Project Overview

This research is based upon work supported by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research Genomic Science program under Award Number DE-SC0020163. Cross-Kingdom Interactions is largely an expansion of work from the Phage & Fauna project, which was completed under Award Number DE-SC0016247.


Decades of research have identified key microbial mediators of terrestrial nutrient cycling, their edaphic sensitivities, and the functional genes and enzymes involved. While many aspects of bacterial, fungal, and microfaunal mediation of nutrient cycling are reasonably well understood, we know that the organisms mediating the relevant processes interact in a complex biotic milieu and their impacts on nutrient cycling are poorly understood. We posit that cross- kingdom interactions shape nitrogen (N) cycling and the resulting plant/microbe nutrient availability and loss pathways. These interaction networks, involving bacteria, fungi, archaea, protists, microfauna and viruses, are differentially influenced by soil habitats (rhizosphere, detritusphere, hyphosphere, bulk soil), and their characteristic resource supply rates and substrate availability. 

Our project asks how cross-kingdom and within-kingdom interactions provide a functional framework for N cycling in soil. Do greater complexities of biotic interactions result in a more robust N-cycle with higher rates of turnover and nutrient transformation?

Many agree the time is ripe to apply new techniques, including stable isotope probing (SIP) ‘omics, Random Matrix Theory co-occurrence networks, NanoSIMS imaging, and LC-MS MS metabolomics to classically-taught soil bioweb concepts—such as the Auxiliary Microbial Loop hypothesis3 (protozoal grazing that liberates nutrients in the rhizosphere)—to gain a quantitative and mechanistic understanding of how interacting organisms shape the magnitude, complexity and speed of soil nutrient cycling processes. To achieve these goals across the scales of trophic complexities, we have compiled a strong, multidisciplinary team, with expertise in microbial ecology, soil viruses, microfauna, fungi, community systems biology (genomics, proteomics, metabolomics), SIP, network analysis, and microbe-based N-modeling.

Based on our extensive research background exploring C- and N-transformations in California annual grassland soils, we propose to explore the effects on N- and C-cycling of predation, competition, and cooperative interactions—among viruses, bacteria, archaea, arbuscular mycorrhizal fungi (AMF), saprotrophic fungi, microfauna, and roots. Our previous research on soil nutrient dynamics (including mineralization/immobilization, macromolecular N breakdown and control of proteases and chitinases by quorum control, nitrification and denitrification) provides a powerful foundation for the work of Cross Kingdom Interactions.

To learn more about what we’ve already discovered on the subject of Cross-Kingdom Interactions, visit our Publications & Products page.

Primary Research Interests

1. Nitrogen and Carbon mineralization/immobilization
2. Depolymerization of macromolecular organic Nitrogen compounds
3. Nitrification and denitrification
4. Nitrogen and Carbon transfers by fungi and fauna that enable or limit Nitrogen-cycling
5. Links between soil biotic interactions and Carbon-cycling