wet land soil Targeted loci environmental. soil metagenome

Though the use of metagenomic methods to sample below-ground fungal communitiesis common, the use of similar methods to sample plants from their undergroundstructures is not. In this study we use high throughput sequencing of the ribulosebisphosphatecarboxylase large subunit (rbcL) plastid marker to study the plantcommunity as well as the internal transcribed spacer and large subunit ribosomal DNA(rDNA) markers to investigate the fungal community from two wetland sites. Observedcommunity richness and composition varied by marker. The two rDNA markersdetected complementary sets of fungal taxa and total fungal composition clusteredaccording to primer rather than by site. The composition of the most abundant plants,however, clustered according to sites as expected. We suggest that future studiesconsider using multiple genetic markers, ideally generated from different primer sets, todetect a more taxonomically diverse suite of taxa compared with what can be detectedby any single marker alone. Conclusions drawn from the presence of even the mostfrequently observed taxa should be made with caution without corroborating lines ofevidence.