An interactive 3D simulator of a growing plant root system — either a taproot system (dicot) or a fibrous system (monocot) — being colonised by an arbuscular mycorrhizal (AM) fungus. It runs entirely in the browser.
https://schornacklabslcu.github.io/MycorRhize3D/
Controls: left-drag to orbit, scroll to zoom, right-drag to pan. On phones the side panel and the graph collapse to buttons so the 3D view fills the screen.
Roots and mycorrhizal fungi form one of the oldest and most widespread symbioses on Earth (~400 million years old). In the arbuscular mycorrhizal symbiosis, a soil fungus enters the root, spreads through the cortex, and builds tree-like feeding structures (arbuscules) that trade soil phosphorus and nitrogen for plant sugars and lipids. Because the fungus lives inside the root, watching colonisation spread in real time in an intact, living root system was historically very hard.
This simulator's behaviour is inspired by Timoneda, Yunusov, Quan, Gavrin, Brockington & Schornack (2021), "MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation," PLOS Biology 19(7): e3001326. In this manuscript we engineered plants to produce a vivid red betalain pigment (betanin) specifically in cells where the fungus (Rhizophagus irregularis) had colonised, so that fungal spread could be followed live and in colour across whole root systems of Medicago truncatula and Nicotiana benthamiana. It was the first time this hidden process could be seen unfolding in real time in living plants.
That work is why colonised root tissue is drawn in red here — the red front spreading along the roots is the visual analogue of the MycoRed reporter lighting up as the fungus advances.
The simulator is an illustrative teaching model, not a reproduction of the paper's data. Its rules echo established root-architecture and colonisation concepts:
- Root architecture — choose a taproot (one dominant gravitropic primary root with recursively branching laterals, à la CRootBox / ArchiSimple) or a fibrous system (many thin, similar-diameter adventitious primaries emerging together from the crown and fanning outward and down, with no dominant root, as in grasses and other monocots). Both feature an apical zone that stays unbranched, thin rounded tips that thicken to mature diameter, and collision-avoidance so roots fill the soil volume. Branching depth and the maximum length of each root order are independently adjustable.
- Colonisation dynamics — infection begins where a growing root crosses the germination radius of a fungal spore (scattered randomly or confined to a defined cube of inoculum). From each entry point the fungus spreads bidirectionally along the root, cannot colonise a set distance behind the growing tip, and each infection event has a finite lifetime after which it stops advancing — echoing the patchy, locally-limited colonisation seen experimentally. Crossing a root–lateral junction can be set to happen freely, after an adjustable time delay, or not at all.
- Live readout — a dual-axis chart tracks total root length (grey) against colonised length (red) over time.
Every parameter above is adjustable with live sliders, and a Randomize button rolls a fresh root architecture.
- Rendering: three.js (r160).
- Scientific inspiration: Timoneda A, Yunusov T, Quan C, Gavrin A, Brockington SF, Schornack S. MycoRed: Betalain pigments enable in vivo real-time visualisation of arbuscular mycorrhizal colonisation. PLOS Biology, 2021. https://doi.org/10.1371/journal.pbio.3001326
MIT — do what you like; attribution appreciated.