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

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.