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Identifying Hot Spots and Hot Moments of Metabolic Activity in Salt Marsh Sediments through BONCAT-FISH Microscale Mapping

Active Dates 9/1/2021-8/31/2024
Program Area Environmental Systems Science
Project Description
Identifying Hot Spots and Hot Moments of Metabolic Activity in Salt Marsh Sediments Through BONCAT-FISH Microscale Mapping

J. Marlow, Boston University (Principal Investigator)

Complex microbial communities are essential constituents of soil and sediment ecosystems: they modulate nutrient and metabolite flux in ways that filter runoff, determine greenhouse gas emissions, and support higher trophic levels. However, our ability to derive net biogeochemical fluxes from knowledge of a community’s constituents is limited by a lack of suitable methods connecting metabolic activity on a single-cell level to emergent, bulk processes. In salt marsh sediments, where redox zones are highly compressed due to substantial organic loading, this challenge is particularly pronounced: connections between dominant electron-donating (carbon) and electron-accepting (sulfur) metabolic cycles lack spatial and temporal specificity.

We aim to fill these knowledge gaps in three specific ways. First, we will enhance our newly developed microscale metabolic mapping technique to identify the “hot spots” of metabolic activity in intact salt marsh sediment. The approach combines in situ incubations, substrate analog probing, resin embedding, µ-CT scanning, and correlative fluorescence and electron microscopy to map the pore network, mineral grains, all biomass, and the anabolically active subset of organisms. To link identity and catabolic function with spatial and anabolic information, we will incorporate multiplexed fluorescence in situ hybridization into the workflow, targeting known lineages (through 16S rRNA hybridization) and specific carbon- and sulfur-processing metabolic pathways (through mRNA hybridization). Second, by deploying the approach across daily and seasonal cycles, we will clarify the “hot moments” of particular microenvironments and metabolisms. For example, we anticipate measurable shifts from photosynthesis-derived carbon sources to chemolithotrophically-derived carbon sources as drivers of sulfate reduction during the day and night, respectively. Finally, we will optimize a metabolic model using the microscale map information as well as measurements of bulk carbon and sulfur metabolite changes over the course of the incubations. By tuning environmentally-relevant parameters to link cell-centered “bottom-up” activity with net “top-down” bulk measurements, we will advance efforts to build a scale-aware, predictive understanding of how complex environmental microbiomes shape emergent biogeochemical fluxes.

We anticipate that the proposed work will generate several ecosystem-specific and interdisciplinary outcomes. At Little Sippewissett Salt Marsh, we will clarify the spatiotemporal links between the microbial community and carbon and sulfur cycling; understanding these mechanistic details of ecosystem function will allow us to better predict changes in biodiversity and emergent biogeochemical fluxes, particularly in the context of continued environmental change. More broadly, by building microscale maps of metabolic activity in the context of an intact and mineralogically diverse sediment column, fundamental principles that structure environmental microbiomes will emerge. For example, our workflow will expose relationships between a cell’s metabolic activity and its microenvironment – pore connectivity, mineral identity, and the function and distance of microbial neighbors. By incorporating these primary data into flux balance analysis – reaction transport models, we will provide a blueprint for scientists to directly link bottom-up, single cell ecophysiological measurements with top-down assessments of net fluxes for microbiomes, environments, and biogeochemical cycles of interest.
Award Recipient(s)
  • Boston University (PI: Marlow, Jeffrey)