Integrating deep microbial dynamics in the critical zone – IRONSTONE

The deep subsurface is conventionally thought as a carbon and energy-poor environment, with limited microbial growth and biogeochemical process rates. In recent years, there has been increasing evidence of the existence of deep microbial communities, able to actively respond to changes in hydrological and geochemical changes. These subsurface communities are thought to catalyse a large array of redox reactions but their impact on geochemical processes, rates and fluxes have remained largely elusive so far. IRONSTONE assembles an interdisciplinary team of scientists with complementary expertise in Earth sciences, microbial ecology and fluid mechanics to explore the interplay between hydrological, geochemical and microbial processes in the critical zone. The central hypothesis that will be tested is that flow and chemical gradients enhance microbial activity at depth by promoting the formation of redox driven habitats and triggering biogeochemical processes that would not occur in homogeneous environments. By investigating the mechanisms and scales that control these microbial hot spots and hot moments, IRONSTONE will provide a new understanding of how microbially enhanced reactivity influence landscape-scale biogeochemical fluxes.
For this purpose, IRONSTONE will focus on iron oxidation and iron oxidizing bacteria (FeOB). Iron redox transformations play a central role in global biogeochemical cycles and FeOB are primary producer of organic carbon that potentially strongly influence deep microbial communities. We recently demonstrated that mixing between superficial oxygenated water and deep iron-rich groundwater drives the formation of microoxic environments, where FeOB can thrive in deep fractured rocks. This mechanism is likely representative of the dynamics of other microorganisms that depend on electron donors and acceptors that are spatially segregated, leading to strongly enhanced microbial activity in mixing zones. As such, it may profoundly change representations and models of deep subsurface environments.
IRONSTONE will rely on an original methodology coupling microfluidics, genomics, geochemistry and hydrology to understand and quantify the dynamics of FeOB hot spots and their impact on critical zone cycles and fluxes. This methodology may be extended to a range of microorganisms and reactions. IRONSTONE will make the most of the rapid developments in microfluidics and microimaging to interrogate the concept of geochemical gradients at microscale. Innovative microfluidic devices and experiments will allow observing growth, distribution and morphology of mineralized FeOB colonies subjected to precise concentrations or gradients of O2 and Fe(II) (WP1). These microscale observation will be combined with the characterization of reactive pathways and geochemical fluxes associated to FeOB hot spots formation and degradation (WP2). For this, IRONSTONE will couple metagenomics and metatranscriptomics, isotopic labelling, and microimaging, molecular and thermodynamics approaches. Upscaling to field scale will be investigated using novel tracer tests based on continuous dissolved gas and isotopic measurements, including isotopic fractionation of O2, to quantify microbiological controls on reactions and elemental fluxes (WP3).
The highly interdisciplinary approach developed in IRONSTONE will thus provide new opportunities to understand how spatial heterogeneity and temporal variation of environmental conditions affect the dynamics of microbial growth and the kinetics of microbially catalyzed reactions in the subsurface, leading to a new framework to integrate deep microbial dynamics in critical zone cycles and fluxes.