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Chapter 38 : Decomposition and Fungal Community Structure in Aquatic Environments

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Abstract:

This chapter focuses on leaf decomposition in streams, which is dominated by aquatic hyphomycetes. It emphasizes on methods used to analyze the decomposition of various substrates and on methods to characterize fungal community structure. The procedures used to collect and expose leaves in streams will affect several interdependent aspects of decomposition. The use of dried material in litter bags has been the method of choice to study decay in submerged or emergent macrophytes. Their decomposition is therefore best studied by marking individual plants or leaves with electrical cable ties and measuring decay and microbial colonization in situ. Application of this technique has profoundly altered our view of the fungal involvement in macrophyte decomposition in marshes. Many of the considerations for choosing and collecting samples apply regardless of subsequent analysis. The great advantage of molecular methods is that they are based on a much greater number of unique traits than traditional approaches (primarily nucleotide sequences rather than morphological data), resulting in much higher resolution. In addition, molecular traits are essentially independent of life stage; there is no need to induce a reproductive stage to allow unequivocal identification and phylogenetic assessment. Currently, neither molecular nor traditional methods lead to comprehensive species lists; therefore statistical evaluations are needed to extrapolate from our samples to ecosystems.

Citation: Bärlocher F. 2007. Decomposition and Fungal Community Structure in Aquatic Environments, p 469-478. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch38

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Microbial Ecology
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Denaturing Gradient Gel Electrophoresis
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Confocal Laser Scanning Microscopy
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Restriction Fragment Length Polymorphism
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Confocal Laser Scanning Microscopy
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Restriction Fragment Length Polymorphism
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Confocal Laser Scanning Microscopy
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References

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Tables

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TABLE 1

Fungal primers for amplifying DNA from environmental samples, the adjacent genes, and presumed degrees of specificity

Citation: Bärlocher F. 2007. Decomposition and Fungal Community Structure in Aquatic Environments, p 469-478. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch38

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