The microbiology of nitrification has been extensively studied, but the ecology and environmental impact of the process has received less attention. The reason for this has more to do with the difficulties of conducting field experiments to examine the links with other processes which cause losses of nitrogen, than a failure to appreciate its importance in agricultural systems. This project was designed to overcome some of the limitations of existing field techniques to enable simultaneous measurements of nitrification and the major processes of N supply (mineralization) and N loss (denitrification and leaching) to be examined. The study proceeded in three distinct phases: firstly, soils with contrasting N management histories were examined, using laboratory assays for potential activities. Clear differences which resulted from higher N inputs were established, with correspondingly higher nitrifying activities. For example, in a fertilized soil, mmoniaoxidizers produced 48.4 compared with 1.3 nM NO2- g-1 soil h-1 in an unfertilized soil. Potential nitrite-oxidizing rates were 93.4 and 62.5 nM g-1 h-1, respectively. Assays of enzyme kinetics, therefore confirmed the higher nitrifying activity in the fertilized soil, but demonstrated a lower affinity of the enzyme for N02 substrate, with Km values of 436 and 310 gM NO2--N, respectively. Nitrifying rates in soils from grass-clover swards were intermediate between the fertilized and unfertilized soils. Secondly, a new field incubation technique was developed and used to obtain actual rates by concurrent measurements of the major N cycling processes. A strong correlation was established between nitrification and denitrification (r2 = 0.98). The measurements were verified by comparison with other independent methods. Net rates of nitrification in the same soil type ranged from 0.55 - 1.17 kg N ha-1 d-1, with the highest rates in the fertilized soil. Over 70% of the mineralized N was nitrified, of which 80% was subsequently lost (i. e. either denitrified or leached). Thirdly, the practical implications of these findings were examined in greater detail using 15N labelling techniques which enabled process rates (net and gross) to be established in a model of the N cycle. When nitrification was inhibited, there were no significant differences between gross or net mineralization rates in the soils from the three swards, which indicated that N-immobilization could be directly influenced by the level of nitrifying activity in these soils. The influence of nitrification in determining the pathways of N loss from grassland soils was quantified in this study. From a detailed investigation of the processes involved in N cycling, it was deduced that nitrification was also one of the major factors in determining the outcome of competition for inorganic N between plant and microbial biomasses.

Pressurized hot water and DTPA-Sorbitol are two relatively new soil boron (B) extraction methods with potential to replace the cumbersome hot water extraction. The objective of this research is to produce data in support of acceptance or rejection of these two alternative B extractions. The three soil tests were used to extract B from samples of calcareous sand and silt loam and limed, loamy fine sand treated with 10 levels of B and incubated for 7 and 28 d. As B application increased so did extractable B with each extraction method. High correlations (r of 0.977 to 0.999) were observed between extractable B and rate of B application with all three methods. Hot water generally extracted the least and pressurized hot water the most B regardless of soil type, rate of application or duration of incubation. Greenhouse and field experiments were conducted on one limed acid and two alkaline soils naturally low in B to test alfalfa response to B fertilizer. Values from the three soil extraction methods were correlated to yield, B tissue concentration and total B removal of alfalfa. In greenhouse studies with varying levels of soil applied B, highly significant relationships exist between extractable soil B and both tissue B concentration and total B removal. Correlations between yield and extractable soil B were impossible to obtain because of a lack of alfalfa yield responses to applied boron. All three methods accurately predict plant B tissue concentrations and total B removal. The field experiment produced a significant positive relationship between total alfalfa yield and extractable B using hot water and pressurized hot water extractions, but not using DTPA-Sorbitol. The results observed in this research support pressurized hot water extraction as the better of the two alternatives to replace hot water extraction in a broad range of soil types.

Conserving the environment is an issue that is gaining popularity day by day. Phosphorus transfer from agricultural soils is an important environmental issue that is being closely observed as the transport of phosphorous to water bodies is adversely affecting water quality due to accelerated eutrophication. It is important to establish phosphorous models that accurately account for soil test phosphorous. Standard models like SWAT (Soil and Water Assessment Tool) and EPIC (Environmental Policy Integrated Climate) were designed for serving this purpose. They are now used as the basis for developing new models that can more accurately account for the phosphorus transport, depending on local soil conditions and external factors like climate, addition of biochar or other soil amendments. Our research involved development of new methods from published data that are applied to different soils from Kentucky that are incubated for various time periods, with and without the addition of biochar amendments. Changes in the soil labile phosphorus content after phosphorus addition to and depletion from these incubated soils was measured to discern the effect of biochar on the rates of phosphorus transport. The measured labile phosphorus was further analyzed using statistical analysis software drawing comparisons among treatments without biochar, with low temperature biochar and high temperature biochar for specific soil-biochar combinations. Loamy sand soils with both pine chips and switch grass biochar types have shown slightly increased leeching of phosphorus upon addition of biochar whereas clay loam soils have not shown any significant change upon addition of biochar.

This thesis examines sulfide oxidation in 4 physically and mineralogically diverse acid sulfate soil (ASS) materials collected from coastal floodplain sites in north-eastern New South Wales. The aim of this study is to gain further understanding of the process of sulfide oxidation in ASS materials, which will allow improved and more effective management strategies to be applied to these materials. The process of sulfide oxidation was examined using laboratory incubation experiments. The oxidation of pyrite was the primary cause of initial acidification of the ASS materials studied. Although the acid volatile sulfur fraction increased in concentration by an order of magnitude over the initial 8 days of incubation, the subsequent oxidation of this fraction did not result in substantial acidification. Sulfate (SO42-) was the dominant sulfur species produced from sulfide oxidation, however, water-soluble SO42- was a poor indicator of the extent of sulfide oxidation. The sulfoxyanion intermediates thiosulfate (S2O32-) and tetrathionate(S4O62-) were only detected in the early stages of incubation, and their relative abundance appeared to be pH dependent. The diminishing presence of these 2 sulfur species as oxidation progressed was indicative that ferric iron (Fe3+) and bacterial catalysis were driving the oxidation processes. The rate of sulfide oxidation, and consequent rate of acidification, was highly dependent on the soil pH and oxygen availability. Accelerated sulfide oxidation was only observed at low pH (i.e. pH < 4.0) when oxygen availability was not limited. The application of sub-optimal amounts of neutralising agents prevented severe soil acidification in the short-term (i.e. up to 2 months), but had little effect on decreasing the rate of sulfide oxidation and acidification in the long-term. Sub-optimal amounts of CaCO3 accelerated sulfide oxidation and acidification of the peaty marcasitic ASS material resulting in elevated soluble Fe and Al concentrations. For some of the ASS materials, sub-optimal applications of seawater-neutralised bauxite refinery residue (SNBRR) also resulted in elevated soluble Al concentrations. The response of partially-oxidised ASS materials to the exclusion of oxygen was variable. The rate of sulfide oxidation, acidification and the production of soluble oxidation products generally decreased markedly when subjected to anoxia. However, especially in highly acidic ASS materials (i.e. pH < 3.5), sulfide oxidation and acidification generally occurred (albeit at much slower rates), most probably due to oxidation by Fe3+. Rapid sulfide re-formation occurred in the peat ASS material that had been oxidised for 63 days, with 0.47% reduced inorganic sulfur (SCR) formed over 60 days of anoxia. Biogeochemical sulfide formation consumes acidity, however, sulfide re-formation was ineffective in reversing acidification under the conditions of this experiment. The peroxide oxidation methods examined were method dependent and substantially underestimated peroxide oxidisable sulfur, sulfidic acidity and net acidity. The precipitation of jarosite during peroxide oxidation was a major factor contributing to the underestimation in these ASS materials. Clay mineral dissolution may contribute towards the underestimation of both sulfidic and net acidity using peroxide oxidation methods. The atmospheric loss of sulfur and acidity was also identified as a possible additional interference. This study has shown that the initial pH of an ASS material is a useful indicator (additional to those already used) of the potential environmental hazard of an ASS material when oxygen is expected to be non-limiting, such as when ASS materials are excavated and stockpiled. The recommended action criteria need to be reassessed as the data indicate that the current criteria are conservative for alkaline and neutral ASS materials, but should be lowered for all acidic ASS materials (i.e. pH < 5.5) to 0.03% sulfide regardless of texture. Alternative strategies are necessary for the management of ASS materials that are subject to oxidation when the addition of optimal rates of neutralising materials cannot be ensured. The treatment of sites containing actual ASS materials by management strategies that rely on oxygen exclusion need to be accompanied by strategies that include either acid neutralisation or containment in order to reduce acid export from the site. The peroxide oxidation methods examined were subject to substantial interferences, and consequently are unable to reliably provide accurate measurements of the reduced inorganic sulfur fraction, sulfidic acidity, and net acidity in ASS materials.

Soils are the largest pool of carbon (C) in terrestrial ecosystems and store 1500 Gt of C in their soil organic matter (SOM). SOM is a dynamic, complex and heterogeneous mixture, which influences soil quality through a wide range of soil properties. Labile SOM comprises a small fraction of total SOM (approximately 5%), but due to its rapid turnover has been suggested to be most vulnerable to loss following soil disturbance. This research was undertaken to examine the consequences of soil disturbance on labile SOM, its availability and protection in soils using the isotopic analysis of soil-respired CO₂ (δ¹³CO₂). A range of soils were incubated in both the short- (minutes) and long-term (months) to assess changes in labile SOM. Shifts in soil-respired δ¹³CO₂ over the course of soil incubations were found to reflect changes in labile substrate utilisation. There was a rapid depletion of δ¹³CO₂ (from a starting range between -22.5 and -23.9‰, to between -25.8 and -27.5‰) immediately after soil sampling. These initial changes in δ¹³CO₂ indicated an increased availability of labile SOM following the disturbance of coring the soil and starting the incubations. Subsequently δ¹³CO₂ reverted back to the initial, relatively enriched starting values, but this took several months and was due to labile SOM pools becoming exhausted. A subsequent study was undertaken to test if soil-respired δ¹³CO₂ values are a direct function of the amount of labile SOM and soil physical conditions. A range of pasture soils were incubated in the short-term (300 minutes), and changes in soil-respired δ¹³CO₂ were measured along with physical and chemical soil properties. Equilibrium soil-respired δ¹³CO₂, observed after the initial rapid depletion and stabilisation, was a function of the amount of labile SOM (measured as hot water extractable C, HWEC), total soil C and soil protection capacity (measured as specific soil surface area, SSA). An independent experimental approach to assess the effect of SSA, where labile SOM was immobilised onto allophane – a clay mineral with large, active surface area – indicated limited availability of labile SOM through more enriched δ¹³CO₂ (in a range between -20.5 and -20.6 ‰) and a significant (up to three times) reduction in HWEC. In the third study, isotopic measurements were coupled with CO₂ evolution rates to directly test whether equilibrium soil-respired δ¹³CO₂ can reflect labile SOM vulnerability to loss. Soils were sampled from an experimental tillage trial with different management treatments (chemical fallow, arable cropping and permanent pasture) with a range of C inputs and soil disturbance regimes. Soils were incubated in the short- (300 minutes) and long-term (600 days) and changes in δ¹³CO₂ and respiration rates measured. Physical and chemical fractionation methods were used to quantify the amount of labile SOM. Pasture soils were characterised by higher labile SOM estimates (HWEC; sand-sized C; labile C respired during long-term incubations) than the other soils. Long-term absence of plant inputs in fallow soils resulted in a significant depletion of labile SOM (close to 50% based on sand-sized C and HWEC estimates) compared with pasture soils. The values of δ¹³CO₂ became more depleted in 13C from fallow to pasture soils (from -26.3 ‰ to -28.1 ‰) and, when standardised (against the isotopic composition of the solid soil material), Δ¹³CO₂ values also showed a decrease from fallow to pasture soils (from -0.3 ‰ to -1.1 ‰). Moreover, these patterns in isotopic measures were in strong agreement with the amount of labile SOM and its availability across the soils, and were best explained by the isotopic values of the labile HWEC fraction. Collectively, these results confirm that labile SOM availability and utilisation change immediately after soil disturbance. Moreover, isotopic analysis of soil-respired CO₂ is a powerful technique, which enables us to probe mechanisms and examine the consequences of soil disturbance on labile SOM by reflecting its availability and the degree of SOM protection.

This thesis examines sulfide oxidation in 4 physically and mineralogically diverse acid sulfate soil (ASS) materials collected from coastal floodplain sites in north-eastern New South Wales. The aim of this study is to gain further understanding of the process of sulfide oxidation in ASS materials, which will allow improved and more effective management strategies to be applied to these materials. The process of sulfide oxidation was examined using laboratory incubation experiments. The oxidation of pyrite was the primary cause of initial acidification of the ASS materials studied. Although the acid volatile sulfur fraction increased in concentration by an order of magnitude over the initial 8 days of incubation, the subsequent oxidation of this fraction did not result in substantial acidification. Sulfate (SO42-) was the dominant sulfur species produced from sulfide oxidation, however, water-soluble SO42- was a poor indicator of the extent of sulfide oxidation. The sulfoxyanion intermediates thiosulfate (S2O32-) and tetrathionate(S4O62-) were only detected in the early stages of incubation, and their relative abundance appeared to be pH dependent. The diminishing presence of these 2 sulfur species as oxidation progressed was indicative that ferric iron (Fe3+) and bacterial catalysis were driving the oxidation processes. The rate of sulfide oxidation, and consequent rate of acidification, was highly dependent on the soil pH and oxygen availability. Accelerated sulfide oxidation was only observed at low pH (i.e. pH < 4.0) when oxygen availability was not limited. The application of sub-optimal amounts of neutralising agents prevented severe soil acidification in the short-term (i.e. up to 2 months), but had little effect on decreasing the rate of sulfide oxidation and acidification in the long-term. Sub-optimal amounts of CaCO3 accelerated sulfide oxidation and acidification of the peaty marcasitic ASS material resulting in elevated soluble Fe and Al concentrations. For some of the ASS materials, sub-optimal applications of seawater-neutralised bauxite refinery residue (SNBRR) also resulted in elevated soluble Al concentrations. The response of partially-oxidised ASS materials to the exclusion of oxygen was variable. The rate of sulfide oxidation, acidification and the production of soluble oxidation products generally decreased markedly when subjected to anoxia. However, especially in highly acidic ASS materials (i.e. pH < 3.5), sulfide oxidation and acidification generally occurred (albeit at much slower rates), most probably due to oxidation by Fe3+. Rapid sulfide re-formation occurred in the peat ASS material that had been oxidised for 63 days, with 0.47% reduced inorganic sulfur (SCR) formed over 60 days of anoxia. Biogeochemical sulfide formation consumes acidity, however, sulfide re-formation was ineffective in reversing acidification under the conditions of this experiment. The peroxide oxidation methods examined were method dependent and substantially underestimated peroxide oxidisable sulfur, sulfidic acidity and net acidity. The precipitation of jarosite during peroxide oxidation was a major factor contributing to the underestimation in these ASS materials. Clay mineral dissolution may contribute towards the underestimation of both sulfidic and net acidity using peroxide oxidation methods. The atmospheric loss of sulfur and acidity was also identified as a possible additional interference. This study has shown that the initial pH of an ASS material is a useful indicator (additional to those already used) of the potential environmental hazard of an ASS material when oxygen is expected to be non-limiting, such as when ASS materials are excavated and stockpiled. The recommended action criteria need to be reassessed as the data indicate that the current criteria are conservative for alkaline and neutral ASS materials, but should be lowered for all acidic ASS materials (i.e. pH < 5.5) to 0.03% sulfide regardless of texture. Alternative strategies are necessary for the management of ASS materials that are subject to oxidation when the addition of optimal rates of neutralising materials cannot be ensured. The treatment of sites containing actual ASS materials by management strategies that rely on oxygen exclusion need to be accompanied by strategies that include either acid neutralisation or containment in order to reduce acid export from the site. The peroxide oxidation methods examined were subject to substantial interferences, and consequently are unable to reliably provide accurate measurements of the reduced inorganic sulfur fraction, sulfidic acidity, and net acidity in ASS materials.