Before biological or biogeochemical experimentation, sediments are often manipulated and defaunated with the use of many different approaches and only modest consideration of treatment effects on sediment biogeochemistry and fluxes. Mesocosm experiments require large quantities of sediment and no standard protocol to defaunate and equilibrate muddy sediments before initiation of experiments has been determined.

Using fine-grained sediments, we examined a number of treatments: (1) intact with macroinfauna; (2) intact, macroinfauna individually removed; (3) homogenized surface sediment with macrofauna; (4) homogenized deep sediment without macroinfauna; and (5) intact deep sediment without macroinfauna. In weekly batch core flux incubations, we measured dissolved oxygen, dinitrogen gas, ammonium (NH₄ ), nitrate plus nitrite (NO₃⁻ NO₂⁻), silicate (Si), and soluble reactive phosphorus (SRP) fluxes over a 5-week period. In addition, we determined porewater ammonium concentrations over time.

Different sediment preparation techniques, with the same muddy sediment, significantly affected nutrient and gas fluxes, and the amount of nutrient and gas fluxes differed between sediment preparation techniques. Severely manipulated sediments, such as homogenized treatments, had high initial effluxes but eventually equilibrated to lower and more constant nutrient and gas fluxes. Moreover, biogeochemical flux changes for all treatments became similar after about 2 to 3 weeks. Sieved sediments exhibited low fluxes over the entire 5-week period, and flux rates did not change over time. A feasible method for sediment preparation for mesocosm studies is to use homogenized deep sediment equilibrated over an almost 2-week period. Overall, sediment preparation and the time after sediment manipulation affect sediment biogeochemical processes and must be considered before initiating experiments.