Identifying the microorganisms responsible for specific processes in C cycling remains a major challenge in environmental microbial ecology, one that requires integration of multiple techniques. Stable isotope probing, or SIP, has come to represent a variety of powerful approaches that allow simultaneous identification of identity and function in microbial communities.  Bulk methods such as DNA/RNA-SIP and PLFA-SIP are well developed and allow tracking of a multitude of C substrates (acetate, cellulose, CH₄, CO₂, and plant litter) into specific microbial consumers.  However, to understand the spatio-temporal context of may key C transformations and microbial interactions, new imaging technologies are needed to analyze processes and properties of macromolecule complexes, microbes, plant root cells, soil (micro)aggregates,  phytoplankton and marine snow as they undergo formation and decomposition.  New and sensitive in situ approaches include NanoSIMS single cell analysis, isotope arrays, and combinations of FISH labeling with high resolution isotope imaging.

Results/Conclusions

Recent work illustrates how these powerful new techniques use targeted stable isotope probing to link biological activities to physical and chemical processes.  They may be used in soil systems to study microbial mats or rhizosphere interactions, and in both terrestrial and aquatic systems to link C and other nutrient cycles at the organismal level. These new aproaches may also be of great use in the study of trophic cascades and metabolic networks.  While cross-feeding is often thought of as a confounding effect in SIP-type studies, with fine scale temporal sampling and FISH-SIMS analysis, we have the opportunity trace C flows through microbial foodwebs, to their eventual fate in stabilized organic-mineral complexes.