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Characterizing amino sugar signature in particle size separates of tropical soils is important for further understanding the fate of microbial-derived compounds during the decomposition of soil organic matter (SOM) in tropical agroecosystems. We investigated the impact of land-use changes on the nature, amount and dynamics of amino sugars in soil of the semi-arid northern Tanzania. Samples were collected from the uppermost 10 cm of native woodland, degraded woodland, fields cultivated for 3 and 15 years and homestead fields fertilized with animal manure. The amount of glucosamine, galactosamine, mannosamine and muramic acid were determined in bulk soil and size separates. Compared to the native woodland, a 68% and 72% reduction in total amino sugar contents were found in the 3- and 15-year cultivated fields, respectively. Moreover, 39% of the total amino sugar was lost from the degraded woodland. This may be attributed to accelerated decomposition of amino sugars and/or decreasing microbial biomass input under the semi-arid environment following clear-cutting and cultivation. In contrast, only a 20% decline was found from the fields where animal manure had been applied. Most of the amino sugar depletion occurred from the coarse and fine sand-associated SOM. The decline from the silt and clay-bound amino sugar was relatively small, indicating the importance of organo-mineral associations in the stabilization of microbial-derived sugars in this tropical soil. After 15 years of continuous cultivation, the ratio of glucosamine:galactosamine increased from 1.44 to 2.23, while the ratio of glucosamine:muramic acid increased from 14.5 to 26.5 (P<0.05). These results suggest that cultivation may have led to preferential depletion of bacterial-derived amino sugars (muramic acid and galactosamine) compared with fungal-derived glucosamine.