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Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato

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Abstract

The fungus Cenococcum geophilum Fr. (Dothideomycetes, Ascomycota) is one of the most common ectomycorrhizal fungi in boreal to temperate regions. A series of molecular studies has demonstrated that C. geophilum is monophyletic but a heterogeneous species or a species complex. Here, we revisit the phylogenetic diversity of C. geophilum sensu lato from a regional to intercontinental scale by using new data from Florida (USA) along with existing data in GenBank from Japan, Europe, and North America. The combination of internal transcribed spacer (ITS) ribosomal DNA and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene resolved six well-supported lineages (87–100 % bootstrap values) that are closely related to each other and a seventh lineage that is phylogenetically distinct. A multi-locus analysis (small subunit (SSU), large subunit (LSU), translational elongation factor (TEF), and the largest and second-largest subunits of RNA polymerase II (RPB1 and RPB2)) revealed that the divergent lineage is the sister group to all other known Cenococcum isolates. Isolates of the divergent lineage grow fast on nutrient media and do not form ectomycorrhizas on seedlings of several pine and oak species. Our results indicate that C. geophilum sensu lato includes more phylogenetically distinct cryptic species than have previously been reported. Furthermore, the divergent lineage appears to be a non-mycorrhizal sister group. We discuss the phylogenetic diversity of C. geophilum sensu lato and argue in favor of species recognition based on phylogenetic and ecological information in addition to morphological characteristics. A new genus and species (Pseudocenococcum floridanum gen. et sp. nov.) is proposed to accommodate a divergent and putatively non-mycorrhizal lineage.

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Acknowledgments

This study was supported by Grant-in-Aid for Japan Society for the Promotion of Science (JSPS) Postdoctoral Fellow for Research Abroad (to K. Obase) with additional funding from the University of Florida Institute for Food and Agricultural Sciences (IFAS) (to M. E. Smith). We thank the Interdisciplinary Center for Biotechnology Research (ICBR) at the University of Florida for performing DNA sequencing, the Ordway-Swisher Biological station, the City of Gainesville, and the Austin Cary Memorial Forest for providing study sites. We also thank collaborators at the Smith Mycology Lab at the University of Florida for their assistance.

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Authors and Affiliations

  1. Microbial Ecology Laboratory, Department of Forest Microbiology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan

    Keisuke Obase

  2. Department of Plant Pathology, University of Florida, 2517 Fifield Hall, Gainesville, FL, 32611-0680, USA

    Keisuke Obase & Matthew E. Smith

  3. Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA

    Greg W. Douhan

  4. Cooperative Extension Advisor, Tulare Co., University of California, Tulare, CA, 93274, USA

    Greg W. Douhan

  5. Laboratory of Forest Pathology and Mycology, Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan

    Yosuke Matsuda

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  1. Keisuke Obase
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Correspondence to Keisuke Obase.

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Fig. S1

ITS and GAPDH phylogenetic tree constructed using the Maximum Likelihood method. Clade numbers correspond to those detailed in Figure 2. Bootstrap values higher than 70 % are indicated at the nodes (1000 replications). (GIF 5777 kb)

High resolution image (TIF 939 kb)

Fig. S2ᅟ

Phylogenetic trees of Dothideomycetes based on each of five different loci highlighting the placement of Cenococcum geophilum sensu lato (Cg), Pseudocenococcum floridanum (Pf) and members of Glonium (Gl). Phylogenetic placement was inferred using the Maximum Likelihood method based on the SSU, LSU, TEF, RPB1 and RPB2 regions. Bootstrap values higher than 80 % are indicated at the nodes (1000 replications). (GIF 6134 kb)

(GIF 1092 kb)

High resolution image-1 (TIF 1164 kb)

High resolution image-2 (TIF 247 kb)

Fig. S3ᅟ

Operational taxonomic units (OTUs) partitioned by PTP analysis. (GIF 5686 kb)

(GIF 1791 kb)

High resolution image-1 (TIF 733 kb)

High resolution image-2 (TIF 196 kb)

Fig. S4

Mycelial growth of Cenococcum geophilum sensu lato and Pseudocenococcum floridanum isolates after four weeks incubation on MMN agar media. Data are presented as mean values from three replicates with standard deviations. The clade number is shown for each C. geophilum isolate. (GIF 1666 kb)

High resolution image (TIF 752 kb)

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Obase, K., Douhan, G.W., Matsuda, Y. et al. Revisiting phylogenetic diversity and cryptic species of Cenococcum geophilum sensu lato. Mycorrhiza 26, 529–540 (2016). https://doi.org/10.1007/s00572-016-0690-7

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