretion rates depending on locally variable nutrient conditions and thus enables simulations of trophically interacting bacterial species within a complex medium such as , but not limited to , soil .', 'The heavy computational burden related to the motility of individual bacterial cells and the numerous iterations of the FBA requires the reduction of genome-scale metabolic networks using the previously published redGEM [36] and lumpGEM [37] algorithms .', 'The implementation of reduced-scale metabolic models ( rGEM ) significantly reduced the computational time whilst retaining the salient features and predictability offered by the genome-scale models ( GEM ) ( Table 1 ) .', 'Although such a reduction ( GEM to rGEM ) may not be crucial for very small physical domains , simulations of ecologically relevant systems where gradients of environmental variables persist would require spatial domains with a few thousand nodes .', 'For example , in the micromodel comparison ( Fig 3 ) we considered approximately 3000 nodes and two species , thus solving 6000 FBA problems per time step; hence , the use of rGEM greatly improved computational efficiency .', 'Compared to other individual based metabolic models the primary benefit of reduced models is not due to the physical domain size ( e . g . BacArena simulates domains containing 100 by 100 grid nodes [22] ) , but the small time step dictated by the motility algorithm and related large number of iterations in total .', 'Except for E . coli , all reduced-scale models perform very similarly to their genome-scale counterparts .', 'Reactions which have a net flux difference greater than 10 mmol/gDw/h are predominantly attributed to internal cycles within the genome-scale models or cycling of nutrients between compartments of the genome-scale model that are absent in the reduced-scale model , as has been previously reported [39] .', 'There is a discrepancy in acetate metabolism between the reduced-scale and genome-scale models of E . coli .', 'This is due to overoptimistic predictions of the genome-scale model where the predicted high fluxes can only be achieved through net CO2 fixation , which is unlikely [39] .', 'The main difference between a group of spatiotemporal metabolic models and the newly developed IndiMeSH lies in the ability of the latter to represent complex habitats such as soil , including pore spaces , aqueous phase configurations and related constraints to chemical diffusion and bacterial dispersion .', 'The IndiMeSH model is designed for a different range of applications than the COMETS model; however , we obtained comparable simulation scenarios through simple adjustments to the physical and biological domain of the model .', 'These include the representation of bacterial cells as super agents as well as a reduction in velocity to account for growth on agar .', 'The use of super agents has been implemented in the past [44 , 45] and in other studies have been shown to have limited effects on simulation results as long as the scaling ratio is sufficiently small [46] .', 'Using these modifications , IndiMeSH accurately reproduced the COMETS results .', 'These simulations rely on an appropriate reduction of the genome-scale models preserving the stoichiometric relations between consumed and excreted nutrients and demonstrate the ability of IndiMeSh to replicate and predict bacterial growth based on trophic interactions , a process ubiquitous in dense bacterial hotspots .', 'Since both COMETS and IndiMeSH are essentially two-dimensional simulations , the oxygen concentration was kept artificially low to imitate conditions experienced by the layer of cells close to the agar itself .', 'In reality , a bacterial colony growing on agar is a dynamic system where oxygen is consumed at the periphery , resulting in multiple micro niches and redox conditions within the colony itself [47] .', 'Individual-based models coupled with metabolic networks focusing on colony growth are able to capture this phenomenon well [23] , however the scale of those models restricts simulations of a large domain with hundreds of colonies .', 'The importance of emergent spatial patterns and bacterial spatial organization prompted us to examine how IndiMeSH reproduces previously published experimental data of bacterial distributions in micrometric pore networks dominated by carbon-oxygen counter gradients [13] .', 'The original IBM represented facultative anaerobes as obligate anaerobes , which resulted in consistent discrepancies between model and experimental results especially for facultative anaerobes proliferating close to the oxygenated peripheral ports .', 'Integration of metabolic networks as a means of growth calculation enabled us to capture the segregation of facultative anaerobes into a denitrifying population close to the carbon source and a subpopulation using aerobic respiration ( Fig 3 ) .', 'Despite possibilities to represent facultative anaerobes using Monod kinetics and an arbitrary oxygen-threshold-switching strategy ( e . g . [15] ) , IndiMeSH managed to capture the facultative behavior more naturally without an artificial construct of bimodal metabolism .', 'Originally , the interaction between the two species suggested an indirect commensalism where the anaerobes were required to release sufficient carbon to the periphery for complete oxygen consumption by the aerobes and provision of an anoxic niche .', 'Through the integration of metabolic networks and additional intermediate metabolites in the form of acetate ( to ensure mass balance of carbon within the simulation ) , the cooperation between the species was shown to be a passive interaction where acetate was produced due to a lack of electron acceptor ( not sufficient nitrate available ) at the central port .', 'Diffusion of acetate to the periphery enabled the aerobic community ( both facultative anaerobes and obligate aerobes ) to grow closer to the oxygen-rich peripheral port .', 'This mechanism is less susceptible to perturbations and provides a more plausible explanation for cooperation compared to the scenario where one species “farms” the other .', 'Abrupt perturbations are ubiquitous in all natural systems such as soil , either due to rapid changes in hydration conditions following rainfall or irrigation , or chemical alteration by the application of fertilizer or contaminants to the soil , or physical alterations such as tillage or rapid soil compaction .', 'To test the capability of IndiMeSH to simulate such dynamic changes in environmental conditions , a simulation scenario was created where a change in electron donor availability alters the macroscopic conditions within a soil aggregate cross-section based on experimental results of glucose perfusion in soil aggregates [24] .', 'These experimental results describe a non-uniform effect in space as evidenced from peeling off 1 mm of the aggregate with 1 . 6 fold increase in bacterial total abundance in the periphery relative to 1 . 3 in the core ( in the numerical experiment we observed 2 . 5 fold outer to 1 . 1 inner ) .', 'The interpretation we provide to these interesting experimental results is that the perfusion with glucose alleviates the carbon flux limitations in natural aggregates , which is controlled by the inner ( largely anaerobic ) population .', 'The perfusion creates a situation where carbon and oxygen become available at the periphery and promote the rapid growth during the availability window ( until the carbon pulse is consumed ) .', 'In the simulation , the total population size starts to decline after peaking around 8 days into the simulation .', 'This is not easily verified in the experimental data , but acknowledging that only a fraction of the total population was reported to be dividing ( approximately 4 . 5% to 8 . 2% of the total population [24] ) , assuming that the population has reached steady state or is declining does not seem farfetched .', 'These simulations represent a scenario where the physical representation of soil in the form of angular pore networks plays a crucial in shaping the diffusional landscape of the microbial habitat and overall population growth–a unique feature of the presented model framework .', 'An important aspect differentiating IndiMeSH from other current spatiotemporal metabolic network models is the accuracy with which the physical habitat of the bacterial cells is represented .', 'Angular pore networks enable to link the aqueous phase configuration dictated by the pore geometry to the underlying chemical conditions and ultimately to the spatial landscape of bacterial metabolism .', 'For the same matric potential , pore networks of different mean diameter expose bacteria to fundamentally different growth conditions as shown for instance in Fig 5B at -1 kPa .', 'Both the medium and small pore networks are saturated ( nearly 100% ) at this matric potential whereas the pore network containing large pores is desaturated with profound consequences for oxygen diffusion dynamics and bacterial motility .', 'Potentially more important is the ability of IndiMeSH to capture the change in aqueous phase configuration for the same pore network at varying matric potentials .', 'As shown in Fig 5E , the change in matric potential not only alters the magnitude of nutrient consumption but also the relative ratio of for instance glucose to nitrate consumption .', 'In wet conditions , the community is split into two distinct sub populations with one growing anaerobically via denitrification and producing acetate at the center and a second which grows via aerobic respiration of acetate at the periphery of the domain ( Fig 5F ) .', 'In dry conditions , aerobic respiration is favored due to the increased gaseous diffusion at -10 kPa ( Fig 5C ) .', 'The difference in population size depending on hydration conditions is due to the reduction in carbon diffusion under dry conditions .', 'It is important to note that these contrasting conditions emerge due to a single change in model input files–the matric potential–which induces substantial changes to both the physicochemical aspects of the model as well as bacterial growth strategy .', 'Hence , the physical description of the pore habitat , related diffusional constraints and bacterial self-organization in complex pore systems are features that distinguish IndiMeSH from other current spatiotemporal metabolic models such as COMETS[21] or BacArena[22] .', 'IndiMeSH offers a representation of metabolic versatility with an individual-based model of bacterial life in soil habitats .', 'Metabolic networks enabled a natural transition between aerobic and anaerobic pathways and associated nutrient consumption patterns , inducing trophic interactions without prior assumptions , as required by mathematical models using simple growth kinetics .', 'The detailed description of the physical habitat and aqueous phase and emergent nutrient diffusion fields give rise to complex metabolic landscapes with changes in metabolic activity at the millimeter scale .', 'Due to the modular design of the IndiMeSH model , individual components can be modified to represent , for instance , a differe
['Introduction', 'Methods', 'Results', 'Discussion']
['Natural soil is characterized as a complex habitat with patchy hydrated islands and spatially variable nutrients that is in a constant state of change due to wetting-drying dynamics .', 'Soil microbial activity is often concentrated in sparsely distributed hotspots that contribute disproportionally to macroscopic biogeochemical nutrient cycling and greenhouse gas emissions .', 'The mechanistic representation of such dynamic hotspots requires new modeling approaches capable of representing the interplay between dynamic local conditions and the versatile microbial metabolic adaptations .', 'We have developed IndiMeSH ( Individual-based Metabolic network model for Soil Habitats ) as a spatially explicit model for the physical and chemical microenvironments of soil , combined with an individual-based representation of bacterial motility and growth using adaptive metabolic networks .', 'The model uses angular pore networks and a physically based description of the aqueous phase as a backbone for nutrient diffusion and bacterial dispersal combined with dynamic flux balance analysis to calculate growth rates depending on local nutrient conditions .', 'To maximize computational efficiency , reduced scale metabolic networks are used for the simulation scenarios and evaluated strategically to the genome scale model .', 'IndiMeSH was compared to a well-established population-based spatiotemporal metabolic network model ( COMETS ) and to experimental data of bacterial spatial organization in pore networks mimicking soil aggregates .', 'IndiMeSH was then used to strategically study dynamic response of a bacterial community to abrupt environmental perturbations and the influence of habitat geometry and hydration conditions .', 'Results illustrate that IndiMeSH is capable of representing trophic interactions among bacterial species , predicting the spatial organization and segregation of bacterial populations due to oxygen and carbon gradients , and provides insights into dynamic community responses as a consequence of environmental changes .', 'The modular design of IndiMeSH and its implementation are adaptable , allowing it to represent a wide variety of experimental and in silico microbial systems .']
['Soil bacterial communities are key players in global biogeochemical cycles and drive other soil regulatory and provisional ecosystem functions .', 'Despite the relatively high bacterial abundance found in fertile soil , bacteria occupy only a small fraction of the soil surfaces and often form hotspots with disproportionate contributions to observed biogenic fluxes .', 'As soil opacity and complexity limit detailed observations of such hotspots in situ , we have developed a modeling platform , IndiMeSH ( Individual-based Metabolic network model for Soil Habitats ) , to enable systematic study of dense multispecies bacterial communities within a structured habitat resembling ( but not limited ) to soil .', 'The model is capable of representing multispecies trophic interactions and spatial self-organization in response to nutrient gradients , as confirmed in comparison with published results .', 'IndiMeSH offers new opportunities for quantifying bacterial hotspot formation and dynamics and observe their resilience and response to perturbations in hydration and nutrient conditions .']
['carbohydrate metabolism', 'medicine and health sciences', 'chemical compounds', 'pathology and laboratory medicine', 'oxygen', 'pathogens', 'metabolic networks', 'carbohydrates', 'glucose metabolism', 'organic compounds', 'glucose', 'simulation and modeling', 'oxygen metabolism', 'network analysis', 'bacteria', 'research and analysis methods', 'computer and information sciences', 'chemistry', 'pathogen motility', 'biochemistry', 'chemical elements', 'organic chemistry', 'virulence factors', 'monosaccharides', 'biology and life sciences', 'physical sciences', 'metabolism', 'organisms']