Biogeochemical Transformations

The interplay of geology, chemistry, and biology among Earth systems is critically important for keeping Earth’s air and water clean and plants healthy. Our biogeochemical transformations expertise crosses scientific boundaries to investigate how nutrients, contaminants, and other chemical compounds move and change in the environment. With new information on how these exchanges occur, we can develop and improve predictive models to anticipate and manage their effects on both human and natural systems.

The science

From Earth’s layers beneath our feet to the atmosphere overhead, biogeochemical transformations underlie the cycling of carbon, nitrogen, iron, and other elements that are essential to life. At EMSL, our Biogeochemical Transformations Integrated Research Platform helps researchers answer fundamental questions about chemical, physical, hydrologic, microbial, and atmospheric interactions that affect the transformation and mobility of critical nutrients, contaminants, aerosols, particles, and compounds within the environment.

We use the latest platforms and approaches to gain new insights into the physiochemical effects of nutrient cycling in the environment, the interactions between metabolic pathways, and the dynamics of microbial communities. From molecular structures and activity, to cellular and community-scale processes, we seek to improve scientific understanding of microbial metabolism and nutrient cycling in the environment.

How we do the science

EMSL’s biogeochemical expertise combines multiple scientific disciplines and data visualization approaches with multiscale modeling platforms.

• We have a suite of assaying methods related to sequencing, enzymatic activity probing, fractionation, aggregation, CO₂ respiration, and more for soil microbiology investigations.
• X-ray computed tomography is used to obtain three-dimensional microstructural information on plant/soil samples. A wide spatial resolution range can be covered, from centimeter-scale to nanoscale, using different instruments to visualize and volumetrically analyze the morphology and distribution of pores, soil moisture content, and organic matter.
• Helium ion microscopy and scanning electron microscopy are employed to investigate fungal-driven mineral weathering and carbon and other plant nutrient allocation in arid, semi-arid, sub-humid, and humid environments.
• Mass spectrometry and nuclear magnetic resonance are used to attain high-resolution chemical information about soil organic matter. Our mass spectrometry imaging capabilities are capable of encompassing a range of spatial scales to perform molecular and/or element mapping with high resolution and isotope sensitivity.
• Pore water chemistry is determined using analytical techniques including inductively coupled plasma mass spectrometry and ion chromatography. Soil mineralogy is investigated using X-ray diffraction.
• Mössbauer spectroscopy provides information on chemical speciation, e.g., ⁵⁷Fe compounds, and gives insight into their redox chemistry.
• X-ray photoelectron spectroscopy can provide elemental analysis and chemical-state information from the very top of sample surfaces for elements critical to geochemical cycling (C, N, O). N-depth compositional information is also available via Ar+ ion beam depth profiling.

We also steward the open-source NWChem computational chemistry code for quantum chemistry and electronic-structure calculations. Insights gained from these integrated capabilities help us develop and refine algorithms and models for predicting complex coupled systems.

Research in action

Heavy elements in sediments

Identifying chemical forms of uranium in sediments is key to understanding how the contaminant reacts and moves in the environment. A recent EMSL user project analyzed sediment samples with our high-spatial-resolution secondary ion mass spectrometer and found that uranium attached itself to organic matter, not inorganic minerals. This finding suggests that uranium may be more mobile and widespread than expected, and have implications for regulatory contamination limits, monitoring periods, and remediation strategies.

Microbes in sediments

Researchers involved with the WHONDRS and Subsurface Science Focus Area projects are also looking at microbial communities in hyporheic zones—the sediments beneath a waterway or along the water’s edge—for their potential to respire or fix nutrients during various environmental conditions. The combination of field data and EMSL statistical modeling approaches link fine-scale processes with larger-scale seasonal dynamics to infer ecological processes through space and time.

Nutrients in sediments

EMSL researchers are currently studying calcium and soil organic matter (SOM) interactions to better understand molecular-level processes that influence nutrient cycling in alkaline soils. Results from our field site in Warden, Washington, show that calcium-containing minerals play a critical role in SOM stabilization. In turn, SOM stabilization leads to nutrient availability. In the lab, the research team is investigating why this happens. The current thought is that larger molecules, with a greater number of nucleophilic functional groups, are stabilized when organic molecules aggregate in the soils through cation bridging. Through this process, greater quantities of nutrients are absorbed.