Discovery of novel intermediate forms redefines the fungal tree of life

Journal name:
Nature
Volume:
474,
Pages:
200–203
Date published:
DOI:
doi:10.1038/nature09984
Received
Accepted
Published online

Fungi are the principal degraders of biomass in terrestrial ecosystems and establish important interactions with plants and animals1, 2, 3. However, our current understanding of fungal evolutionary diversity is incomplete4 and is based upon species amenable to growth in culture1. These culturable fungi are typically yeast or filamentous forms, bound by a rigid cell wall rich in chitin. Evolution of this body plan was thought critical for the success of the Fungi, enabling them to adapt to heterogeneous habitats and live by osmotrophy: extracellular digestion followed by nutrient uptake5. Here we investigate the ecology and cell biology of a previously undescribed and highly diverse form of eukaryotic life that branches with the Fungi, using environmental DNA analyses combined with fluorescent detection via DNA probes. This clade is present in numerous ecosystems including soil, freshwater and aquatic sediments. Phylogenetic analyses using multiple ribosomal RNA genes place this clade with Rozella, the putative primary branch of the fungal kingdom1. Tyramide signal amplification coupled with group-specific fluorescence in situ hybridization reveals that the target cells are small eukaryotes of 3–5μm in length, capable of forming a microtubule-based flagellum. Co-staining with cell wall markers demonstrates that representatives from the clade do not produce a chitin-rich cell wall during any of the life cycle stages observed and therefore do not conform to the standard fungal body plan5. We name this highly diverse clade the cryptomycota in anticipation of formal classification.

At a glance

Figures

  1. Identification of the cryptomycota.
    Figure 1: Identification of the cryptomycota.

    a, Phylogeny demonstrates a diverse clade of environmental sequences (coloured dots) branching at the base of the Fungi. MrBayes tree topology was calculated from an alignment of 100 sequences and 1,012 DNA characters. Support values are summarized by black dots (indicating at least 0.9 Bayesian posterior probability and 80% bootstrap support by ML and Log-Det distance methods) or by black rings (Bayesian posterior probability above 0.6 and bootstrap support above 50%). The key node showing monophyly of cryptomycota encompassing Rozella is marked with actual values, with the SSU–5.8S–LSU support value (Supplementary Fig. 2a) shown in red. Shortened branches are in grey. Sequences targeted by the probes/primers are labelled on the tree. b, Provenance list of environmental DNA sequences. c, Schematic representation of the positions of primers (arrows) and probes (green hexagons) on a partial rDNA gene array (grey). d, TSA-FISH identification of cryptomycota cells (green) and DAPI staining of microbial community (blue). Scale bar, 10μm.

  2. Structural properties of cryptomycota cells and evidence for different life cycle stages.
    Figure 2: Structural properties of cryptomycota cells and evidence for different life cycle stages.

    a, Micrographs showing flagella on cryptomycota cells, as detected by TAT1 tubulin antibody. b, Single cells without a chitin cell wall, as inferred by non-binding of wheat germ agglutinin (WGA). c, Non-flagellate putative cysts (lack of TAT1 signal indicates absence of flagellum), without a chitin/cellulose cell wall, as inferred by non-binding of calcofluor white. d, Cryptomycota cells attached to a second-party cell. Bright field differential interference contrast (DIC) shows filamentous structure of the second-party cell. e, Cryptomycota cells attached to a second-party cell; residual staining identifies the boundary of the second-party cell and WGA identifies absence of chitin during attachment. Scale bars, 10μm. f, Putative cryptomycota skeleton life cycle (letters in brackets refer to micrographs ae). This life cycle is limited to stages identified using TSA-FISH so additional stages are likely to remain unobserved (for example, sporangia stages and cell division) and the order of transition remains hypothetical. Furthermore, the diversity of the cryptomycota group strongly indicates that there are likely to be numerous life-cycle variations within the group, so this life cycle is unlikely to represent the wider diversity of cryptomycota.

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GenBank/EMBL/DDBJ

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Author information

Affiliations

  1. School of Biosciences, University of Exeter, Exeter EX4 4QD, UK

    • Meredith D. M. Jones,
    • Martin J. Egan &
    • Thomas A. Richards
  2. Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK

    • Meredith D. M. Jones,
    • David Bass &
    • Thomas A. Richards
  3. Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain

    • Irene Forn &
    • Ramon Massana
  4. Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK

    • Catarina Gadelha
  5. Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston Massachusetts 02115, USA

    • Martin J. Egan

Contributions

This study was conceived by T.A.R. and M.D.M.J. with assistance from D.B. and R.M.. M.D.M.J. performed the molecular biology experiments with assistance from I.F. (FISH), C.G. (immunolocalization) and M.J.E. (microscopy). T.A.R. performed the bioinformatics and phylogenetic analysis. T.A.R. and M.D.M.J. wrote the paper with assistance from D.B. and R.M.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

Novel sequence data have been deposited in GenBank under accession numbers FJ687265, FJ687267 and FJ687268.

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Supplementary information

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  1. Supplementary Information (23M)

    This file contains Supplementary Figures 1-7 with legends and Supplementary Tables 1-6.

Comments

  1. Report this comment #22010

    Russell Paterson said:

    There is a discussion about whether these organisms are fungi in another Nature Comments page. Hence, someone could usefully test for ergosterol in the cell membrane which is almost fungal specific (Paterson 2005), especially as there is no cell wall. There is a staining method and some genes are known (send email address for more information).
    Reference
    Paterson (2005). Microbiology, 151, 641.

    R Russell M Paterson
    Micoteca da Universidade do Minho
    Centre of Biological Engineering
    University of Minho
    Portugal

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