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Mycorrhiza

, Volume 22, Issue 4, pp 309–315 | Cite as

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

  • Håvard Kauserud
  • Surendra Kumar
  • Anne K. Brysting
  • Jenni Nordén
  • Tor Carlsen
Original Paper

Abstract

In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences were clustered into OTUs as proxies for species using single linkage clustering (BLASTClust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone library datasets — even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had little impact when applying the same sequencing technique on replicate samples.

Keywords

Ectomycorrhiza Community ecology 454 pyrosequencing Sanger sequencing Bistorta vivipara 

Notes

Acknowledgments

The University of Oslo is acknowledged for financial support and three anonymous reviewers for helpful comments. We thank biology students at the University of Oslo who did the field work and initiated this work as a part of a course project.

Supplementary material

572_2011_403_MOESM1_ESM.doc (188 kb)
Table S1 Number of reads obtained from all OTUs, distributed on plant root systems and replicates. Top blast hits are shown along with identity, query coverage, and GC content of the representative sequence. (DOC 188 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Håvard Kauserud
    • 1
  • Surendra Kumar
    • 1
  • Anne K. Brysting
    • 2
  • Jenni Nordén
    • 1
  • Tor Carlsen
    • 1
  1. 1.Department of Biology, Microbial Evolution Research Group (MERG)University of OsloOsloNorway
  2. 2.Department of BiologyCentre for Ecological and Evolutionary Synthesis (CEES)OsloNorway

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