Effect of Soil pH Increase by Biochar on NO,N2O and N2 Production during Denitrification in Acid Soils

Biochar (BC) application to soil suppresses emission of nitrous- (N₂O) and nitric oxide (NO), but the mechanisms are unclear. One of the most prominent features of BC is its alkalizing effect in soils, which may affect denitrification and its product stoichiometry directly or indirectly. We conducted laboratory experiments with anoxic slurries of acid Acrisols from Indonesia and Zambia and two contrasting BCs produced locally from rice husk and cacao shell. Dose-dependent responses of denitrification and gaseous products (NO, N₂O and N₂) were assessed by high-resolution gas kinetics and related to the alkalizing effect of the BCs. To delineate the pH effect from other BC effects, we removed part of the alkalinity by leaching the BCs with water and acid prior to incubation. Uncharred cacao shell and sodium hydroxide (NaOH) were also included in the study. The untreated BCs suppressed N₂O and NO and increased N₂ production during denitrification, irrespective of the effect on denitrification rate. The extent of N₂O and NO suppression was dose-dependent and increased with the alkalizing effect of the two BC types, which was strongest for cacao shell BC. Acid leaching of BC, which decreased its alkalizing effect, reduced or eliminated the ability of BC to suppress N₂O and NO net production. Just like untreated BCs, NaOH reduced net production of N₂O and NO while increasing that of N₂. This confirms the importance of altered soil pH for denitrification product stoichiometry. Addition of uncharred cacao shell stimulated denitrification strongly due to availability of labile carbon but only minor effects on the product stoichiometry of denitrification were found, in accordance with its modest effect on soil pH. Our study indicates that stimulation of denitrification was mainly due to increases in labile carbon whereas change in product stoichiometry was mainly due to a change in soil pH.     

Contributions of Autotrophic and Heterotrophic Nitrifiers to Soil NO and N2O Emissions

Soil emission of gaseous N oxides during nitrification of ammonium represents loss of an available plant nutrient and has an important impact on the chemistry of the atmosphere. We used selective inhibitors and a glucose amendment in a factorial design to determine the relative contributions of autotrophic ammonium oxidizers, autotrophic nitrite oxidizers, and heterotrophic nitrifiers to nitric oxide (NO) and nitrous oxide (N₂O) emissions from aerobically incubated soil following the addition of 160 mg of N as ammonium sulfate kg⁻¹. Without added C, peak NO emissions of 4 μg of N kg⁻¹ h⁻¹ were increased to 15 μg of N kg⁻¹ h⁻¹ by the addition of sodium chlorate, a nitrite oxidation inhibitor, but were reduced to 0.01 μg of N kg⁻¹ h⁻¹ in the presence of nitrapyrin [2-chloro-6-(trichloromethyl)-pyridine], an inhibitor of autotrophic ammonium oxidation. Carbon-amended soils had somewhat higher NO emission rates from these three treatments (6, 18, and 0.1 μg of N kg⁻¹ h⁻¹ after treatment with glucose, sodium chlorate, or nitrapyrin, respectively) until the glucose was exhausted but lower rates during the remainder of the incubation. Nitrous oxide emission levels exhibited trends similar to those observed for NO but were about 20 times lower. Periodic soil chemical analyses showed no increase in the nitrate concentration of soil treated with sodium chlorate until after the period of peak NO and N₂O emissions; the nitrate concentration of soil treated with nitrapyrin remained unchanged throughout the incubation. These results suggest that chemoautotrophic ammonium-oxidizing bacteria are the predominant source of NO and N₂O produced during nitrification in soil.     

Contributions of Autotrophic and Heterotrophic Nitrifiers to Soil NO and N(2)O Emissions

Soil emission of gaseous N oxides during nitrification of ammonium represents loss of an available plant nutrient and has an important impact on the chemistry of the atmosphere. We used selective inhibitors and a glucose amendment in a factorial design to determine the relative contributions of autotrophic ammonium oxidizers, autotrophic nitrite oxidizers, and heterotrophic nitrifiers to nitric oxide (NO) and nitrous oxide (N(2)O) emissions from aerobically incubated soil following the addition of 160 mg of N as ammonium sulfate kg. Without added C, peak NO emissions of 4 mug of N kg h were increased to 15 mug of N kg h by the addition of sodium chlorate, a nitrite oxidation inhibitor, but were reduced to 0.01 mug of N kg h in the presence of nitrapyrin [2-chloro-6-(trichloromethyl)-pyridine], an inhibitor of autotrophic ammonium oxidation. Carbon-amended soils had somewhat higher NO emission rates from these three treatments (6, 18, and 0.1 mug of N kg h after treatment with glucose, sodium chlorate, or nitrapyrin, respectively) until the glucose was exhausted but lower rates during the remainder of the incubation. Nitrous oxide emission levels exhibited trends similar to those observed for NO but were about 20 times lower. Periodic soil chemical analyses showed no increase in the nitrate concentration of soil treated with sodium chlorate until after the period of peak NO and N(2)O emissions; the nitrate concentration of soil treated with nitrapyrin remained unchanged throughout the incubation. These results suggest that chemoautotrophic ammonium-oxidizing bacteria are the predominant source of NO and N(2)O produced during nitrification in soil.     

Effects of Biochar Addition on CO2 and N2O Emissions following Fertilizer Application to a Cultivated Grassland Soil

Carbon (C) sequestration potential of biochar should be considered together with emission of greenhouse gases when applied to soils. In this study, we investigated CO₂ and N₂O emissions following the application of rice husk biochars to cultivated grassland soils and related gas emissions tos oil C and nitrogen (N) dynamics. Treatments included biochar addition (CHAR, NO CHAR) and amendment (COMPOST, UREA, NO FERT). The biochar application rate was 0.3% by weight. The temporal pattern of CO₂ emissions differed according to biochar addition and amendments. CO₂ emissions from the COMPOST soils were significantly higher than those from the UREA and NO FERT soils and less CO₂ emission was observed when biochar and compost were applied together during the summer. Overall N₂O emission was significantly influenced by the interaction between biochar and amendments. In UREA soil, biochar addition increased N₂O emission by 49% compared to the control, while in the COMPOST and NO FERT soils, biochar did not have an effect on N₂O emission. Two possible mechanisms were proposed to explain the higher N₂O emissions upon biochar addition to UREA soil than other soils. Labile C in the biochar may have stimulated microbial N mineralization in the C-limited soil used in our study, resulting in an increase in N₂O emission. Biochar may also have provided the soil with the ability to retain mineral N, leading to increased N₂O emission. The overall results imply that biochar addition can increase C sequestration when applied together with compost, and might stimulate N₂O emission when applied to soil amended with urea.     

Dynamics of Soil Denitrifier Populations: Relationships between Enzyme Activity, Most-Probable-Number Counts, and Actual N Gas Loss

To better understand temporal variability in soil denitrification, denitrifying enzyme activity (DEA) and denitrifier populations (as determined by most-probable-number [MPN] counts) were measured in field and laboratory experiments. Measurements of DEA and MPN provided highly contradictory indications of denitrifier dynamics. In laboratory incubations, under conditions favoring active denitrification, the synthesis of new denitrifying enzymes and the actual amount of denitrification were closely related. In other experiments, however, both DEA and MPN counts were poor indicators of actual denitrification. In some cases, we found significant increases in DEA but no significant production of N gas. Except with unnaturally high substrate amendments, changes in DEA were small relative both to the persistently high DEA background and to changes in MPN. As estimated by MPN counts, denitrifier populations increased significantly during denitrification events. It was apparent that only a small fraction of the denitrifiers were included in the MPN counts, but it appeared that this isolatable fraction increased during periods of active denitrifier growth. Use of DEA as an index of biomass of cells which have synthesized denitrifying enzymes suggested that denitrifier populations were persistent, stable, and much larger than indicated by MPN procedures.     

High-Resolution Denitrification Kinetics in Pasture Soils Link N2O Emissions to pH,and Denitrification to C Mineralization

Denitrification in pasture soils is mediated by microbial and physicochemical processes leading to nitrogen loss through the emission of N₂O and N₂. It is known that N₂O reduction to N₂ is impaired by low soil pH yet controversy remains as inconsistent use of soil pH measurement methods by researchers, and differences in analytical methods between studies, undermine direct comparison of results. In addition, the link between denitrification and N₂O emissions in response to carbon (C) mineralization and pH in different pasture soils is still not well described. We hypothesized that potential denitrification rate and aerobic respiration rate would be positively associated with soils. This relationship was predicted to be more robust when a high resolution analysis is performed as opposed to a single time point comparison. We tested this by characterizing 13 different temperate pasture soils from northern and southern hemispheres sites (Ireland and New Zealand) using a fully automated-high-resolution GC detection system that allowed us to detect a wide range of gas emissions simultaneously. We also compared the impact of using different extractants for determining pH on our conclusions. In all pH measurements, soil pH was strongly and negatively associated with both N₂O production index (IN₂O) and N₂O/(N₂O+N₂) product ratio. Furthermore, emission kinetics across all soils revealed that the denitrification rates under anoxic conditions (NO+N₂O+N₂ μmol N/h/vial) were significantly associated with C mineralization (CO₂ μmol/h/vial) measured both under oxic (r² = 0.62, p = 0.0015) and anoxic (r² = 0.89, p<0.0001) conditions.     

pH Dependence of the Isomerase Activity of Protein Disulfide Isomerase: Insights into its Functional Relevance

The isomerase efficacy of the oxidoreductase, protein disulfide isomerase (PDI), has been examined by a simple method. Using this technique, the pH-dependence of relative efficiency of isomerization reactions by PDI has been evaluated and its impact on a key structure-forming step in the oxidative folding pathway of a model protein determined. Results reveal that PDI has a greater relative impact on thiol-disulfide reshuffling (isomerization) reactions and consequently the structure-forming step in oxidative folding at pH 7, as opposed to pH’s 8 and 9. These results suggest that PDI, which possesses an anomalously low thiol pKa, is fine-tuned to catalyze oxidative folding in the lumen of the endoplasmic reticulum where the ambient pH of ∼7 would otherwise retard thiol-disulfide exchange reactions and hinder acquisition of the native fold. The pH-dependent impact on isomerization catalysis has important implications for the development of synthetic chaperones for in vivo and in vitro applications.     

Influence of nutrient solution pH on N2O and N2 emissions from a soilless culture system

The influence of nutrient solution pH on the emission of N2O and N2 was investigated during cultivation of cucumbers in a closed-loop rockwool system. Between pH 4 and 7 these gaseous nitrogen losses increased from 1.6 to 21.1% of the N fertilizer input. This was equivalent to average flux rates of 0.06 and 0.85 kg nitrogen per hectare greenhouse area and day, respectively. The N2O/N2 ratio was inversely related to the total gaseous nitrogen losses. At neutral pH dinitrogen was the main emission product, whereas more acidic conditions favoured the emission of nitrous oxide. The pH effects were probably not indirectly affected by root respiration or exudation as much as by a direct inhibition of the activity of denitrifying microorganisms due to high H+ concentrations since similar results were obtained in unplanted nutrient solution systems with the addition of glucose as carbon source. Despite the low microbial denitrification activity under acidic conditions, nitrogen balance deficits of up to one-fifth of the N input still occurred. It is suggested these losses were predominantly caused by chemodenitrification.     

Peroxisome Size Provides Insights into the Function of Autophagy-related Proteins

Autophagy is a major pathway of intracellular degradation mediated by formation of autophagosomes. Recently, autophagy was implicated in the degradation of intracellular bacteria, whose size often exceeds the capacity of normal autophagosomes. However, the adaptations of the autophagic machinery for sequestration of large cargos were unknown. Here we developed a yeast model system to study the effect of cargo size on the requirement of autophagy-related (Atg) proteins. We controlled the size of peroxisomes before their turnover by pexophagy, the selective autophagy of peroxisomes, and found that peroxisome size determines the requirement of Atg11 and Atg26. Small peroxisomes can be degraded without these proteins. However, Atg26 becomes essential for degradation of medium peroxisomes. Additionally, the pexophagy-specific phagophore assembly site, organized by the dual interaction of Atg30 with functionally active Atg11 and Atg17, becomes essential for degradation of large peroxisomes. In contrast, Atg28 is partially required for all autophagy-related pathways independent of cargo size, suggesting it is a component of the core autophagic machinery. As a rule, the larger the cargo, the more cargo-specific Atg proteins become essential for its sequestration.     

Monitoring the Size and Metabolic Activity of the Bacterial Community during Biostimulation of Fuel-Contaminated Soil using Competitive PCR and RT-PCR

Efforts to understand and improve soil bioremediation are limited by our ability to determine how treatment variables affect microbial communities. A method was developed to monitor the density and metabolic activity of the total bacterial community in soil. This method was used to monitor the bacterial community in microcosms of Arctic soil after addition of N plus P to stimulate biodegradation of hydrocarbon contaminants. During 29 days of incubation, the total petroleum hydrocarbon level in the soil was reduced from 850 to 360 mg/g of soil. DNA and RNA were extracted from soil using a bead beating method, purified by ammonium acetate precipitation, and assayed by competitive PCR and RT-PCR assays with universal bacterial primers. The copy number of 16S rDNA in the soil microbial community was relatively stable and ranged from 1.7 × 109 to 4.5 × 109/g of soil throughout the incubation. The copy number of 16S rRNA changed substantially and ranged from 5.6 × 1010 to 1.0 × 1012/g of soil. The rRNA:rDNA ratio was highest during the phase of fastest hydrocarbon biodegradation. These results suggest that the treatment to stimulate hydrocarbon biodegradation did not substantially change the density of the bacterial community but did transiently increase its overall metabolic activity.     

Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F_ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.     

Effects of Shading Soybean Plants on N2O Emission from Soil

The effect of photosynthesis on N₂O emission from soil was investigated by shading soybean (Gycline max. L) plant at flowering, pod-setting and grain-filling stages. The results showed that by stopping photosynthesis through shading the plants stimulated N₂O emission significantly at flowering stage and pod-setting stage, and suppressed N₂O emission dramatically at grain-filling stage. At flowering stage, soybean species seem to rely mainly on fertilizer N and shaded plants decreased the N uptake. Interaction between the relative increase in available N for N₂O production by shading and the presence of root exudates promoted N transformation (nitrification/denitrification) and N₂O emission. At pod-setting stage, the available soil nitrogen seems to be a critical limiting factor and without substantial release of symbiotically fixed N through plant roots, resulted in a weak effect of shading on N₂O emission. At grain-filling stage, available N for N₂O production was derived from symbiotically fixed N and was greatly affected by photosynthesis. These results indicated that the effect of soybean growth on N₂O emission from soil varies with plant growth stages as available N for N₂O production is mainly from fertilizer N and organic mineralization during the early growth of soybean plants, while N₂O emission is controlled by the quantity and perhaps also the quality of root exudates, which is closely related with plant photosynthesis in the late season of soybean growth.     

New Insights into Syndecan-2 Expression and Tumourigenic Activity in Colon Carcinoma Cells

Adhesion receptors play crucial roles in the neoplastic transformation of normal cells through induction of cancer-specific cellular behaviour and morphology. This implies that cancer cells likely express and utilize a distinct set of adhesion receptors during carcinogenesis. Colon cancer is an excellent model system for the study of this process, since both molecular genetic and morphological changes have been well established for this disease. We recently reported increased expression of the cell surface adhesion receptor, syndecan-2, in several colon carcinoma cell lines. Indeed, increased syndecan-2 expression was necessary for tumourigenic activity, suggesting that syndecan-2 might have value as both a new diagnostic marker and a possible therapeutic target. Here, we review recent advances in understanding the role of syndecan-2 in the carcinogenesis of colon cells, and discuss a leading role for this molecule in a new era for colon cancer treatment.     

Effect of pH and substitution of H2O for D2O on oxygen liberation by chloroplasts

The rate of dark relaxation of the oxygen evolving system in chloroplasts is shown to depend on the value of the surface charge of some chloroplast membrane component having protein nature and isoelectric point at pH 6.0. The substitution of H2O for D2O leads to isoelectric point shift of this protein.     

Nitrous Oxide (N2O) Emissions from Subsurface Soils of Agricultural Ecosystems

Ecosystems - Nitrous oxide (N2O) is a major greenhouse gas and cultivated soils are the most important anthropogenic source. N2O production and consumption are known to occur at depths below the A...     

Soil core method for direct simultaneous determination of N2 and N2O emissions from forest soils

In order to quantify N₂-emissions from a spruce and a beech site at the Höglwald Forest, a new measuring system was developed, that allowed simultaneous, direct determination of N₂- and N₂O-emission with high accuracy (detection limit approx. 10 g N m^–2 h^–1 for N₂ and <1 g for N₂O) using a gas-flow core method. This method requires exchange of the soil atmosphere with an artificial atmosphere, that differs only in that N₂ is substituted by He. The measuring system, the methodology of measurements and validation experiments are described in detail. Due to the huge heterogeneity of denitrification activity in different soil cores taken from our forest sites, no general trends of N₂ and N₂O production in relation to soil moisture and temperature could be demonstrated. Based on reasonable number of measurements, this work gives for the first time an estimate of the magnitude of N₂-losses from temperate forest soils. Both the magnitude of N₂-emissions (spruce: 7.2±0.7 kg N₂-N ha^–1 yr^–1; beech: 12.4±3.1 kg N₂-N ha^–1 yr^–1), as well as the N₂O–N₂ ratio (spruce: 0.136±0.04; beech: 0.52±0.19) were significantly higher for soils from the beech sites as compared to soils from the spruce site. The results suggests that N₂-emissions from N-saturated forest soils, still receiving high loads of atmospheric N-deposition, are approx. 30% of atmospheric N-input at the spruce site, and approx. 50% at the beech site. Our results demonstrate that losses of nitrogen in the form of N₂ cannot be neglected in the context of calculating N-balances for given forest sites.