Methods for assessing microbial trophic interactions

One of the greatest roadblocks to understanding microbial interactions and nutrient flow in the environment is the lack of appropriate methodologies to quantitatively study these processes at a meaningful spatial scale. In the Orphan lab, we are actively engaging in the development and application of compatible fluorescence and stable isotope based methods for tracking the flow of carbon, nitrogen and sulfur within individual environmental microorganisms. Applied in concert with geochemical and isotopic analyses in the environment, we are attempting to address fundamental ecological and biogeochemical processes from the prospective of individual cells in the environment. Specific objectives include characterizing the within population heterogeneity in activity and substrate use, niche diversification, interspecies metabolite transfer/ syntrophy, influence of physical associations between microorganisms on activity and phenotype, and trophic dynamics between bacteria, archaea, viruses and microeukaryotes. The combination of these microscopy-based, multi-disciplinary methods provide a unique and critical perspective on microscale dynamics within ecosystems that is highly synergistic with the now widely used meta ‘omics techniques.

Tracking the flow of carbon and nitrogen from host to virus in marine environments

(Ally Pasulka, NSF postdoctoral fellow, with collaborators Kay Bidle, Rutgers, Matt Sullivan, OSU)

While the collective impact of viral activity has become more apparent over the last decade, new research directions are needed to extend beyond counts of viral-like particles and fill critical gaps in our understanding of the biogeochemical impact of viruses in ocean ecosystems. The development of tools to study virus-host interactions within a complex microbial community at the resolution of individual viral particles will provide an unprecedented means to partition carbon (C) and nitrogen (N) flow within and between viruses, their prey (autotrophic or heterotrophic) and the environment.

Specifically we aim to:

1. Develop and refine methods for quantifying stable isotope ratios of carbon 13 and nitrogen 15 in viral particles using nanoscale secondary ionization mass spectrometry (nanoSIMS) in order to track C and N exchange between viruses and host microorganisms.

2. Apply approaches developed in Objective 1 in order to quantify the amount of viral activity stemming from different production pathways (e.g., autotrophic vs. heterotrophic production as determined by C and N enrichment) in the natural environment.

To learn more about nanoSIMS, visit

Collaborative project: quantitative measurements of mixotrophy in protists

(Dave Caron and Karla Heidelberg, USC)