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Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species

  • Plant Microbe Interactions
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Abstract

Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF) or non-arbuscular mycorrhizal (non-AMF) fungi and then tested whether habitat or host identity influenced these fungal communities. Approximately 14% of the sequences represented AMF taxa (44 OTUs) with the majority belonging to Glomus groups A and B. Non-AMF sequences represented 186 OTUs belonging to Ascomycota (58%), Basidiomycota (26%), Zygomycota (14%), and Chytridiomycota (2%) phyla. Total AMF and non-AMF richness were similar between habitats but varied among host species. AMF richness and diversity per root sample also varied among host species and were highest in T. ceratophorum compared with T. officinale and P. viscosum. In contrast, non-AMF richness and diversity per root sample were similar among host species except in the willow understory where diversity was reduced in T. officinale. Fungal community composition was influenced by host identity but not habitat. Specifically, T. officinale hosted a different AMF community than T. ceratophorum and P. viscosum while P. viscosum hosted a different non-AMF community than T. ceratophorum and T. officinale. Our results suggest that host identity has a stronger effect on rhizosphere fungi than habitat. Furthermore, although host identity influenced both AMF and non-AMF, this effect was stronger for the mutualistic AMF community.

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Acknowledgments

A NSF doctoral dissertation improvement grant (DEB-0808000) and the University of Missouri funded this study. Lori Eggert at the University of Missouri and the Division of Biology and Ecological Genomics Institute at Kansas State University provided access to their facilities. Ernesto Almira at the Interdisciplinary Center for Biotechnology Research at the University of Florida provided the 454 pyrosequencing service. Gavin Conant assisted with post-sequencing analysis. Candace Galen, Lori Eggert, Marc Brock, Maarja Opik, and three anonymous reviewers commented on the manuscript.

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  1. Katie M. Becklin

    Present address: Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA

Authors and Affiliations

  1. Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA

    Katie M. Becklin & Kate L. Hertweck

  2. Division of Biological Sciences, Kansas State University, Manhattan, KS, 66506, USA

    Ari Jumpponen

  3. 1200 Sunnyside Avenue, 5032 Haworth Hall, Lawrence, KS, 66045, USA

    Katie M. Becklin

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Correspondence to Katie M. Becklin.

Electronic Supplementary Materials

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Appendix A

Sequence alignment and neighbor-joining tree for the full dataset including AMF OTUs, non-AMF OTUs, and reference sequences. GenBank accession numbers are listed with abbreviated taxon names for reference sequences. (NEX 10837 kb)

Appendix B

Sequence alignment and neighbor-joining tree for the AMF dataset including AMF OTUs, reference sequences, and outgroup taxa. Reference sequences represent either the highest BLASTN matches from GenBank or consensus sequences from Schüßler et al. [42]. GenBank accession numbers are listed for the BLASTN matches. Accession numbers for all other reference sequences are listed in Schüßler et al. (NEX 367 kb)

Table S1

GenBank accession number, top BLASTN match, and phylogenetic assignment for each 454 operational taxonomic unit (OTU). OTUs were designated based on 97% sequence similarity. (PDF 78 kb)

Table S2

Number of sequences, number of operational taxonomic units (OTUs), and relative abundance of each OTU per root sample collected from T. ceratophorum, T. officinale, and P. viscosum plants in open meadow and willow understory habitats. OTUs were designated based on 97% sequence similarity. (PDF 189 kb)

Figure S1

Mean (±SE) AMF richness, diversity, and evenness per root sample based on OTUs designated at 90%, 95%, 97%, and 99% sequence similarity. a, d OTU richness by habitat (a) and host species (d); b, e Shannon’s diversity index by habitat (b) and host species (e); c, f OTU evenness by habitat (c) and host species (f). In (a–c), open and solid circles represent samples from the open meadow and willow understory, respectively. In (d–f), symbols represent samples from T. ceratophorum (circles), T. officinale (squares), and P. viscosum (triangles). *P ≤ 0.05; **P ≤ 0.01, significant habitat or host effect. The decrease in OTU richness and diversity at 99% similarity was due to an increased number of singletons, which were subsequently removed from the dataset. (JPEG 74 kb)

High-resolution image (TIFF 731 kb)

Figure S2

Mean (±SE) non-AMF richness, diversity, and evenness per root sample based on OTUs designated at 90%, 95%, 97%, and 99% sequence similarity. a OTU richness by habitat and host species; b Shannon’s diversity index by habitat and host species; c OTU evenness by habitat and host species. Symbols represent samples from T. ceratophorum (circles), T. officinale (squares), and P. viscosum (triangles). Open and solid symbols represent samples from the open meadow and willow understory, respectively. *P ≤ 0.05; **P ≤ 0.01, significant habitat by host interaction. (JPEG 40 kb)

High-resolution image (TIFF 408 kb)

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Becklin, K.M., Hertweck, K.L. & Jumpponen, A. Host Identity Impacts Rhizosphere Fungal Communities Associated with Three Alpine Plant Species. Microb Ecol 63, 682–693 (2012). https://doi.org/10.1007/s00248-011-9968-7

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