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In recent decades, ecologists have investigated the effects of shrub encroachment on regional carbon cycling in semi-arid and arid regions. Although differences in carbon sequestration and stocks have been recognized in different soil layers, the vertical changes in soil organic carbon (SOC) at the molecular level following shrub encroachment remain unexplored. In this study, we used biomarkers to assess the impacts of shrub encroachment on SOC composition.

We collected soil samples along the 1-m profile within shrub patches and grassy matrix in three typical shrub-encroached grassland (SEG) sites in Inner Mongolia, and quantified the vertical distribution of the biomarkers, including free lipids, bound lipids and lignin-derived phenols.

The principal component analysis (PCA) of the biomarker data showed that samples in the grassy matrix had strong positive loadings along the first two components (PCs); in contrast, samples in the upper 50 cm of the shrub patches had negative loadings along the first component (PC1) as well as a narrower range. The acid to aldehyde ratios of the vanillyl and syringyl type monomers increased simultaneously along the 1-m profile in the grassy matrix; however, this trend was not observed in the shrub patches. In addition, the vanillyls to syringyls to cinnamyls ratio was approximately 3:2:1 in the shrub patches and 3:2:1 or 2:2:1 in the grassy matrix.

Shrub encroachment altered the vertical patterns in SOC composition, especially in the upper 50 cm, as well as the oxidation status of lignin-derived phenols along the entire 1-m profile. Further, shrub encroachment influenced the soil carbon composition under the shrub canopy as well as in the grassy matrix due to the sprawling canopies and the horizontal extension of the root systems of the encroaching shrubs. These results provided new insights into the vertical patterns of SOC changes after shrub encroachment at the molecular level and have important implications for understanding the mechanisms of soil carbon dynamics with changes in vegetation structure and composition.