This dataset contains root water uptake estimated from soil moisture contents from the 12 macrocosms used in the Jena-Ecotron Experiment in 2012. This experiment was conducted in the Montpellier European Ecotron (CNRS, France) an advanced controlled environment facility for ecosystem research, and aimed at understanding the impact of plant species richness (4 vs. 16 species) for ecosystem carbon and water fluxes.The soil monoliths used in this experiment contained plant communities originating from the long- term Jena Experiment (50°57.1' N, 11°37.5' E, 130 m above sea level; mean annual temperature 9.3°C, mean annual precipitation 587 mm) established in May 2002. Twelve plots from the Jena Experiment were selected for the Jena-Ecotron study according to the following criteria: (1) the four functional groups grasses, legumes, small and tall herbs were present, (2) realized species numbers were close to sown species richness, and (3) plots were equally distributed across the experimental field site to account for different soil textures. Large monoliths (2 m² surface area, diameter of 1.6 m, 2 m depth with a weight of 7 to 8 tons) including intact soil and vegetation were excavated from the twelve plots in December 2011 and placed in lysimeters. In March 2012, before the start of the vegetation growth, the lysimeters were transported and installed in the Macrocosms platform of the Montpellier European Ecotron.A water balance method was used to estimate daily root water uptake profiles and thus daily ecosystem ET from diurnal fluctuation of soil water content measurements (Guderle & Hildebrandt, 2015; doi:10.5194/hess-19-409-2015). The method consists in applying a running regression over multiple time steps on soil water content time series of each measurement depth. Here we used measurements with a temporal resolution of 1 minute from 10 cm, 20 cm, 30 cm and 60 cm depth. We split up the time series by fitting a linear function to each day and night branch of the time series in order to disentangle soil water flow and actual root water uptake. In a prior investigation we found the main transpiration time lasted from 5:30 am to 6:30 pm so that the onset of the day and night branch was fixed to these times. Night time transpiration was low (< 23 % of the day time transpiration) and therefore neglected (Milcu et al. 2016). Subsequently, the root water uptake profile was integrated over the entire soil profile to determine the ET per one m² surface and day. The modelled ET was furthermore multiplied by the factor two in order to upscale the modelled ET to the surface of one lysimeter which is two m².Root water uptake values are provided as absolute values (cm d-1) and as percentage values for the days 25 June 2012, 28 June 2012, 29 June 2012, 17 July 2012 and 18 July 2012 for 10 cm, 20 cm, 30 cm and 60 cm depth. Root water uptake as percentage was calculated as ratio of root water uptake of individual layers to the sum of total root water uptake from 10 cm to 60 cm depths multiplied by 100.

There are two types of missing values contained in datasets from the Jena Experiment. Empty cells represent missing values that result from the design of the experiment. Empty cells result when the respective value does not occur in the design and could thus not be measured. For example, in the case of species-specific biomass cells are left blank, when the species was not sown in the respective plot. Missing values that resulted from methodological problems, sampling errors, or lost samples/data are marked with "-9999".This dataset is part of a collection of measurements of the Jena-Ecotron Experiment, which was part of the Jena Experiment.