The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

S. K. Schmidt; K. L. Wilson; A. F. Meyer; C. W. Schadt; T. M. Porter; J. M. Moncalvo

doi:10.1128/9781555815509.ch4

Chapter 4 : The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

Authors: S. K. Schmidt¹, K. L. Wilson², A. F. Meyer³, C. W. Schadt⁴, T. M. Porter⁵, J. M. Moncalvo⁶

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Affiliations: 1: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 2: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 3: Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; 4: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6038; 5: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; 6: Department of Ecology and Evolutionary Biology, University of Toronto, and Department of Natural History, Royal Ontario Museum, Toronto, ON M5S 2C6, Canada

Content Type: Monograph

Publication Year: 2008

Category: Genomics and Bioinformatics; Environmental Microbiology

Book DOI: 10.1128/9781555815509

Chapter DOI: 10.1128/9781555815509.ch4

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Abstract:

Molecular surveys of soil fungi have received much less attention despite the fact that fungi dominate decomposition and nutrient cycles in many soils. The ability to sequence fungal DNA from soil samples has opened up a new realm of possibilities for identifying new fungal groups. A clone library approximates a random sample of fungi in the soil, and is likely to be biased toward some groups of fungi over others based on variables in each step of the procedure used. The Assembling the Fungal Tree of Life (AFTOL) initiative has definitively clarified the phylogenetic tree for all known fungi. Three rDNA regions are commonly used to identify fungi: the 18S small subunit (SSU); the internal transcriber spacer sequences ITS-1 and ITS-2; and the 28S large subunit (LSU). This chapter reviews the new fungal lineages that have been discovered in various soil libraries over the past 10 years. Most soil libraries to date have discovered new fungi only at the genus or species level. The chapter talks about two main discoveries, Chytridiomycota and Ascomycota, after reviewing other important but unrelated clades that have also been discovered in soil libraries. It is important to flesh out the fungal family tree as quickly as possible, as it is possible that many of the missing fungi can go extinct before it is known that they ever existed.

Citation: Schmidt S, Wilson K, Meyer A, Schadt C, Porter T, Moncalvo J. 2008. The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil, p 55-66. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch4

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The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

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FIGURE 1

Composite tree from a Bayesian analysis of LSU rRNA genes showing the relative position of Soil Clone Group I ( Schadt et al., 2003 ; Porter et al., 2008 ) between the Taphrinomycotina and Saccharomycotina subphyla, and Groups II and III within the Pezizomycotina subphylum as reported by Schadt et al. (2003) .

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FIGURE 1

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FIGURE 2

Phylogenetic tree of environmental sequences of the Chytridiomycota and Zygomycota from high-altitude soil clone libraries. This tree consists of library clones (in rectangles), nBLAST matches of the clones, and selected guide sequences, and was constructed using Bayesian methods. Clone sequences of uncultured organisms that are nBLAST matches of the high-altitude soil clones are ovals. Support values are Bayesian posterior probabilities, and bootstraps using parsimony and neighbor joining methods (Bayes/MP/NJ). Selected posterior probabilities are those greater than 95%; selected bootstraps are those recovered greater than 50%. The TAL 6 clade represents novel chytrid sequences at the ordinal level. Two other novel lineages are also shown, T3 BA7 and T3 BF2. Zygomycete clones SF1 D5 and SF1 G7, found under snow in forest soils in Colorado, are members of a recently described snow mold consortium ( Schmidt et al., 2007 , 2008).

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FIGURE 2

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Tables

The Missing Fungi: New Insights from Culture-Independent Molecular Studies of Soil

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TABLE 1

Biogeographic distribution of SCGI in rDNA clone libraries of soils a

TABLE 1

Biogeographic distribution of SCGI in rDNA clone libraries of soils a