Deep-rooted perennials alter microbial respiration and chemical composition of carbon in density fractions along soil depth profiles

• Deep-rooted perennials differentially alter CO 2 and SOC along depth profiles. • Microbes under deep-rooted perennials respire plant-derived C at shallow soil layers. • Deep-rooted perennials increase aliphatic C in free light fractions at depth. Growing deep-rooted perennials has been proposed to increase soil organic carbon (SOC) stocks and mitigate CO 2 emissions. Yet, we know little about the bioavailability and chemical properties of SOC under deep-rooted perennials and shallow-rooted annuals. Improving our understanding of the role of deep-rooted perennials for belowground C storage is critical, as root growth has the potential to both increase SOC stock and accelerate loss of existing SOC. Here, we assessed the effects of >10 years of land conversion from shallow-rooted annuals (maize) to deep-rooted perennials (switchgrass) on SOC bioavailability (microbial respiration, Δ 14 C-CO 2 ), mineral-associated SOC (density fractionation), and SOC turnover and composition ( 14 C-SOC, DRIFT spectroscopy) in surface soils (0–20 cm) and subsoils (90–120 cm) at two sites with sandy and silty soils. We demonstrate that switchgrass enhanced microbial respiration of recently-fixed C in surface soils. Switchgrass increased Δ 14 C values of the free light fraction in subsoil of the sandy site, by supplying aliphatic C (putative simple plant C) into the soil. In contrast, maize input less root C into the soil, and at one site increased the decomposition of older SOC, which indicates that overall microbial C demand outpaced plant C inputs. These results highlight that deep-rooted perennials stimulate the transfer of more atmospheric C to both surface and subsoils than shallow-rooted annuals, that newly generated SOC under deep-rooted perennials is relatively less protected from decomposition, and that reaping the C benefits of deep-rooted perennials could require maintaining the land cover as a perennial cropping system.