Abstract
We have previously reported the design of a new PCR primer pair that allows amplification of a broad range of eubacterial 16S rDNA sequences from ectomycorrhizae (ECM) without co-amplification of plastid or mitochondrial sequences. Here, we report using a similar primer combination to generate three small 16S rDNA libraries from tuberculate ECM of Rhizopogon spp., two from R. vinicolor ECM (libraries Rvi18 and Rvi24) and one from R. vesiculosus ECM (library Rve13). At the class level, libraries were dominated by sequences from the Alphaproteobacteria, Gammaproteobacteria, and Acidobacteria, with some Sphingobacteria, Actinobacteria, Planctomycetacia, and Verrucomicrobiae present as well. Based on the parsimony test implemented in TreeClimber, libraries Rvi18 and Rvi24 were significantly different from Rve13 at the α = 0.05 level, while they were only borderline significantly different from each other (p = 0.07). Differences between Rvi and Rve libraries were primarily due to differences in the number of Alphaproteobacteria sequences and specifically sequences from the Rhizobiales, which were more common in the Rve13 library. It is currently unknown what drives these differences between eubacterial communities. Amplification success for eubacterial 16S rDNA sequences was generally low in this study indicating low abundance of bacteria on tuberculate ECM. Attempts to amplify nitrogenase reductase (nifH) sequences were unsuccessful.
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Acknowledgements
The authors thank Susie Dunham for facilitation fieldwork conducted in Oregon and two anonymous reviewers for their very insightful comments. The study was supported by NSF grant DEB-0137531 to AMK.
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Supplementary Table 1
Classification of 16S rDNA sequences according to the RDB Classifier. Percentages indicate bootstrap confidence estimates in individual classifications (Wang et al. 2007) (DOC 64.0 KB).
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Kretzer, A.M., King, Z.R. & Bai, S. Bacterial communities associated with tuberculate ectomycorrhizae of Rhizopogon spp.. Mycorrhiza 19, 277–282 (2009). https://doi.org/10.1007/s00572-008-0213-2
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DOI: https://doi.org/10.1007/s00572-008-0213-2