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Soil organic matter (SOM) is a key indicator of soil quality, regulating major soil processes and functions such as soil organic carbon (SOC) storage and cycling, microbial biomass and activity, and nutrient storage and cycling in agro-ecosystems. There has been increasing interest in these functions of SOM, and how they are impacted by management practices in different farming systems. However, there is limited understanding of how, and to what extent, soil structural units (termed "aggregate-size classes") with different SOM bioavailability, influenced by contrasting tillage practices, mediate these soil processes. Moreover, knowledge on the allocation dynamics of newly assimilated C and N in crop–soil systems, with implications for nutrient use efficiency and crop productivity, is also limited. An improved understanding of these inter-relationships will provide insights into identifying land management practices with potential to increase SOM storage, while enhancing plant available nutrients, nutrient use efficiency and therefore crop productivity at farm scale.

A series of experiments was carried out to enhance understanding of the impact of different management practices on key soil processes and functions such as: soil structural stability; carbon and nutrient cycling, availability and storage; microbial biomass and activity; and the coupling between plant C input and soil nutrient availability or N uptake by plants. These processes were examined in bulk soil and/or in different aggregate-size classes. The experiments reported in Chapters 2-5 were performed using soils from three long-term (16-46 years) sites, i.e. the Condobolin (NSW) and Merredin (WA) sites, on a Luvisol, with a semi-arid or a Mediterranean climate, respectively, and the Hermitage (QLD) site, on a Vertisol, with a sub-tropical climate. The practices at Condobolin comprised conventional (CT) and reduced tillage (RT) with mixed crop-pasture rotation, no-till (NT) with continuous cropping, and perennial pasture (PP. The practices at Merredin comprised stubble either retained (SR) or burnt (SB) under direct-drilled continuous cropping. The practices at Hermitage comprised a factorial combination of CT, NT, SR, SB, with either 0 (0N) or 90 kg urea-N ha^-1 (90N) in a continuous cropping system. For the study in Chapter 2, dry and wet sieving techniques were used to separate mega- (> 2 mm), macro- (2-0.25 mm), micro-aggregate (0.25-0.053 mm) and silt-plus-clay (< 0.053 mm) fractions. The impact of management on soil structural stability, and total SOC and nutrient [N, phosphorus (P) and sulphur (S)] stocks in these differently sized aggregate classes was quantified at different soil depths (i.e. 0-10 cm, 10-20 cm and 20-30 cm depths). To understand the processes of SOC mineralisation and the release of plant available nutrients, as impacted by different tillage management practices, the surface layer (0-10 cm) bulk soil and soil aggregates [mega-aggregate, macro-aggregate and micro-aggregate (<0.25 mm)] were incubated at 22 ± 0.5 ̊C and 60% of water holding capacity for 126 days with or without crop residue amendments (Chapter 3-5).

The first study (Chapter 2) demonstrated that management practices with relatively low or no soil disturbance improved soil structure in the Luvisol at Condobolin, while the high clay content in the Vertisol at Hermitage may have overridden the effect of tillage, and therefore, management had minimal impact on soil structure stability. Further, this study found minor to modest impacts of long-term management practices on soil C gain and N, S and P stocks across the field sites. The so-called improved management practices such as perennial pasture at Condobolin, and no-till, stubble retention and fertilisation at Hermitage showed relatively higher SOC and nutrient stocks than management practices with disturbance through tillage plus stubble burning. The findings suggest that the least disturbed systems along with stubble retention and fertilisation can enhance agricultural sustainability by increasing SOC and nutrient concentrations, particularly in micro-aggregates or micro-structures.

The second study, (Chapter 3), showed that SOM has a significant fertiliser value in terms of the supply of plant available N, P and S, and management practices can significantly influence the release of plant available nutrients from SOM. In this experiment, bulk soils (Luvisol and Vertisol) collected from 14 long-term management practices across the three long-term field sites were incubated for 126 days. The mineralisation of SOC and the release of nutrients were higher in the CT versus RT and NT, and the SR versus SB practices in both soils. This study found a continuous release of plant available N across all the management practices over the study period, whereas, the release of available P and S was evident only during the first 30 days, after which P and S availability decreased, probably because microbial immobilisation or clay fixation of P and S predominated, particularly in the Vertisol. These findings suggest that SOM is a direct source of nutrients for crop growth, and management practices involving soil disturbance along with organic matter (residues) input can promote SOM mineralisation and the release of plant available nutrients in farming systems.

The third study, another incubation study (Chapter 4), suggested that SOM can continuously release plant available nutrients (particularly P and S) over 126 days after incorporation of residues. In this experiment, crop residues [canola (Brassica napus: δ¹³C 124‰) or wheat (Triticum aestivum: δ¹³C 461‰) stem] were added to Luvisol (δ¹³C -24.7‰) and Vertisol (δ¹³C -18.5‰) sampled from the contrasting tillage (CT or RT and NT) treatments and incubated for 126 days. This study found that crop residue input into the tilled systems stimulated native SOC mineralisation by ~100-300% across both soils. Both SOC mineralisation and the release of plant available nutrients varied with tillage intensity (CT or RT > NT), residue type (canola > wheat), and soil type (Vertisol > Luvisol). This study also found that crop residue input (cf. control) did not change the magnitude of net available N over the study period, possibly due to stronger N immobilisation than mineralisation. However, a significant amount of available P and S was released in both soils over 126 days. Therefore, this study suggests that, in addition to the likely release of available P and S from the residues via mineralisation, considerable quantities of available P and S may have been released from the soil reserves via positive priming of SOM mineralisation (as demonstrated in our study) and possibly via dissolution/desorption reactions in the soils.

Results from the fourth study (Chapter 5) demonstrated that the differently sized aggregate classes had a smaller effect, compared with the effects of tillage intensity, residue type and soil clay content/type, on the priming of native SOC mineralisation and nutrient (N, P and S) release dynamics in the soils. In this laboratory incubation study, the ¹³C-labelled canola or wheat stem residues were added into the three dry aggregate-size classes, collected from contrasting tillage systems on the Luvisol and Vertisol, and incubated for 126 days. This study found that crop residue input (versus no residue input) stimulated SOC mineralisation in all three aggregatesize classes in both soils. The native SOC mineralisation varied with tillage intensity (CT > RT > NT) (in the Luvisol only), residue type (canola > wheat), and aggregate-size classes (macro- ≥ micro- > mega-aggregates) in both soils. Crop residue input into the soil aggregates (cf. no residue input) maintained the release of available N over the study period, likely due to the dominance of microbial N immobilisation versus mineralisation induced by the relatively C-rich and nutrient-poor crop residues. An interesting finding is that incorporation of crop residues released a considerable amount of plant available nutrients (particularly P and S) from the soil aggregate reserves, most likely via different biological (e.g. priming) and chemical (e.g. nutrient desorption and mineral dissolution) mechanisms. Further, micro- and/or macro- versus mega-aggregates, canola versus wheat residue input, and Vertisol versus Luvisol had higher plant available nutrients in till versus no-till systems.

To understand the allocation dynamics of newly assimilated C and N in a canola crop-soil system with different tillage and N fertilisation treatments, a field-based ¹³C¹⁵N isotopic study was performed at Wagga Wagga, NSW (Chapter 6). Results from this study showed that short-term tillage and N fertilisation can increase belowground allocation of newly assimilated C and plant uptake of soil-released N, under a semi-arid environment. In this study, in situ ¹³CO₂ and urea-¹⁵N pulse labelling was conducted during the canola flowering stage. Despite no short-term effect of management practices on total SOC and N stocks, aggregate stability, microbial biomass, and ¹³C retention in different aggregate-size classes, this study found greater new root C input to 1 m depth, plant N uptake and canola seed yield under a low-intensity tillage (cf.. no-till) and N fertilisation (cf. no N) system.

To conclude, the studies showed that tillage along with stubble retention and/or N fertilisation can stimulate SOM decomposition and the release of plant available nutrients, while enhancing plant derived-C input and nutrient uptake, with positive implications for crop productivity in farming systems. On the contrary, the least disturbed systems such as perennial pasture or no-till along with stubble retention and N fertilisation can increase SOC and nutrient concentrations in micro-structures, although these systems (cf.. tilled systems) gave modest gains in SOC and nutrient stocks. Using tillage to encourage nutrient release should be planned strategically, as the timing of nutrient release from the stimulated SOM decomposition needs to be aligned with crop demand to maximise efficiency of use of nutrients. A further consideration is the trade-off with climate change mitigation, as encouraging SOM mineralisation via tillage will decrease SOC stocks, particularly in surface soil layers.

Dry bean (Phaseolus vulgaris) and maize (Zea mays) are two of the most important staple grain crops for many developing countries. These crops are the main sources of proteins and carbohydrates in the diet of millions of people in these countries. The highest cultivation percentage of these crops is carried out under rain-fed conditions, therefore weather conditions have a stronger influence on its development and production. Currently, there are no studies of how climate change will affect these crops, neither how will be the new dynamic of pathogenic organisms (pests and diseases) for these crops, or which new pests or diseases might attack dry bean or maize. By having the scenarios of these changes we can reduce and change cropping patterns to mitigate the effects of climate change on these staple crops, placing high priority on food security. In this study we describe the changes on climate suitability for two staples crops and some of their pests and diseases (described below) at a global level using CLIMEX, using two Global Circulation Models (GCMs) (CSIRO-Mk3.0 and MIROC-H), assuming an A2 emissions scenario for 2050 and 2100. At the moment, the climate change effects on these diseases and plagues are unknown, as well as the consequences that these effects could have on maize and common bean production and the subsequent supply of these staple crops.

In the first part of this study, the crop modelled is maize. At the global level, maize is the third most important crop on the basis of harvested area. Given its importance, an assessment of the variation in regional climatic suitability under climate change is critical. CliMond 10'data were used to model the potential current and future climate distribution of maize at the global scale. The change in area under future climate was analysed at continental level and for major maize producing countries of the world. Regions between the tropics of Cancer and Capricorn indicate the highest loss of climatic suitability, contrary to poleward regions that exhibit an increase of suitability. South America shows the highest loss of climatic suitability, followed by Africa and Oceania. Asia, Europe and North America exhibit an increase in climatic suitability. This chapter indicates that globally, large areas that are currently suitable for maize cultivation will suffer from heat and dry stresses that may constrain production. For the first time, a model was applied worldwide, allowing for a better understanding of areas that are currently suitable and that may remain suitable for maize.

In the second part of the study, the fall armyworm (FAW, Spodoptera frugiperda), a maize insect pest, was modelled. FAW (Lepidoptera: Noctuidae), is an endemic and important agricultural pest in America. Several outbreaks have occurred with losses estimated at millions of dollars. Insects are affected by climate factors, and climate change may affect geographical range, growth rate, abundance, survival, mortality, number of generations per year and other characteristics. These effects are difficult to project due to the complex interactions among insects, hosts and predators. The aim of the current research is to project the impact of climate change on future suitability for the expansion and final range of FAW as well as highlight the risk of damage due to the pest under current and future conditions. The possible number of generations was estimated to exceed five in the south-eastern USA by 2100. A unique modelling approach linking environmental suitability and number of generations was developed to project the risks of FAW damage. The results show changes in suitability and risk across America, with an increase in the northern hemisphere and decreases or extinction in the southern hemisphere, except for southern Brazil, Uruguay, Paraguay and northern Argentina, which indicate high future levels of risk. The current study highlights the possible extinction of a tropical pest in areas near the Equator. The two GCMs both projected increases in the low-risk category of 40% by 2050 and 23% by 2100, with the medium- and high-risk categories decreasing by >50% by 2050 and >39% by 2100, compared with the current risk. In general, agricultural pest management may become more challenging under future climate change and variation, and thus, understanding and quantifying the possible impacts of FAW under future climate conditions is essential for the future economic production of crops.

The third study was about maize fungal diseases. Common rust (Puccinia sorghi) and southern rust (Puccinia polysora) are two of the most important foliar maize diseases worldwide. These fungi have caused severe economic loss to maize yields worldwide. The current and future potential distribution of these diseases was modelled with CLIMEX using the known current geographic locations of the rusts, growth and stress indices. The current projection shows areas with marginal to optimal suitability in all the continents. The models for future projections display a general reduction in the Southern Hemisphere and increase in the Northern Hemisphere, especially for the southern rust. The overlay of the General Circulation Models produce an estimation of the common areas under risk for future climate conditions for the simultaneous occurrence for both corn rusts, with a reduction of the medium-and high-risk categories by 2100. This study highlights the possible effects of climate change at a global level for common and southern rust, as well as the risk of occurrence of both diseases in common areas for future climate that could be particularly harmful for crops.

In the fourth study, the model of common bean was performed. Crops experience different climate stresses during development. The magnitude of damage will depend on the phenological stage of the crop and the stress duration. Climate change could intensify some or all of these stresses, thus negatively impacting agriculture. An assessment of staple crop productivity, quality and climatically suitable areas under climate change conditions is necessary to undertake any global initiatives to tackle food security issues. The common bean (Phaseolus vulgaris L.) is a staple crop and the main source of proteins and nutrients in Africa and Latin America. The purpose of this study is to develop a process-oriented niche model (CLIMEX) to assess the impacts of climate change on the current and future potential distribution of common bean and to use this model to investigate the changes in heat, cold, dry and wet stresses under climate change. In this study, we used A2 and A1B emission scenarios and two different global climate models, CSIRO-Mk3.0 and MIROC-H, for the years 2050 and 2100. Our results indicate future climate conditions are more favourable for common bean cultivation in the Northern Hemisphere, but are less favourable in the Southern Hemisphere. Heat and dry stresses are the main factors limiting and reducing common bean distribution under current and future projected conditions. Africa and Latin America are projected to decrease with respect to suitability for common bean cultivation. The model projections indicate that a shift in the common bean productive areas is highly likely with a loss of suitability of the current common bean cultivation areas and an increase in cold regions such as Canada, the Nordic countries and Russia. The results indicate the likelihood of changes in climatic suitability and the distribution of common bean at a global scale under a future climate, which will affect regions where this legume is a staple crop and an important source of household income. Regions in the Northern Hemisphere could take advantage of the increase in suitability by increasing the production and exportation of this grain.

In the fifth study, we used the overlays of the distributions of beet armyworm (Spodoptera exigua), a secondary common bean insect pest, soybean rust (Phakopsora pachyrhizi), a secondary fungal diseases of common bean and P. vulgaris as potential host to demonstrate and assess their interactions. Worldwide, crop pests (pathogens and insects, CPs) affect agricultural crops detrimentally. These negative effects, coupled with the impact of climate change, are a cause of major nutritional and economic losses. Secondary pathogens may increase in importance under global warming conditions. The use of species distribution models, such as CLIMEX, is invaluable for projecting current and future suitability of CP localities. The soybean rust and beet armyworm model projections show consistent agreement with the known global distribution. In the current scenario, suitable climate conditions for both CPs are predicted in all continents. A general reduction in suitability between the Tropic of Cancer and the Tropic of Capricorn is likely under future scenarios. Regarding the risk of these CPs occurring in common bean, a reduction is likely for the middle and the end of the century. The most relevant findings of this study were the reduction of the suitable areas for the CPs, the reduction of the risk under future scenarios and the similarity of trends for the CPs and host. The current results highlight the relation between and the coevolution of host and pathogens. Thus, the study overlays the distributions of two CPs and a potential host to demonstrate and assess their interactions, which has rarely been performed previously in climate change studies.

In the last study, we focus our study on Mexico to analyse in depth the global models previously performed. A general reduction in suitability for maize and common bean as well as for the plagues and diseases under study is shown through for territory by the middle and end of the century. The reduction of suitability may be caused by the increase of heat and dry stresses. We also propose a methodology of downscaling and other techniques to improve the model in CLIMEX of the current and future suitability of the species under study. Later we will be able to continue doing the same investigations in other countries to discover their particular strengths and weaknesses for the future productions of these two staple crops under climate change.