Soil Microbiology at the University of California, Berkeley
Firestone Lab


1.  Cross-Kingdom Interactions (2019-2022)

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

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 understood, the organisms involved interact in the complex biotic milieu of soil; we have little understanding of how these 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 a more robust N-cycle with 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 address the following objectives:

  1. Determine how biotic interactions (among viruses, bacteria, fungi, and microfauna) control key N-cycle transformations.
  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.

2. Sustainable Biofuels (2015-2021)

Establishment to senescence: plant-microbe and microbe-microbe interactions mediate switchgrass sustainability

Switchgrass, a perennial grass native to the midwest and prairie states, has been identified as an ideal crop for biofuel conversion, with high biomass yield. Our work focuses on sustainable production of switchgrass for biofuel through beneficial association with soil microorganisms. Certain soil microorganisms aid plants in nutrient acquisition and drought tolerance, acting as plant probiotics. We study growth of switchgrass on marginal lands that are not suitable for most crop production to understand how switchgrass association with soil microorganisms may improve plant growth and soil carbon storage in low nutrient, low water input soils. Our research focuses on four key objectives:

  1. Identify high- and low-performing SG genotypes in marginal soils; determine the functional succession of SG-associated microbial communities during successful SG establishment.
  2. Characterize plant-microbe and microbe-microbe interactions in switchgrass and its microbiome, particularly when challenged by water or nutrient stress.
  3. Determine how low-input switchgrass production in marginal soils may enhance ecosystem sustainability metrics such as: C storage, nutrient availability, soil food webs.
  4. Integrate and synthesize experimental data to reveal plant-microbes interactions and the underlying mechanisms critical to switchgrass effects on ecosystem sustainability.

3. Microbes Persist: System Biology of the Soil Microbiome (2018-2021)

The ultimate goal of this LBNL SFA project is to determine how microbial
ecophysiology, population dynamics, and mineral-microbe interactions regulate
cellular-C persistence under changing moisture regimes. The long term objectives are

  1. Use SIP-metagenomics to delineate how changing water regimes shape activity of
    specific microbial populations and expression of ecophysiological traits that impact the
    fate of cellular and plant C.
  2. Quantify and assess mechanisms of mortality in the soil microbiome focusing on phage
    lysis and water stress) and their contribution to C turnover and the biochemistry of
    microbial residues.
  3. Measure how the soil microbiome and its biochemical products (cell wall materials, cytosol, extracellular polymeric substances, exo-enzymes) interact with contrasting mineral assemblages to control both short- and long-term soil C persistence.
  4. Synthesize quantitative, genome-scale ecophysiological trait data, population specific growth and mortality rates, and SOM metrics to parameterize models of microbial functional guilds and SOM turnover to effectively predict the long-aspired connection between soil microbiomes and soil C fate.

4. Extracellular Polysaccharides in Soil (2020-2021)

Metagenomic prediction of microbial extracellular polysaccharide synthesis and mineral association in soil.  

The purpose of Alex Greenlon’s postdoctoral research is to gain mechanistic and population-specific insights into microbial EPS production in soil, and the environmental and soil factors that affect it. This research will yield mechanistic insights into the how soil factors related to agricultural management influence EPS production and soil structure, as well as nominate soil microbial taxa that could be relevant for the development of microbial technologies to secure long-term soil fertility and carbon storage. The project addresses three specific objectives: 

  • Identify the dominant soil microorganisms  utilizing plant carbon to synthesize EPS
  • Measure the response of these microbial populations to varying soil moisture and source of plant carbon 
  • Quantify the production of EPS molecules by distinct microbial populations

5. Tracing Carbon Flow through Soil Food Webs (2016-2020)

Directing traffic in the rhizosphere: how phage and fauna shape the flow and fate of root carbon through microbial pathways

Soil surrounding plant roots, the ‘rhizosphere’, is a nexus of biological activity. Stimulated by exudates and root decay, rhizosphere organisms (bacteria, archaea, fungi, fauna, and viruses) interact to form critical pathways that move carbon (C) from root tissue to surrounding soil, and ultimately regulate  the fate of soil C. The pathway of C flow through the soil food web can influence whether C is stabilized in soil, the largest active terrestrial C reservoir globally. Climate change can alter precipitation regimes which may result in changes to the pathways of C flow through the soil food web. We use a combination of stable isotope tracing, multi-omic analysis, and network analysis to investigate our research questions:

  1. How do fungi mediate the flux and fate of root C?
  2. What roles do phage play in controlling carbon flow in rhizosphere soil?
  3. How do faunal interactions in the soil food web mediate C flow and fate in the rhizosphere?

6. Microbial Mediation of Soil Carbon Dynamics (2013-2017)

Mapping soil carbon from cradle to grave: drafting a molecular blueprint for Carbon transformation from roots to stabilized soil organic Carbon

Soils store more carbon (2,300 Gt) than the atmosphere and biosphere combined, the second largest active carbon reservoir after the ocean. Plants are the primary source of soil carbon, photosynthesizing atmospheric CO2 and releasing carbon into the soil through plant roots. Soil microbes are the primary mediators or this plant-derived carbon, metabolizing and transforming soil carbon compounds. The primary objective of our work is to determine how organic C decomposition and stabilization processes in soil are impacted by the interactions between plant roots and the soil microbial community (bacteria, archaea, fungi, microfauna). To accomplish this objective, we are:

  1. Tracking the functional succession of microbial communities during the transformation of root exudates and decaying root litter under ambient and elevated CO2.
  2. Measuring how the composition and quantity of root C affects the enzymatic capacities of the root microbiome and ultimately impacts C sorption/desorption from mineral surfaces.
  3. Parameterizing a trait-based model of the microbial community functions that predicts carbon stabilization and turnover in the rhizosphere.

7. Microbial Ecology in the Critical Zone (2013-2019)

Eel River Critical Zone Observatory

The Eel River Critical Zone Observatory is a multi-disciplinary research collaborative based at the University of California, Berkeley.  Our research focus is to explore how biotic and abiotic factors interact in the near-surface environment (from bedrock to tree tops) and how these relationships impact environmental processes.

California’s Eel River CZO is rooted in intensive field monitoring in the critical zone, which follows watershed currencies (water, solutes, gases, biota, sediment, energy, and momentum) through a subsurface physical environment and microbial ecosystem of the critical zone into the terrestrial ecosystem, up into the atmosphere, and out through drainage networks to the coastal ocean. Our work connects tree physiology, water, and nutrients to microbial ecology, trace gas production, and other watershed currencies.