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The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses

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Abstract

Bacteria have been observed to grow with fungi, and those that associate with ectomycorrhizal fungi have often been thought of as symbionts that may either increase or decrease ectomycorrhizal formation rate or provide other unaccounted benefits. To explore this symbiosis from a community ecology perspective, we sampled ectomycorrhizal root tips over a 3-year period and used 454 pyrosequencing to identify the bacteria that live inside the ectomycorrhizal root tips. The results showed that fungal community composition within the same soil core and fungal taxonomic identity had a stronger effect on bacterial community composition than sample year or site. Members of the Burkholderiales and Rhizobiales were most highly represented, reflecting many previous reports of these bacteria in association with fungi. The repeated occurrences of these two bacterial orders suggest that they may be symbiotic with their fungal hosts, although the nature of such mechanisms, be it symbiotic diazotrophy or otherwise, remains to be thoroughly tested.

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Acknowledgments

We thank the two anonymous reviewers for very useful suggestions and guest editor Emma Sayer for the attention to details that have much improved this manuscript. This work was supported by an NSF-GRFP and the UC Berkeley Dissertation Year Award to NHN.

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Correspondence to Nhu H. Nguyen.

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Table S1

A list of ECM samples that were successfully sequenced and identified as belonging to a single fungus. These samples were then subjected to 454 pyrosequencing to identify the bacterial associates. The names of these species were applied by matching their sequences to each other (within 97 % sequence similarity), to more than 600 vouchered specimens at the study site, and by phylogenetic inference when appropriate. (XLSX 62 kb)

Table S2

Rarified OTU table (144 sequences per sample) of the “complete EM” dataset. The “common EM” dataset was a subset of this table. The table includes fungal species identification (see the Methods section for explanation). Representative sequences were picked from the most common sequence type for that OTU. (XLSX 434 kb)

Table S3

More refined identification matches of the most frequently found bacterial OTUs. The “% identity” column also contains the confidence % from the Ribosomal Database Project Classifier. See Table S2 for matching sequences to the OTU_ID. T = matches to the type strain of the species. NA = no accession numbers given because matches were made through the RDP Classifier. (XLSX 55 kb)

Table S4

Comparison of bacterial communities associated with each fungal species across multiple years using the adonis test. Letters indicate significant groupings with p < 0.05. NA, not applicable because data was not available for that comparison. (XLSX 38 kb)

Figure S1

PCoA ordination plot of the bacterial associates within the root-tips of the five common EM species showing loose clustering of the microbiome of fungal species across years. Filled squares = Tricholoma imbricatum, open circles = Tomentella sublilacina, filled triangles = Russula cerolens, × = Rhizopogon salebrosus, open diamonds = Clavulina sp. (PDF 78 kb)

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Nguyen, N.H., Bruns, T.D. The Microbiome of Pinus muricata Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses. Microb Ecol 69, 914–921 (2015). https://doi.org/10.1007/s00248-015-0574-y

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