We investigated how the co-presence of macrophytes and macroinvertebrates in organic substrates lowers methane emissions and nutrient transport, due to radial oxygen loss and bioirrigation. Laboratory incubations were performed to measure ebullitive methane fluxes and dissolved gas and nutrient fluxes from sediments in presence of macrophytes and macrofauna.

The experiment was carried out in the laboratory, under controlled conditions. Sediment, macrophytes and macroinvertebrates were collected in the field and then transported to the laboratory. Sieved sediment was transferred to 24 microcosms: 12 were used for ebullition measurements and 12 underwent batch incubations for dissolved gas and nutrient fluxes measurement. Four treatments (with 6 replicates) were tested: bare sediment (S), sediment with oligochaetes (SO), sediment with macrophytes (SV) and sediment with oligochaetes and macrophytes (SOV). 

Half of the microcosms (n = 12, 4 treatments x 3 replicates) was provided with an underwater system to collect the gas bubbles released from the sediments, which consisted in an 8 cm i.d. inverted transparent glass funnel maintained vertically 30 cm above the microcosms surface by a glass stick; the far end of the funnel fitted a 40-ml glass vial filled with water. At time intervals varying between 1-2 days the 12 vials were removed from the funnels, maintained upside-down and closed underwater and with lids provided with a rubber septum, weighed and replaced with new ones. All vials were previously filled with water, closed with lids and weighed.

The second set of microcosms (n = 12) underwent light and dark batch incubations on days 1, 5 and 10 for flux measurements at water-sediment interface. Incubations were carried out according to the international standard protocol reported in Dalsgaard et al. (2000). Shortly before the incubation microcosms were included into plexiglass liners (i.d. 8 cm, height 30 cm) equipped with a stirring unit. The incubations started when all liners were capped with gas-tight lids and lasted two hours to keep O₂ concentration within ±20% of the initial value. Water samples were collected at the beginning and at the end of the incubation from each liner.

Data are reported in .txt and include methane ebullitive rates and dissolved gas and nutrient fluxes in the four tested treatments during a 12-day experiment. There are no missing values and ebullitive methane fluxes are expressed in mmol CH₄ m^-2h^-1, whereas fluxes of dissolved gas and nutrients are expressed in mmol m^-2d^-1.