The hypothesis of this study is that the variable hydrological regime of intermittent lakes and wetlands affects the primary productivity, decomposition and root fungal colonisation of Phragmites australis, with effects on the whole ecosystem metabolism. The above-ground biomass of reed stands was monitored in littoral and riparian stands of Lake Cerknica, under different water levels. Leaf and culm litter decomposition was also studied at three locations, from predominantly dry to permanently submerged. Root colonisation by fungi was monitored across two seasons in the littoral reed stand. The primary productivity of the littoral stands was related to a variable degree with water levels and air temperature in July in the current year. In the riparian reeds, only monthly temperatures in October of the previous year were important. The submersion duration of the litter enhanced the decomposition rates. The frequency of fungal colonisation of reed roots was decreasing with the submersion time length. Overall, roots were colonised by arbuscules, hyphae, vesicles, hyphal coils and microsclerotia. The main outcomes of this study deals with the role of intermittent hydrological conditions in determining the structure and functioning of reed-dominated lacustrine wetlands, which are exposed to climate threats.

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The intermittent Lake Cerknica comprises a variety of wetland habitats, which support numerous species, many of them included on the Red List. The exchange of wet and dry periods influences the through-flow of energy and the turnover of matter in the lake. In the last five decades, the water level fluctuations were highly variable. Since 1961 the May and June water levels have shown a decreasing trend line, in October the trend line revealed an increase, while from November to February no changes of trend could be observed. High water levels in winter and during the peak vegetation season negatively affected reed productivity. The decomposition of reed leaves increased with the wetness of the survey location, while the soil mineralisation rate was only slightly related to soil wetness. In comparison to the tributaries, the lake water contained relatively low amount of nutrients, which was a consequence of a densely vegetated area.Keywords Decomposition · Evapotranspiration · Intermittent lake · Phragmites australis · Wetland habitats IntroductionLake Cerknica is an intermittent wetland appearing at the bottom of the Cerknica polje karst depression. It is characterised by extreme inter-annual water level fluctuations, which are the result of a high precipitation rate and water runoff into an extensive underground drainage system in carbonate rocks. The catchment area of the lake extends over 475 km 2 . The majority of the lake's inflow consists of karstic waters (80%), while only one tributary brings surface water (15%). The amount of water in the lake depends on precipitation and potential evapotranspiration of the