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Microbes are often the largest biomass in an ecosystem, yet are not often considered in classical ecology. Problems with the study of the ecology of microbes come from the difficulties in applying the isolation and culture techniques that were so successful in medical studies but are not effective in the environment. Most environmental microbes simply will not grow in culture. The problem of assessing the impact of microbes on ecosystems is further complicated as the most significant impact of a microbial community on an ecosystem is the result of metabolic activities. Inactive microbes can be a food source, but the biogeochemical metabolism of the active microbes have the greatest impact on the environment. In stable soils and sediments, only a tiny proportion of the potential metabolic capacity and versatility of that community is being actively expressed at a given time. Microbes in these environments are poised to rapidly take advantage of nutrients that become available following a disturbance. This dramatic reaction to disturbance makes measuring the metabolic activity of microbes in undisturbed soil a significant challenge. Heterogeneity on the scale of the microbes in the distribution of nutrients, carbon sources, water, ions, or terminal electron acceptors in soils is a significant complication. The assumptions of colligative properties of solutions for soil environments in the estimations of kinetics is one of the reasons that engineers have so much trouble making successful models for in situ bioremediation in these heterogeneous soils and sediments. How then, can soil microbial community ecology be approached? The hypothesis that many of the responses of monocultures of microbes to specific conditions will predict the responses of these organisms to specific conditions in the soil community seems to hold true. This theory is being tested using genetically engineered microbes with "reporters" in biofilms and can be examined in soils, if the analysis does not apply selective pressures that can distort the in situ conditions. The knowledge of physiological responses of monocultures, and the structural modifications they produce, provides a mechanism to predict the responses of a community to specific change. In characterizing the microbial community in situ, there are advantages to analyzing lipid membranes, because all viable cells are enclosed in lipid membranes containing polar lipids. If specific organisms have sufficiently unusual lipids in their membranes then these lipids can serve as "signatures" to define the community structure. If there are specific conditions that result in structural modifications of the lipids, then the detection of these modifications can be utilized to define the ecology of the microniche of that organism and thus of at least a portion of the microbial community. This gives insight into the microbes' nutritional/physiological status and the suitability of the local environment. The presence of polar lipids can define the viable biomass, as no cell can function without an intact membrane which contains polar lipids. The activation of endogenous phospholipase activity with cell death can leave traces of the recent lysis in the diglyceride structure. The detection of specific genes can define the limits of adaptation but not always reflect current metabolic activity. That most complex ecosystem with the most diverse biota and versatile biochemistry, soil, is finally approachable on both a holistic and utterly reductionest scale, thanks in large measure to the prescient insight of Per Brinck who introduced Chemical Ecology to Lund University and the rest of the world.
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