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1. While 13 C-depleted carbon derived from biogenic methane can substantially contribute to the benthic secondary production in deep stratified lakes, its role in shallow lakes is less clear. We investigated the dynamics of δ13 C and δ15 N in the larvae of Chironomus plumosus throughout an annual cycle in two ecologically distinct basins (open-water plankton-dominated and sheltered macrophyte- covered) of a large (270 km2 ), shallow, polymictic and eutrophic lake (Võrtsjärv, Estonia, North Europe). The larval stable isotopic compositions were linked to the presence of methane-oxidising bacteria (MOB) in larval guts and sediments. 2. Molecular detection of MOB revealed their presence in various sediment types, but stable isotope (SI) analysis revealed clear differences in the feeding of chironomid larvae between the plankton- and macrophyte-dominated habitats. 3. In the plankton-dominated habitat, the mean δ13 C values of larvae remained relatively constant (−38.3‰ to −35.5‰) and corresponded closely to the sediment δ13 C values. Mean δ13 C values of chironomid larvae were generally lower in macrophyte-dominated habitats (−43.4‰ to −33.0‰), and both seasonal and individual variation in larval δ13 C values were more pronounced. MOB presence in larval guts proved a dietary contribution from biogenic methane in macrophyte-dominated habitats. Both the SI and molecular results indicated that MOB could help support larvae even during the cold temperature-limited and ice- covered periods. 4. Our study indicates that methane-derived carbon makes a low but steady contri- bution to the larval chironomids throughout an annual cycle in large shallow Võrtsjärv. However, this contribution can be substantially higher in the lake habitats with abundant macrophytes. The study provides further evidence that a carbon flow pathway from biogenic methane can contribute to the benthic food web under variable habitat conditions in a shallow polymictic lake. Funding information: Estonian Research Council, Grant/Award Number: IUT 21-02, PUT 134, PUT 1389 Funding information: Estonian Research Council, Grant/Award Number: IUT 21-02, PUT 134, PUT 1389

Summary Biogenic methane as an alternative carbon and energy source for freshwater organisms has been receiving increasing attention, but the phenomenon is still poorly understood for shallow lakes. We measured the carbon and nitrogen stable isotope signatures (δ13C, δ15N) for key groups of pelagic and benthic organisms, including crustacean zooplankton, chironomid larvae, young-of-the-year and adult fish, to assess whether biogenic methane contributes to pelagic and benthic food webs in a large, shallow lake, Lake Vortsjarv, Estonia. In the southern part of the lake, covered by macrophytes, crustacean zooplankton showed strong seasonal variation of δ13C, with the lowest values occurring in the period of oxygen depletion. Chironomid (Chironomus plumosus) larvae showed high isotopic variability within the lake, with strongly 13C-depleted and 15N-depleted signatures (down to δ13C −64.0‰ and δ15N −2.6‰) in the macrophyte-covered area. Our results indicate that carbon derived from biogenic methane can contribute seasonally to the benthic food web and, to some extent, also to the pelagic food web, where the lake is covered by macrophytes. Moreover, δ13C values for roach (Rutilus rutilus), perch (Perca fluviatilis) and pike (Esox lucius) from the macrophyte-dominated area were on average 3.5‰ lower than those for the same fish from the plankton-dominated lake area, suggesting some carbon derived from methane is transferred up through the food web. Although no direct evidence is available, our results, together with previous studies of the lake, suggest that protozoans could be a potentially important link from methane-oxidising bacteria to animals higher in the web.

Summary 1. As grazers on picoplankton and nanoplankton, planktonic ciliates form an important link in pelagic food webs. Ciliate communities may be controlled by predation by metazooplankton. In eutrophic systems, however, where the number of large crustaceans is often low, the mechanisms that regulate ciliate dynamics have rarely been described. 2. We conducted an enclosure experiment with natural and screened (145 μm) summer plankton communities to investigate the effect of the small-sized crustacean zooplankton on ciliate community structure and the microbial loop in a shallow eutrophic lake. 3. The removal of the larger fraction of crustaceans initiated a decrease in total ciliate abundance. At the community level, we observed a substantial increase in large-sized predacious ciliates (>100 μm) and a simultaneous decrease in the abundance of smaller ciliates (