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Chapter 42 : Methods for Studying Terrestrial Fungal Ecology and Diversity

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Abstract:

Fungi are of fundamental importance in terrestrial ecosystems, and their roles and importance are usually overlooked or underestimated by ecologists who study plants or animals. Filamentous fungi with a habit of exuding adhesive extracellular polysaccharides or mucopolysaccharides are important in soil stabilization through the formation of microaggregates and the binding of aggregates and particles. In the human environment, fungi are important in many food and industrial fermentations, but they also cause food spoilage and grow unwanted in our living and working spaces, creating problems of environmental health. This chapter highlights the fundamentals of discovering and identifying fungi in these diverse environments. The fundamentally different biologies of different groups of fungi mean that no single method will work to discover or isolate all fungi in any material or area. For this reason, some general methods are presented, which users may need to modify to study their fungi of particular interest. Biodiversity of Fungi presents an extensive review of this topic.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42

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Image of FIGURE 1
FIGURE 1

The major types of fungi. (a) : , showing the correct method of collecting macrofungi; inset, eight ascospores are produced in each sac-like ascus in this (photo by G. L. Barron, University of Guelph). (b) : , associated with a fairy ring in Wyoming. (c) : attacking nematodes (drawing by G. L. Barron, University of Guelph, from reference ). (d) : a spore and hyphae of an endomyorrhizal fungus washed from soil. (e) : , a striking and common fungus from soil. The inset shows a close-up of the sporangiospores (both photos by G. L. Barron, University of Guelph). (f) Vegetative cells and ascus of , an ascomycetous yeast.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42
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Image of FIGURE 2
FIGURE 2

Sampling designs: stratified random (left side) and regular grid (right). The heavy horizontal line represents the baseline, filled circles represent 10-m intervals from which sampling transects are struck at 90° to the baseline, and open circles represent sampling plots 4 m2 in area, with a radius of 1.14 m ( ). In stratified random sampling, sample plots are located on the transects at distances taken from a random numbers table, e.g., in the left line, with their centers at 6.33 m from the baseline, and then 2.17, 5.94, 4.67, and 8.07 m from the center of the previous plot.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42
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Image of FIGURE 3
FIGURE 3

Collecting and culturing macrofungi (a to d) and microfungi (e to f). (a) Taking notes on a fresh collection of , using a color guide ( ); (b) making a tissue culture from a fruiting body of ; (c) the procedure for obtaining a spore print; (d) a spore print; (e) a soil sprinkle plate for isolation of nematophagous fungi; (f) particle washing to remove spores of abundantly sporulating molds to selectively recover more recalcitrant fungi from soil, including . In this example, 5 g of soil was first dispersed by shaking for 1 h at 4°C in 0.1 M sodium pyrophosphate decahydrate and then poured through sieves of 250- and 53-μm mesh. Particles remaining on the 53-μm mesh sieve were washed with a stream of tap water. The remaining organic materials may be picked up in a 1-ml, broad-bore pipette and inoculated onto agar or in liquid medium or used in DNA extractions that are enriched for filamentous fungi.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42
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Image of FIGURE 4
FIGURE 4

(a) Preparation of the Air-O-Cell spore trap. (b) Separate the cassette by breaking the shrink seal. (c) Mark the ends of the inlet slit. (d) Remove the gel-coated glass wafer and gently lower it, gel side up, onto a drop of clear lactic acid. Using the placement marks, adjust the wafer so that the sampled area lies parallel to the sides of the microscope slide. (e) Hang a drop of mounting fluid on a coverslip and gently lower it onto the gel surface. (f) Completed mount.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42
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Tables

Generic image for table
TABLE 1

Ranking of indoor versus outdoor air spora

cts, counts.

1 = most abundant.

LOD, limit of detection.

Citation: Thorn R, Scott J, Lachance M. 2007. Methods for Studying Terrestrial Fungal Ecology and Diversity, p 929-951. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch42

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