Biophysics & Biochemistry

Everything that flows through a mycorrhizal network must cross at least one biological membrane. The biophysics of those membranes — their lipid composition, the proton gradients across them, and the transporter proteins embedded in them — sets the rules for what can move, in which direction, and how fast. This module zooms into the molecular machinery underlying the abstract fluxes used in the ODE of Module 2.

The fungal membrane and the proton motive force

Fungal hyphae are bounded by a phospholipid plasma membrane and a rigid chitin cell wall (unlike plants, which use cellulose). The membrane lipid ergosterol — the fungal equivalent of cholesterol — concentrates transport proteins into ordered lipid rafts.

The central energy currency of the membrane is the proton motive force (PMF). A plasma membrane H⁺-ATPase pumps protons out of the cell, building both an electrical potential (typically −150 to −250 mV, inside negative) and a pH gradient (about 1.5–2 units, inside alkaline). Together:

$$\Delta G_{\text{PMF}} = F\,\Delta \psi + 2.303\, RT\, \Delta \text{pH}.$$

Every nutrient that enters the fungus — sugars, amino acids, phosphate, sulfate, nitrate — is dragged in against its own gradient by proton-coupled symporters that ride this PMF.Knock out the H⁺-ATPase and nutrient uptake collapses immediately.

Carbon transfer: sucrose → trehalose → lipids

At the symbiotic interface, plant cells secrete sucrose into the apoplastic space using SWEET transporters (Sugar Will Eventually be Exported Transporters). Sucrose can reach millimolar concentrations there. The fungus then either:

1. Hydrolyses it outside — fungal invertases cleave sucrose into glucose + fructose, which are imported by hexose–H⁺ symporters, or
2. Imports it intact via sucrose transporters and cleaves it inside using sucrose synthase, preserving the energy of the glycosidic bond as UDP-glucose.

Inside the hypha, glucose is rapidly converted into trehalose (α-D-glucopyranosyl-α-D-glucopyranoside) — the dominant mobile sugar in fungi — and into glycogen for storage and into triacylglycerol lipid droplets. Long-distance carbon transport through hyphae is partly via these lipid droplets, ferried along actin filaments by myosin V motors at several micrometres per second. This is an active, ATP-dependent process, not passive diffusion.

Phosphorus: the headline nutrient

Soil phosphorus is the limiting nutrient that the symbiosis is built around. In most soils, free orthophosphate (H₂PO₄⁻ / HPO₄²⁻) is present at less than 10 µM — tightly bound to iron and aluminium oxides and inaccessible to thick roots. Fungal hyphae penetrate micropores in soil aggregates that roots cannot.

Hyphal phosphate-H⁺ symporters (high-affinity Major Facilitator Superfamily transporters) import phosphate with stoichiometry of 2–4 H⁺ per Pi against a concentration gradient of three to four orders of magnitude — possible only because the PMF is so steep.

Once inside, phosphate is not transported as the free ion. It is polymerised into long chains of polyphosphate (polyP) — the same phosphoanhydride bond as in ATP, with ΔG°′ ≈ −20 kJ/mol per bond — and stored in vacuoles at concentrations of hundreds of millimolar. PolyP serves three roles at once: a buffer (preventing toxic free-Pi accumulation), a mobile store (transported across the network in vacuoles via cytoplasmic streaming), and an energy reserve.

At the plant interface, vacuolar polyphosphatases hydrolyse polyP back to Pi, which is exported to the apoplast and imported into root cells by plant phosphate transporters such as MtPT4. Thethermodynamic accounting is striking: phosphate moves from a few µM in soil all the way to millimolar concentrations in plant vacuoles — a 1000- to 10 000-fold uphill journey ultimately powered by sunlight via photosynthesis.

The polyphosphate vacuole as a biophysical object

Polyphosphate chains (typically 20–1000 residues, partly neutralised by Mg²⁺/Ca²⁺/K⁺ counterions) form a dense, partially condensed polyelectrolyte gel inside the vacuole. The fungal vacuole is bounded by the tonoplast, which is actively acidified by V-ATPase (using ATP to pump H⁺ in) and by H⁺-pyrophosphatase (recycling metabolic PPi for the same purpose). The combination creates a vacuolar pH of 5.0–5.5 and gives the polyP gel a strong electrostatic identity.

PolyP moves through hyphae inside vacuoles, ferried by actin/myosin transport. Vacuoles deform or undergo regulated fission to navigate narrow hyphal constrictions; recent imaging has revealed extensive tubular vacuolar networks in long hyphae — effectively a vascular system at the organelle scale.

Nitrogen: the GS–GOGAT cycle

Fungi take up nitrogen as ammonium (NH₄⁺, via AMT transporters), nitrate (NO₃⁻, via NRT symporters, reduced by nitrate then nitrite reductase), or amino acids directly. Inorganic N enters amino-acid metabolism via:

$$\text{NH}_4^+ + \text{glutamate} + \text{ATP} \;\xrightarrow{\text{GS}}\; \text{glutamine} \;\xrightarrow{\text{GOGAT}}\; 2\,\text{glutamate}.$$

Glutamine and glutamate (and to a lesser extent alanine) are then the nitrogen carriers handed across the symbiotic interface. The C:N ratio of the exchange is tightly regulated — in a nitrogen-rich environment the plant becomes a less dependent customer and the "exchange rate" shifts.

Signalling: strigolactones, Myc-LCOs, and the calcium oscillation

The handshake begins with the plant. Roots secrete strigolactones (SL) — carotenoid-derived hormones — into the rhizosphere. SL binds an α/β-hydrolase receptor (KAI2/D14 family) on the fungus, triggering hyphal branching, massive mitochondrial activation, and secretion of Myc-LCOs (lipo-chitooligosaccharides, structurally related to rhizobial Nod factors used by nitrogen-fixing bacteria).

Myc-LCOs bind plant LysM-RLK receptors on the plasma membrane. Through an incompletely understood pathway, this signal reaches the inner nuclear envelope and opens CASTOR and POLLUXcation channels, depolarising the envelope and triggering periodic release of nuclear Ca²⁺ via IP₃-gated channels. The result: nuclear calcium oscillations with period 30–100 s, measurable with calcium-sensitive fluorescent reporters.

The oscillations are read by CCaMK via the auto-phosphorylation memory mechanism explained in Module 3. This is precisely the memory-kernel / non-Markovian filter picture: CCaMK's response is a convolution of past Ca²⁺ input against an exponentially decaying memory, preferentially amplifying a narrow band of input frequencies. It is a biological matched filter, tuned to the frequency the fungal partner actually emits.

Water and aquaporins

Water moves across hyphal membranes through aquaporins — six-helix membrane proteins with an hourglass pore lined by two NPA motifs that exclude protons and ions while passing water molecules in single file. Aquaporin gating is regulated by phosphorylation, pH and osmotic stress. At the network level, the fungus reduces the hydraulic resistance between soil water and tree leaves, helping the tree maintain transpiration through dry patches — biophysically described by the van den Honert catenary model of soil → root → leaf → atmosphere water potential drops.

Defensive chemistry — jasmonic acid signalling

When a tree is wounded or attacked, membrane damage releases linolenic acid from chloroplasts. A cascade of lipoxygenase, allene oxide synthase, and β-oxidation produces jasmonic acid (JA), which is conjugated to isoleucine to form the bioactive JA-Ile. JA-Ile binds the F-box protein COI1, triggering ubiquitin-mediated degradation of JAZ repressors, and unblocking the transcription factor MYC2 — which switches on the plant's defence genes. JA and its volatile methyl ester can travel through the mycorrhizal network to neighbouring trees, priming their defences before the herbivore arrives.

Thermodynamics of the exchange

The plant invests up to 30% of its photosynthate in fungal partners — a continuous drain of Gibbs free energy in exchange for phosphorus and nitrogen that would otherwise be inaccessible. But the access to those nutrients allows higher rates of photosynthesis (leaf area, chlorophyll, RuBisCO all are P- and N-limited), which funds more fungal growth and yet more nutrient supply — an autocatalytic positive feedback.

The feedback is regulated by something extraordinary: a biological market. Toby Kiers and colleagues showed that plants preferentially allocate carbon to fungal partners delivering more phosphorus, and fungi preferentially allocate phosphorus to roots delivering more carbon — a market-like reciprocity emerging purely from coupled biochemistry, without neurons, cognition, or intention. It is one of the cleanest demonstrations of how complex apparent cooperation can arise from local exchange rules.