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Summary Factors that affect the respiration of organic carbon by marine bacteria can alter the extent to which the oceans act as a sink of atmospheric carbon dioxide. We designed seawater dilution experiments to assess the effect ofpCO₂enrichment on heterotrophic bacterial community composition and metabolic potential in response to a pulse of phytoplankton‐derived organic carbon. Experiments included treatments of elevated (1000 p.p.m.) and low (250 p.p.m.)pCO₂amended with 10 μmol L⁻¹dissolved organic carbon fromEmiliana huxleyilysates, and were conducted using surface‐seawater collected from the South Pacific Subtropical Gyre. To assess differences in community composition and metabolic potential, shotgun metagenomic libraries were sequenced from low and elevatedpCO₂treatments collected at the start of the experiment and following exponential growth. Our results indicate bacterial communities changed markedly in response to the organic matter pulse over time and were significantly affected bypCO₂enrichment. ElevatedpCO₂also had disproportionate effects on the abundance of sequences related to proton pumps, carbohydrate metabolism, modifications of the phospholipid bilayer, resistance to toxic compounds and conjugative transfer. These results contribute to a growing understanding of the effects of elevatedpCO₂on bacteria‐mediated carbon cycling during phytoplankton bloom conditions in the marine environment.