Defining the roles of microbial taxa in soil nitrogen turnover

This project is a collaboration between Drs. David Myrold and Peter Bottomley of Oregon State University and Dr. Jennifer Pett-Ridge of the Lawrence Livermore National Laboratory. It is supported by the National Science Foundation.

Linking microbial community structure to specific functions of the N cycle has been a long-standing quest of soil microbial ecologists. Recent developments combining the use of stable isotopes with molecular tools (i.e., stable isotope probing, SIP) have made this quest achievable in a qualitative sense. The proposed research will couple a new, high-sensitivity SIP method (Chip-SIP), which uses NanoSIMS isotopic imaging to quantitatively measure incorporation of 15N substrates into microbial rRNA hybridized to a phylogenetic microarray, with the well-established method of 15N isotope dilution to measure N cycling rates in soil. This approach will enable the identification of the different functional groups (and specific taxa within those functional groups) associated with organic N consumption and mineralization, inorganic NH4+ and NO3- consumption, and the interactions among microbial taxa that process N in soil. The functional groups we are interested in examining are heterotrophic bacteria and archaea, saprotrophic and mycorrhizal fungi, and AOA and AOB.


  1. Utilization of N from organic and inorganic sources varies both across and within microbial functional groups.
  2. Suppression of one or more functional groups will alter how taxa of the remaining groups process N over a range of N availability.


To test the first hypothesis, N utilization will be determined in four soils by adding tracer levels (low concentrations, high enrichments) of 15N-labeled substrates (15N,13C-glycine, 15NH4+, or 15NO3-), and then using isotope dilution to calculate gross process rates (mineralization, immobilization, nitrification) and Chip-SIP to identify active (N-assimilating) microorganisms. The second hypothesis will tested in a manipulative experiment, where one or more functional groups will be suppressed (e.g., severing roots, adding group-specific inhibitors), and processing of 15N-labeled substrates will be measured after a short incubation period.