A nitrogen afterglow at atmospheric pressure has recently been described as able to transport active species over long distances in small diameter tubes, with a biocidal effect. For a discharge gas composed of nitrogen, either of high purity or with some controlled ppm of oxygen, survival curves are presented. The afterglow, flowing at 40 slm in a cylindrical quartz tube with 8 mm internal diameter is studied using emission spectroscopy. Fundamental or excited states of atomic or molecular species of parent gases are detected and evaluated. Their absolute concentration is measured along the tube axis. Correlated to transport equations, results give information on the creation and destruction reactions of these species, especially of the O(1S) metastable state of O, the species that has been shown to boost the biocidal effect.