Long-term Liming Experiment Research Articles

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2− reductase) in SoilA suggest that low NO2− concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2− in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2− accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

Long-term liming improves soil fertility and soybean root growth, reflecting improvements in leaf gas exchange and grain yield

Soil acidity is one of the major drivers of yield-limited crop productivity, particularly when combined with dry spells during crop development. Liming is a widely used strategy for alleviating the negative effects of soil acidity, ensuring greater crop root development to assist the plant in periods of low water availability, promoting full photosynthetic activity and, consequently, increasing crop yield. Here, we investigated the long-term effects of surface liming on soil chemical properties as well as soybean root growth, nutrition, photosynthetic parameters and grain yield during three growing seasons (2016–2019) in a region prone to dry spells. The long-term liming experiment was established in 2002. We evaluated the long-term effects of four surface lime rates: control, soil not treated with lime; ½ RLR, soil treated with half the recommended lime rate; 1 RLR, soil treated with the full recommended lime rate; and 2 RLR, soil treated with twice the recommended lime rate. The last lime application occurred in 2016. Our results revealed that increasing lime rates applied to soil surface up to 2 RLR increased soil fertility and root growth, besides to enhance the root distribution along soil profile. These changes contributed to boost soybean leaf photosynthetic pigments and gas exchange, leading to better growth, nutrition and grain yields, despite periods of dry spells. Our results suggested that in tropical agricultural systems with intensive cultivation throughout the agricultural year, higher lime rates can be applied without nutritional imbalances in the soil and plants. Our study provided important clues on how long-term liming changes soil fertility and triggers the cascading effects in improving root growth and distribution, as well as soybean photosynthetic metabolism and yield.

Modelling long-term impacts of fertilization and liming on soil acidification at Rothamsted experimental station

Liming is widely used to reduce the impacts of soil acidification and optimize soil pH for agricultural production. Whether models can simulate the effect of liming on soil pH, and base saturation (BS), and thereby guide lime application, is still largely unknown. Long-term experimental data from a grassland (Park Grass, 1965–2012) and arable land (Sawyers Field, 1962–1972) at Rothamsted Research, UK, were thus used to assess the ability of the VSD+ model to simulate the effects of long-term fertilization and liming on soil acidification. The VSD+ model was capable of simulating observed soil pH and BS changes over time in the long-term liming experiments, except for a treatment in which sulphur (S) was added. Normalized Mean Absolute Errors (NMAE) and Normalized Root Mean Square Errors (NRMSE) of simulated and observed pH values, averaged over the observation periods varied between 0.02 and 0.08 (NMAE) and 0.01–0.05 (NRMSE). The acidity budget results for Park Grass suggest that nitrogen (N) transformations contributed most to acidity production, causing predominantly aluminium (Al) exchange in the topsoil (0–23 cm) followed by base cation (BC) release, but in the treatment with S addition, BC uptake had a nearly similar effect on acidity production. However, in Sawyers Field, the acidity budget suggested that BC uptake was the dominant cause of soil acidification, while the impacts of N transformations were limited. Liming was found to sufficiently replenish BC and decrease Al exchange in the topsoil layer. Overall, the VSD+ model can adequately reconstruct the impacts of fertilizer and liming applications on acid neutralizing processes and related soil pH and BC changes at the soil exchange complex.

Yield responses of arable crops to liming - An evaluation of relationships between yields and soil pH from a long-term liming experiment.

The management of optimal soil pH is fundamental to sustainable crop production. Understanding the lime requirement for arable crops has developed gradually over the last several decades. The aim of this study was to examine the yield-pH relationship for a range of arable crops to understand their response to liming, based on the Long-Term Liming experiments established in 1962 at Rothamsted Research, UK. The main treatments of four different rates of lime and, therefore, four distinctly different soil pH levels were maintained for 35 years at two sites (Rothamsted and Woburn). The pH ranged from 4.4 to 8.0. The lime response was tested on the following crops: spring barley, spring oats, spring beans, spring lupins, winter lupins, potatoes, linseed, winter oilseed rape, winter triticale and winter wheat. Relative yield (RY) was used for non-linear regression analysis to detect site, year and phosphorus (P) fertiliser effects on the relationship with pH. Liming had a highly significant positive effect on soil pH, but overall there was no consistent increase or decrease in soil extractable P (Olsen) or exchangeable K. There were significant site effects detected for RY for most crops which reflect differences in the two soil types. Spring oats and potatoes had very weak responses to lime within the pH range tested. For spring barley, winter triticale, winter wheat and winter oilseed rape significant effects of P fertiliser on the yield-pH relationship were found, although the nature of effects differed between crops and sites. Findings from the Long-Term Liming experiment are invaluable in improving the fundamental understanding on the yield-pH relationship for important arable crops and this has significant implications on selecting crops for rotations. The pH at 90% RY was calculated for selected crops and the beneficial effect of fertiliser P was detected in significantly reducing the critical pH value.

Nitrite kinetics during anoxia: The role of abiotic reactions versus microbial reduction

Anoxic spells in soil induce denitrification, i.e. the sequential reduction NO3−→NO2−→NO→N2O→N2, catalysed by the four enzymes NAR, NIR, NOR and NOS, respectively. Transient accumulation of all intermediates is inevitable, but the concentrations depend on the regulation of gene expression and the physical/chemical properties of the soil. Nitrite is chemically unstable at low pH, decomposing via a conglomerate of abiotic reactions with metals and organic compounds which can result in production of NO, N2O, N2 and nitrosated organic compounds (R-NO). There is evidence that acidic soils accumulate less nitrite than neutral soils, but it is unclear if this is due to high abiotic decomposition rate (VADEC) or fast enzymatic reduction of nitrite (VNIR) at low pH. To investigate this, we monitored the kinetics of NO2−, NO, N2O and N2 during anoxic incubations of three organic soils with pHCaCl2 ranging from 3.4 to 7.2, taken from a long-term liming experiment. In parallel, we determined the rate of abiotic nitrite decay (VADEC) and its product stoichiometry (NO, N2O and R-NO) in gamma-irradiated soils. VADEC was clearly first-order with respect to HNO2 (kHNO2 = 1.4 h−1), N-gas production (NO, N2O and N2) accounted for only ∼50% of VADEC, the rest was ascribed to nitrosation (R-NO). During denitrification (live soil incubation), the nitrite concentrations reached 2–3 mM in the soils with pH 4.9 and 7.2, while the soil with pH 3.4 kept nitrite concentrations at 20–50 μM, except for a short spike reaching 160 μM after 40 h. Estimated rates of nitrite scavenging by the two competing sinks (NIR and ADEC) showed that NIR was the strongst nitrite sink in soil with pH 3.4 (VNIR > VADEC), while VNIR ≈ VADEC in the soil with pH 5.9. In the soil with pH 7.2, VADEC was insignificant. Thus, the regulation of denitrification (high VNIR relative to VNAR) played a crucial role in determining nitrite kinetics, hence the fate of nitrite in acid soils. High nitrite reductase activity effectively minimized abiotic nitrite decomposition and nitrosation of soil organic matter. The results shed light on regulation of denitrification in acid soils, and its implications for the fate of nitrogen during denitrification events.

Emissions of nitrous oxide (N2O) affected by pH-related nitrite accumulation during nitrification of N fertilizers

The potential of nitrogen (N) fertilizer forms to mitigate N2O emissions from agricultural fields is not very well understood. It is known that both reduced and oxidized N forms can be beneficial, depending on site-specific edaphic and climatic conditions. In the present study four laboratory incubation experiments were conducted under conditions that should minimize denitrification to investigate N2O emissions during the nitrification of solid N fertilizers.It was found that on two loamy sand soils with pH values slightly above pH5, urea caused 2.7–3.8 fold higher cumulative N2O emissions than ammonium sulphate (AS). N2O emission rates from urea were accompanied by elevated soil nitrite levels, while those of AS were not. The direct addition of a NaNO2 solution revealed an exponential relationship between soil nitrite levels and cumulative N2O emissions, indicating that soil nitrite induces N2O emissions, probably by nitrite reduction via nitrifier denitrification. When the soil pH was increased to 6.3 (soil from a long-term liming experiment) nitrite accumulation during nitrification was observed for both N forms. Cumulative N2O emissions did not differ between N forms on the latter soil, but N2O emission kinetics were faster for urea. Cumulative N2O emissions from AS at soil pH6.3 were significantly higher than those of AS at pH values around 5.It was concluded that i) nitrite accumulation during nitrification of reduced N fertilizer forms can significantly contribute to N2O emissions under non-denitrifying conditions, ii) the risk of nitrite accumulation increases with higher soil pH values, and iii) that the alkalizing hydrolysis of urea increases the risk of nitrite accumulation and thus higher N2O emissions as well. This mechanism would explain why urea causes higher N2O emissions than fertilizers in the form of ammonium salts.

Effects of liming and selected heavy metals on ammonium release in waterlogged agricultural soils

Many farmlands are periodically flooded or ponded by excessive precipitation resulting in changes to soil chemical and biochemical properties. In this study, one set (eight treatments with four replications) of field-moist surface soils (0–15 cm) and their air-dried counterparts obtained from a long-term liming experiment were incubated at 30 °C under waterlogged conditions for 10 days, and the amounts of net NH4+-N released (soluble and exchangeable) were determined after extraction with 4 M KCl. Another set of three surface soils were used to evaluate the effect of six heavy metals on the NH4+-N release under waterlogged conditions. Results showed that increasing the liming rate from 0 to 17,930 kg ha−1 effective calcium carbonate equivalent increased the average soil pH from 4.98 to 7.06, averages of the amounts of NH4+-N released ranged from 1.6 to 5.2 mg N kg−1 field-moist soil, and the corresponding amounts released in air-dried soils ranged from 18.9 to 32.9 mg N kg−1 soil. This increase of the amount NH4+-N released in air-dried soil samples is presumably due to a slaking effect. At 5 mmol kg−1 soil, all six heavy metals inhibited the NH4+-N released. The relative effectiveness of the heavy metals in inhibition of the NH4+-N released varied among the three soils. Lead(II) was the most effective inhibitor of NH4+-N release in Clarion and Harps soils and Cd(II) in Harps soil. Cobalt(II), Cu(II), and Cd(II) were the least effective inhibitors of NH4+-N release in Clarion, Harps, and Okoboji soils, respectively.

Impaired reduction of N2O to N2 in acid soils is due to a posttranscriptional interference with the expression of nosZ.

ABSTRACTAccumulating empirical evidence over the last 60 years has shown that the reduction of N2O to N2 is impaired by low soil pH, suggesting that liming of acid soils may reduce N2O emissions. This option has not gained much momentum in global change research, however, possibly due to limited understanding of why low pH interferes with N2O reductase. We hypothesized that the reason is that denitrifying organisms in soils are unable to assemble functional N2O reductase (N2OR) at low pH, as shown to be the case for the model strain Paracoccus denitrificans. We tested this by experiments with bacteria extracted from soils by density gradient centrifugation. The soils were sampled from a long-term liming experiment (soil pH 4.0, 6.1, and 8.0). The cells were incubated (stirred batches, He atmosphere) at pH levels ranging from 5.7 to 7.6, while gas kinetics (NO, N2O, and N2) and abundances of relevant denitrification genes (nirS, nirK, and nosZ) and their transcripts were monitored. Cells from the most acidic soil (pH 4.0) were unable to reduce N2O at any pH. These results warrant a closer inspection of denitrification communities of very acidic soils. Cells from the neutral soils were unable to produce functional N2OR at pH values of ≤6.1, despite significant transcription of the nosZ gene. The N2OR expressed successfully at pH 7.0, however, was functional over the entire pH range tested (5.7 to 7.6). These observations lend strong support to our hypothesis: low soil pH diminishes/prevents reduction of N2O, primarily by precluding a successful assembly of functional N2O reductase.

Changes in the content and composition of humus in the sandy loamy soddy-podzolic soil in a long-term liming experiment

The effect of liming on organic matter in sandy loamy soddy-podzolic soil was studied. The study was performed on samples taken from the 50-year-long experiment established by Prof. Kornilov in 1957. It was shown that liming had almost no effect on the total humus content in the soil. The humus composition was studied using two fractionation methods of the humus substances by the Ponomareva-Plotnikova procedure. The regrouping of the humus fractions occurred due to the changes in the mobility of soil mineral components, which involved a regular increase in the content of the Ca-bound fraction of humic acids (HA-2) at the expense of the HA-1 fraction bound to the mobile forms of R2O3 reliable at the lime rates equivalent to the total acidity and higher. The levels of the stabilization of the different HA fractions were considered, as well as the stability of the changes in the humus composition during 50 years.

Soil bacterial and fungal communities across a pH gradient in an arable soil

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

The N 2O product ratio of nitrification and its dependence on long-term changes in soil pH

The contribution of nitrification to the emission of nitrous oxide (N 2O) from soils may be large, but its regulation is not well understood. The soil pH appears to play a central role for controlling N 2O emissions from soil, partly by affecting the N 2O product ratios of both denitrification (N 2O/(N 2+N 2O)) and nitrification (N 2O/(NO 2 −+NO 3 −). Mechanisms responsible for apparently high N 2O product ratios of nitrification in acid soils are uncertain. We have investigated the pH regulation of the N 2O product ratio of nitrification in a series of experiments with slurries of soils from long-term liming experiments, spanning a pH range from 4.1 to 7.8. 15N labelled nitrate (NO 3 −) was added to assess nitrification rates by pool dilution and to distinguish between N 2O from NO 3 − reduction and NH 3 oxidation. Sterilized soil slurries were used to determine the rates of chemodenitrification (i.e. the production of nitric oxide (NO) and N 2O from the chemical decomposition of nitrite (NO 2 −)) as a function of NO 2 − concentrations. Additions of NO 2 − to aerobic soil slurries (with 15N labelled NO 3 − added) were used to assess its potential for inducing denitrification at aerobic conditions. For soils with pH⩾5, we found that the N 2O product ratios for nitrification were low (0.2–0.9‰) and comparable to values found in pure cultures of ammonia-oxidizing bacteria. In mineral soils we found only a minor increase in the N 2O product ratio with increasing soil pH, but the effect was so weak that it justifies a constant N 2O product ratio of nitrification for N 2O emission models. For the soils with pH 4.1 and 4.2, the apparent N 2O product ratio of nitrification was 2 orders of magnitude higher than above pH 5 (76‰ and 14‰). This could partly be accounted for by the rates of chemodenitrification of NO 2 −. We further found convincing evidence for NO 2 −-induction of aerobic denitrification in acid soils. The study underlines the role of NO 2 −, both for regulating denitrification and for the apparent nitrifier-derived N 2O emission.

Experiences with liming in European countries - results of long-term experiments

Liming was and still is carried out in many European forests since the beginning of the 1980s. Main objectives of compensation liming is to neutralize actual acidic deposition in order to prevent further soil acidification, to increase base saturation and acid buffering capacity of the soil. This paper evaluates results from long-term liming experiments throughout Europe using different amounts and forms of liming materials. Differences in forest ecosystem reaction to liming can be caused by amount, form and frequency of the application, and by the solubility, reaction kinetics, contents and composition of the material used. Furthermore, other factors like climate, site history, management, environmental conditions (e.g. actual and historical deposition rates), humus form, C/N ratio, nitrogen stores, and the soil chemical properties (e.g. pH, base saturation, CEC) may strongly influence the effects of liming treatments. Element budgets of forested ecosystems on a plot or watershed scale provide a very useful tool to integrate the various effects of additional Mg inputs via liming/fertilization.

Biomass carbon measurements and substrate utilization patterns of microbial populations from soils amended with cadmium, copper, or zinc

Samples of a sandy loam soil taken from a long-term liming experiment in southeast England were amended with solutions of metal sulfate salts. Soils with a range of pHs were amended to contain Cu, Cd, or Zn at concentrations around the maximum permissible values for these metals in agricultural land receiving sewage sludge. After a 3-year equilibration period, the microbial biomass was determined by the fumigation-extraction technique. These results were compared with data from substrate utilization patterns of microbial populations extracted by using a weak salt solution. There was no reduction in microbial biomass due to pH or metal treatment in any of the soils except the Cu treatment. Principal-component analysis of the respiration patterns in Biolog plates demonstrated effects of both pH and metal treatment on the extracted microbial population which were independent of gross biomass size. pH and soil amendments with Cu and Zn were found to reduce the metabolic potential of the extracted soil microbial population.

Liming and re-liming needs of acidic soils used for crop - pasture rotations

Summary. In a long-term liming experiment in north-eastern Victoria, we have re-applied lime and applied gypsum (1992 season) to assess wheat grain yield responses with on-going changes in soil pH and extractable aluminium. An acid-sensitive wheat (cv. Oxley) was grown in 2 seasons (1992–93), 12 years after initial applications of lime. Where lime (2.5 t/ha) was applied in 1992 to a previously unlimed soil, grain yield was increased by 19 and 46% respectively in the 2 seasons. However, the yield from these newly limed plots was well below the yields obtained from plots limed in 1980. Re-liming plots limed in 1980 resulted in further yield increases, with lime re-applied at 2.5 t/ha increasing yields by 12% in both seasons. Gypsum decreased grain yields on unlimed soil in the year of application but in the second year gave increases in yield. Whilst pH had changed little in the unlimed soil over the 12 years, the concentrations of extractable aluminium in the root zone increased substantially such that these concentrations far exceed levels which may affect acid-sensitive wheats. Liming at 2.5 t/ha did reduce the aluminium at 0–10 cm depth, but the concentrations at 10–20 cm depth (11.7 mg/kg) are likely to restrict grain yield. The data illustrate the progressive nature of soil acidification and the risk to wheat productivity through delaying treating this soil degradation problem.

Boron retention in limed forest mor

Boron (B) retention was studied in the mor humus of podzolic soil from boreal Norway spruce (Picea abies (L.) Karst.) forests. In a long-term liming experiment, ground limestone had been applied 30 years earlier and again 12 years before sampling. Additionally a short-term field experiment was done to separate the effect of increased pH from calcium (Ca) addition. In the short-term experiment the treatments were control and two doses of CaCO 3, CaSO 4 and sodium + potassium (Na + K) carbonate mixture. These treatments were applied in the year before sampling. The B retention data conformed to a Freundlich model better than to a Langmuir model. Considerable B adsorption occurred, probably mostly due to the large organic matter content of mor. Liming significantly increased the quantity of adsorbed B in both experiments. Incubation with added B for 8 weeks considerably increased B retention and reduced the difference between limed and unlimed soil. CaSO 4 had no effect on B retention characteristics, whereas Na + K treatment caused changes similar to those of lime. Therefore Ca probably has little influence on B adsorption in this pH range (3.0–5.9).

Changes in soil pH and exchangeable calcium in two liming experiments on contrasting soils over 12 years

SummarySoils were analysed from two long-term liming experiments on a sandy-clay loam at Rothamsted and a loamy sand at Woburn. Plots given four levels of limestone factorially combined with phosphate and potassium fertilizers (with magnesium subplots in 1974) were cropped with beans, barley, potatoes and oats from 1963 to 1974.The smallest limestone applications (5 t CaCO3/ha) increased soil pH the following year to values predicted by lime-requirement determinations using a standard advisory method. The larger limestone applications (10 and 20 t/ha) increased pH proportionally less. Soil pH decreased after the first year with 5 t/ha in both experiments but increased at the 20 t/ha rate for 6 years in the sandy-clay loam and for 3 years in the loamy sand before starting to decline.Exchangeable calcium (soluble in N ammonium acetate) decreased at approximately linear rates in all plots of both experiments from the first year. Slopes of the regressions were smaller at low than at higher rates of liming, depending primarily on the average pH. Rates of CaCO3 losses from the surface 23 cm of soil ranged from 225 to 823 kg/ha per year at Rothamsted and from 307 to 852 kg/ha per year at Woburn.Observed rates of Ca loss were compared with an empirical relationship suggested by Gasser (1973) between annual Ca losses and soil pH under average rainfall conditions and estimates based on a model system.

Liming effects on the response of potatoes and oats to phosphorus, potassium and magnesium fertilizers

SummaryIn two long-term liming experiments on a sandy-clay loam at Rothamsted and a loamy sand at Woburn the responses of potatoes in 1974 and oats in 1975 to cumulative dressings of superphosphate and potassium chloride applied since 1962 and magnesium sulphate applied in 1974 were measured at four pH levels within the range pH 4–pH 7.Yields of both crops were similar over the whole pH range when standard rates of NPKMg fertilizers were given. Without added P and Mg, yields of potatoes were much smaller on the more acid soils, but without K, yields were larger. A similar pattern of yield responses to P and Mg fertilizers occurred with oats but there were no differences between the small responses to K additions over the whole pH range.Analyses of potato leaves sampled at the 10% flowering stage showed differences related to the yield effects for K and Mg but not for P. Yield responses were associated with concentrations less than 4% K and 0·18% Mg in the dry matter of topmost fully mature leaves.The differences in yield response caused by liming were not associated with differences in ‘available’ nutrients in the soils (determined using standard methods).