Aim of our model

The dry lab played a crucial role in advancing our project by complementing wet lab experiments. We used computational models to simulate biological processes, predict potential outcomes, and provide deeper insights into complex systems.

Initially, we considered a variety of approaches, including the use of diffusion models to study biofilm expansion and simulations of plant growth with and without our engineered bacteria. However, we realized that focusing on the metabolic alterations in our bacteria after induced to produce a hyper-robust biofilm is crucial. This area is where computational modeling can significantly advance our project's progression. Specifically, our objective was to gain insight into the growth costs associated with biofilm production, its limits, and how the bacterial metabolic network behaves under different realistic conditions, including laboratory media, bulk soil, rhizosphere environments, and drought.

Flux Balance Analysis (FBA) proved to be a valuable tool to address these questions. It is a method of simulating the metabolism of mostly single-celled organisms and offers insights into how our genetically modified bacteria will perform in agricultural applications, which cannot be investigated in field experiments due to Swiss regulations.

We have made all our code available here, including all scripts, data, graphs, and tables so that future iGEM teams and other interested parties can utilize the scripts for their analyses or as a starting point on how to work with FBA.

What is Flux Balance Analysis?

Overview

FBA is used to reconstruct genome-scale metabolic networks to study the biochemical processes within a cell and to predict its growth based on the maximization of a biologically significant objective function, usually biomass production1. A metabolic network maps the chemical reactions within an organism that convert nutrients into energy and synthesize the essential building blocks required for growth and maintenance. These models include all known metabolic reactions and the genes encoding the enzymes required to catalyze those reactions. A genome-scale metabolic model (GEM) includes all the metabolically relevant genes for the organism of interest. It contains a set of m metabolites, one of n stoichiometric reactions between these metabolites, and the rules linking genes to their corresponding reactions and their flux, meaning the rate of flow of molecules through a metabolic reaction. Defining and modeling a GEM is the first step in FBA.

Figure 1: Workflow used when working with FBA. Created using BioRender.com

The second step involves making some key assumptions about the model’s functions and structure. The most important assumption in FBA is the steady-state assumption. This means that we assume the concentrations of all metabolites to remain constant over time. This makes it possible to solve the optimization problem using linear programming. Next, we define an expected flux range for each reaction, considering important details like reaction directionality and efficiency.

FBA requires an objective function to optimize for. Usually, an artificial ‘biomass production’ reaction is used as the objective function, because it is a good approximation to the growth rate of the organism. All the flux calculations aim to maximize this process.

In a third step, we need to specify the so-called exchange reactions responsible for importing and exporting nutrients to and from the cell, to simulate the environment in which our organism grows. They vary significantly under different conditions and must be considered with great care to ensure the model produces accurate and reliable results.

Formal Definition

In this section we will look in more detail at the mathematical representation of the metabolism and the computational methods used in an FBA. This is mainly intended for readers who are particularly interested in the computational background.

Formally, the steady state assumption is described as follows:

Let $v_i \in \mathbb{R}$ be the flux through the $i$-th reaction, where $i \in \{1,...,n\} \subset \mathbb{N}$, usually in $\frac{mmol}{gDW \cdot h}$, $x$ a metabolite with concentration $[x]$, and $s_i \in \mathbb{R}$ be the stoichiometric coefficient of in the reaction. Then $$\sum_{i=0}^n s_i \cdot v_i = \frac{d}{dt} [x] = 0.$$ Since we can write a stoichiometric $m \times n$ matrix $\mathbf{S}$ containing the coefficient for each metabolite and coefficient and $\mathbf{v} \in \mathbb{R}^n$ a vector containing all the fluxes, we get $$\mathbf{Sv} = 0.$$ The additional assumptions for the bounds of each reaction flux are defined in two vectors $\mathbf{a},\mathbf{b} \in \mathbb{R}^n$. The first one contains all lower bounds and the second all upper bounds. The objective function $f(\mathbf{v})$ is what the FBA optimizes by solving for the flux distribution in the network. The problem solved by the FBA is thus described by $$\max_{\mathbf{v} \in \mathbb{R}^n} f(\mathbf{v}), \text{ such that } \mathbf{Sv}=0,$$ $$a_i \leq v_i \leq b_i \ \forall i \in \{1,...,n\}$$

Let’s consider a simple example to make this concept easier to understand:

Figure 2: Simple example of a metabolic network. Created with BioRender.com

In this example we have five metabolites in the internal compartment $(A, B, C, D, E)$ and four metabolites in the external compartment $(A\_e, B\_e, C\_e, E\_e)$. There are seven reactions involving these metabolites: four exchange reactions $({EX}\_A, {EX}\_B, {EX}\_C, {EX}\_E)$, which transport metabolites between the internal and external compartments, and three internal reactions $(R_1, R_2, R_3)$, where metabolites are converted into other metabolites.

Instead of having this long list of reactions, we can very efficiently describe this network in a stoichiometric $m \times n$ matrix $\mathbf{S}$, where each row represents a metabolite, and each column represents a reaction. Often there are a few other reactions added to $\mathbf S$, one of which is the biomass reaction, which is not a real biochemical reaction but rather a summary of several reactions that describe the growth rate of the organism.

This matrix defines a set of linear equations which can be solved by relatively simple algorithms optimizing for the maximal flux in the objective function, meaning the highest achievable rate of the desired metabolic process under the given constraints.

Earlier, we mentioned solving a linear programming problem. But what does that actually mean? In our project, we used the Python library COBRApy, which relies on a solver called the GNU Linear Programming Kit (GLPK). GLPK uses the Simplex algorithm at its core. This algorithm works by iterating along the edges of the feasible solution space—determined by the constraints of the metabolic network—to find the optimal solution, such as maximizing biomass production. The solver then returns the flux values we are interested in analyzing.

Project Structure

We divided our modeling process into different stages to have a more manageable overview over the project. Each stage increases in complexity, providing a deeper understanding of the metabolic behavior of our bacteria across various perspectives and conditions.

Stage 0: Exploring our GEM

The GEM iJN1463

Microbial metabolic networks show both shared pathways and significant species-specific variations in nutrient utilization, absorption, metabolism, and biomass production4. For Pseudomonas sp. IsoF, the bacterium employed in our RhyzUp project, no genome-scale metabolic model (GEM) is available, and only a limited number of metabolic pathways have been researched. Given the infeasibility of constructing a new metabolic network without extensive experimental validation, we opted to use a GEM from a related species, Pseudomonas putida. P. putida is frequently used as a reference organism in experiments involving Pseudomonas sp. IsoF, particularly the well-characterized strain P. putida KT2440, which is also the case in the laboratory our wet lab team is working at.

Our FBA is based on the publicly accessible iJN1463 model of P. putida KT24403. This comprehensive metabolic reconstruction incorporates 1462 genes, 2927 reactions, and 2153 metabolites, representing a significant expansion of the reactome compared to previous models5. The model's robustness is further enhanced by its validation through in-vivo growth screens, making it an ideal foundation for our analysis. While our experimental design and analysis are based on P. putida KT2440, the computational scripts developed for this project could be readily applied to a Pseudomonas sp. IsoF GEM, should one become available in the future. This approach allows for flexibility and potential expansion of our research as more species-specific data becomes accessible.

How to test a biofilm?

The biofilm of Pseudomonas putida KT2440 is primarily composed of the structural proteins LapA and LapF, along with the exopolysaccharides cellulose, alginate, and P. putida exopolysaccharides A (Pea) and B (Peb)6. There is no specific biofilm forming reaction in the model because these components are secreted outside the cell to form the biofilm structure externally. As a result, we do not analyze the biofilm as a whole, but individual biofilm components.

Although LapA is a crucial biofilm matrix component in P. putida, its regulation involves cyclic diguanylate (c-di-GMP) binding to LapD, which modulates LapG activity and controls LapA's presence on the cell surface, rather than direct metabolic pathways6. The metabolic pathways for Pea and Peb exopolysaccharides in P. putida KT2440 are not yet sufficiently known to incorporate them meaningfully into our model. Future research should aim to integrate Pea and Peb into the model, including their specific production ratios, to more accurately represent the biofilm composition of P. putida KT2440.

Therefore, we focus our analysis on cellulose and alginate, two components with well-defined metabolic pathways. For cellulose there is only one exchange reaction present in the model (ID=EX_cell4_e).

Alginate has several exchange reactions in the model, so we researched which target reaction would be most useful. Alginate is an important biofilm component, particularly under water-limiting conditions7. Alginate biosynthesis involves distinct metabolic pathways for the production and incorporation of differentially linked and acetylated subunits. We decided to use the reaction between the activated precursor GDP-mannuronic acid, a key regulatory step in the alginate pathway, and prealginate (Reaction ID=PALGSKT)8, rather than on the exchange reactions of alginate subunit. This approach allowed us to consider different alginate variants that may be produced in response to varying environmental contexts. As acetyl-CoA is a substrate for the biomass reaction, it is a limiting factor. This suggests that under nutrient-limited conditions, our model may favor alginate pathways that are less dependent on acetylation. The extent to which P. putida KT2440 relies on acetylated alginate should be tested in vivo for further refinement of the model.

Adding c-di-GMP

Stage 1: Cost Analysis of Biofilm Components on Growth Rate

The first experimental step with our model was to evaluate the cost of biofilm production by assessing its impact on the growth rate of Pseudomonas putida KT2440 using the preset condition of the model. This was done by analyzing the biomass exchange reaction (ID = BIOMASS_KT2440_WT3) and focusing on two key biofilm components: cellulose and alginate (details in Stage 0). When optimizing the biomass reaction under the given conditions, no biofilm components are produced. Therefore, we set the lower bounds of cellulose and alginate reaction to the value 0 and then linearly increased it, thereby forcing the bacteria in our model to secrete these biofilm components. For each increment, the model was reoptimized to maximize the biomass production and the associated flux value is saved. The model was used in the preset conditions when downloaded from BiGG models.3

The biologically significant range for cellulose extrusion, from 0 mmol/gDW/h to 1.37 mmol/gDW/h, and for alginate extrusion, up to 1.26 mmol/gDW/h, is linear. Biomass production should never have a negative value, as a decrease in biomass would indicate cell death, so values below 0 were not being considered. The linearity may be caused by the simplicity of the available nutrients, as here glucose is the main carbon source in the medium. In Stage 3, we repeated the experiments under different, more complex nutrient conditions (see Stage 3 for details). From this first analysis we can see the direct correlation between increased biofilm production and decreased biomass production, indicating that producing biofilm components is quite costly for the bacteria. The linear relationship suggests a trade-off, as glucose is either used for biomass growth or diverted to produce biofilm components like cellulose and alginate.

Stage 2: Gene Assays

In a collaborative project between wet and dry lab, one of the key responsibilities of the dry lab is to identify areas where the wet lab's processes can be optimized or advanced, as well as finding promising experimental approaches. For stage 2, we performed a gene assay to evaluate whether the metabolism of P. putida KT2440 could potentially be improved by knocking out genes, thus freeing up energy for biofilm production.

In the first step, we knocked out each gene individually and identified those whose deletion did not result in immediate death of the cell. We used this approach to reduce the number of genes to analyze, thereby minimizing computational time as much as possible. This resulted in a list of 1138 genes that are likely nonessential for the survival of P. putida KT2440.

We conclude from the results that the metabolism of P. putidaKT2440 is highly efficient, and it cannot be improved by simply knocking out a part of it. For future investigation we would suggest working on some knock-ins as addition to the metabolic network. We revisited these experiments in different media during stage 3 to see if knockouts could improve the efficiency in more complex environments.

Stage 3: Experiments in Soil Conditions

Early on in the process of finding the dry lab project, we recognized the value of simulating soil conditions to bridge the gap between the wet lab experiments and real-world applications. Given that field trials with genetically engineered bacteria are prohibited in Switzerland, simulating realistic conditions became the only way to obtain "field data”.

Our dry lab team simulated various application-oriented conditions and compared the performance of our organism as biofilm production was increased under each setting. We focused on the following conditions:

We made a script that helps read in these conditions and automatically changes the lower bound of the exchange reactions (link to script), which makes adjusting the model to other conditions easier. Link

For each of these new models we ran adapted versions of the previous in silico experiments (See stage 1 and stage 2. The six experiments include:

The following section focuses on the combined cost analysis and gene assays for improved cellulose and alginate production. All data, graphs and scripts used in the analysis are available on our repository.

As expected from the results of stage 1 and the similarities between the preset of the iJN1463 model and the M9 glucose minimal medium, the relationship between alginate, cellulose and biomass is highly linear. This outcome is not surprising, as glucose serves as the sole carbon source for all three reactions and there is no metabolic flexibility in this simple medium. When the organism is forced to produce cellulose and/or alginate, the substrate is no longer available to produce biomass.

In the more nutrient-rich and complex LB medium, we observe a significant difference. Biomass yield is higher, and more biofilm components can be produced. It is about three times higher when no biofilm is produced. Also, cellulose or alginate production can be pushed to values about three times higher compared to the glucose minimal medium condition.
The relationship between cellulose, alginate and biomass in LB medium is not linear. The production rates of pre-alginate and cellulose can each be increased up to 1.03 mmol/gDW/h. Further increase would result in higher cost of biomass per unit of biofilm-component synthesized. At this threshold, biomass production is reduced to 1.10 mmol/gDW/h, 66% of its maximum.

The graphs for soil, rhizosphere and drought conditions look very similar. They show a largely linear relationship with biomass production peaking at approximately 26 µmol/gDW/h. All conditions also show comparable levels of biofilm production before growth drops below 0. From these results, we conclude that the changes between the different conditions do not have a great effect on our modified bacteria. Although this model does not account for changes in bacterial social behavior and other complex changes between these conditions, the results demonstrate that P. putida KT2440 is metabolically resilient to environmental stress, making it a strong candidate for combating drought and enhancing plant growth.

Interestingly, when optimizing the biomass function, we observed that P. putida KT2440 does not take up water across different conditions, which explains its resilience to drought. This observation is based on the analysis of metabolites taken up and secreted under varying conditions (Link to repository - see FBA_different_conditions.xlsx). This may seem surprising, but they align with the assumptions and constraints established within our model. Additionally, we found that amino acids serve as the sole nitrogen sources for the bacteria, highlighting a strong dependence on them, as they also play a major role in carbon flux.

To better visualize the scale in differences between maximal biomass production capacity in each environment we combined the cellulose production data in one graph.

In the gene assays, we found no improvements for cellulose or alginate by knocking out single genes in either the M9 glucose minimal or LB medium. Interestingly, we found multiple genes improving cellulose production in each of the assays for soil, rhizosphere, and drought conditions without negatively impacting biomass production.

Stage 4: Impact of nutrient variability on biomass production

We evaluated the model's sensitivity to nutrient variations to assess whether supplementation would benefit field applications or not. For the initial analysis, we selected phosphorus and potassium for being common in fertilizers, as well as calcium and magnesium due to their significant flux patterns observed together with the water uptake in Stage 3.

Although nitrogen is also a key fertilizer component, Stage 3 revealed that the bacteria expel large amounts of ammonium (NH₄⁺) and prefer amino acids as their nitrogen source. The model tested uptake from 0 to 1000 µmol/gDW/h. Each nutrient quickly reached saturation, providing minimal growth benefit beyond that point. Therefore, supplementing the soil with these nutrients is likely to be unproductive for the growth of P. putida KT2440.

A clear correlation between the limitation of amino acid and polysaccharide uptake and biomass production is evident.

While supplementing both could be beneficial, their rapid metabolization by rhizobial bacteria would require frequent applications.
Instead, we recommend applying a highly concentrated version of our product as close to the roots as possible to enhance the likelihood of colonization, rather than relying on extensive nutrient supplementation.

Assumptions and Limitations

As it is impossible to perfectly replicate real-world conditions in a model, we made assumptions to approximate the system.
First we adopted the standard assumptions used in FBA (See What is Flux Balance Analysis). These include the implicit assumption that the metabolic network underlying the model is comprehensive enough to accurately represent our organism of interest, P. sp. IsoF and the steady-state assumption necessary to solve the linear programming problem in FBA.

As mentioned in Stage 0, there is no available model for Pseudomonas sp. IsoF, therefore in dry lab we worked with a model of the P. putida KT2440 strain, namely iJN1463. Furthermore, we assumed that all the organisms try to maximize their growth and therefore we choose biomass production (ID = ​​BIOMASS_KT2440_WT3) as the objective value.

Due to the heterogeneous nature of soil and rhizosphere environments and the resulting data complexity, we assumed that drought has the same effects in both the rhizosphere and bulk soil. Furthermore, given the complex structure of biofilms and their dependence on environmental factors, we focused only on the two main components: cellulose and alginate. Additionally, our simulation of a single cell metabolic network does not include the effect bacterial community interactions can have.

Given the heterogeneous nature of soil, we used a single in silico soil in our experiments, but due to the wide variation in soil composition based on land use and location, we made necessary simplifications to build our model.

Discussion

Throughout the modeling of RhyzUp, we made several key observations, which we would like to highlight and summarize in this section. Utilizing FBA to assess the cost of hyper-robust biofilm production proved to be a valuable approach (See Aim).

In the first stage of our project, we demonstrated that biofilm production is metabolically costly for bacteria, directly reducing biomass production. Given the trade-off between biofilm formation and biomass growth, symbiotic relationships with plants must provide substantial benefits to be advantageous for bacteria. In the case of P. putida KT2440, being a rhizobacteria, these benefits clearly outweigh the associated metabolic costs. Therefore, the wet lab's focus on producing a hyper-robust biofilm only when the bacteria are near the plant roots, where it has the strongest benefit for plants, is well-founded.

In the second stage, we observed that P. putida KT2440 exhibits high metabolic efficiency even in simple media with limited carbon sources. Consequently, knocking out individual genes does not enhance cellulose or alginate production. To achieve a more efficient metabolism, newly introduced genes would need to be added to enable new pathways.

As we shifted our focus to more complex media, particularly in the third stage, we demonstrated that both the cost and maximum quantity of biofilm production are highly dependent on the nutritional complexity of the environment. We observed significant differences between simple and complex media, such as M9 glucose minimal medium and LB medium, as well as between laboratory and natural conditions. The nutritionally rich LB medium allowed the bacteria to produce the most biomass and biofilm components. The evaluated range of up to 1.03 mmol/gDW/h cellulose and alginate production can assist the wet lab in fine-tuning gene expression strength, allowing them to take advantage of the reduced metabolic cost of biofilm production within that range.

Conversely, there are only minor variations among different soil conditions. The biomass production and the costs associated with increased biofilm are comparable across bulk soil, rhizosphere, and drought conditions, suggesting that P. putida KT2440 is well-suited to withstand drought while enhancing plant resilience. Given that the results indicate improved performance in nutritionally richer environments, we anticipate that the bacteria will naturally migrate towards the roots, benefiting the wet lab's construct by remaining concentrated in close proximity to them. In the gene assay conducted under more complex conditions, we successfully identified a list of genes that the wet lab could further investigate to enhance cellulose production in soil conditions.

Finally, in the last stage, we observed that polysaccharides and amino acids significantly impacted biomass production, while other essential nutrients did not enhance growth beyond a low saturation threshold. Consequently, we concluded that active supplementation would be inefficient, as key nutrients like sugars and amino acids are metabolized quickly and would require frequent reapplication, leading to increased labor on the side of farmers.

In conclusion, by using our model, we were able to find multiple ideas that could be implemented by the wet lab and can be researched in follow-up studies. Furthermore, we laid a path for future teams trying to work with simulations in soil, proving that it is possible to model soil conditions and show how defining and implementing conditions can be approached. We also found plenty of data supporting the wet lab’s design decisions, showing that our construct makes sense and is based on a solid scientific foundation.

Outlook

To improve on the limitations outlined earlier (See Limitations), future research should prioritize the development of a GEM for Pseudomonas sp. IsoF and focus on collecting more experimental data under defined conditions, including soil, rhizosphere, drought, and potentially biofilm environments. Given the inherent heterogeneity of soil ecosystems, we recommend repeating the experiments from stages 3 and 4 using different in silico soil models. It would be particularly valuable to compare results from soils associated with diverse land-use types, such as arable land, settlements, forests, meadows, and alpine grasslands. Our SDM2 model provides a solid foundation for this work, and its flexible design means that incorporating new soil types would primarily require access to detailed soil composition data for each land use.

Additionally, to better assess the competitiveness of Pseudomonas sp. IsoF, we propose conducting competition tests using FBA on common rhizosphere bacteria. By comparing the growth rates of different species under the same conditions applied to P. putida KT2440 (See Stage 3 for soil design details), we can use growth rate as a proxy for competitive ability. Faster-growing bacteria typically have an advantage when competing for limited resources like nutrients and space, reflecting greater efficiency in resource utilization.

Our preliminary search has identified several potential models for inclusion in this analysis, such as iCN718 (Acinetobacter baumannii AYE)17, iYO844 (Bacillus subtilis subsp. subtilis strain 168)18, and iJYQ746 (Bacillus amyloliquefaciens)19.

However, it is important to note that this estimation may be conservative, as Pseudomonas sp. IsoF possesses a distinct competitive advantage due to its Type IVB Secretion System (T4BSS). This system allows P. sp. IsoF to kill a wide range of Gram-negative bacterial competitors by delivering toxic effectors in a contact-dependent manner20.

Looking ahead, integrating these competition experiments into a Pseudomonas sp. IsoF model, along with varying soil types, will enhance our understanding of microbial dynamics and further clarify the role of Pseudomonas sp. IsoF in agricultural ecosystems, particularly in biofilm production.

Update

Between the wiki freeze and the Grand Jamboree, we continued working on our models and achieved additional results, which we present in this section.

We focused on the competition test described in the outlook section. As a proof of concept, we selected two GEMs of soil bacteria, a gram-positive and a gram-negative strain, that our bacterium would likely compete with in field applications. For the gram-positive bacterium, we used Bacillus subtilis str. 168 and used its GEM, iYO84418, and for the gram-negative bacterium, we chose Xanthomonas phaseoli pv. manihotis , using its GEM, iXpm155621. We adapted both models to our established soil conditions in stage 3 and analyzed their biomass production in the given environment. Assuming that growth rate is a reasonable proxy for competitiveness - where a bacterium gains a competitive advantage by outgrowing others - we compared their biomass production levels to those of our pre-established P. putida KT2440 model.

Figure 24: P. putida KT2440 shows a metabolic competition advantage to two other soil bacteria even when producing the biofilm component cellulose.

As shown in Figure 24, the P. putida KT2440 model outperforms both competitors and can even be induced to produce cellulose before the cost becomes too high and the growth rate falls below that of the others. This result is very promising, but it requires further testing and verification/validation from the wet lab.