Optimizing Cryo-Focused Pyrolysis GC/MS for Tracing Soil Organic Matter Across Diverse Ecosystems

The cycling of organic matter in terrestrial soils and
sediments
is central to a range of biogeochemical processes that regulate nutrient
cycling, crop productivity, trace gas emissions, and contaminant transport.
Pyrolysis-gas chromatography/mass spectrometry (py-GC/MS) is a powerful
tool for characterizing bulk soil organic matter (SOM) at the molecular
level. In this study, we used a cryo-focused py-GC/MS system to analyze
soil samples from seven diverse ecosystems: vernal pool, prairie pothole,
temperate forest, tropical forest, tundra, wildfire-affected boreal
forest, and grassland. We addressed a key bottleneck in molecular-level
SOM characterization by developing an automated data analysis pipeline
to optimize py-GC/MS and complementary evolved gas analysis/mass spectrometry
(EGA/MS) methods, incorporating advanced tools for peak deconvolution,
developing a custom compound class library, and implementing fragmentation
spectrum-based molecular networking for the first time. This improved
workflow was applied to soil samples from all seven ecosystems, including
multiple depths and density fractions. Our findings demonstrate that
ecosystem type plays a dominant role in shaping compositional differences
in SOM. We also identified trends in the source of SOM compounds (e.g.,
microbial vs plant-derived) across soil depth and density fractions,
which are critical for understanding persistence and turnover of SOM.
Our molecular networking analysis indicated that although many compounds
are widespread across ecosystems, others are restricted to specific
environments, such as wetlands. This underscores the utility of molecular-level
data in elucidating the complexity of SOM composition and the environmental
drivers that shape it. Such molecular-level insights can deepen our
knowledge of biogeochemical SOM cycles.