Comparing diversity of fungi from living leaves using culturing and high-throughput environmental sequencing

ABSTRACT

High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected. Here we use high-throughput amplicon sequencing from bulk DNA extracts to test the impact that biases associated with culture-based methods had on an earlier study that compared the influence of site and host on fungal diversity in Nothofagaceae forests in New Zealand. Both detection methods sampled tissue from the same set of symptomless, living leaves. We found that both the culturing and high-throughput approaches show that host is a stronger driver of fungal community structure than site, but that both methods have some taxonomic biases. We also found that the individual trees selected for high-throughput sampling can impact the alpha-diversity detected and through this could potentially affect subsequent analyses based on a comparison of this diversity.

KEYWORDS:

• Fungal endophytes
• Nothofagaceae
• pyrosequencing
• sampling bias
• UNITE species hypothesis

Supplemental data

Supplemental data for this article can be accessed on the publisher’s Web site.

ACKNOWLEDGMENTS

Ngati Rangi, the New Zealand Department of Conservation, and the Auckland Council are thanked for allowing Nothofagaceae leaf material to be collected on land they manage. Karyn Hoksbergen, Paula Wilkie (Landcare Research), Sarah Hoffman, Rose Williams, and Renee Johansen (Auckland University) assisted with the culturing. Renee Johansen and Jerry Cooper (Landcare Research) are thanked for advice on use of the UPARSE pipeline.

FUNDING

This research was supported through the Landcare Research Systematics Portfolio, with Core funding support from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment.

Additional information

Funding

This research was supported through the Landcare Research Systematics Portfolio, with Core funding support from the Science and Innovation Group of the New Zealand Ministry of Business, Innovation and Employment.