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Chapter 57 : Quantifying the Metabolic Activity of Soil- and Plant-Associated Microbes
The seemingly infinite variety of metabolic processes and products suggests potential for a correspondingly vast array of detection methodologies, and the scope of available technology for monitoring microbial metabolic activity is increasing so rapidly that it is difficult to catalog the available methods. Soil, the rhizosphere, and the phyllosphere are populated by complex communities of organisms, including microbes (bacteria, archaea, fungi, and protists) but also typically including plant and animal components. The rhizosphere and phyllosphere are defined by the presence of a plant, so it is inherently impossible to characterize microbial activity in these habitats through the study of genetically uniform microbial strains in isolation. Respirometry is increasingly being used for determination of biodegradation kinetics, and microcosm screening studies often are performed under controlled conditions to evaluate biodegradability potential and options for bioremediation. Several methods for estimating the metabolic activity levels of microbial populations involve quantification of cellular pools and rates of synthesis of specific biochemical components including RNA, DNA, ATP, and total adenine nucleotide. A number of methods for the quantification of metabolic activity and/or biomass of individuals, populations, or microbial communities involve direct microscopic observation of cells. This chapter has attempted to provide an overview of a number of these new methodologies, but it only presents a snapshot in time, as the number of new techniques and the opportunities they present for environmental microbiology continue to rapidly expand.