Quantitative information on the ecophysiology of individual microorganisms is generally limited because it is difficult to assign specific metabolic activities to identified single cells. Here, we develop and apply a method, Halogen In Situ HybridizationSecondary Ion Mass Spectroscopy (HISH-SIMS), and show that it allows simultaneous phylogenetic identification and quantitation of metabolic activities of single microbial cells in the environment. Using HISH-SIMS, individual cells of the anaerobic, phototropic bacteria Chromatium okenii, Lamprocystis purpurea, and Chlorobium clathratiforme inhabiting the oligotrophic, meromictic Lake Cadagno were analyzed with respect to H 13 CO3 ؊ and 15 NH4 ؉ assimilation. Metabolic rates were found to vary greatly between individual cells of the same species, showing that microbial populations in the environment are heterogeneous, being comprised of physiologically distinct individuals. Furthermore, C. okenii, the least abundant species representing Ϸ0.3% of the total cell number, contributed more than 40% of the total uptake of ammonium and 70% of the total uptake of carbon in the system, thereby emphasizing that numerically inconspicuous microbes can play a significant role in the nitrogen and carbon cycles in the environment. By introducing this quantification method for the ecophysiological roles of individual cells, our study opens a variety of possibilities of research in environmental microbiology, especially by increasing the ability to examine the ecophysiological roles of individual cells, including those of less abundant and less active microbes, and by the capacity to track not only nitrogen and carbon but also phosphorus, sulfur, and other biological element flows within microbial communities.anaerobic phototrophs ͉ nanoSIMS

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Abstract. Sulfur isotope analysis of atmospheric aerosols is a well established tool for identifying sources of sulfur in the atmosphere, estimating emission factors, and tracing the spread of sulfur from anthropogenic sources through ecosystems. Conventional gas mass spectrometry averages the isotopic compositions of several different types of sulfur aerosol particles, and therefore masks the individual isotopic signatures. In contrast, the new single particle technique presented here determines the isotopic signature of the individual particles. Primary aerosol particles retain the original isotopic signature of their source. The isotopic composition of secondary sulfates depends on the isotopic composition of precursor SO2 and the oxidation process. The fractionation with respect to the source SO2 is −9‰ for homogeneous and +16.5‰ for heterogeneous oxidation. The sulfur isotope ratio of secondary sulfate particles can therefore be used to identify the oxidation pathway by which this sulfate was formed. With the new single particle technique, different types of primary and secondary sulfates were first identified based on their chemical composition, and then their individual isotopic signature was measured separately. Our samples were collected in Mainz, Germany, in an urban environment. Secondary sulfates (ammonium sulfate, gypsum, mixed sulfates) and coatings on silicates or organic aerosol dominated sulfate loadings in our samples. Comparison of the chemical and isotopic composition of secondary sulfates showed that the isotopic composition was homogeneous, independent of the chemical composition. This is typical for particles that derive from in-cloud processing. The isotopic composition of the source SO2 of secondary sulfates was calculated based on the isotopic composition of particles with known oxidation pathway and showed a strong dependence on wind direction. The contribution of heterogeneous oxidation to the formation of secondary sulfate was highly variable (35–75%) on day-to-day basis and depended on meteorological conditions.