Arbuscular mycorrhizal fungi (AMF) are well-known plant symbionts which provide enhanced phosphorus
uptake as well as other benefits to their host plants. Quantification of mycorrhizal density and
root colonization has traditionally been performed by root staining and microscopic examination methods,
which are time-consuming, laborious, and difficult to reproduce between laboratories. A number of
biochemical markers for estimating mycorrhizal hyphae and spores have been published. In this study
we grew maize plants in three different soils in a replicated greenhouse experiment and compared the
results from two microscopic methods, spore density and root colonization, to the results from three lipid
biomarker methods: neutral lipid fatty acid, phospholipid fatty acid, and ester-linked fatty acid analysis.
Ester-linked fatty acid analysis gave consistent results for both spore density and root colonization, but
neutral lipid fatty acid analysis had the highest correlation to AMF spore counts. Phospholipid fatty acid
analysis was not correlated to spore density and did not reproducibly correlate to root colonization.