Overview: The Microbiotron will be a modular system of 48 soil-plant incubation chambers, each individually instrumented and controlled by a centralized system that will allow us to (1) control, replicate, and monitor soil conditions and processes and (2) manipulate and analyze microbial communities and their activities over time. The modular chamber design will allow users to swap alternative functionalities via interchangeable tops and wall panels, which will enable use across a broad range of UW-Madison labs and disciplines. For example, a lab focused on soil C cycling might require a gas-tight chamber with an automated gas flux sampling system, and the ability to sub-sample soils throughout the incubation, while a lab focused on plant-microbe interactions might require quantitative root growth imaging and an open-air system. To make this transition, we would switch out the gas-tight tops containing integrated gas flux measurement ports for an open top, and switch out the soil sampling port side-panel for a root imaging camera panel. Thus, the chambers will be highly expandable and easy to diversify for an extremely wide range of potential experiments. In addition, while we have chosen mid-sized chamber dimensions for this first iteration of the instrument, future grant proposals can easily solicit funds for construction of larger or smaller chambers.

Environmental control: Microbiotron chambers will be individually sensored for experimental control of soil moisture and temperature for up to 48 chambers per project run. Soil nutrient concentrations can be manipulated via direct additions of fertilizer solutions to soils, or more tightly via addition of aqueous solutions to the metered drip irrigation system. In addition, the gas-tight nature of the chambers will allow for manipulation of headspace gas concentrations, notably CO₂. For specific purposes, the headspace could be enriched in stable isotopes (e.g., ¹³C and ¹⁵N) to allow tracing of elemental flows through the plant-soil-microbial system. Replicate chambers will allow experimenters to use natural or artificially constructed soils to study the influence of soil type, texture, bulk density, mineralogy, and pH on microbial activity and ecosystem functions.

Microbial control: To understand soil microbial functioning, the manipulation and control of microbial community composition is necessary. Thus, a key feature of the Microbiotron will be the ability to effectively sterilize chambers between projects, allowing experimenters to initiate the microbial community of their choosing in each chamber. Manipulation methods include: inoculation with naturally divergent whole communities, targeted inoculation of specific microbial taxa from culture, and subtraction of microbial groups via chemical additions (irradiation, heat sterilization, fungicides, anti-bacterial compounds). Combining direct manipulations of initial microbial communities with indirect manipulation imposed by environmental conditions will allow investigators to create the necessary variability to tease apart the contributions of individual microbial taxa or groups to plant health and ecosystem processes.

Measured variables: Each chamber will be connected to an array of equipment and sensors (Fig. 2) allowing for the continuous monitoring of soil environmental conditions (moisture, temperature, and gas fluxes, etc.). Soil greenhouse gas dynamics and plant and microbial nutrient availability are both fundamentally tied to soil biogeochemical cycles driven by microbes – in particular, C and N fluxes. Thus, the Microbiotron will include 5-gas measurement capabilities with a Picarro Cavity Ring-Down Spectrometer (CRDS) G2508, capable of measuring soil gas fluxes of the 3 major greenhouse gases (CO₂, CH₄, N₂O) and NH₃ a central pathway for N loss from ecosystems. Access to the soil-root system via removable panels will allow for repeated, minimally destructive sampling of soil and root tissue. These samples can then be analyzed via any number of methods to characterize soil chemistry and microbial community composition and function. Transparent chamber walls will allow for imaging of root systems, necessary to calculate rates of root growth and turnover, and root architecture. Finally, water flow-through can be collected to determine leaching rates for key soil nutrients, soil/root metabolites, and dissolved organic carbon.