Environmental and ecological change across Angkor’s transition inferred from untargeted molecular fingerprints

Angkor was the capital of the Khmer Empire during approximately 9th to 15th CE. It relied on a sophisticated water management system to sustain a vast low-density urban population. For the last two decades, the decline of Angkor has been linked to hydroclimatic instability in combination with infrastructural failure. Recent archaeological evidence suggests that the decline of elite occupation within the civic-ceremonial core may have begun earlier, resulting from additional social, political, or economic drivers. Understanding the timing and potential causes of such changes is crucial for assessing the vulnerability of complex urban systems.Sedimentary molecular biomarkers can provide insights into paleoenvironmental and anthropogenic changes. In particular, untargeted molecular fingerprinting is not constrained by predefined compound lists and analyzes thousands of molecular features simultaneously. This enables the detection of complex and overlapping source inputs and facilitates the identification of broader molecular shifts potentially associated with changing land use, ecosystem functioning, and anthropogenic activity.Here we apply an untargeted molecular fingerprinting framework using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS) to characterize sedimentary organic matter in lipid extracts from a sediment core retrieved from a pond inside the temple of Angkor Wat. GC×GC substantially increases chromatographic resolution and enables the detection of thousands of chemical features without a priori hypotheses and is thus suitable for the untargeted analyses. We investigate temporal shifts in molecular composition across the Angkorian and post-Angkorian periods to evaluate changes in organic matter inputs, microbial processing, and water quality, and discuss their implications for changes in urban land use and occupation patterns at the temple complex.