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

Characterizing Bacterial–Fungal Interactions Within Soil Niches and Across Soil Mineralogies


Nayela Zeba1* (, Mengting Yuan1, Wesley Sparagon2, Siyang Jian3, Zheng Shi3, Katerina Estera-Molina1,4, Gaetan Martin2, Tai Maaz2, Jonathan Deenik2, Jizhong Zhou3, Jennifer Pett-Ridge4, Nhu Nguyen2


1University of California–Berkeley; 2University of Hawai’i–Mānoa; 3University of Oklahoma; 4Lawrence Livermore National Laboratory


This work aims to develop a quantitative and mechanistic framework for understanding how bacterial–fungal interactions (BFIs) influence carbon (C) stabilization and mineralization within soil niches and across soil mineralogies. Leveraging principles of community systems biology and ecology, this experimental strategy combines stable isotope probing (SIP), SIP-assisted meta-omics, field mesocosms, soil process rate monitoring, and microbe-informed ecosystem modeling. Objectives include: (1) investigating the influence of various C sources (e.g., rhizodeposits, hyphal deposits, and litter) on grassland BFIs and their subsequent effects on the fates of these photosynthates; (2) examining the role of BFIs in promoting C stability within soil aggregates and on mineral surfaces, and their impact on C destabilization in soils across mineralogies; and (3) assessing how drought conditions, in conjunction with C source and soil mineralogy, shape BFIs and the soil processes they govern.


Bacteria and fungi are dominant soil microbes that play crucial roles in biogeochemical cycling. While cross-domain interactions in soil are well-documented, a mechanistic understanding of BFIs and their influence on biogeochemical cycling of essential soil nutrients under differing soil mineralogy is still lacking. This study comprises a field experiment at the University of California Hopland Research and Extension Center with ingrowth cores of different mesh sizes to separate soil niches. These cores were incubated in a randomized block design plot under rain-out shelters and subject to either 90% or 50% of ambient precipitation. A subset of hyphosphere cores (i.e., 44µm mesh allowing fungal hyphae and bacteria to permeate but excluding roots) and negative controls (i.e., 0.45µm mesh preventing hyphae from crossing) were excluded from receiving rhizodeposits and litter for two growth seasons. These treatments represented C depleted conditions. The research team monitored carbon dioxide (CO2) efflux from the cores and soil moisture levels within the plots. Preliminary findings from a mixed-effects model indicated a significant effect of both precipitation level and core type on CO2 efflux. Efflux was, on average, 10% lower under 50% precipitation from September 2023 to January 2024. This was consistent with 14% lower soil moisture under 50% precipitation from October to December 2023.

Furthermore, a significant interaction between mesh size and soil moisture was observed to influence CO2 flux rates. Efflux from the 44µm mesh cores was 15% higher than that from the 0.45µm cores, likely linked to fungal hyphae activity within the 44µm mesh cores. Also being monitored is CO2 efflux from 830µm mesh cores representing the rhizosphere (i.e., allowing roots, fungal hyphae, and bacteria to cross) to gain further insights into the role of BFIs on CO2 flux dynamics across soil niches. In spring 2024, the research team aims to label the grasses growing adjacent to the cores with 13CO2 followed by soil sampling for chemical and microbial analyses. The objective is to quantify the transportation of photosynthetic C into the cores via hyphae, identify the soil C pools that the photosynthetic C is transformed into, and characterize the bacterial and fungal taxa involved in these processes.

To characterize BFIs across soil mineralogy, this project aims to conduct a parallel field-based mesocosm experiment in which the same ingrowth cores will be deployed into intact megaliths of five soil types with distinct clay mineralogies from Hawai’i’s O’ahu Island. A similar 13CO2 labeling event will be carried out to measure how soil mineralogy interplays with BFI-mediated C dynamics.

Lastly, the research team tested model frameworks to represent the diversified interactions between bacteria and fungi in soils. Sensitivity analysis demonstrated that the initial fungi to bacteria ratio and fungi/bacteria enzyme production rates are key parameters regulating competition between bacteria and fungi. After developing a suitable model framework, the team aims to integrate CO2 effluxes, C pool sizes, 13C enrichment, and SIP-derived metagenomic data from the above experiments into a new generation of omics-informed, niche-identified Microbial ENzyme Decomposition model.

Funding Information

This work was funded by the DOE Office of Science, BER Program, grant no. DE-SC0023106 awarded to Nhu Nguyen, Mengting Yuan, Tai Maaz, Jonathan Deenik, Jizhong Zhou, Jennifer Pett-Ridge, and Mary Firestone. Work at Lawrence Livermore National Laboratory (LLNL) is performed under the auspices of the DOE by LLNL under Contract DE-AC52-07NA27344.