We obtained spectra of the pre-main sequence star AU Microscopii during a transit of its Neptune-sized planet to investigate its orbit and atmosphere. We used the high-dispersion near-infrared spectrograph IRD on the Subaru telescope to detect the Doppler shadow from the planet and constrain the projected stellar obliquity. Modeling of the observed planetary Doppler shadow suggests a spin-orbit alignment of the system ($lambda=-4.7_{-6.4}^{+6.8}$ degrees), but additional observations are needed to confirm this finding. We use both the IRD data and spectra obtained with NIRSPEC on Keck-II to search for absorption in the 1083 nm line of metastable triplet He I by the planets atmosphere and place an upper limit for the equivalent width of 3.7 mAA at 99 $%$ confidence. With this limit and a Parker wind model we constrain the escape rate from the atmosphere to $<0.15-0.45, M_{oplus}$ Gyr$^{-1}$, comparable to the rates predicted by an XUV energy-limited escape calculation and hydrodynamic models, but refinement of the planet mass is needed for rigorous tests.
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