Agricultural biotechnology, such as genetic modification, has been proposed as a way to face food security and climate change. All new crop varieties with altered genetics must be subjected to safety assessments to fulfil regulatory requirements, prior to marketing and/or commercial release. The aim of this thesis is to undertake part of the safety assessment of transgenic plants, using emerging molecular biology technologies. Initially, the molecular characterisation of two genetically modified plants were performed using long read DNA sequencing. Results demonstrate the capability of this technique to characterise transgenes located in complex and or repetitive regions of the plant genomes, in a fast and cost effective way with simple and robust bioinformatic pipelines that would be broadly applicable and accessible. Then, a reliable methodology was developed using droplet digital PCR tools for the detection of transgenes in a variety of complex pasture based products relevant to livestock industries. Later, a toxicological assessment of the high energy perennial ryegrass was performed using a metabolomics approach. The current study indicates that the new technologies can provide a highly reliable and efficient solution for the safety assessment. This thesis represents a contribution in the use of new technologies to improve the risk assessment procedure of genetically modified plants.

Microbes are a vital part of ecosystems and play key roles in the essential processes of the functioning. In agriculture, microbial ecology has wide reaching impacts on crop growth and quality commodity production. As a high value agricultural product, wine is a useful model for elucidating the effects of microbial ecology from the vineyard to the winery. Microbial growth and metabolism is an inherent component of wine production, influencing grapevine health and productivity, conversion of sugar to ethanol during fermentation, and the flavour, aroma and quality of finished wines. Recent advances in genetic sequencing and metagenomic approaches has extended our understanding of microbial distribution patterns and established the unique biogeography model in viticulture. While the contributions of microbial biogeography to wine metabolites and regional distinctiveness (known as terroir, a well-recognised and celebrated character in wine industry), and by which mechanisms, remain tenuous. This thesis focuses on the microbial biogeography of wine, the interplay between microbial patterns and affecting factors, and how these patterns drive wine quality and styles. I begin by investigating the distribution patterns of bacteria and fungi at large scale, and their roles in shaping wine characteristics. Samples were collected from vineyard soil, grape must, and wine ferments across six geographically separated wine-producing regions in southern Australia (~ 400 km). Soil and grape must microbiota exhibited distinctive regional patterns, as well as wine aroma profiles. Associations among soil and wine microbiota, abiotic factors (weather and soil properties), and wine regionality were modelled, highlighting that fungal communities was the most important driver of wine aroma profiles. Source tracking wine-related fungi in the vineyard suggests that soil is a source reservoir of grape- and must-associated fungi which might be translocated via xylem sap. I then move on to elucidate the fungal ecology within vineyards. Fungal communities were characterised over space and time that associated with the grapevine (grapes, flowers, leaves, roots, root zone soil) during the annual growth cycle (flowering, fruit set, veraison, and harvest). Fungi were significantly influenced by the grapevine habitat and plant development stage, with little influences from the geographic location (<5 km). The developmental stage of veraison, where grapes undergo a dramatic change in metabolism and start ripening process, saw a distinct shift in fungal communities. A core fungal microbiota of grapevines (based on abundance-occupancy models) existed over space and time which drove the seasonal community succession. Beyond coinciding with the changing plant metabolism and physiology, strong correlations with solar radiation and water status suggests that the core microbiota changes with respect to the changing environments during plant development. I further investigate fungal contributions to wine aroma profiles by quantifying multiple layers of fungi, combining metagenomics and population genetics. Fungal communities were characterised associated with Pinot Noir and Chardonnay grape must/juice and ferments coming from three wine estates (including 11 vineyards) in the Mornington Peninsula wine region. At this scale (< 12 km), fungal communities, yeast populations, and Saccharomyces cerevisiae populations differentiated between geographic origins (estate/vineyard), with influences from the grape variety. During spontaneous fermentation, growth and dominance of S. cerevisiae reshaped the fungal community and structured the biodiversity at strain level. Associations between fungal microbiota and wine metabolites highlights the primary role of S. cerevisiae in determining wine aroma profiles at sub-regional scale. Overall, this thesis provides a significant body of knowledge to the microbial ecology field. Using vineyards, grapes, and wine as a model system, these findings relate microbial biogeography, environments, and quality agricultural commodity production. It provides fundamental perspectives to conserve the biodiversity and functioning for sustainable agriculture under the changing climate.

Most of the lentil and field pea grown in Australia are exported to India and surrounding countries, to the Middle East, Turkey and North Africa. While each country may utilise pulses differently, common to all, is that quality is based on the visual characteristics of the whole-grain and split-pulse, and its cooking quality. One of the objectives of pulse-breeding programs is to ensure that the quality traits of new varieties align with the preferences defined by the export markets. Pulse-quality traits were historically determined using empirical tests to quantify seed size, colour, contamination and defects. Since many of these tests are time-consuming to perform, comprehensive quality evaluation is reserved for advanced germplasm. Therefore, adoption of rapid and objective methods would improve efficiency and consistency of quality evaluation and enable comprehensive assessment of early generation lines. Technological advances in digital imaging and machine learning has seen a broad application of machine vision to assess agricultural products. While there is extensive research in this field, there are still relatively few machine vision methods which have been developed for the quality-assessment of lentil and field pea grains. Within this study, rapid and objective methods were developed to assess three grain-traits, which related to visual characteristics of lentil and field pea and were identified to be important within breeding programs. The targeted applications were the classification of broad market classes of field pea, quantitation of bleaching discoloration within the ‘green pea’ market class and classification of split and dehulled fractions of lentil and field pea post milling. Machine vision algorithms were developed based on the analysis of multispectral images. Linear discriminant analysis, based on image-derived colour, shape and size features, was used for the classification of field pea market classes. The model was applied to sound and defective grain samples, achieving perfect classification of sound grain and distinguishing sound from defective grain with 97% accuracy. The extent of bleaching in green field pea samples was quantified through an objective model which was developed on visible reflectance spectra (spectrophotometric analysis) and subsequently adapted for image-based analysis of grain colour. The image-derived colour scores closely matched the spectrophotometric analysis and additionally enabled the distribution or uniformity of bleaching to be objectively quantified within each sample. Furthermore, through the image analysis scoring system, the relative susceptibility to bleaching, of each genotype, was also quantified. Milled fractions of lentil and field pea were classified through the application of artificial neural networks, where network architectures and inputs were compared. A convolutional neural network, trained on image-derived feature distributions, was found to be the most accurate and computationally efficient model. Machine vision is an expanding field of research which offers the potential for consistent, accurate and rapid product-quality evaluation. The results of this study demonstrate the efficacy of machine vision applications throughout the pulse value chain and particularly within germplasm enhancement programs. Adoption of machine vision systems can increase the capacity for comprehensive screening at all stages of breeding which is currently not practicable through standard assessment methods.

The recovery of P from organic waste streams (known as organic amendments, OA) is becoming increasingly popular. Besides a source of P, OA have also been reported to increase soil P availability and reduce P adsorption in acidic soil. The main mechanism involves the reduction in the soil P adsorption sites (especially Al and Fe) by the organic anion producing compounds of the OA. Organic anions form organometallic complexes in the soil to reduce P adsorption. The potential representative organic anion producing compounds of the OA are phenolic and carbonyl compounds. The phenolic and carbonyl compounds usually represent the aromatic (such as benzoic, hydroxybenzoic, protocatechuic acids etc) and aliphatic (such as oxalic, malic, citric etc) organic acids, respectively. This study aimed to investigate if these signature phenolics and carbonyl compounds of the OA can be used to predict their role in soil P availability for future prescriptive applications. An acidic soil (Red Chromosol) from the Rutherglen, northeast of Victoria, Australia was collected and waste from two different streams namely food waste and biosolid and their three different processed forms (untreated or raw, biochar and compost) were utilized as sources of OA in this study. Nuclear magnetic resonance (NMR) spectroscopy was utilized to identify forms of C (solid-state 13C NMR) and P compounds (solution-state 31P NMR) in the OA. The effect of OA on soil P availability was studied in a 110-day laboratory incubation study. Further, some selected representative compounds of phenolic and carbonyl C of OA (aromatic and aliphatic organic acids) were tested against soil P availability in another 110-day laboratory incubation experiment. Finally, a plant bioassay experiment with Triticale (genus Triticosecale) was conducted to understand the effect of both OA and organic acid on soil P availability and plant P uptake with or without the addition of external P. Results from incubation of OA with soil showed an increase in soil P availability (Olsen P) and a decrease in soil P buffering capacity, (PBC). An additional increase in soil Olsen P was observed above the total amount of Olsen P from OA that was added. It might imply that this additive increase of the soil Olsen P was due to the substitution of previously fixed P by the action of organic anions (coming from the dissociation of phenolic and carbonyl compounds) and formation of the stable organometallic complexes. This was further supported by a strong and positive correlation between the delta Olsen P (difference between observed and expected Olsen P) and phenolic and carbonyl C content of the OA. The phenolic and carbonyl C content of the OA also showed a significant correlation with the decrease of soil PBC (delta PBC, the difference between treatment and control). In both correlation studies, the ratio of phenolic to carbonyl C compounds of OA showed a strong correlation with soil P availability compared to their total abundance. The contrasting nature of phenolic and carbonyl compounds was speculated as to the reason why there was a high correlation between soil P availability and the ratio of phenolic to carbonyl C content of OA. The OA with a nearly equal abundance of phenolic to carbonyl C content showed a maximum increase in soil P availability. Therefore, it was concluded that the ratio of phenolic and carbonyl C content of OA could be used to predict P availability in acidic soil. In the next study, some naturally occurring aromatic organic acids (representative of the phenolic compounds) and aliphatic organic acids (representative of the carbonyl compounds) were added either individually or in combination (at 1:1 ratio of aliphatic and aromatic organic acids). The experimental results suggested that aliphatic organic acids were more effective in increasing soil P availability and decreasing soil PBC compared to aromatic organic acids. However, the effect of aliphatic organic acids on increasing soil P availability was prolonged when applied in combination with aromatic organic acids at 1:1 ratio. Therefore, this study concluded that the effect of an OA can be predicted based on their phenolic and carbonyl C content. Finally, the results from the plant bioassay experiment showed that the addition of OA increased the soil P availability irrespective of addition of external P to the soil. As hypothesized in the previous study, this increase in soil P availability after OA addition was expected to show a strong correlation with the ratio of phenolic to carbonyl C content of the OA. The correlation study between the soil P availability and the ratio of phenolic to carbonyl C content of the OA showed a moderate to weak correlation. The differences in those studies (laboratory incubation vs pot) were speculated as to the reason for obtaining this moderate to week correlation between the soil P availability and ratio of phenolic to carbonyl C content of the OA. In the plant bioassay experiment, OA and P were added simultaneously to the soil. Therefore, a competition between organic anions (which was coming from dissociation of organic acid compounds of OA) and P and was expected to increase P availability in the soil by reducing P adsorption. However, the preferential sorption of P by Al and Fe compared to organic anions was speculated as the main reason for observed moderate correlation. The phenolic and carbonyl C content of OA would correlate strongly with the soil P availability if OA were added first (which might reduce P sorption by forming organometallic complexes) and then P to the soil as also observed in previous study. Therefore, it was concluded that the phenolic and carbonyl C content of the OA would predict soil P availability better if OA was first added (which would form organometallic complexes) and then P added to the soil rather than adding both simultaneously. The addition of OA significantly increased the plant P uptake and showed a positive correlation with soil Olsen P. There it was concluded that soil Olsen P was a good indicator of plant P availability. In the plant bioassay experiment, organic acid treatments showed no significant effect on soil P availability and plant P uptake compared to the control. This might be due to the addition of organic acids at 10 times lower concentration in this experiment compared to the previous incubation experiment. In conclusion, this thesis showed that the ratio of the phenolic to carbonyl C content of the organic amendments could be used to predict the role of organic amendments on increasing soil P availability. The availability of fertilizer P could also be predicted by phenolic and carbonyl C content, if OA added first and then P added to the soil compared to their simultaneous addition. The OA with a nearly equal abundance of phenolic and carbonyl C content would have a maximum effect on increasing soil P availability. This knowledge would be beneficial for farmers, agricultural landholders and especially OA producers to assess the impact of their organic waste products on soil P availability in the quickest possible time based on the abundance of the signature C compounds (phenolic and carbonyl).

The quality of cooked meat is valuable for consumers and meat industry. The aim of this research was to identify structural determinants of the quality of cooked meat. Muscle type (bovine semitendinosus, psoas major, biceps femoris), cooking temperature (45 C to 85 C), ageing time (14 vs 0 days in beef; prolonged 15 vs conventional 3 days in pork), enzyme inhibition (with/without cathepsin inhibitor) and fibre type (bovine masseter 100 percent type I; cutaneous trunci 93 percent type II) were investigated factors affecting meat quality. Methods for measuring quality (cooking loss and Warner- Bratzler shear force (WBSF)), structural changes (shrinkage) and protein denaturation [Differential Scanning Calorimetry (DSC) and Fourier Transform Infrared (FTIR) microspectroscopy] were used. Cooking loss was higher in semitendinosus compared to biceps femoris and psoas major; and it increased with temperature in beef and pork. Cooking loss increased with ageing of beef independent of temperature and muscle type; and decreased with prolonged ageing compared to conventional ageing, of pork (cooked at 70 C and 80 C). The denaturation enthalpy of masseter and cutaneous trunci explained 58 and 59 percent of the variation in cooking loss, respectively. Reduction of WBSF in bovine muscles rich in collagen (all but psoas major) with cooking at 60 C to 65 C was attributed to collagen denaturation. The increase in WBSF in unaged beef with cooking at 70 C and 80 C was attributed to intact titin denaturation. In relation to shrinkage, 3D laser scanning was compared to caliper measurements, and was found inferior in measuring volume and predicting cooking loss. Cuboids` transverse and longitudinal shrinkage were higher in muscles with higher collagen content and sarcomere length, respectively. Transverse shrinkage started 5 C higher in psoas major fibre fragments, compared to semitendinosus and biceps femoris, likely due to predominant type I fibres. It was proven that transverse and longitudinal shrinkage of fibre fragments is caused by myosin and actin/titin denaturation, respectively. Since ageing reduced the longitudinal shrinkage of cooked beef (biceps femoris and psoas major cuboids at 80 C, semitendinosus and biceps femoris fibre fragments at temperatures greater or equal to 75 C) and pork, an important role of titin in longitudinal shrinkage was hypothesized. Cathepsin inhibition reduced the longitudinal shrinkage (semitendinosus, biceps femoris, psoas major cooked at temperatures greater than 75 C), and increased the transverse shrinkage (semitendinosus at temperatures greater or equal to 60 C) of fibre fragments. Longitudinal and transverse shrinkage were major contributors to cooking loss (beef and pork) and WBSF (beef), respectively. Cutaneous trunci had higher cooking loss (at temperatures lower or equal to 75 C), higher transverse (at temperatures lower or equal to 60 C), longitudinal (at temperatures lower or equal to 80 C) and volume shrinkage of fibre fragments (at temperatures lower or equal to 65 C); as well as lower transition temperature of myosin, higher reduction in alpha-helix and beta-sheet, and higher, compared to masseter, formation of beta-aggregated strands, random coil and aromatic side chains (at temperatures lower or equal to 60 C). The differences in protein denaturation and shrinkage between masseter and cutaneous trunci cooked at 55 C were attributed to the myosin isoform, while the differences in muscle fibre and connective tissue proteins’ denaturation at 60 C and 65 C were pH dependent. Myosin (isoform, denaturation), actin (denaturation), titin (degradation, denaturation), collagen (content, denaturation) and sarcomere length were proven or postulated, as structural determinants of the quality of cooked meat.

The main objectives of this project were to: 1) show that lettuce anthracnose propagules that persist in soil from a previous lettuce crop may be controlled by a cold tolerant strain of Trichoderma inoculated just before the pathogen becomes active and virulent, reducing incidence and severity, and, 2) determine if liquid cultures containing Trichoderma secondary metabolites (TSMs) can be sprayed for maximum leaf coverage to reduce the incidence and severity of the disease when condition for disease are ideal. Lettuce anthracnose Microdochium panattonianum (MP) is a key winter disease in Victoria, Australia, and other temperate regions in the world. Cultural methods to reduce the severity of this disease are not practical nor economically feasible. While chemical control can be achieved it is not flawless and can cause health issues. Propagules of MP persist in soil sheltered in leaf debris and germinate with the onset of cold and wet conditions in the subsequent winter. Unfortunately, this pathogen has received little scientific attention but as winters become wetter this disease is causing greater loss and this body of work offers a more sustainable management tool. Trichoderma species are common saprophytic fungi in soils rich in organic matter. They have a proven ability to control crop diseases with a multiplicity of strategies including parasitism, competition, antibiosis and, at the same time, stimulating plant defences and growth. However, these natural processes vary with species and strains of Trichoderma. This research project showed that the incidence and severity of the lettuce anthracnose can be reduced by applying Trichoderma cold tolerant strains to the soil. Secondly, it showed that spraying Trichoderma liquid filtrates containing metabolites to the leaves also reduced and managed lettuce anthracnose. From a pool of 27 Trichoderma isolates, 8 grew at 10 C degrees. These 8 isolates were characterised morphologically in vitro under different culturing conditions of temperature, pH and media. Some isolates were identified by molecular techniques to species while others still require more investigation. Tests in vitro on solid media prepared with liquid filtrates confirmed that liquid filtrates from one isolate related to T. viride and one from T. composticola affected the morphology and growth of MP. These filtrates contained 6 pentyl-alpha-pyrone (6PP,) a volatile metabolite with a characteristic coconut smell. Other Trichoderma liquid filtrates containing metabolites such as cytosporone S and 6PP, produced by some strains of T. aureoviride, T. atroviride and Trichoderma sp., killed the pathogen. Fourteen isolates produced 6PP, a well-documented Trichoderma secondary metabolite (TSM). Of these, some have been identified as T. viride, T. composticola, T. atroviride, T. paratroviride, T. neokoningii and T. asperelloides. Others are yet to be fully identified to species. Isolates of T. harzianum, T. polysporum. T aureoviride, T. longibrachiatum and T. spirale did not produce this metabolite.Isolates of Trichoderma, TC1, CAROL, 71558 and 1536 require further identification because they were outliers on the phylogenetic tree. None of these isolates produced 6PP.Challenged isolates produced higher quantities of 6PP than did the individual liquid cultures. Trichoderma atroviride (PMF) from New Zealand produced 137 mg/l of 6PP, but when challenged by Trichoderma paratroviride (NSW) the 6PP concentration was 160 mg/l. Incidence and severity of MP were reduced significantly in a field trial using the cold tolerant isolate 356 related to T. composticola. TSMs applied as foliar sprays have the potential to control many foliar diseases in crops and is a new field of research. The use of Trichoderma cold tolerant strains for control of winter active pathogens is a new strategy for the use of Trichoderma products.

Intensive livestock production systems, such as cattle feedlots, play an important role in meeting the increasing global demand for animal products, driven by a growing population and increasing affluence. These intensive systems account for a significant proportion (~39%) of global atmospheric ammonia (NH3), which is released from the large amounts of manure generated. In cattle feedlots, the loss of NH3 represents about 75% of the excreted nitrogen (N) in the manure and this has important implications for environmental pollution. Consideration of management strategies to reduce this loss provides potential to obtain N enriched manures that can be used as fertilizer. A number of mitigation techniques have been shown to reduce NH3 loss from manure. These include: acidifying agents and urease inhibitors (both requiring frequent reapplication), dietary manipulation (can affect animal productivity) and manure compaction and covering (only applicable to stockpiled manure). Lignite (brown coal) has a demonstrated capacity to suppress NH3 emission from manure by 30-66% and is seen as a more effective, practical and potentially long lasting option. Lignite’s ability to effectively reduce the loss of NH3 from manure has been credited to its pH, cation exchange capacity (CEC), pH buffer capacity and labile carbon (C) content. However, we do not fully understand what the actual capacity for N retention by lignite is, or the main mechanisms by which lignite retains N, and how these are influenced by the properties of the lignite and changes in the environmental conditions when lignite is mixed with other materials (such as manure). Also, the impact of lignite on the quality of the manure during deposition, storage, processing (such as composting) and land application, has not been studied. The objectives of this study were to: (i) characterize different lignite materials for their capacity for nitrogen retention, and to understand the mechanisms of N retention; (ii) determine how lignite amendment of manure affects the composting process under both field and laboratory conditions by monitoring changes in biochemical parameters and gaseous emissions that occur during composting, and (iii) determine the C and N mineralization from non composted and composted manure applied to soil and how this is influenced by lignite. The capacity for N retention by lignite, and the mechanisms of N retention were determined by characterizing five lignites sourced from Victorian brown coal deposits. The chemical properties that were examined for each lignite (e.g. pH, total and labile C, forms of C, pH buffering capacity, CEC, etc.) were related to its ammonium (NH4+) adsorption capacity as a function of pH and also to the biological immobilization of N in the lignite. The properties of the lignites, their capacity for NH4+ adsorption and the immobilization of N, were determined through a series of laboratory experiments involving SEM, 13C NMR spectroscopy, sample digestion and extraction, batch adsorption isotherms techniques, and controlled environment incubations. Lignite’s impact on composting of manure was assessed under field (windrow) conditions to determine the benefits under typical industry scale management processes. The mechanisms by which lignite affected composting of manure was determined under laboratory (in-vessel) conditions. Changes in biochemical parameters (e.g. N forms, organic matter and pH), emissions of NH3 and greenhouse gases (GHG), as well as compost maturity indices, were monitored. Lignite’s effect on C and N mineralization from manure (non-composted and composted) when applied to soil, was determined through a laboratory incubation experiment which monitored CO2 evolution (as a measure of C mineralized) and changes in NH4+ and NO3- concentration in soil (as a measure of N mineralized) over a period of 40 days. The mechanism by which lignite retains N was found to be mainly through pH dependent adsorption of NH4+ on exchange sites of deprotonated carboxyl groups. The maximum NH4+ adsorption capacity (Qmax) increased up to 3 fold when pH was increased from 3.6 to ~7. Biological immobilization of N was insignificant (e.g. maximum of 0.1 mg N g-1 lignite) compared to NH4+ adsorption on exchange sites (e.g. highest Qmax of 25.6 mg NH4+-N g-1 lignite at pH ~7). These findings suggest lignite’s ability to suppresses NH3 from manure occurs by i) initially favouring the formation of NH4+ over NH3 due to the acidic pH of the lignite, and ii) deprotonation of more carboxyl groups with continuous deposition of alkaline manure leading to increased CEC of the lignite and increased retention of NH4+. Amending manure with lignite did not inhibit the composting of manure. The addition of lignite suppressed the emission of NH3 from manure during both field windrow (by 45%) and laboratory in-vessel (by 35-54%) composting. Lignite addition reduced the emissions of GHGs (12-23% for CO2, 58-72% for N2O and 52-59% for CH4) during in-vessel composting. However, during windrow composting, addition of lignite caused the emissions of GHGs to increase (41% for CO2, 136% for N2O, and from -5.0 mg kg-1 initial dry matter (DMi) day-1 in the manure only to 9.8 mg kg-1 DMi day-1 for CH4). The higher emissions of CH4 and N2O were presumed to be due to anaerobic pockets that developed within the lignite treated windrow resulting from the small particle size of the lignite, and facilitated by the largely passive aeration method (unlike the forced aeration for in-vessel composting) used during the windrow composting. For the in-vessel composting, lignite addition to manure increased the organic matter (OM) and N contents of the final compost by 10-19 and 28-38% respectively, and also the germination index, a measure of compost maturity, (from 71% to 90-113%). These changes were not observed under windrow composting conditions likely due to the passive aeration method used. In addition, the effect of lignite in the windrow compost may have differed to that in the in-vessel systems because i) the mode of manure collection using large scale field equipment meant that the lignite content of the manure was estimated based upon that applied but could have been less due to some being left on the pen surface, and ii) the source of soil used in the cattle pens was quite alkaline (pH 8.8) which may have reduced the lignite pH effect. Lignite addition to the manure suppressed microbial activity (soil respiration) which reduced the mineralization of C from the manure when applied to soil, more noticeably when the manure was composted. Over a 40-day incubation period, with non-composted manure application rates of 30 and 60 t ha-1 soil, the C mineralized was 26.4 to 27.8% for manure only, and with lignite amendment it was 16.3 to 21.4%. The corresponding C mineralized in the composted manure was 12.4 to 14.1% and 3.5 to 6.5%. The addition of lignite had a mixed effect on N mineralized from manure when applied to soil. The N mineralized was significantly higher in the non-composted manure amended with Loy Yang lignite (10.4 to 13.5% for 30 and 60 t ha-1) than with Bacchus Marsh lignite (4.1 to 9.8%) and non-composted manure only (3.2 to 8.7%). For composted manure, there was no significant difference between N mineralized in the manure only (4.8 to 6.7%) and the lignite treatments (2.5 to 7.8%). Results presented in this study, for the first time, show the dominant N retention mechanism by lignite in manure, its influence on biochemical changes and gaseous emissions during manure composting under both laboratory and field conditions, and finally how the lignite impacts nutrient mineralization from non-composted and composted manure when applied to soil. In conclusion, this study shows lignite’s capacity to mitigate the emissions of both NH3 and GHGs from manure under optimum composting conditions. Hence, in intensive livestock production systems, lignite has the ability to improve the agronomic value of the large volumes of manure generated and reduce the environmental pollution associated with livestock production and manure management. Lignite addition to manure, especially when composted, has the potential to increase soil OM and improve long term soil health due to the inhibitory effect of lignite on C mineralization from manure. The findings of this study provide the option for the use of lignite as a tool for sustainable livestock production in intensive livestock industry.

Antimicrobial resistance (AMR) has become a global issue for human and animal health and welfare. It narrows down the choice of antimicrobials to treat infections and increases the costs of treatment. Effective antimicrobial stewardship is critical to ensure antimicrobials are used appropriately. Monitoring the antimicrobial resistance genes (ARGs) in bacteria is one of the important parts of antimicrobial stewardship. Bacteria in animal faeces harbor various ARGs. The traditional culture-based approaches to detect ARGs in the faecal bacteria are limited to the culturable bacteria, which only represent a small fraction of the faecal microbiome. The culture-independent approaches, such as high-throughput qPCR (HT-qPCR) and the next generation sequencing, bypass the limitation of culture and allow us to characterise the ARG profiles of the total bacterial community. These approaches have been widely used to detect and quantify ARGs in the faecal microbiomes of animals in various countries, but few of such studies have been done in Australia. In this project, faecal samples were collected from foals, calves, chickens and pigs, raised in commercial farms. The foals and chickens had no history of antimicrobial treatment. Calves were expected to have low chance being exposed to antimicrobials and only the pigs might be medicated. ARGs of the major antimicrobial classes, mobile genetic elements (MGEs) and metal resistance genes (MRGs) in the faecal samples were detected and quantified using a HT-qPCR array. The faecal microbiomes were determined by amplifying the V3-V4 region of the bacterial 16S rRNA gene and sequencing the amplicons on an Illumina platform. In addition, environmental swabs were collected from the chicken and pig farms and the microbiome and ARGs profiles of the swab samples were analysed to determine whether the environmental sampling could be used to study ARGs in animals raised intensively on a large scale. Overall, tetracycline resistance genes (tet) encoding ribosomal protection proteins and macrolide resistance genes (mef and erm) were the dominant ARGs in the faecal samples regardless of the animal species. The high level of these genes could be explained by the predominance of the potential bacterial hosts, such as Bacteroides spp., in the faecal microbiomes. The ubiquitous presence of the tet and mef/erm genes in animals suggested these genes are persistent and are not necessarily associated with the antimicrobial usage. On the other hand, the faecal samples had very low level of extended spectrum beta lactamase genes, blaCMY and blaCTX-M, carbapenems resistance gene cphA, fluoroquinolones resistance gene qnrB and virginiamycin resistance gene vatE, which suggested animals with low antimicrobial exposure had low risk of carrying ARGs that confer resistance to antimicrobials of high clinical concern. Manure belt swabs collected in the cage chicken sheds were appropriate to study ARGs associated with caged poultry. However, the floor swabs in the chicken and pig farms did not reflect the ARG profiles of the animal faeces due to insufficient biomass for DNA extraction or great changes in the microbiome composition compared to the faeces. In conclusion, this project showed that HT-PCR is an efficient method to screen a range of ARGs in complex samples. Analysis of ARG profile of animals without antimicrobial exposure set the baseline of presence and abundance of ARGs in animal faeces. Diverse ARGs detected in these animals suggests the persistence of ARGs in faecal microbiome. The results are useful for future studies investigating whether the current antimicrobial use practices can select and enrich pre-existing ARGs in farm animals.

Lentil is one of the important pulse crops in the world; however, its production is threatened by economically important diseases. Two of the devastating seedborne diseases of this crop, across the world and in Australia, are Ascochyta blight, caused by Ascochyta lentis, and Botrytis grey mould, caused by Botrytis cinerea and Botrytis fabae. Lack of genetically diverse sources of disease resistance in cultivated lentil varieties has increased dependence on fungicides to control these diseases. However, still, huge production losses are recorded worldwide as overuse of fungicides has resulted in the pathogen adaptation by mutations leading to their resistance and a reduction of fungicides efficiency. Therefore, there is a dire need for the development of an environmentally friendly physical method to be implemented in the integrated disease management scheme in pulse crops, including lentil. Microwave radiation is a sustainable and environmentally safe technology for food and agricultural processing. Its use for thermal treatment has shown great potential for sterilisation of food material as well as eradication of pests and pathogens from agricultural commodities. However, its potential in the grain industry and the control of related pathogens have not been fully explored, probably due to the concerns related to the resulting grain quality. Additionally, the indirect use of microwave, as a source for processing gas to produce non-thermal plasma followed by treatment of the seeds with the plasma, has recently gained a lot of attention. Therefore, the present study aimed to develop a thermal or non-thermal process, based on microwave radiation, to disinfect lentil seeds from its seed borne pathogens. The potential of a microwave multi mode cavity with a turntable for the eradication of AB of lentil seeds at different seed moisture contents, microwave powers, and exposure times was evaluated. This process was assumed to be like the industrial scale microwave system, with a conveyor belt, in terms of heat uniformity and efficiency of pathogen control. It was proven that the pathogen could be removed faster at higher seed moisture content; however, the seed viability was also more susceptible to microwave radiation at the higher seed moisture content (19% wet based). Infected seed percentage (IS%) reduced from 17% to 8.9%, at a seed moisture content of 9.1%, by applying a 100% power level (maximum 1100 W) for 51 s without a significant seed germination loss. Nevertheless, seed vigour (measured by electrical conductivity) was negatively affected by these process parameters. Investigation of heat uniformity in this process showed that the difference between hot and cold spots could reach as high as 50 C, which may account for the seed vigour loss before completing the eradication of the pathogen. To improve heat uniformity, a microwave fluidised bed was designed and manufactured. The efficiency of this process, in the eradication of seed borne Botrytis grey mould of lentil seeds, was firstly evaluated by investigation of the effective factors, including microwave power, exposure time, air temperature and seed moisture content with responses of IS%, seed germination, seed vigour, seeds bed temperature, and moisture loss. The results showed that a 30% reduction in IS% could be achieved by applying microwave power of 300 W and air temperature of 60 C or microwave power of 400 W and air temperature of 50 C for 10 min at the seed moisture content of 18%, without a significant reduction in seed viability and vigour. The temperature history, measured at two points in the fluidised bed using fibre optic probes, showed that the difference between hot and cold spot did not exceed 5 C. It confirmed that there was a very good heat uniformity in the microwave fluidised bed process. Evaluation of the effect of factors in the previous study showed that exposure time was an effective factor in reducing the IS%, while it did not have a significant effect on seed germination. To determine whether more reduction of the IS% could be achieved at prolonged exposure time, IS% reduction was examined in a drying experiment in the microwave fluidised bed dryer at the same process parameters as the previous experiment. The drying kinetics and time saving, compared with the conventional fluidised bed, were also studied. The results confirmed that the same reduction of the IS% occurred, and therefore increasing exposure time did not improve the reduction of the infected seeds; however, it proved to be a very effective drying process (more than 54% reduction in the drying time). It means that the greatest reduction in infected seeds occurred during the first 10 min of the process. The reason for not having more reduction in IS% after a specific time could be the very fast desiccation of the pathogen during the treatments, which increased its thermal resistance and subsequently the minimum power, or temperature required for its eradication. The seeds, which were dried in the previous experiment, were evaluated for any quality changes by examining their antioxidant enzyme activities, cooking quality, and their macronutrient using Fourier transform infrared (FTIR) micro spectroscopy. It was concluded that there was no significant quality deterioration in the most efficient process parameters (400 W & 50 C). In conclusion, there is great potential for microwave disinfection of lentil seeds under the condition where the hot spot is controlled so as not to harm the seed quality. It could be achieved by microwave assisted drying with at least a 54% reduction in the drying time compared with conventional fluidised bed drying. One hundred percent eradication might not be achieved, but it can be considered as part of an integrated disease management process in lentil crops, with the ultimate goal of reducing initial fungicide application for seed treatment and later applications for the crop. However, there might be concerns over the heat tolerance of different grains and different batches of the same grain, which was the reason for considering the non-thermal treatment with microwave plasma. Finally, the non thermal process of plasma, created from a microwave source, was examined for its potential in the eradication of Botrytis grey mould from lentil seeds. Non thermal plasma is the fourth state of the matter produced by energizing a gas and consists of various reactive species including atoms, ions, and radicals, which is a very promising non chemical method of seed disinfection with a growth enhancement effect. Two modes of treatment were considered: direct argon plasma at low power (400 W); and treatment with the afterglow of the air or air and argon plasma (10 s and 100 s) followed by holding the seeds in the trapped processed gas for 5 min to 24 h. There was a 41% reduction in the infected seed percentage (IS%) after 100 s of treatment with the afterglow of air plasma following by 24 h holding and a 32.3% reduction occurred when they were treated by 30% air and 70% argon plasma for 10 s and 60 min holding time. No significant change was observed in antioxidant enzyme activities of the treated seeds, except for triggering of catalase activity after 24 h of holding time. However, lentil seeds colour changed towards redness and yellowness after prolonged treatment time (400 s) or holding time (24 h). Therefore, the afterglow of microwave plasma or plasma processed air could be further explored as a great tool for the disinfection of grains, without any negative effect on their viability. Overall, both microwave fluidised bed and the afterglow of microwave plasma were able to reduce the seed-borne Botrytis grey mould of lentil seeds without any adverse effect on the seed viability. Microwave fluidesed bed would be useful when drying and disinfection are simultaneously desirable as the disinfection was just achievable at high seed moisture content with very fast drying of the seeds. However, the disinfection of dry lentil seeds was possible using the treatment with the afterglow of the plasma. Therefore, plasma treatment could be further explored for the treatment of other grains and their related pathogens if the dry seeds need to be disinfected.

ABSTRACT Some farms remain in the ownership of one family for several generations and others do not. This study is about family farms in Australia used for growing crops, running beef cattle and sheep, or operating with a mix of these activities. Why and how has the same family operated a farm for generations and why and how do other such family farms cease to continue in the same ownership? This work investigates the question of inter-generational succession of family farm businesses in the context in which there are three main aims of owners of family farm business. The definition of the three main aims is to provide adequately for retirement; pass on to heirs a farm that has reasonable prospects of being a sound economic proposition and financially viable and has potential for future improvements in productivity and growth of wealth for the farming child or children, provide a share of resources for the non–farming children that they consider being adequately commensurate with their entitlement and that they are content with that share. There is a large body of work about farm management economics and business growth. Rarely does farm management literature document the process of succession, or investigate, develop and report theory about the many factors that contribute to enabling a farm to remain in the ownership of one family. Studies that concentrate on the human, technical or the economic elements of farm management overlook the question of succession. Usually studies focusing on succession are unburdened by the complexities of farm economics. Knowing how and why farm families manage to ‘farm for generations’, or fail to do so, remains the domain of the farm families and their stories about attempted inter-generational succession. A mix of research methods was used to investigate the question of inter-generational succession of family farming businesses, in the context of farm economic theory and theory about the growth of the firm. Surveys of farmers and agricultural professionals and case studies of the farm succession experiences of families have been documented. The possibilities open for farm families discussed and an analysis of historical records of farm firms has been undertaken. Explorations of the options facing some current farming businesses and what they would need to do now to achieve successful succession have been used to illuminate the research questions about inter-generational succession. Central to the question of farm succession are the attitudes and attributes, experiences and actions of the owner-managers who run farm businesses. The real situations of farm owners, family members and managers, who have been through or will go through succession, have been investigated in this study. A pilot survey through an advisor network provided an assessment of over 6,000 of the 52,000-broad acre family farms in Australia. The case study method was used to analyse and contrast attributes, attitudes and actions of sixteen family businesses; half of these family businesses will continue farming, half will not do so. The historical records of 100 case study businesses were explored and their stories of succession documented. Succession analysis and planning was done for five current family farm operations facing up to succession. In 2016, 48 per cent of the 52,000-broad-acre farm businesses in Australia had an annual gross value of sales of $230,000, or less. There is no likelihood that farms with such low annual income will achieve the three main aims of succession. Most of the owners of broad-acre family farm businesses do not have a succession plan, do not intend to develop a succession plan for their business and do not have the scale to achieve the three main aims. For those farm businesses that have adequate scale, this alone will not ensure there will be a business for the next generation that has reasonable prospects of being a sound economic proposition and financially viable and has potential for future improvements in productivity and growth of wealth for the farming child or children. Farm families cannot achieve the three main aims of succession unless the business generates economic returns and annual cash flows and builds wealth at a level and consistency above the average for the district and the industry. Farm businesses must farm well, over a long time, for the three aims of succession to be achievable and for succession hopes and plans to become reality. Most broad-acre farm families in Australia cannot aspire to achieve the three main aims. The reasons are many and complex ranging from the economics and finance of farming to the scale and medium-term profitability of the business, to planning and intent, and the always-complex interpersonal relationships of families. This is of course as it must be. How else can the family farms that achieve succession grow, to be able to pass on the farm to family decades hence?

Climate variability and extreme climate events such as heat waves, droughts, extreme precipitation and frost occurrences are increasingly challenging the agricultural systems in Australia and globally. Despite this, the majority of the previous climate change studies have focused on the influence of average climate change on agricultural systems, which risks underestimating the impacts of climatic changes. In south eastern (SE) Australia, climate variability has increased in recent decades accompanying an increased frequency and severity of extreme climate events such as heat waves and droughts. The objective of this research was to investigate the impacts of changing climate variability and extreme climate events on pasture systems in SE Australia using biophysical modelling and controlled experimental approaches. Year to year variability in pasture yields has many consequences on the key management decisions such as stocking rates and the timing of the reproductive cycle. Changes to the pasture growth patterns were investigated at five sites in SE Australia ranging from medium rainfall, warm temperate climate at Wagga Wagga in southern New South Wales to high rainfall, cool temperate climate at Elliott in Tasmania using DairyMod biophysical software over the period 1960-2015. Across the sites, winter production has increased, spring pasture growth has decreased and year to year yield variability during autumn and spring seasons has increased in the most recent period (2002-2015) compared to 1988-2001. Increased number of days with water and temperature limitation together with increased spring and summer soil moisture deficit are in line with the simulated changes in pasture growth patterns, suggesting that adaptations such as incorporating deep rooting and heat tolerant species should be prioritized to stabilize pasture production. The year to year variability in pasture yield was better explained when extreme climate indices were used in combination with climate averages, as compared with climate average alone. Extreme climate indices together with the average climate variables explained more yield variability at the medium rainfall sites (eg. Wagga Wagga R2=0.89) than high rainfall sites (eg. Elliott R2=0.70) indicating that medium rainfall sites are more sensitive to the changes in rainfall distribution and high temperatures. Increased occurrences of dry months, wet months during the winter and spring, number of hot days above 30 C and the duration of hot days in a year decreased pasture yields highlighting the importance of considering extreme climate events in future climate change studies on agricultural systems. El-Nino Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) are two major rainfall drivers that influence rainfall variability in Australia and their phases reach the peak during the spring season which is the major pasture growing season in SE Australia. Each driver has a dry and hot phase (El-Nino and IOD(+)) and a cool and wet phase (La-Nina and IOD(-)). The influence of these phases individually and in combination were investigated on simulated annual pasture production from 1950-2015 in five sites in SE Australia. In dry and hot phases of both of ENSO and IOD (El-Nino and IOD(+)), lower pasture production was simulated, while the phases responsible for the wet and cool climate increased the yield. When combined ENSO-IOD phases were examined, the highest yields resulted when the La-Nina phases coincided with IOD(-) or neutral, whilst the El-Nino with IOD(+) phases led to the lowest yields. Forecast analysis revealed that the effects of climate driver phases emerge at the end of winter, but this is not a sufficient lead time for making important pasture management decisions. Therefore, further studies are warranted to increase the forecast ability of each climate driver phase to use them in agriculture decision making. Climate models project increased frequency of extreme climate events in SE Australia in the future. A controlled environmental experiment was conducted to investigate growth and physiological responses of four summer active temperate perennial pasture species to consecutive 7-day heat and drought stresses. Exposure of perennial ryegrass, tall fescue, cocksfoot and chicory to consecutive moderate (30/20 C, day/night) and severe (35/25 C, day/night) heat and drought stress revealed that all the species can acclimate to moderate combined heat and drought stress by maintaining the physiological functions such as photosynthesis, maximum photochemical efficiency of photosystem II, cell membrane permeability and relative leaf water content. However, chicory was the only species that maintained the above physiological processes under consecutive severe heat and drought stresses while all grass species decline to the minimum values. Plants that were irrigated showed cooler canopies than non-irrigated plants during high temperature treatments and this transpirational cooling mitigated the impacts of heat stress in all species. Leaf temperature data measured using infrared images during the experiment were used to validate the leaf energy budget equation and the calculated leaf temperatures (using the energy budget) were used to model heat stress impacts on perennial ryegrass in DairyMod model. The leaf temperature calculation incorporates the interaction of air temperature and soil water through the feedback effects of transpiration through stomata. The simulations run with calculated leaf temperatures predicted the observed reduction of photosynthesis accurately while air temperature simulations overestimated the actual impacts under moderate temperature, indicating that leaf temperature more accurately represents the environment under which plants are grown under heat stress rather than air temperature. Further, the DairyMod high temperature stress recovery function (T sum) for perennial ryegrass was parameterized using measured data of the experiment. The findings demonstrated that simulations of DairyMod can be improved using leaf temperature and parameterizing heat stress recovery functions. In conclusion, this research highlighted that the climate variability and extreme events have changed the pasture growth patterns in SE Australia in the recent period (2002-2015) therefore, climate variability and extreme climate events need to be fully considered in the future climate change studies. Chicory may be a more adapted pasture species in temperate livestock areas where extreme summer heat and moisture stresses limit summer feed supply. Leaf temperature modelling improves the heat stress simulations in the DairyMod model and this approach can also be used in other crop simulation models to improve high temperature stress modelling. Future research should aim to identify the plant traits and key metabolic processes in Chicory that confer greater heat stress tolerance and what other species would have similar traits. Future research on climate change impacts should also aim to determine critical combinations of extreme events that would result in tipping points for farming systems.

Nigeria is an agrarian economy with over seventy percent of the population engaged in agriculture. However, the nation depends heavily on food imports. Nigerian food producers are predominantly resource-constrained poor farmers, who are the most food insecure. Nigerian agriculture is chiefly conducted to meet household food requirement but is gradually transitioning to semi-subsistence agriculture. Agriculture was once the mainstay of Nigeria. The Nigerian agricultural sector was abandoned for the oil sector in the early 1970s. This neglect has negative consequences on the country’s agriculture. Presently, Nigerian agriculture is characterized by low performance. Nigeria, once a net food exporter has become a net food importer. With a view to enhancing the performance of Nigeria farmers, improved technologies have been developed and disseminated to farmers. In spite of this, there is food insecurity and poverty intensification in the country. This raises the questions whether or not farmers are adopting these technologies and the efficacy of these technologies in enhancing farmer performance and alleviating poverty in the country. Yam is a significant crop in Nigeria. It is a highly prized crop in the country. It has sociocultural, medicinal, nutritional and economic value. It is nutritionally superior to comparable crops including sweet potato and taro. Notwithstanding, yam farmers in Nigeria are performing poorly. Yam production in Nigeria is mainly impeded by high cost, unavailability of planting material, and over reliance on labour-intensive traditional yam production methods which are expensive, encourage the use of low quality planting materials, and inhibit mechanization of yam production. Yam Minisett Technology (YMT) is an on-farm yam multiplication technique which enables development of high quality planting materials for yam production. The aim of this project is to ascertain the potential of new technology and increased farmers efficiency for wellbeing improvement with reference to yam production and YMT in Nigeria. The specific objectives of this project are to: (i) describe yam production in Nigeria; (ii) compare farm activities and yam production systems in Nigeria; (iii) examine indicators and determinants of performance of yam producers (performance indicators being technical and economic); (iv) examine the role of technology adoption on farmer performance and wellbeing; (v) assess the superiority of seed yam from YMT over other planting materials; and (vi) ascertain determinants of adoption of improved technology. A multi-stage sampling technique was adopted to elicit cross-sectional data from three hundred and sixty yam farmers (120 respondents per State) in three yam-producing States of Nigeria. The States were Benue, Enugu and Ondo. The States are located in different agro-ecological zones of Nigeria and use different methods for yam production. Data were drawn from two Local Government Areas (LGAs) in each State. The LGAs were Katsina-Ala and Buruku in Benue State, Nkanu-east and Uzo-Uwani in Enugu State, and Ose and Owo in Ondo State. Primary and secondary data were used in this investigation. Primary data were collected from the respondents by using a well-structured questionnaire, direct observation and by interviewing farmers. Secondary data were obtained from databases, websites and literature. Data collected include socioeconomic data, resource endowment and utilization data, input and output data, data on farming systems and techniques, attitudinal data, environmental data and health data. Data were analyzed with descriptive statistics, econometrics and economic models. Descriptive statistics were used to describe yam production. An econometric model (stochastic frontier analysis) was used to evaluate the indicators of performance of yam farmers. Two functional forms, the Cobb-Douglas and the Translog production and cost functions, were used to investigate the production and cost of yam. The models were compared for goodness-of-fit. The best functional form was used to determine the technical and economic efficiency and factors influencing efficiency. Metafrontier analysis was used to test the presence of environment/technology gaps between States. The impact of YMT adoption on yam farmer performance was investigated using Propensity Score Matching. Factors influencing adoption were determined with Probit model. Gross Margin (GM) analysis was used to determine the profitability of yam with and without YMT. Partial budgeting was also performed to confirm the profitability of YMT. Net return was used to compare the yam cropping systems. The stochastic frontier analysis showed that, on average, Nigerian yam farmers in those States were not fully efficient in yam production. Benue State was technically efficient in yam production. Both Benue and Enugu yam farmers were relatively economically efficient. The performance (technical and economic efficiency) of Nigerian yam farmers is influenced by farmer’s socioeconomic profile, decisions, and access to inputs and facilities. Yam production is affected by farm size, quantity of planting material, labour and capital input. Cost of yam is determined by output, capital input, rent on land, planting material, wage rate and price of fertilizer. The result of the metafrontier analysis revealed that the production environment and technology for yam differ between States in Nigeria. Benue and Ondo States have more favourable environments for yam production. Enugu yam farmers are operating in a more restrictive environment. GM analysis established that yam production is relatively profitable. Yam had a higher GM than other root and tuber crops. Yam/Maize is the most profitable cropping system in Nigeria. Embracing Yam/Maize intercrop and increased investment in yam production can contribute to improving the poverty status in Nigeria. The adoption of YMT has the potential to improve farmer performance and wellbeing in Nigeria. YMT is a viable seed yam production technique. Yam production using YMT is more profitable than the traditional yam production techniques. Adopters of YMT in Nigeria outperformed non-adopters.