Kinetics and electron transport of soil hydrogenases catalyzing the oxidation of atmospheric hydrogen

The soil hydrogenases of chernozem and eolian sand were different with respect to their kinetic properties. Increase of soil moisture above optimum moisture content or prior incubation of the soils under very high H₂-mixing ratios (i.e. 1%) resulted in a decrease of V_max or in an increase of the K_m of the H₂ oxidation reaction. Under anaerobic conditions, the K_m for H₂ was higher and V_max was lower than under aerobic conditions. The anaerobic H₂-oxidation activity of both soils was stimulated by the addition of artificial electron acceptors with redox potentials of at least 80 mV. Ferricyanide as the most efficient stimulator did not function as a final electron acceptor for anaerobic H₂-oxidation, but acted as a catalyst by bypassing a rate-limiting electron transport step. In eolian sand, the aerobic as well as the anaerobic activity for atmospheric H₂ oxidation decreased upon exposure to very high H₂-mixing ratios (i.e. 1%). A similar effect was observed after incubation with ferricyanide which enabled the inflow of excess electrons from soil reductants or added NADH into the electron transport system of the soil hydrogenase with anaerobic activity. The activity for atmospheric H₂ oxidation was regenerated during incubation in H₂-free atmospheres, especially in the presence of oxygen. Inhibition and regeneration were probably due to alterations in components of the soil hydrogenases caused by the extent of a maximal electron flow through the electron transport system of the soil hydrogenases. Two classes of hydrogenase activities were discerned in eolian sand: one predominantly active under aerobic and the other under anaerobic conditions.     

Efficiency of acetylene reduction (nitrogen fixation) in soil: Effect of type and concentration of available carbohydrate

Sandy loam field soil and Acer saccharum (maple) forest soil were amended with different concentrations of glucose and mannitol and incubated at different pO₂ levels. Nitrogenase activity was determined by repeated 1-h C₂H₂ reduction assays performed at the ambient pO₂ of incubation. Calculated efficiencies of N₂ fixation increased with increasing anaerobiosis and with decreasing added carbohydrate concentration. Efficiencies up to 30 mg N₂ fixed per gram of glucose consumed were obtained under anaerobic conditions in the presence of 0.25% (w/w) glucose. Evidence suggested that low aerobic efficiencies were caused by intense competition for carbohydrate and by lower pH values attained. High concentrations (up to 3.0% w/w) of glucose under aerobic conditions suppressed the development of N₂ase activity. Mannitol supported N₂ase activity the development of which was very much delayed under aerobic conditions but little delayed under anaerobic conditions.     

Effect of the herbicide glyphosate on respiration and hydrogen consumption in soil

The effect of glyphosate on soil respiration and Hz oxidation in an agricultural soil was investigated. The effects of the pure herbicide and commercial formulation, Roundup® (Monsanto Company), were compared in soil under both aerobic and anaerobic conditions. Both formulations stimulated O₂ uptake as well as aerobic and anaerobic CO₂ evolution. Roundup caused more stimulation than glyphosate under aerobic incubation conditions; the formulations had an equal effect on anaerobic CO₂ evolution. Hydrogen oxidation was inhibited by both formulations in aerobic and anaerobic soil. Aerobic H₂ oxidation was inhibited to the same extent by both formulations; Roundup had a stronger inhibitory effect on anaerobic H₂ oxidation than did glyphosate.     

Effects of organic amendments on evolution of ethylene and other hydrocarbons from soil

Evolution of C₂H₄ from soils under anaerobic conditions was stimulated by amendment with cereal straw, but hay had little effect. Temporary restoration of aerobic conditions resulted in large increases in C₃ and C₄ hydrocarbons, with both straw and hay amendments. Several known products of the fermentative degradation of carbohydrate increased the evolution of hydrocarbons under anaerobic, and to a greater extent, under aerobic conditions. In particular, ethanol and butyric acid promoted the formation of C₂H₄ and propylene, respectively. The association between degradation products and C₂H₄ suggests that both may be implicated when root growth is adversely affected by the anaerobic decomposition of plant residues.     

Short-term partitioning of <Superscript>14</Superscript>C-[U]-glucose in the soil microbial pool under varied aeration status

The effect of soil aeration status on carbon partitioning of a labelled organic substrate (¹⁴C-[U]-glucose) into CO₂, microbial biomass, and extra-cellular metabolites is described. The soil was incubated in a continuous flow incubation apparatus under four different aeration conditions: (1) permanently aerobic, (2) permanently anaerobic, (3) shifted from anaerobic to aerobic, and (4) shifted from aerobic to anaerobic. The soil was pre-incubated for 10 days either under aerobic or under anaerobic conditions. Afterwards, glucose was added (315 g C g^–1) and the soils were incubated for 72 h according to four treatments: aerobic or anaerobic conditions maintained, aerobic conditions shifted to anaerobic conditions and anaerobic conditions shifted to aerobic conditions. Carbon partitioning was measured 0, 8, 16, 24, 48 and 72 h after the glucose addition. In permanently aerobic conditions, the largest part of the consumed glucose was built into microbial biomass (72%), much less was mineralised to CO₂ (27%), and only a negligible portion was transformed to soluble extra-cellular metabolites. Microbial metabolism was strongly inhibited when aeration conditions were changed from aerobic to anaerobic, with only about 35% of the added glucose consumed during the incubation. The consumed glucose was transformed proportionally to microbial biomass and CO₂. In permanently anaerobic conditions, 42% of the consumed glucose was transformed into microbial biomass, 30% to CO₂, and 28% to extra-cellular metabolites. After a shift of anaerobic to aerobic conditions, microbial metabolism was not suppressed and the consumed glucose was transformed mainly to microbial biomass (75%) and CO₂ (23%). Concomitant mineralisation of soil organic carbon was always lower in anaerobic than in aerobic conditions.     

Function of the methanogenic community in mangrove soils as influenced by the chemical properties of the hydrosphere

Coastal ecosystems represent a potential additional source of the greenhouse gas methane (CH₄) that has been insufficiently quantified. Thus, to understand the mechanisms controlling greenhouse gas emissions in these ecosystems, this study investigated CH₄ emissions from and the related microbial properties of mangrove soils. Soil and gas samples were collected from several plots at different distances from the seashore in Soc Trang and Ca Mau in Vietnam, and the Sundarbans in India. Soil samples were incubated under different conditions, i.e., anaerobic or aerobic, and the microbial properties of each soil sample with the addition of different amounts of seawater were analyzed. Relatively high CH₄ fluxes and production were detected during the aerobic incubation of samples from the seashore plots in Soc Trang and Ca Mau. However, CH₄ production was reduced under anaerobic conditions [soil electrical conductivity (EC): 179–289 mS m^?1, pH (H₂O): 7.45–8.10] compared with aerobic conditions [water content: 38.9–109.2%, EC: 187–299 mS m^?1, pH (H₂O): 6.86–7.72], but it increased with increasing sulfate concentration, soil EC and cellulase activity and lowering soil pH under anaerobic conditions. Furthermore, mangrove soil with a relatively high level of total organic carbon (C) exhibited relatively high CH₄ production when diluted 4-fold with seawater under anaerobic conditions [water content: 38.9–109.2%, EC: 533 mS m^?1, pH (H₂O): 6.67]. Nearly all of the DNA bands excised from polymerase chain reaction-denaturing gradient gel electrophoresis contained identical sequences related to archaea from the class Halobacteria. The high potential of the seashore plot for CH₄ emissions could be due to the enhancement of cellulase activity under the intermittent oxygen supply, which promotes polysaccharide depolymerization and subsequently increases anaerobic methanogenic activities during tidal flooding. This study also indicates that the major archaea responsible for CH₄ production require a particular hydrospheric salt concentration and soil pH.     

Effect of alternate aerobic and anaerobic conditions on redox potential,organic matter decomposition and nitrogen loss in a flooded soil

The effect of several cycles of varying length of alternate aerobic and anaerobic conditions on redox potential, organic matter decomposition and loss of added and native nitrogen was investigated under laboratory conditions in flooded soil incubated for 128 days. Redox potential decreased rapidly when air was replaced with argon for the short-time cycles, but decreased more slowly where the aerobic period was long enough to permit build-up of nitrate. The minimum redox potential reached during the anaerobic period was generally lower for the longer cycles, but in all cases was low enough for denitrification to occur. Rate of decomposition of organic matter was faster in the treatments with a greater number of alternate aerobic and anaerobic periods. Total N (native and applied) losses as high as 24.3 per cent occurred in the treatment with the maximum number of cycles and with alternate aerobic and anaerobic periods of 2 and 2 days. Increasing the durations of the aerobic-anaerobic periods decreased the loss of N. A maximum loss of 63.0 per cent of applied ¹⁵NH₄-N resulted from the shortest (2 and 2 day) aerobic and anaerobic incubation. For soil undergoing frequent changes in aeration status the only labelled N that remained at the end of incubation was found in the organic fraction. Loss of N may have been even greater if labelled inorganic N had not been immobilized by microorganisms decomposing the added rice straw. The greater loss of N resulting from the 2 and 2 day aerobic-anaerobic incubation shows that, in soils where the redox potential falls low enough for denitrification to occur, increasing the frequency of changing from aerobic to anaerobic conditions will increase the loss of N.     

Heterotrophy-coordinated diazotrophy is associated with significant changes of rare taxa in soil microbiome

Soil heterotrophic respiration during decomposition of carbon (C)-rich organic matter plays a vital role in sustaining soil fertility. However, it remains poorly understood whether dinitrogen (N₂) fixation occurs in support of soil heterotrophic respiration. In this study, ¹⁵N₂-tracing indicated that strong N₂ fixation occurred during heterotrophic respiration of carbon-rich glucose. Soil organic ¹⁵N increased from 0.37 atom% to 2.50 atom% under aerobic conditions and to 4.23 atom% under anaerobic conditions, while the concomitant CO₂ flux increased by 12.0-fold under aerobic conditions and 5.18-fold under anaerobic conditions. Soil N₂ fixation was completely absent in soils replete with inorganic N, although soil N bioavailability did not alter soil respiration. High-throughput sequencing of the 16S rRNA gene further indicated that: i) under aerobic conditions, only 15.2% of soil microbiome responded positively to glucose addition, and these responses were significantly associated with soil respiration and N₂ fixation and ii) under anaerobic conditions, the percentage of responses was even lower at 5.70%. Intriguingly, more than 95% of these responses were originally rare with < 0.5% relative abundance in background soils, including typical N₂-fixing heterotrophs such as Azotobacter and Clostridium and well-recognized non-N₂-fixing heterotrophs such as Sporosarcina, Agromyces, and Sedimentibacter. These results suggest that only a small portion of the soil microbiome could respond quickly to the amendment of readily accessible organic C in a fluvo-aquic soil and highlighted that rare phylotypes might have played more important roles than previously appreciated in catalyzing soil C and nitrogen turnovers. Our study indicates that N₂ fixation could be closely associated with microbial turnover of soil organic C when available in excess.     

Effect of blending urea with pyrite or coating urea with polymer on ammonia volatilization loss from surface-applied prilled urea

Laboratory studies on a sandy clay loam (Typic Ustochrept) alkaline soil showed that NH₃ volatilization loss from surface-applied prilled urea during an 8-dya incubation under aerobic conditions was 27.5% of applied N (400 kg N ha^-1) and was reduced to 8.9% when the urea was blended physically with pyrite in a 1:2 ratio; under anaerobic conditions the values for urea and pyrite-urea were 19.3 and 16.9%, respectively. Other treatments tested were urea-gypsum, neemcake-coated urea and polymer-coated urea. A 6% polymer coating showed the least NH₃ volatilization under anaerobic conditions and was next best to pyrite-urea under aerobic conditions. A 3% polymer coating was slightly inferior to the 6% coating. Urea-gypsum and neemcake-coated urea did not differ very much from urea alone under anaerobic conditions, but under aerobic conditions neemcake-urea showed a significantly lower total NH₃ loss compared to prilled urea alone and urea-gypsum.     

Carbon, Nitrogen and Phosphorus Tranformations are Related to Age of a Constructe Wetland

Two horizontal constructed wetlands with subsurface flow (CWs) of different age were monitored in a 2-year study. One of the CWs was new, while the second one had been in operation for 5 years in the first year of study. Transformations of C, P, and N were measured in each CW in the substrate of the vegetated bed under both aerobic and anaerobic conditions, and their rates were compared. C was mineralized in both CWs under both aerobic and anaerobic conditions, but mineralization rates differed between the CWs; they were cca ten times higher in the established CW compared to the new CW. Dissolved reactive phosphorus (DRP) was immobilized under aerobic conditions but was mobilized under anaerobic conditions. DRP transformation was cca five times faster in the established CW. Nitrification occurred under aerobic conditions at similar rates in both CWs. NH₄ ⁺ concentration decreased under both aerobic and anaerobic conditions, but there was large variability. The age of the CW affected C mineralization rates and DRP immobilization rates under aerobic conditions and mobilization rates under anaerobic conditions; they increased as the CWs maturated, while no effect of CW age was observed on nitrogen removal rates.     

Laboratory study of phosphorus forms and test procedures on soils under aerobic and anaerobic conditions

The inorganic forms of phosphorus in nine samples of surface soils from the Nainital Tarai of India were determined by a series of extractions with different reagents after incubation for 45 days under aerobic or anaerobic conditions. The forms of phosphorus in samples incubated under aerobic conditions and the pH range of 7.2–8.5 indicated that the soils had been subject to slight chemical weathering. Anaerobic incubation to simulate conditions in lowland rice paddies converted part of the inorganic phosphorus into more labile forms, based on changes in amounts of isotopically exchangeable phosphorus. Amounts of the element converted to more labile forms differed among the nine soil samples.A better correlation was found between amounts of phosphorus extracted by 0.5M NaHCO³ (Olsen's method) than by 0.03N NH₄F in 0.25N HCl (Bray's method) and the isotopically exchangeable phosphorus. The better correlation suggests that the bicarbonate extraction would be the better method for estimating “availablelrd phosphorus in soils of lowland rice paddies. Recalibration of the test prior to such use seems desirable to allow for increases in amounts of phosphorus in labile forms after soils have been shifted from aerobic to anaerobic conditions.     

Enhancement of aerobic nitrogenase activity (acetylene reduction assay) by phenol in soils and the rhizosphere of cereals

By addition of phenol at concentrations between 0.1 and 10 mmol·l^?1, nitrogenase activity (acetylene reduction assay) is enhanced by a factor of 5 in the rhizosphere of Pennisetum glaucum (pearl millet) incubated under 20% O₂. No increase is found under microaerobic conditions. This enhancement effect is also noticed in a soil amended with a sucrose concentration of 20 mmol·l^?1. Under those conditions, however, an enhancement is found under aerobic as well as under microaerobic conditions and a further increase of the phenol added reduces the activity to almost zero. A 4-fold increase of N₂-fixation by phenol addition under aerobic conditions was determined with homogenous sediments from a fresh water lake while anaerobic N₂-fixation was already slightly reduced by the same concentration added. Excised roots of Sorghum nutans CSH 5 failed to show any phenol enhancement of nitrogenase activity. After a preincubation of 6h, inhibition of nitrogenase activity under air by addition of 1 mmol·l^?1 was much more pronounced than under microaerobic conditions.     

Sensitivity of Nitrogen Mineralization Indicators to Crop and Soil Management

Abstract

Soil nitrogen (N) mineralization indicators are useful only if they are sensitive to management practices. The precision of measurement and the sensitivity of the following indicators to crop sequence, tillage, and liming effects were compared: (i) mineral N production during a 24‐day incubation under aerobic conditions, (ii) ammonium (NH₄)‐N production under waterlogged conditions, (iii and iv) hot potassium chloride (KCl)–extractable and hydrolyzable NH₄‐N (the latter obtained by subtracting initial NH₄‐N from extracted NH₄‐N), and (v) protease activity. The coefficients of variation decreased in this order: protease activity>KCl‐hydrolyzable NH₄‐N>aerobic incubation>KCl‐extractable NH₄‐N=anaerobic incubation. Most of the test results obtained using the indicators were correlated with each other. Mineralizable N measured by aerobic and anaerobic incubation was sensitive to tillage, liming, and crop sequences, especially when using soil 5‐cm deep. Hot KCl‐extractable NH₄‐N was influenced by tillage but not liming, and less sensitive than the incubation procedures to crop sequence. The protease assay produced no significant test. It was concluded that anaerobic incubation can provide a relatively sensitive assessment of management effects on soil mineralizable N.     

Evaluating the effect of liming on N<Subscript>2</Subscript>O fluxes from denitrification in an Andosol using the acetylene inhibition and <Superscript>15</Superscript>N isotope tracer methods

We assessed the effect of liming on (1) N₂O production by denitrification under aerobic conditions using the ¹⁵N tracer method (experiment 1); and (2) the reduction of N₂O to N₂ under anaerobic conditions using the acetylene inhibition method (experiment 2). A Mollic Andosol with three lime treatments (unlimed soil, 4 and 20 mg CaCO₃ kg^?1) was incubated at 15 and 25 °C for 22 days at 50% and then 80% WFPS with or without 200 mg N kg^?1 added as ¹⁵N enriched KNO₃ in experiment 1. In experiment 2, the limed and unlimed soils were incubated under completely anaerobic conditions for 44 h (with or without 100 mg N kg^?1 as KNO₃). In experiment 1, limed treatments increased N₂O fluxes at 50% WFPS but decreased these fluxes at 80% WFPS. At 25 °C, cumulative N₂O and ¹⁵N₂O emissions in the high lime treatment were the lowest (with at least 30% less ¹⁵N₂O and total N₂O than the unlimed soil). Under anaerobic conditions, the high lime treatment showed at least 50% less N₂O than the unlimed treatment at both temperatures with or without KNO₃ addition but showed enhanced N₂ production. Our results suggest that the positive effect of liming on the mitigation of N₂O evolution from soil was influenced by soil temperature and moisture conditions.     

A Numerical Approach to Simulate the Biogeochemical Involvement in a Coastal Reduced Groundwater Environment

Bacteria-mediated reduction processes play a decisive role in the water quality alterations in the subsurface environment of coastal aquifers. Availability of organic carbon as the electron donor with other electron acceptors such as NO₃ ^?, MnO₂, Fe(OH)₃ and SO₄ ^2? induces different bacteria to activate under aerobic and anaerobic conditions. A two-dimensional reactive transport model has been developed to simulate the bacteria-mediated reduction reactions in a coastal aquifer. The model explains the utilisation of O₂, NO₃ ^?, MnO₂, Fe(OH)₃ and SO₄ ^2? as electron acceptors for the oxidation of organic carbon in the aquifer under aerobic and anaerobic conditions. The conceptual model consists of three different phases named as bio phase, mobile phase and matrix phase. Model parameters are adopted from literature on bacteria-mediated multi-component modelling and bioremediation processes. Monod kinetic equation is assumed to formulate the bacterial growth. The model explains the behaviours of aerobic and anaerobic bacteria under the availability of organic carbon. Two scenarios are tested and numerical results are discussed. The present numerical study highlights the possibility of the simulation of the formation of reduced environments in coastal aquifers which has not received much attention of groundwater modelling community yet.     

Effects of transient anaerobic conditions in the presence of acetylene on subsequent aerobic respiration and N2O emission by soil aggregates

Our objective was to assess the effect of anaerobic conditioning in the presence of acetylene on subsequent aerobic respiration and N₂O emission at the scale of soil aggregates. Nitrous oxide production was measured in intact soil aggregates Δ (compacted aggregates without visible porosity) and Γ (aggregates with visible porosity) incubated under oxic conditions, with or without anaerobic conditioning for 6 d. N₂O emissions were much higher in aggregates that had been submitted to anaerobic conditioning than in aggregates that did not experience this conditioning, although very little NO₃⁻ remained in soil after the anaerobic period. ¹⁵N isotope tracing technique was used to check whether N₂O came from nitrification or denitrification. The results showed that denitrification was the major process responsible for N₂O emissions. The aerobic CO₂ production rate was also measured in intact soil aggregates. It was greater in aggregates submitted to anaerobic conditioning than in those that were not, suggesting that the anaerobic conditioning lead to an accumulation of small compounds including fatty acids that are readily available for microbial decomposition in aerobic conditions. This process increases the aerobic CO₂ production and favours the N₂O emissions through denitrification.     

Effect of sediment pH and oxidation-reduction potential on PCB mineralization

Microbial mineralization rates of a ¹⁴C-labelled PCB mixture were determined in PCB-contaminated Capitol Lake, LA, sediment under controlled pH and redox conditions. Mineralization rates were inferred from the activity of ¹⁴CO₂ evolved from the sediment suspensions. Sediment pH and redox potential significantly affected PCB mineralization. Mineralization rates were higher under moderately aerobic conditions (microaerophilic) ( + 250 mV) than under aerobic conditions ( + 500 mV) or anaerobic conditions (0 mV and ?200 mV). PCB mineralization rates in moderately aerobic sediment were 30 to 40 fold higher than those in anaerobic sediment. Sediment conditions in the oxidized surface layer would promote PCB mineralization. Sediment pH and redox potential were shown to be two sediment parameters which can be managed to enhance degradation of PCBs in contaminated sediment.     

Production and stability of ethylene in soil

Summary One of the major factors affecting the production and stability of ethylene (C₂H₄) in soil is its water content. This study was conducted to determine the effect of unsaturated vs. saturated conditions on the production and stability of C₂H₄ in soil. L-Methionine and D-glucose were added alone and in combination at 1.0 and 5.0 g kg^-1 soil, respectively. The addition of l-methionine significantly promoted C₂H₄ production at field capacity to a much greater extent than under waterlogged conditions. Glucose was equally effective under both moisture regimes, while the combined application of both amendments (l-methionine and d-glucose) led to the release of significantly higher amounts of C₂H₄ under saturated conditions. Antibiotic experiments revealed that under aerobic conditions, l-methionine may be more efficiently converted to C₂H₄ by soil fungi, while in glucose-amended soil, both bacteria and fungi are active in generating C₂H₄. C₂H₄ was more stable under saturated conditions. The magnitude of C₂H₄ removal from the headspace after 3 days of incubation under unsaturated conditions (25.7%) was comparable to that after 6 days under saturated conditions (24.1%). The loss of C₂H₄ was approximately 10-fold greater in non-sterilized soil than in sterilized (autoclaved) soil, both maintained at field capacity, indicating that a biotic component has a major influence on C₂H₄ stability. Kinetic analysis revealed that the C₂H₄ loss/degradation in nonautoclaved soil under aerobic conditions followed a firstorder reaction, with a rate constant (k) of 0.115 day^-1 and a half-life (t _1/2) of 6.0 days.     

Denitrification potentials: Measurement of seasonal variation using a short-term anaerobic incubation technique

A short-term anaerobic incubation technique using the C₂H₂ inhibition of N₂O-reductase for comparing denitrification potentials of soils is described. Twenty grams of soil with added NO^?1₃ are incubated in the presence of He and 0.1 atm C₂H₂ at 25°C and 0 soil matric potential for 8 h. N₂O evolution is linear within 60 to 120 min. The denitrification potential of soils stored at 4°C decreased markedly over 21 days of storage in accordance with changes in the available C. Denitrification under an anaerobic atmosphere was observed at 4 C. Denitrification potentials were independent of NO^?3₃ concentrations above 25 μg NO^?₃-N g^?1 soil. Biphasic linear rates of N₂O evolution were observed in one soil. Incubation of this soil with chloramphenicol suggested the first linear phase is attributable to the in situ enzyme activity at the time of sampling. The second linear phase is indicative of the dentrification potential and is attributed to the full induction of denitrifying enzymes. The denitrification potential of a soil was maintained at or close to the maximum for 8 months of the year. During midsummer months the denitrification potential decreased markedly and the soil demonstrated a biphasic rate of denitrification suggesting an in situ denitrification activity less than the maximum potential. Results indicate that the maximum denitrification potential of this soil may often be limited not by NO^?₃ but by available C.     

Specific rates of net methylmercury production in lake sediments

Specific rates of Hg (²⁰³HgCl₂) methylation and McHg (¹⁴CH₃HgI) demethylation in aerobic and anaerobic conditions were determined in samples of surface sediments (0 to 2 cm) taken from five small headwater lakes in Southern Finland. The highest rates of methylation were measured in anaerobic conditions. However, the importance of aerobic methylation increased with increasing Fe and Mn content in sediment. There was little difference between aerobic and anaerobic demethylation. The results demonstrate that the net McHg production in lake sediments depends on the individual characteristics of the lake, particularly pH and and sediment properties. These characteristics seem to affect demethylation in anaerobic conditions and methylation in aerobic conditions.