The biological pump plays a pivotal role in the global carbon cycle, and accurately quantifying net community production (NCP) is essential for assessing its efficiency. However, the classic light and dark bottle incubation technique often leads to a systematic overestimation of bacterial respiration (BR) due to the "bottle effect," introducing significant uncertainties into NCP estimates. In this study, we propose and validate a novel correction model that successfully accounts for BR in incubation systems for the first time. Experimental data from the Chinese marginal seas indicate that BR is overestimated by an average of 200% after 24-hour incubations using the traditional method, resulting in a ~20% overestimation of community respiration. This overestimation is particularly pronounced in oligotrophic bacterial communities with low biomass or productivity. Corrected NCP data suggest that certain regions previously classified as net heterotrophic were, in fact, misidentified due to inflated BR estimates. These findings highlight the potential overestimation of heterotrophic regions based on bottle incubation, underscoring the need to reassess global ocean metabolic balances. Overall, this study provides a critical reference for the accurate estimation of bacterial carbon flux, with important implications for assessing the efficiency of the biological pump.

bottle incubation, bacterial respiration, community respiration, metabolic balance