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Estuaries are among the most productive of aquatic ecosystems. Yet the collective understanding of patterns and drivers of primary production in estuaries is incomplete, in part due to complex hydrodynamics and multiple controlling factors that vary at a range of temporal and spatial scales. A whole-ecosystem experiment was conducted in a deep, pelagically dominated terminal channel of the Sacramento-San Joaquin Delta (California, USA) that seasonally appears to become nitrogen limited, to test whether adding calcium nitrate would stimulate primary productivity or increase phytoplankton density. Production did not respond consistently to fertilization, in part because nitrate and phytoplankton were dispersed away from the manipulated area within 1–3 days. Temporal and spatial patterns of gross primary production were more strongly related to stratification and light availability (i.e., turbidity) than nitrogen, highlighting the role of hydrodynamics in regulating system production. Similarly, chlorophyll was positively related not only to stratification but also to nitrogen—with a positive interaction—suggesting stratification may trigger nutrient limitation. The average rate of primary production (4.3 g O2 m−2 d−1), metabolic N demand (0.023 mg N L−1 d−1), and ambient dissolved inorganic nitrogen concentration (0.03 mg N L−1) indicate that nitrogen can become limiting in time and space, especially during episodic stratification events when phytoplankton are isolated within the photic zone, or farther upstream where water clarity increases, dispersive flux decreases, and stratification is stronger and more frequent. The role of hydrodynamics in organizing habitat connectivity and regulating physical and chemical processes at multiple temporal and spatial scales is critical for determining resource availability and evaluating biogeochemical processes in estuaries.

The impacts of wildfire smoke on lake habitats remains unclear. We determined the metabolic response to smoke in the epi‐pelagic and two littoral habitats in Castle Lake, California. We compared light regime, gross primary production, ecosystem respiration, and net ecosystem production in years with and without smoke. During the smoke period incident ultraviolet‐B (UV‐B) radiation and photosynthetically active radiation (PAR) decreased by 53% and 28%, respectively, while the water column extinction coefficient of UV‐B and PAR increased by 20% and 18% respectively. Epi‐pelagic productivity increased during smoke cover because of decreased solar inputs. PAR values remained sufficient to saturate productivity, suggesting observed differences were primarily the result of changes in UV‐B. Littoral‐benthic productivity did not change, possibly reflecting adaptation to high‐intensity UV‐B light in these habitats. Our results highlight the importance of understanding how prolonged wildfire smoke alters the amount of energy produced from specific habitats in lakes. Plain Language Summary: Large wildfires are increasing worldwide, but the impacts of wildfire smoke on lakes are unknown. We determined how photosynthetic activity and organism's respiration respond to smoke in the offshore and nearshore habitats in a mountain lake. Smoke limited the damage to algae caused by ultraviolet‐B radiation, resulting in increased offshore photosynthesis. Photosynthesis in the nearshore habitat did not change during smoke cover, possibly because organisms in shallow habitats have adapted to the higher intensity of damaging ultraviolet‐B radiation. Our results highlight the importance of understanding how prolonged smoke conditions can alter lakes' energy flows and food webs. Key Points: Wildfire smoke reduced ultraviolet‐B and photosynthetically active radiationLake habitats respond differently to changes in light from smoke, pelagic primary production increased with no change to littoral metabolismSmoke alters energy flows with implications for food web structure in lakes [ABSTRACT FROM AUTHOR]

Ecosystem metabolism is a key ecological attribute and easy to describe, but quantifying metabolism in estuaries is challenging. Properly scaling measurements through time and space requires consideration of hydrodynamics and mixing water from heterogeneous sources, making any estimation uncertain. Here, we compared three methods for modeling ecosystem metabolism in a portion of the Sacramento‐San Joaquin Delta. Metabolism estimates based on laboratory incubations, continuous in situ buoys, and an oxygen isotope approach all indicated the system was net heterotrophic, and calculated rates were comparable in magnitude when averaged over the 2‐month study. Daily metabolic rates based on in situ buoys were the most variable, likely due to horizontal and vertical advection and poor portrayal of the dissolved oxygen budget. After temporally averaging in situ buoy estimates or smoothing the dissolved oxygen time series for tidal effects, rates were more comparable to the other methods, which may be necessary to account for tidal advection and unbalanced contributions from subhabitats within the metabolic footprint. Incubation‐based rates represent the finest temporal and spatial scale and only account for pelagic processes, which may explain why incubation‐based rates were lower than the other two methods. The oxygen isotope method provided temporally and spatially integrated rates that were bracketed by the other two methods and may be a valuable tool in systems matching the model requirements. Because uncertainty arises in each method from a number of assumptions and scaling calculations, the resolution of metabolic rates in estuaries is likely coarser and more variable than in other aquatic ecosystems. [ABSTRACT FROM AUTHOR]