Soil Food Webs
Soil food webs contain complex mixtures of organisms whose interactions mediate the flow of carbon (C) through ecosystems. The smaller fauna (protozoa and nematodes) in concert with larger animals (metazoa) form the machinery of ecosystem C and nutrient transformation through their interactions with fungi, bacteria, and plants. Soil surrounding plant roots, called the rhizosphere, is a nexus for this biological activity. However, It is not well understood how rhizosphere organisms control dynamics of soil organic matter (SOM) and respond to changing precipitation patterns. While interactions between roots and microbes have been intensively studied, little is known about how other members of the soil food web (fungi, fauna, and viruses) and how their interactions control the movement of C through soil. Changes in precipitation affect soil structure, water content, biotic interactions, and alter the physiology of plants, all of which can influence soil fauna abundance and composition and change soil food web structure.
Protozoa, nematodes and micro and mesofauna that require water films or relatively high moisture content to be active, produce latent but viable structures such as cysts and egg masses during drought, from which new generations of organisms arise when optimal conditions return. However, prolonged drought periods can also lead to elimination of key soil functional groups that may keep the soil environment from returning to its original functional state. To understand the effect of drought in terrestrial systems, it is important to take a holistic approach that considers all of the compartments of the soil food web and their contribution to C flow.
Arbuscular mycorrhizal fungi (AMF), obtain C from their host plant in exchange for increased access to nutrients, and can consume up to 20% of the C fixed by plants. AMF perform a variety of beneficial functions for plants, for example, they improve plants’ drought tolerance by improving osmoregulation, reducing oxidative stress, altering root hydraulic properties, and other mechanisms. However, much is still unknown about the significance of these mechanisms. While drought generally decreases photosynthesis rates, reflected in the total plant-fixed C allocated to AMF, it is possible that proportionally more C is allocated to AMF under drought conditions.
Research at HREC, led by the Firestone lab, assessed the roles of whole food-webs in SOM transformation and stabilization by exploring how multi-domain interactions (bacteria-fungi-phages-microfauna) control rhizosphere C cycling. They explored, mapped, and quantified the complex webs of biotic interactions that mediate and control flows of plant root C into soil and thus addressed many of the foundational knowledge gaps in rhizosphere ecology.
To achieve these goals, researchers formed a multidisciplinary team, with expertise in microbial ecology, soil fauna, fungi, community systems biology (genomics, proteomics, metabolomics), stable isotope probing, and the theory, and analysis and modeling of ecological networks (including food-web modeling). Using a combination of molecular methods and isotope techniques, they quantified the amount of root C redistributed by arbuscular mycorrhizal hyphae (AMF) into soil and applied multi-omics analyses to identify (and follow) phage and their role in C cycle in rhizosphere soil. Combining these gene-based and metagenomic-based technologies with stable isotopes allowed the researchers to follow C from roots to faunal food sources, to faunal predators, and ultimately to CO2 in heavy fractions of soil. By integrating experiments, network theory, and modeling, they generated a broader systems-level understanding of these exceedingly complex interactions.