Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Fungal-Bacterial Interactions: Bridging Soil Niches in Regulating Carbon and Nitrogen Processes


Nhu H. Nguyen1*, Jonathan Deenik1, Jennifer Pett-Ridge2, Mengting Yuan3, Jizhong Zhou4, Siyang Jian4, Tai Maaz1, and Katerina Estera-Molina2,3


1University of Hawaiʻi–Mānoa; 2Lawrence Livermore National Laboratory; 3University of California–Berkeley; and 4University of Oklahoma


As dominant groups of soil microbes, fungi and bacteria together drive essential biogeochemical cycles belowground. However, the dynamics, mechanisms, and ecological implications of bacterial-fungal interactions (BFIs) are poorly understood, especially on the community level and under abiotic stress. The goal is to build a quantitative and mechanistic framework to address how BFIs determine the availability and fate of C and N across the complexity of soil niches. The three interrelated objectives each addresses a critical factor determining the behavior of BFIs across soil C source, mineralogy, and water availability:(1) measure how grassland BFIs are shaped by the availability of different C source, and in turn mediate soil C and N mineralization; (2) determine how BFIs may mediate C stabilization and mineralization via aggregation and mineral surface interaction across soils of different mineralogies; and (3) quantify how reduced water availability interplays with C source, C availability, and soil mineralogy in structuring BFIs and BFI-mediated soil processes.


Fungi and bacteria are the two dominant groups of soil organisms that consume, process, and translocate plant-derived organic matter and thus are critical to global nutrient cycling. Fungal hyphal networks are important gateways for C and nutrient exchanges between plants and soils, and there is an increasing recognition that such processes are co-mediated by their interactions with bacteria. Yet the understanding of these interactions has generally been correlative, and the mechanisms of these interactions in the context of nutrient cycling are far from understood. The team hypothesize that bacterial-fungal interactions (BFIs) fundamentally determine the outcomes of soil ecosystem function by enabling C and N mineralization, competing for limited nutrients, and contributing to soil organo-mineral interactions and aggregate formation. Through this project, researchers aim to build a quantitative and mechanistic framework of how BFIs can change soil processes, the availability and the fate of C and N across the complexity of soil niches in different soil types and abiotic conditions. Researchers will present the initial concepts of this project through a set of three experiments: (1) Characterize how Mediterranean and tropical grasslands BFIs are shaped by the availability of different C source, and quantify soil C and N mineralization mediated by the BFIs; (2) Understand whether and how BFIs mediate C stabilization and destabilization in soils of different mineralogies; and (3) Quantify how drought interplays with C source, C availability, and soil mineralogy in influencing BFIs and BFI-mediated soil processes.

Researchers propose three major tasks that scale in complexity, starting with a field experiment where the team will segregate soil niche compartments by using ingrowth cores that sequentially exclude incoming roots and fungi. This allows researchers to trace 13C in isotopically labeled photosynthate as it moves through these niche compartments. Next, in a field-based mesocosm experiment, researchers will deploy the same ingrowth cores into intact megaliths of different soil types and use 13C and 15N tracers to measure how soil mineralogy interplay with microbial processes that influence the incorporation of these tracers into soil aggregates and mineral surfaces. Next, researchers will fine-tune the mechanisms that control BFIs in a laboratory soil microcosm experiment that measures the molecules involved when bacteria and fungi come into direct contact and the functional outcomes of these interactions. These three experiments will be performed under a drought treatment that can help address how microbial interactions can change with environmental conditions. Finally, researchers will integrate the data from these experiments using network analysis and omics-informed, niche-identified ecosystem (MEND) modeling.

The project will address the gap resulting from the over-simplified culture-based BFI studies and the mainly correlative field surveys of fungal-bacterial co-occurrence. Leveraging the above methods and technologies, researchers will be able to identify the mechanisms important to BFIs across broad grassland ecosystems, quantify C and N dynamics, model interactions in natural soil environments, and use this powerful set of data to better predict terrestrial C and N cycles under climate change.

Funding Information

This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0023106. Work at LLNL is performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.