Root Mycorrhizal Mycobiome in Pinus densiflora Accessed by Long- and Short-read NGS Techniques
Ki Hyeong Park* and Young Woon Lim
School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, South Korea
Pinus densiflora is a dominant pine tree, but its habitat is diminishing due to climate change and plant disease in South Korea. Mycorrhizal fungi are expected to have a massive potential in forest management, but precise identification of host-associated mycorrhizal fungi is required beforehand. For the diversity survey of mycorrhizal mycobiome, Next-generation sequencing (NGS) has become a more efficient tool compared to classic methods. However, the widely-used short-read NGS technologies have limitations in taxonomic assignments. The alternative long-read NGS technologies also have their own weakness in sequencing depth and potential biases. To overcome these drawbacks, we employed two NGS platforms, Illumina MiSeq and PacBio Sequel, to characterize the overall mycorrhizal mycobiome directly associated with the root of 80 P. densiflora in 16 pine forests across South Korea, then identified them using a custom database implemented with sequences of Korean sporocarps. Despite the lower sequencing depth of PacBio Sequel, PacBio dataset featured better taxonomic resolution in species level. Datasets from both methods commonly detected most mycorrhizal taxa. However, they featured a significant difference in abundance and frequency for each taxon, although the community structure, as well as the influence of spatial distance, climate, and soil properties on mycobiome was generally similar between platforms. Using two different sequencing platforms, we could identify taxa that would not have been seen if only one platform was used. The results of our study provide detailed information on the composition and distribution of mycorrhizal fungi associated with Korean P. densiflora.