Cross-Kingdom Interactions: the Foundation for Nutrient Cycling in Grassland Soils

Mary Firestone, University of California, Berkeley (Principal Investigator)

Joanne Emerson, University of California, Davis (Co-Investigator)

Nhu Nguyen, University of Hawai'i at Manoa (Co-Investigator)

Jizhong Zhou, University of Oklahoma (Co-Investigator)

Jennifer Pett-Ridge, Erin Nuccio, Lawrence Livermore National Lab (Co-Investigators) 

Javier Ceja-Navarro, Eoin Brodie, Trent Northen, Kateryna Zhalnina, Lawrence Berkeley National Lab (Co-Investigators)

The below-ground microbial world is a jungle: dominated by competition, predation, parasitism, cooperation, and mutualism.  While the importance of ecological interactions is well understood for macro-organisms above ground, the roles of analogous microbial interactions in controlling soil nutrient cycling are largely unknown. 

Decades of research have identified key microbial mediators of terrestrial nutrient cycling, their environmental sensitivities, and the functional genes and enzymes involved. Many aspects of bacterial, fungal, and microfaunal mediation of nutrient cycling are thoroughly documented.  However, the organisms involved in nitrogen cycling interact in an extremely complex soil habitat. We have little understanding of how biotic interactions shape nutrient cycling in soil.  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 higher rates of turnover and nutrient transformation?   We propose to explore the effects on N- and C-cycling of predation, competition, and cooperative/antagonistic interactions—among viruses, bacteria, archaea, arbuscular mycorrhizal fungi (AMF), saprotrophic fungi, microfauna, and roots. Our extensive past research on soil nutrient dynamics, pathways of root C-flow in soil, and exploration of biotic interactions associated with roots and decomposing litter provides a powerful foundation for the proposed research. 

We will:

1.  Determine how biotic interactions (among viruses, bacteria, fungi, and microfauna) control key N-cycle transformations including depolymerization of macromolecular organic N compounds, N- mineralization and immobilization, as well as nitrification and denitrification.

2. Assess how the spatial compartmentalization and transfer between soil compartments by fungal hyphae and mobile fauna determines the occurrence and rates of N-cycling processes.

Our multidisciplinary team, with expertise in microbial ecology, soil viruses, microfauna, fungi, community systems biology (genomics, proteomics, metabolomics), stable isotope probing, network analysis and food-web modeling will conduct greenhouse mesocosm experiments, small-scale viral and faunal lab experiments, and large-scale field experiments along with evaluation and synthesis of existing datasets in order to disentangle the importance of biotic interactions in controlling nutrient cycling.  Combining multiple novel stable isotope techniques with current molecular methods will allow us to explore, map, and quantify the complex web of biotic interactions that mediate and control N-cycling in soil.   Techniques will include stable isotope-based methods, metagenome and metatranscriptome sequencing, exometabolomics, as well as network analysis and system modeling that incorporate key microbial determinants. Without knowledge of the main viral, bacterial, fungal, faunal, and root interactions belowground, our attempts to model or predict terrestrial nutrient cycling will remain rudimentary.