Nanosims Isotopic Imaging of C and N Assimilation in Complex Microbial Communities

Early developments in light microscopy revolutionized our understanding of the physical relationships microorganisms build with each other and their surroundings. Now, recently-developed imaging methods allow insight into the chemical relationships microorganisms build. Using techniques including imaging mass spectrometry (e.g. SIMS, NanoSIMS), spectroscopy and synchrotron-based approaches (e.g. STXM/NEXAFS), microbe-microbe, microbe-mineral, and microbe-organic matter interactions can be characterized at a scale and specificity not previously possible. This presentation will focus on the ecological roles uncultivated microorganisms that would traditionally have been inferred from diversity and genomic studies.

To directly measure functions of uncultivated microbes, isotope-labeling experiments provide a useful means to investigate environmental ecophysiology and allow quantitative measurement of nutrient transfers between cell types, symbionts and consortia. The combination of Nano-Secondary Ion Mass Spectrometry (NanoSIMS) analysis, in situ labeling and high resolution microscopy allows isotopic analysis to be linked to phylogeny and morphology and holds great promise for fine-scale studies of microbial systems.  In NanoSIMS analysis, samples are sputtered with an energetic primary beam (Cs+, O-) liberating secondary ions that are separated by a mass spectrometer and detected by a suite of electron multipliers.  A high sensitivity isotope ratio ‘map’ can then be generated for the analyzed cells.  When NanoSIMS analyses are used in combination with techniques that target specific taxa or molecules (e.g. CARD-FISH, “El-FISH”), high-density microarrays (“CHIP-SIP”) or spatially resolved spectroscopy (STXM/NEXAFS), these techniques allow precise, high-resolution, quantitative measurement of molecular and isotopic patterns in an undisturbed sample.

Data from studies using these approaches in diverse microbial habitats (microbial mats, insect gut, rhizosphere soil, seawater) will be presented to illustrate taxon-specific differences in the incorporation of organic substrates. Our initial results suggest that high microbial diversity at both the species and genomic level results in functional differences that can be quantitatively measured in natural communities. These data considerably expand our concept of bacterial resource partitioning based on temporal and small-scale spatial habitat use by adding relative rates of substrate utilization as a critical component of the bacterial niche.