FungPy: A Python Package to Simulate Plant Hyphosphere Interactions to Model interactions between plant, arbuscular mycorrizhea fungi (AMF) and bacteria

Abhishek Dash

Mentors: Dr. Ali Navid and Dr. John R. Casey, Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory.

Date/Time: August 23rd, 2024 at 2:40pm.

Abstract: Arbuscular Mycorrizhas or AMF is a fungal species that is known to interact with plant roots and various bacterial species present. It is known to enhance access to nutrients and improve drought resistance in most plant species. The goal of FungPy is to model and simulate these interactions to predict optimal fungal-plant partnerships with the goal of optimizing crop yields. FungPy is a Python based package that emulates various parts of the plant root system including a nutrient grid and nutrients that diffuse through it, the hyphal network of the AMF and the mycelium or the fungal mass. Furthermore, an interactive dashboard was also designed to interactively view the growth of the Fungi.

FungPy was successfully developed and its results were consistent with an existing model (Plant Hyphosphere Simulator). FungPy improved upon the existing model through parameterization, higher efficiency and the ability to parallelize different simulations high-performance computing clusters. FungPy successfully modeled the growth and interactions between Pancium Virgatum (switchgrass) and the AMF species Rhizophagus Irregularis. The modeling results were consistent with imaging data that was collected, showing that the modeling of the hyphal network was within a reasonable threshold. Furthermore, an interactive dashboard was developed to effectively visualize the hyphal growth and related graphs.

FungPy is ready for deployment to compare various Fungal-Plant partnerships. Due to the data not being available, different species will be compared at a future point of time to determine the optimal plant-AMF combination. While imaging of metabolites and flux balance analysis between genome scale models between Fungal and Bacterial species was investigated, future iterations of FungPy will support the above.