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Arbuscular mycorrhizal fungi (AMF) colonize the plant root endosphere and extend the host’s resource network. However, little is known about the method to characterize the intraradical AMF communities of a specific tree species in forests. Therefore, we aimed at testing a method for characterizing and comparing the extra- and intraradical AMF communities of  Cryptomeria japonica  (Cupressaceae). In February 2020, we tracked and sampled roots from 5 target trees and the surrounding soil and confirmed their identity using plan DNA barcoding methods. After a microscopic analysis of mycorrhizal root colonization, we used Illumina amplicon sequencing to characterize the corresponding AMF communities. The  C. japonica  roots were colonized by AMF, displaying the Paris- and Arum-types of mycorrhizae. At 100% sequence identity, amplicon sequences of the small-subunit nuclear ribosomal RNA gene clustered into 155 operational taxonomic units (OTUs), 33 and 139 in the intra- and extraradical AMF communities, respectively, corresponding to three families and five genera. Nevertheless, only  Acaulospora, Glomus , and  Rhizophagus  were detected in the root samples. The AMF communities did not significantly differ between the root and the surrounding soil, but we observed a significant nestedness pattern in the community. To avoid erroneous conclusions, combining plant DNA barcoding with amplicon sequencing is a reliable approach, which we recommend for future studies to describe the intraradical AMF community of a specific tree species in forests.

Amplicon sequencing reveals the arbuscular mycorrhizal fungal community composition in Cryptomeria japonica at one local site