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Streams generally are affected by multiple stressors acting at different timescales. Periphyton, often the most important primary producer in these ecosystems, may respond to short-term impacts as well as to different long-term environmental conditions with potentially various changes in community structure. Here, we experimentally investigated the effects of sudden flow pulses on periphyton communities as a way to mimic extreme precipitation events in lowland streams that are predicted to occur more often with climate change in some regions. Using outdoor flumes, we allowed periphyton to colonise nutrient-diffusion substrates under two light conditions (50% shade and fully open) and nutrient availabilities (control, with access only to stream nutrients, and N–P-enriched) along a gradient in baseflows (0.43 to 2.17 L/s). After one month, we exposed the communities to a flow pulse (two-fold peak flow increase to simulate conditions of a potentially high disturbance) and analysed the responses of biomass and taxonomic composition. Flow pulse promoted periphyton growth in the lowest range of the baseflow but led to biomass reduction in the highest range. Light was the second major driver of biomass accrual, whereas nutrient enrichment had a strong effect on community composition both before and after the pulse (i.e., diatom dominance vs. green algae dominance in scenarios without and with enrichment, respectively). In all treatments, the flow pulse promoted a higher taxonomic richness, suggesting a partial reset of the succession of the periphyton communities. However, independent of flow and resources, periphyton communities showed low ecological resistance against the pulse with changes in chlorophyll a, biovolume and taxonomic richness to the pulse. We demonstrated that the effects of pulses on periphyton are similar in terms of biomass but varied strongly regarding composition depending on their initial structure, which is in turn mediated by the baseflow normally experienced by the systems, and on light and nutrient availability. Our results highlight the importance of testing multiple stressors, such as an increase in extreme events, under a wide range of environmental conditions (i.e., flow regime, trophic state, light availability). This approach allows us to detect potential interaction effects and non-linear responses, and highlights that the environmental settings ultimately determine the net effects of flow pulses on community structure and probably also on several important ecosystem processes.

Shallow aquatic systems exchange large amounts of carbon dioxide (CO2) and methane (CH4) with the atmosphere. The production and consumption of both gases is determined by the interplay between abiotic (such as oxygen availability) and biotic (such as community structure and trophic interactions) factors. Fish communities play a key role in driving carbon fluxes in benthic and pelagic habitats. Previous studies indicate that trophic interactions in the water column, as well as in the benthic zone can strongly affect aquatic CO2 and CH4 net emissions. However, the overall effect of fish on both pelagic and benthic processes remains largely unresolved, representing the main focus of our experimental study. We evaluated the effects of benthic and pelagic fish on zooplankton and macroinvertebrates; on CO2 and CH4 diffusion and ebullition, as well as on CH4 production and oxidation, using a full-factorial aquarium experiment. We compared five treatments: absence of fish (control); permanent presence of benthivorous fish (common carps, benthic) or zooplanktivorous fish (sticklebacks, pelagic); and intermittent presence of carps or sticklebacks. We found trophic and non-trophic effects of fish on CO2 and CH4 emissions. Intermittent presence of benthivorous fish promoted a short-term increase in CH4 ebullition, probably due to the physical disturbance of the sediment. As CH4 ebullition was the major contributor to the total greenhouse gas (GHG) emissions, incidental bioturbation by benthivorous fish was a key factor triggering total carbon emissions from our aquariums. Trophic effects impacted GHG dynamics in different ways in the water column and the sediment. Fish predation on zooplankton led to a top-down trophic cascade effect on methane-oxidising bacteria. This effect was, however, not strong enough as to substantially alter CH4 diffusion rates. Top-down trophic effects of zooplanktivorous and benthivorous fish on benthic macroinvertebrates, however, were more pronounced. Continuous fish predation reduced benthic macroinvertebrates biomass decreasing the oxygen penetration depth, which in turn strongly reduced water–atmosphere CO2 fluxes while it increased CH4 emission. Our work shows that fish can strongly impact GHG production and consumption processes as well as emission pathways, through trophic and non-trophic effects. Furthermore, our findings suggest their impact on benthic organisms is an important factor regulating carbon (CO2 and CH4) emissions.

Summary 1. Different behavioural responses of planktonic animals to their main predators, fish, have been reported from shallow lakes. In north temperate lakes, large-bodied zooplankton may seek refuge from predation among macrophytes, whereas in subtropical lakes, avoidance of macrophytes has been observed. The prevalent behaviour probably depends on the characteristics of the fish community, which in Mediterranean lakes is typically dispersed in both the open water zone and in the littoral, as in temperate lakes, and is dominated by small size classes, as in subtropical lakes. 2. We performed ‘habitat choice’ experiments to test the response of Daphnia magna to predation cues at both the horizontal and vertical level by mimicking a ‘shallow littoral’ zone with plants and a ‘deeper pelagic’ zone with sediments. 3. Initial separate response experiments showed that natural plants, artificial plants and predation cues all repelled D. magna in the absence of other stimuli, while sediments alone did not trigger any significant response by D. magna. 4. The habitat choice experiments showed that, in the presence of predation cues and absence of plants, Daphnia moved towards areas with sediment. In the presence of both plants and sediments, Daphnia moved away from the plants towards the sediments under both shallow and deep water treatment conditions. 5. Based on these results, we suggest that Daphnia in Mediterranean shallow lakes avoid submerged macrophytes and instead prefer to hide near the sediment when exposed to predation risk, as also observed in subtropical shallow lakes. This pattern is not likely to change with water level alterations, a common feature of lakes in the region, even if the effectiveness of the refuge may be reduced.

Summary 1. Filamentous green algae (FGA) may represent an alternative state in high-nutrient shallow temperate lakes. Furthermore, a clear water state is sometimes associated with the dominance of FGA; however, the mechanisms involved remain uncertain. 2. We hypothesised that FGA may promote a clear water state by directly suppressing phytoplankton growth, mostly via the release of allelochemicals, and that this interaction may be affected by temperature. 3. We examined the relationships between FGA, phytoplanktonic chlorophyll a concentrations and zooplankton in a series of mesocosms (2.8 m3) mimicking enriched shallow ponds now and in a future warmer climate (0 and c. 5 °C above ambient temperatures). We then tested the potential allelopathic effects of FGA (Cladophora sp. and Spirogyra sp.) on phytoplankton using several short-term microcosms and laboratory experiments. 4. Mesocosms with FGA evidenced lower phytoplanktonic chlorophyll a concentrations than those without. Zooplankton and zooplankton : phytoplankton biomass ratios did not differ between mesocosms with and without FGA, suggesting that grazing was not responsible for the negative effects on phytoplanktonic biomass (chlorophyll a). 5. Our field microcosm experiments demonstrated that FGA strongly suppressed the growth of natural phytoplankton at non-limiting nutrient conditions and regardless of phytoplankton initial concentrations or micronutrients addition. Furthermore, we found that the negative effect of FGA on phytoplankton growth increased up to 49% under high incubation temperatures. The experiment performed using FGA filtrates confirmed that the inhibitory effect of FGA on phytoplankton may be attributed to allelochemicals. 6. Our results suggest that FGA control of phytoplankton growth may be an important mechanism for stabilising clear water in shallow temperate lakes dominated by FGA and that FGA may play a larger role when lakes get warmer.

SUMMARY 1. Shallow lakes and ponds contribute disproportionally to species richness relative to other aquatic ecosystems. In-lake conditions (e.g. presence of submerged plants) seem to play a key role in determining diversity, as has been demonstrated for temperate lakes. When water quality deteriorates and turbidity increases, conditions in such lakes are affected drastically resulting in a loss of diversity. However, it is not clear whether subtropical lakes show the same pattern and whether the richness of all groups reacts similarly to environmental changes. 2. Our aim was to analyse the main factors explaining patterns of species richness in plankton, fish and submerged macrophyte assemblages in both turbid and clear subtropical shallow lakes. We analysed abiotic and biotic features of 18 subtropical, small- to mediumsized, shallow lakes along the Uruguayan coast. We compared both turbid and clear ecosystem states and evaluated the relative variance explained by the factors measured. 3. Variables describing lake and catchment morphology, as well as the percentage of the water column occupied by submerged macrophytes (%PVI) and water turbidity, had strong effects on taxon richness. Interestingly, individual biotic groups had dissimilar richness patterns. Macrophyte %PVI decreased with increasing lake area, while fish species richness showed the opposite pattern. Phytoplankton species richness increased with macrophyte %PVI, while the zooplankton richness pattern varied depending on the taxonomic group considered. 4. Overall, our results indicate that, as found for temperate lakes, a greater submerged plant cover promotes higher species richness in several groups, and that this may overwhelm the otherwise expected positive effect of lake size on species richness. On the other hand, small-bodied zooplankton predominated in lakes with high plant abundance. Our findings concur with recent studies, indicating that refuge capacity of aquatic plants might be weaker in (sub)tropical than in temperate shallow lakes.