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The effects of changing the amount of silica in the cell wall of diatom prey, on the production, decomposition rate and sinking velocity of fecal pellets of the calanoid copepod, Calanus sinicus, were examined. Using different light intensities to control the growth of the diatom Thalassiosira weissflogii also led to the accumulation of different amounts of biogenic silica. Copepods were then fed with either low (~ 1600 cells L−1) or high (~ 8000 cells L−1) concentrations of this diatom. Copepods fed on a high concentration of diatoms with high silica content, exhibited a lower grazing rate and lower fecal pellet production rate than those fed on a high concentration of diatoms with low silica content. However, there was no difference in either the grazing or fecal pellet production rates at low prey concentrations with high or low silica content. The size of the fecal pellets produced was only affected by the prey concentration, and not by the silica content of prey. In addition, the degradation rate of the fecal pellets was much higher for copepods fed a low-silica diet than for those fed on a high-silica diet. Significantly lower densities and sinking rates only occurred in the fecal pellets of copepods fed a low-silica diet and a low prey concentration. Calculating the L-ratio (the ratio of degradation rate:sinking rate) for each group indicated that the fecal pellets produced by copepods fed on highly silicified diatoms are likely to transport both biogenic silica and organic carbon to the deep layer; whereas those produced following the consumption of low-silica diatoms are likely to decompose in the mixing layer.