In the present research, nicotine alkaloid production by Nicotiana tabacum (tobacco) hairy roots and tropane alkaloid production by Hyoscyamus niger hairy roots were investigated. The first objective of this research was to improve the oxygen mass transfer in hairy root cultures with microbubbles. Oxygen was shown as a critical nutrient for the growth of tobacco and H. niger hairy roots. In a 1-liter fermentor, microbubble dispersion improved the oxygen mass transfer, tobacco hairy root growth, and nicotine production in the medium. In a novel ground-joint column bioreactor, microbubbles enhanced the oxygen mass transfer and the growth of H. niger hairy roots. The second objective of this research was to enhance the release of alkaloids from the hairy roots into the culture medium. In a l-liter fermentor, nicotine concentration in medium was improved by adjusting the medium pH to 6. Unlike the nicotine alkaloid, hyoscyamine concentration in medium was not detectable at medium pH 6, whereas hyoscyamine in medium increased to 42 mg l-1 at medium pH 3. Similar to the hyoscyamine, scopolamine in medium increased from 0.1 to 11 mg l-1 when the medium pH was adjusted from 6 to 3. The release of alkaloids into culture medium provides opportunities to isolate a high-value alkaloid directly from the culture fluid, and reduces the cost of product recovery.