In the field and pot experiments, we measured CH4 emissions at 7-day intervals by the static closed-chamber method (27). We measured CH4 emissions from 1 or 2 weeks after rice transplanting to harvest. On each sampling day, we collected four gas samples at 5- or 10-min intervals for each plot or pot. Gas samples were taken between 9:00 and 11:00 a.m. The CH4 concentrations were determined by a gas chromatograph (Agilent 7890A, USA). Emission rates of CH4 (F) were calculated as followsEmbedded Imagewhere ΔCT is the change in CH4 concentration (mg liter−1 hour−1) in the chamber determined by linear regression, V is the volume of the chamber (liter), and A is the enclosed surface area (m2). For our flux rate estimates, we only accepted measurements for which r2 > 0.90; less than 5% of the measurements were discarded.

In the incubation experiment, we measured CH4 emissions at 3-day intervals. We put the beakers into 500-ml jars and sealed the jars. We collected 10 ml of gas from the jar at 0 and 24 hours after sealing the jar. Emission rates of CH4 (F) were calculated as followsEmbedded Imagewhere ΔCT is the change in CH4 concentration (μg liter−1 hour−1) in the jar, V is the volume of the jar (liter), and S is the soil weight (g).

In the field experiment, we measured the abundances of methanogens and methanotrophs of air-dried soils after 12 years of straw incorporation. In the pot experiment, we collected fresh soil samples from the root bags 4 weeks after rice transplanting, when CH4 emissions were relatively high and significantly different among treatments, and 9 weeks after rice transplanting at the end of the experiment. We used the Power Soil DNA Isolation kit (MoBio, USA) to extract soil DNA from 0.25 g of soil. The copy numbers of mcrA and pmoA genes represent the abundances of methanogens and methanotrophs, respectively, and were quantified using quantitative real-time polymerase chain reaction (PCR). We used the primer pairs mcrAf/mcrAr and A189f/A682r to quantify the mcrA and pmoA genes, respectively (33, 34). We performed the quantitative real-time PCR in CFX96 (Bio-Rad, USA).

In the field experiment, rice yield was measured at maturity stage, and aboveground biomass was calculated by rice yield and harvest index. In the pot experiment, we harvested plants and measured aboveground biomass and root biomass 9 weeks after rice transplanting. Rice plants were oven-dried at 70°C to achieve a constant weight.

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