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Intensive forest harvest techniques have the potential to alter soil carbon and nutrient stocks and biogeochemical processes. We investigated how differing levels of organic matter removal (OMR) during timber harvest influenced the long-term stability of nitrification and the microbes regulating this process. Nitrification is limited by the activity of ammonia oxidizing bacteria (AOB) and archaea (AOA); however, reports on the relative contribution of each of these groups to forest soil nitrification have varied and have not been investigated in response to OMR. The influence of soil depth on the structure and function of the ammonia-oxidizing community has also been underreported and was included in this study. We quantified soil physicochemical properties including concentrations of ammonium (NH4+) and nitrite (NO2−) + nitrate (NO3−), and also coupled next generation sequencing and qPCR of the amoA gene to a whole-soil assay that stimulates nitrification and allows for the discrimination of AOA-from AOB-activity using 1-octyne, which inhibits bacterial ammonia monooxygenase activity. Soils were collected (1 m depth) from replicated loblolly pine (Pinus taeda L.) stands subjected to three different intensities of OMR (i.e., unharvested control, bole-only harvest, and whole-tree harvest + forest floor removal). Increasing intensity of OMR and increasing soil depth lead to significant reductions in concentrations of in situ NH4+ and NO2− + NO3−. Sequencing and subsequent annotation of the ammonia oxidizing community revealed that AOA were dominated by Crenarchaeota and AOB were dominated by Nitrosospira spp. The abundance of both bacterial and archaeal amoA were influenced by OMR and soil depth; furthermore, archaeal amoA was more abundant than bacterial amoA across all soil depths and the ratio of AOA to AOB increased with depth. Community structure of AOA and AOB were influenced by soil depth; however, only AOB were altered by OMR. Soil incubations revealed nitrification was N-limited in these forest soils. Furthermore, AOA- and AOB-contributions to total nitrification were nearly equivalent in surface soils; however, AOA contribution increased to 75% at 1 m. In general, the highest rates of nitrification occurred in the soils taken from unharvested control stands; however, OMR treatment differences were only significant when soils were amended with high levels of ammonia indicating that at ambient levels, intensive OMR may not lead to long-term alterations in nitrification potential.
•AOA and AOB amoA abundance is altered by organic matter removal.•AOB, but not AOA, community structure is altered by organic matter removal.•AOA, but not total and AOB, nitrification is altered by organic matter removal at low NH4+ levels.•Soil depth reduces AOB abundance and alters AOA and AOB community structure.