Abstract Plant, soil, and aquatic microbiomes interact, but scientists often study them independently. Integrating knowledge across these traditionally separate subdisciplines will generate better understanding of microbial ecological properties. Interactions among plant, soil, and aquatic microbiomes, as well as anthropogenic factors, influence important ecosystem processes, including greenhouse gas fluxes, crop production, nonnative species control, and nutrient flux from terrestrial to aquatic habitats. Terrestrial microbiomes influence nutrient retention and particle movement, thereby influencing the composition and functioning of aquatic microbiomes, which, themselves, govern water quality, and the potential for harmful algal blooms. Understanding how microbiomes drive links among terrestrial (plant and soil) and aquatic habitats will inform management decisions influencing ecosystem services. In the present article, we synthesize knowledge of microbiomes from traditionally disparate fields and how they mediate connections across physically separated systems. We identify knowledge gaps currently limiting our abilities to actualize microbiome management approaches for addressing environmental problems and optimize ecosystem services.

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Current understanding of the relationship between nitrate (NO3−) uptake and energy cycling in lotic environments comes from studies conducted in low‐nutrient (NO3− < 1 mg‐N L−1), small (discharge <1 m3 s−1) systems. Recent advances in sensor technology have allowed for continuous estimates of whole‐river NO3− uptake, allowing us to address how the relationship between nutrient uptake and metabolism changes over time and space in larger rivers. We used a six‐month, controlled nitrogen (N) waste release into the eighth order Kansas River (USA) as an ecosystem level nutrient addition experiment. We deployed four NO3− and dissolved oxygen sensors along a 33 km study reach, from February to May 2018, to assess the spatiotemporal relationship between nutrient uptake and stream metabolism during the waste addition. Contrary to our prediction, we did not find evidence of uptake saturation despite an extreme increase in nutrient supply during winter, a period of generally lower biological activity. Although high uptake rates were observed across the study reach, they were uncorrelated to gross primary production. Overall, despite winter temperatures, NO3− uptake rates were high compared to small streams and rivers. We provide evidence that large rivers can be effective ecosystems for retaining and transforming nutrients, while showing that the fine‐scale mechanisms that regulate nutrient retention in large rivers are still largely unknown.