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Abstract Understanding which factors shape and maintain biodiversity is essential to understand how ecosystems respond to crises. Biodiversity observed in ecological communities is a result of the interaction of various factors which can be classified as either neutral‐ or niche‐based. The importance of these processes has been debated, but many scientists believe that both processes are important. Here, we use unique ecosystems in groundwater‐filled lava caves near Lake Mývatn, to examine the importance of neutral‐ versus niche‐based factors for shaping invertebrate communities. We studied diversity in benthic and epibenthic invertebrate communities and related them to ecological variables. We hypothesized that if neutral processes are the main drivers of community structure we would not see any clear relationship between the structure of community within caves and ecological factors. If niche‐based processes are important we should see clear relationships between community structure and variation in ecological variables across caves. Both communities were species poor, with low densities of invertebrates, showing the resource limited and oligotrophic nature of these systems. Unusually for Icelandic freshwater ecosystems, the benthic communities were not dominated by Chironomidae (Diptera) larvae, but rather by crustaceans, mainly Cladocera. The epibenthic communities were not shaped by environmental variables, suggesting that they may have been structured primarily by neutral processes. The benthic communities were shaped by the availability of energy, and to some extent pH, suggesting that niche‐based processes were important drivers of community structure, although neutral processes may still be relevant. The results suggest that both processes are important for invertebrate communities in freshwater, and research should focus on understanding both of these processes. The ponds we studied are representative of a number of freshwater ecosystems that are extremely vulnerable for human disturbance, making it even more important to understand how their biodiversity is shaped and maintained.

Abstract Ecosystem engineers can have diverse and conflicting effects on their ecosystems, and the balance between these effects can depend on the physical environment. This context dependence means that environmental variation can produce large differences in engineer effects through space and time. Here, we explore how local variability in environmental conditions can lead to large spatiotemporal variation in the effect of tube‐building midges on benthic ecosystem metabolism in a shallow subarctic lake. Using field experiments, we found that midge engineering increases both gross primary production (GPP) and respiration (RESP) in the sediment. Gross primary production and RESP have opposing influences on net ecosystem production, and the net effect of midges on the benthic ecosystem depends on the balance between their effects on GPP and RESP. Variation in light mediates this balance—under high light conditions, primary producers are able to exploit the structural benefits provided by midges, while in the dark, the elevation of respiration from midge engineering predominates. Benthic light levels vary spatially and temporally due to episodic cyanobacterial blooms that prevent almost all light from reaching the benthos. By quantifying the nonlinear relationship between midge engineering and light, we were able to project ecosystem‐wide consequences of natural variation in light conditions across the lake. Our results illustrate how the sign and magnitude of ecosystem‐wide effects of ecosystem engineers can vary through space and time.