Identification and Classification of AMF
With few defining features, these fungi are often identified by features of their spores (e.g. shape, hyphal attachment, and wall characteristics), by their branching pattern inside of roots, and by features of their arbuscules and vesicles.
To observe all of these features, spores must be isolated from soil collections and AM roots must be cleaned and stained so that fungal features can be observed.
Unlike most other fungi, glomeromycotan spores are often large enough to see with the naked eye (i.e. 40–800 μm diameter, compared to the 5–20 μm diameter of most other fungal spores). This large size allows for the spores to be easily sieved from soil collections, with the number of spores being a metric that can also be used to understand the habits of the fungus and its relative abundance in a given habitat.
Depending on the age, health, and climate of their habitat, AM spores may be found in low or abundant numbers. Sand dunes may only host four spores per cubic centimeter, established woodlands (which host a high number of ectomycorrhiza-forming plant species) can host 1–5 spores per gram of soil, and agricultural sites may have 9–89 spores per gram of soil. In agricultural sites that are frequently tilled, heavy-sporing Glomus species tend to dominate as they do not rely on hyphal spread to reach new plants as much as other genera of AM fungi.
For root colonization observations, roots are surface washed and then cleared of their contents (for example, by boiling them in a bath of potassium hydroxide) before staining them with lab-grade stains or diluted pen inks. Samples of tissue are then observed under a microscope to approximate the amount of total root mass that is colonized by the fungus, while also noting the features in the hyphal branching, arbuscules, and vesicles. Beyond helping identify the fungus, the root colonization percentage can be used to compare infection rates between fungal species, or between fungus-plant pairings, or to qualify the success of an inoculation attempt in the lab or in the field.
If spores are not found in soil samples, wild plants can be harvested and potted in “traps” that are designed to collect AM fungi that exit their roots. One of the challenges with this work is that these fungi are known to dramatically change their appearance and habits as their environmental conditions shift, making lab-based observations potentially quite different from AM dynamics in the field.