We present composite spectra constructed from a sample of 242,150 Lyman-alpha (Lya) forest absorbers at redshifts 2.4<z<3.1 identified in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) as part of Data Release 9 of the Sloan Di
gital Sky Survey III. We select forest absorbers by their flux in bins 138 km/s wide (approximately the size of the BOSS resolution element). We split these absorbers into five samples spanning the range of flux -0.05 < F<0.45. Tests on a smaller sample of high-resolution spectra show that our three strongest absorption bins would probe circumgalactic regions (projected separation < 300 proper kpc and |Delta v| < 300km/s) in about 60% of cases for very high signal-to-noise ratio. Within this subset, weakening Lya absorption is associated with decreasing purity of circumgalactic selection once BOSS noise is included. Our weaker two Lya absorption samples are dominated by the intergalactic medium. We present composite spectra of these samples and a catalogue of measured absorption features from HI and 13 metal ionization species, all of which we make available to the community. We compare measurements of seven Lyman series transitions in our composite spectra to single line models and obtain further constraints from their associated excess Lyman limit opacity. This analysis provides results consistent with column densities over the range 14.4 <~ Log (N_HI) <~ 16.45. We compare our measurements of metal absorption to a variety of simple single-line, single-phase models for a preliminary interpretation. Our results imply clumping on scales down to ~30 pc and near-solar metallicities in the circumgalactic samples, while high-ionization metal absorption consistent with typical IGM densities and metallicities is visible in all samples.
Using a sample of approximately 14,000 z>2.1 quasars observed in the first year of the Baryon Oscillation Spectroscopic Survey (BOSS), we measure the three-dimensional correlation function of absorption in the Lyman-alpha forest. The angle-averaged c
orrelation function of transmitted flux (F = exp(-tau)) is securely detected out to comoving separations of 60 Mpc/h, the first detection of flux correlations across widely separated sightlines. A quadrupole distortion of the redshift-space correlation function by peculiar velocities, the signature of the gravitational instability origin of structure in the Lyman-alpha forest, is also detected at high significance. We obtain a good fit to the data assuming linear theory redshift-space distortion and linear bias of the transmitted flux, relative to the matter fluctuations of a standard LCDM cosmological model (inflationary cold dark matter with a cosmological constant). At 95% confidence, we find a linear bias parameter 0.16<b<0.24 and redshift-distortion parameter 0.44<beta<1.20, at central redshift z=2.25, with a well constrained combination b(1+beta)=0.336 +/- 0.012. The errors on beta are asymmetric, with beta=0 excluded at over 5 sigma confidence level. The value of beta is somewhat low compared to theoretical predictions, and our tests on synthetic data suggest that it is depressed (relative to expectations for the Lyman-alpha forest alone) by the presence of high column density systems and metal line absorption. These results set the stage for cosmological parameter determinations from three-dimensional structure in the Lyman-alpha forest, including anticipated constraints on dark energy from baryon acoustic oscillations.
