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USGS2026

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 data 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.

Environmental Science and Technology↗

USGS2020

Genomic identification of intergeneric hybrids in New World wood-warblers (Aves: Parulidae)

The documentation of hybrids between distantly related taxa can illustrate an initial step to explain how genes might move between species that do not exhibit complete reproductive isolation. In birds, some of the most phylogenetically distant hybrid combinations occur between genera. Traditionally, morphological and plumage characters have been used to assign the identity of the parental species of a putative hybrid, although recently, nuclear introns also have been used. Here, we demonstrate how high-throughput short-read DNA sequence data can be used to identify the parentage of a putative intergeneric hybrid, in this case between a blue-winged warbler ( Vermivora cyanoptera ) and a cerulean warbler ( Setophaga cerulea ). This hybrid had mitochondrial DNA of a cerulean warbler, indicating the maternal parent. For hundreds of single nucleotide polymorphisms within six regions of the nuclear genome that differentiate blue-winged warblers and golden-winged warblers ( Vermivora chrysoptera ), the hybrid had roughly equal ancestry assignment to blue-winged and cerulean warblers, suggesting a blue-winged warbler as the paternal parent species and demonstrating that this was a first generation (F 1 ) hybrid between these species. Unlike other recently characterized intergeneric warbler hybrids, this individual hybrid learned to song match its maternal parent species, suggesting that it might have been the result of an extra-pair mating and raised in a cerulean warbler nest.

Biological Journal of the Linnean Society↗