Lichens are slow-growing niche-constructing organisms formed via scripted symbiotic/mutualist relationships between fungi, algae, and bacteria. We have used quick-freeze deep-etch electron microscopy (QFDEEM), coupled with several additional microscopic techniques, to analyze the Japanese foliose lichen Myelochroa leucotyliza. We have also examined its constituent fungi and algae grown separately (solo) and in co-culture in the laboratory, as well as solo fungi incubated with conditioned algal media (CM) for 9 days. We report our general findings on M. leucotyliza architecture in a Supplement, and focus this report on three findings of particular interest. 1) Plasma membrane differentiations called nubbins are found adjacent to, and at the center of, the cellwall septa in both lichenized and solo hyphae, suggesting a role in cell polarity determination and/or cell-cell communication within the hyphae. 2) Nubbins also localize to the tips of hyphal sub-branches produced by the lichenized but not the solo fungi. These in turn form tip-to-tip contacts (bridges) with one another, suggesting a role in inter-hyphal communication. 3) CM treatment of solo fungi induces a) the production of secondary metabolites, polysaccharides, and lipids; b) a transformation of ER topology and its association with the plasma membrane; and c) a dramatic change in vacuole organization, indicating that the algal growth medium contains soluble materials that trigger fungal differentiation. Keywords: Lichen; Nubbin; Cell-wall septum; Endoplasmic reticulum; Vacuole; Hydrophobin.