To better understand the mechanisms for microcystin-LR (MCLR) biodegradation, the linkage between MCLR-biodegradation kinetics and functional gene expression dynamics was originally investigated with Novosphingobium sp. THN1 as inoculum under various nutrient conditions. Along biodegradation, mlrA gene expression, coupled with mlrD, presented similar trend but was regulated differentially among different conditions. Good positive correlation was observed between MCLR degraded and induction ratios of functional genes until 42 h at respective condition. Compared to those under nutrient-free condition, the stimulated or decelerated biodegradation with dipotassium phosphate (DP) or ammonium chloride (AC) (both at 100 mg L-1) was related to higher or lower up-regulation in mlr gene expression, suggesting that divergent mlr gene expression was one of the reasons for different effects of DP or AC on degradation. However, stimulated degradation with sodium nitrate (100 mg L-1) might involve other mechanisms where mlr expression was not the decisive prerequisite to govern MCLR-biodegradation. (C) 2014 Elsevier Ltd. All rights reserved.