Assessing Functions of Soil Microbes with Isotopic Measurements

Abstract

The difficulty of experimental manipulations, observations, and measurements in the cryptic world of the soil has long hindered studies ofmicrobial functioning in this environment. One promising tool to explore soil microbial functioning, stable isotopemeasurements, is increasingly used to study linksbetweenmicrobesandbiogeochemicalprocesses. Suchmeasurements rely on calculating ratios of heavy to light isotopes of many key biological elements (e. g., 13C:12C, 15N:14N, 18O:16O, 2H:1H, and 34S:32S). Studies can be generally classified into two main types, those using natural abundance levels of isotopes in microbes or microbially produced compounds, and those in which compounds or substances artificially enriched in one or more of the heavy isotopes are applied (tracer studies), and the subsequent fate of the isotopic label followed into different ecosystem components, including microbes. Natural abundance and tracer studies can be used at different levels of resolution, ranging from the whole organism down to specific compound classes (e. g., lipids), specific compounds, or even DNA or RNA unique to a single species. Analyses using gas chromatography on mixtures of volatile compounds linked to isotope ratio mass spectrometry have been particularly widely applied (reviewed in Boschker and Middleburg 2002). Theuse of isotopic techniques has increaseddramatically in the past 15 years, andhasbeen supportedbyavarietyof technological advances, including faster analyses with the widespread adoption of continuous flow isotope ratio mass spectrometry, improvements in our ability to measure hydrogen and oxygen isotope ratios, and steady increases in the quality and variety of compound-specificmeasurements possible. In the following sections, I focus on the use of natural abundance measurements of carbon and nitrogen isotopes to address various research topics in soil microbial ecology, with some discussion of tracer experiments. Useful reviews on natural abundance measurements include Hogberg (1997), Dawson et al. (2002), Hayes (2002) and Werner and Schmidt (2002).