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Work on soils in the HJ Andrews Experimental Forest began with a soil survey conducted in 1962 by Forest Service scientists. Efforts are now underway to update the classification of these soils and map them in a way that will be most useful to researchers. Early work on soil characterization focused largely on hydrologic properties. More recent studies have concentrated on C storage in soils supporting tree stands of different ages, root decomposition, and N fixation. Both early and recent studies have examined effects of forest harvest practices on soil erosion.

In 1997 the DIRT (Detrital Input, Removal, and Trenching) experiment was installed as a part of a national network of similar experiments. The DIRT experiment tests how organic C and respiration respond to treatments of removing litter input, doubling litter input, trenching to remove fine root input, addition of woody detritus, and removal of the A horizon. Other studies have examined the movement of DOC and DON in soils and how soil properties control the release of N following timber harvest.

IIn 1999 the Microbial Observatory at the H.J. Andrews Experimental Forest was established with a grant from the National Science Foundation. This Microbial Observatory is dedicated to the study of bacteria and fungi central to biogeochemical processes in coniferous forest ecosystems in the Central Cascade Mountains of Oregon. Because nitrogen (N) is the most limiting nutrient to tree growth in this ecosystem, research focuses on the functional diversity of microorganisms that perform N cycling processes. Studies primarily examine the microorganisms that produce and consume NO3- because of their pivotal role in supplying N for plant growth and controlling N losses to ground and surface waters as NO3- or to the atmosphere as N2O.

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