Summary: | The interactions established between marine microbes, namely phytoplankton–bacteria, are key to the balance of organic matter export to depth and recycling in the surface ocean. Still, their role in the response of phytoplankton to rising CO<sub>2</sub> concentrations is poorly understood. Here, we show that the response of the cosmopolitan <i>Emiliania huxleyi</i> (<i>E. huxleyi</i>) to increasing CO<sub>2</sub> is affected by the coexistence with bacteria. Specifically, decreased growth rate of <i>E. huxleyi</i> at enhanced CO<sub>2</sub> concentrations was amplified in the bloom phase (potentially also related to nutrient concentrations) and with the coexistence with <i>Idiomarina abyssalis</i> (<i>I. abyssalis</i>) and <i>Brachybacterium</i> sp. In addition, enhanced CO<sub>2</sub> concentrations also affected <i>E. huxleyi</i>’s cellular content estimates, increasing organic and decreasing inorganic carbon, in the presence of <i>I. abyssalis</i>, but not <i>Brachybacterium</i> sp. At the same time, the bacterial isolates only survived in coexistence with <i>E. huxleyi</i>, but exclusively <i>I. abyssalis</i> at present CO<sub>2</sub> concentrations. Bacterial species or group-specific responses to the projected CO<sub>2</sub> rise, together with the concomitant effect on <i>E. huxleyi</i>, might impact the balance between the microbial loop and the export of organic matter, with consequences for atmospheric carbon dioxide.
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