An in situ mesocosm experiment was conducted to assess the N contribution from shallow groundwater upwelling to the total crop N uptake budget. Rice was grown in the field in 61 cm x 47 cm x 40 cm rectangular plastic mesocosms. After tillage, the mesocosms were installed by burying them in the soil such that the upper rim was level with the soil surface. Soil was removed to install the mesocosms, and then the soil was replaced by depth within each mesocosm. Mesocosms were seeded at the same time as the rest of the field. Two treatments were replicated four times in an RCBD design at Sites 1 and 2. The treatments receiving shallow groundwater had 3.5 cm diameter holes drilled in the base to remove 23% of the base area and facilitate water movement between the interior and surrounding subsoil. Treatments without holes excluded shallow groundwater . Surface irrigation water was able to move freely across the surface of all mesocosms. Because surface water is moving uniformly across the surface of each mesocosm treatment, there is no net effect of surface irrigation water N on the assessment of groundwater N contribution. Fertilizer P and K were applied to ensure these nutrients were not limiting plant growth; no N fertilizer was applied. Ten cm long Rhizon MOM pore water samplers were installed at 20 cm depth inside each + groundwater and—groundwater treatments, and additionally at 45 cm depth outside the—groundwater treatment to measure pore water NO3-N and NH4-N throughout the growing season. Soil pore water was sampled six times during the growing season when fields were flooded. Pore water samples were collected using evacuated Exetainer vials acidified with 0.25 mL 1.0 M H2SO4 to pH 2.For determining the amount of N mineralized from field residue during the winter fallow season, chicken fodder system residue samples were collected in fall 2011 and again in spring 2012 to quantify the change in N content of residues during this period.

Residue samples were oven dried and prepared for analysis as described earlier for above ground biomass samples. These samples were used to determine pre- and post-decomposition total C and N in the residue. Estimates of winter decomposition of the rice residue were based on 2011 harvest yield data and spring residue sampling in 8 m2 plots with five replicate samples from each site. Spring samples were collected from the experimental site where all field residue was subsequently removed for the 15N-labeled residue experiment. Residue was weighed in the field and sub-samples were taken for analysis. Soils were analyzed for extractable mineral N using a cold 2 M KCl extraction within 48 h of sampling. Mineral N content was determined using colorimetric methods for NO3-N and NH4-N analyzed on a Shimadzu UV-160 spectrophotometer . The remainder of each sample was air-dried and saved for further analysis. Soil pH, total P, and total K were analyzed at the UC Davis DANR lab, and total C and N were analyzed at the UC Davis Stable Isotope Facility. Soils sampled from the 15N-labeled residue experiment at harvest to 30 cm were sent to the UC Davis Stable Isotope Facility for 15N, total N, and total C analysis using an Elementar Vario EL Cube or Micro Cube elemental analyzer interfaced to a PDZ Europa 20–20 isotope ratio mass spectrometer . Water samples were analyzed using the colorimetric method for extractable NO3-N and NH4-N. Plant tissue total C, total N, and atom % 15N analysis was carried out by the UC Davis Stable Isotope Facility using a PDZ Europa ANCA-GSL elemental analyzer interfaced to a PDZ Europa 20–20 isotope ratio mass spectrometer .Total above ground N uptake in the 15N-labeled residue treatment without N fertilizer was 135 kg N ha-1 and 128 kg N ha-1 . The lower N uptake in these plots compared to the N omission plots described previously could be due to increased N immobilization driven by the crop residue treatments in this experiment. Based on final 15N enrichment at harvest, results indicate less than 3% of the rice N uptake was supplied by the prior year’s crop residue: only 1.9 kg N ha-1 and 3.8 kg N ha-1 .

Of the 15N-labeled residue, 50–70% was recovered in the soil, similar to other studies , suggesting it will potentially be available to subsequent crops and subject to other losses . The contribution to N uptake from the 15N-labeled residue in this study is conservative due to losses that occurred during the partial decomposition prior to incorporation, but the value is still in agreement with earlier studies which show limited contribution from residue in the first year following incorporation of the residues. At each site in this study, when no residue was applied, there was no significant difference in total N uptake compared to the total N in the crop when 15N-residue was applied , suggesting immobilization occurs when rice residue is applied. The intensity of immobilization of soil N is controlled by the chemical characteristics of rice crop residues, and by an increase in soil microbial biomass stimulated by the addition of fresh, labile residue-C. These observations are relevant for N availability during the growing season, even as N immobilization in flooded soils is lower compared to aerobic soils due to reduced microbial activity. The high level of indigenous N supply as shown by the high crop N uptake in the no-residue treatment and the apparent immobilization of 15N-residue supports the conclusion that residue N only contributes a minor amount to the subsequent rice crop. However, considering the cumulative effect of incorporating residues over multiple growing seasons has been found to supply close to20 kg N ha-1 to the crop. Site 1 had higher crop N uptake than Site 2 across all treatments , possibly due to an additional wet-dry cycle that stimulated residue mineralization early in the season at this site .Surface water samples collected during the growing season had levels 0.7 mg L-1 NH4-N and 0.3 mg L-1 NO3-N at all sampling times, making irrigation water a negligible source of N for the crop . The low N concentrations in the surface water also suggest that the N attributed to shallow groundwater was not from surface water that percolated into the subsurface. Using the inlet surface water N concentrations multiplied by ETa , it was estimated that irrigation water contributed 2.9 kg N ha-1 and 3.0 kg N ha-1 . In contrast, shallow groundwater provided 40–60 kg N ha-1 toward total plant N uptake.

Total above ground N uptake in the + groundwater treatment was 122 to 188 kg N ha-1 which was significantly higher than in the—groundwater treatment which was 83 to 127 kg N ha-1. This finding was unexpected and shows that upward movement of previously mineralized N in the shallow groundwater may contribute a substantial amount to total crop N demands in this system. Pore water samples from inside the mesocosms yielded low N concentrations throughout the season ,fodder systems for cattle reflecting active and continual crop uptake. The natural abundance 15N signature of the rice plants suggests that the primary source of N was the same in the presence or absence of shallow groundwater: 0.3685 atom % 15N for both treatments at Site 1, and 0.3683–0.3685 atom % 15N in+ groundwater and—groundwater treatments at Site 2. This indicates a 0.0024–0.0026 atom % 15N enrichment relative to urea , suggesting that N from below 40 cm is likely the result of SOM mineralization. Additionally, samples of groundwater from deeper wells at each site showed high levels of NH4-N up to 18.8 mg L-1 as deep as 5.2 m, and no detectable NO3-N . Because there was no accumulation of NO3-N at depth and because this system is characterized by alternating aerobic and anaerobic conditions, leaching is not evidenced and residual fertilizer from previous years was most likely denitrified and lost from the system. It is therefore reasonable to attribute these subsurface N sources to SOM mineralization.Based on field residue samples collected in fall 2011 and spring 2012, the crop residue remaining at each site prior to spring tillage indicates that approximately 45% of the residue biomass decomposed during the fallow season . Similar values are reported elsewhere for the same residue management practices in California. Accounting for this rate of decomposition is important because it represents rapid C losses and reduces the annual net C balance compared to the total residue biomass input at harvest. Accounting for fallow season decomposition was also the impetus for the partial decomposition of the 15N-labeled residue prior to incorporation in the spring, bringing the C:N ratios of the two materials into close approximation . Losses of C from residues during the fallow season exceeded N mineralization from the residue over the same period, where only an estimated 16.9 to 21.0 kg N ha-1 mineralized . Soil samples from late spring immediately prior to flooding the fields showed NO3-N accumulation of 20.3 to 42.1 kg N ha-1 , a pool of N that for the purposes of this model we assumed was denitrified and lost following flooding. The lower soil NO3-N observed at Site 1 is likely due to an additional early season irrigation flush at this site which may have caused additional N losses. Denitrification and NH3 volatilization are the primary loss mechanisms, and leaching is generally minimal in rice systems.

The fallow season N losses not accounted for in this model result in a lower estimate of winter SOM-N mineralization and consequently decrease the final soil C loss estimate. However, these possible uncertainties are minor as the vast majority of SOM-N mineralization occurred during the growing season .Total annual SOM-N mineralization, the sum of growing and fallow season mineralization, was 302 kg N ha-1 and 279 kg N ha-1 . Based on the C:N ratio of the soil and the total annual N mineralization, the total annual mass of soil C mineralized was 4345 kg C ha-1 and 4136 kg C ha-1 . Accounting for the annual C input from crop residue following fallow season decomposition, the net C loss was 2473 kg C ha-1 and 2241 kg C ha-1 when NUE is assumed at 50% . Soil C loss from this rice system is lower than reported values for other agricultural peat land systems in temperate regions which ranged from 3700–8600 kg C ha-1 yr-1 . Similarly, modeled soil C losses from neighboring islands in the Delta where upland crops are grown ranged from 5000 to 15000 kg C ha-1 yr-1. The lower soil C losses estimated in this study are likely due to the seasonal flooding of the rice fields which reduces SOM oxidation in the system relative to conventional upland crops or pasture. Lower values of NUE correspond to higher rates of soil C loss because an assumption of lower N uptake implies more N, and thus SOM, was mineralized relative to plant N uptake. In general, fertilizer NUE ranges between 30 to 70% in rice systems. In this study, we are considering a range of NUE slightly higher, from 50% to 70% because no accumulation of N was observed in the soil-water system during the growing season based on pore water and soil sampling , suggesting mineralization was fairly synchronized with plant uptake. Also increases in NUE yield marginally smaller reductions in soil C loss, and standard errors are greatly diminished at 50% NUE and above, meaning that within this range the final net soil C loss estimate is less sensitive to the NUE assumption . There is reason to believe the NUE in this N fertilizer omission system is above the 50% threshold, as well-managed rice systems in California have reported NUE above 70%. Considering the effect of our NUE assumption on estimated soil C loss, the probable range of 50–70% NUE would give a range of estimated net soil C loss from 1246–2473kg C ha-1 yr-1 and 1149–2241 kg C ha-1 yr-1 . Using the calculated range of net soil C loss from this study, it is possible to estimate the corresponding soil subsidence under rice production at this site. Because of the limited resolution of soil bulk density measurements in this study, the correlation between soil C loss and subsidence is dependent on an assumption about the fraction of subsidence due directly to C loss versus the effects of compaction and consolidation of the remaining mineral soil material.