ABSTRACT
Soil is a living complex. A wide range of organic materials is degraded by soil: fallen leaves and other plant parts, animal feces, pesticides, and so forth. This function is carried out mainly by soil microorganisms that comprise the detritus food chain in soil. In this food chain, nutrients are converted into available forms that are absorbed by plants, which grow using these nutrients as well as sunlight and water. Thus, soil microorganisms maintain environmental stability and also support plant growth and agricultural production.Soil microbiologists have endeavored to elucidate the relations between the structure of the microbial community and its functions in soil. Functions have been characterized mainly by biochemical approaches: the identification of metabolic pathways, such as nitrification, and measurement of their reaction rates. In biological approaches, specific microorganisms responsible for specific functions in soil have been isolated. However, many soil microorganisms do not grow on laboratory media and only microorganisms adaptable to the culturing conditions can be isolated [1]. In addition, various microorganisms contribute to individual phenomena in the mineral matrix of the soil environment [2]. Microscopic observations have revealed the colonization of a single substrate, such as cellulose, by various microorganisms depending on the amount, location, and stage of decomposition of the substrate in soil [3]. The microorganisms may form a consortia 303
depending on their substrates each other [4]. Activities of these microbial colonies probably also change over time. However, the relations between the structure of the microbial community and its functions remain unclear as suitable methods with which to monitor changes in the microbial community have not been available. It is essential that sensitive methods be developed for measuring temporal changes in size, activities, and composition of the soil microbiota [5]. Various methods using biomarkers for analysis of the microbial communities in soil have been developed: e.g., direct microscopic observation combined with gene probes; analysis of DNA or RNA in soil; analysis of soil lipids, such as ergosterols, phospholipid fatty acids, and isoprenoid quinones.Isoprenoid quinones have been used as biomarkers with which to determine the taxonomic position of isolated microorganisms [6]. The utilization of isoprenoid quinones to characterize a microbial community was pioneered by Hedrick and White [7], who used the ratio of menaquinones to ubiquinones as an indicator of anaerobic versus aerobic metabolism of bacteria in aquatic environments. Subsequently, Hiraishi [8-14] developed a method based on individual quinone species to characterize the microbial community structure in sewage and activated sludge. Each quinone species corresponded to a particular group of aquatic microorganisms. However, utilization of quinone species has been limited mostly to aquatic microorganisms and has not been applied to the microbial community in soil until recently. Thus, isoprenoid quinones have not been utilized and discussed much in terms of being useful biomarkers for the characterization of soil microbial communities [15,16]. Recent advances in studies on isoprenoid quinones as biomarkers have enabled the characterization of the soil microbial community in relation to their functions in soil by the analysis of isoprenoid quinones. In this chapter, quinone profile analysis is introduced and discussed in comparison with other biomarker methods.
