Number of eggs and % Hatch is from collections from all crops supplied for Bt and

Conventional Chemistry Resistance monitoring.

% H. armigera is from crops that attract both Helicoverpa species, cotton and pigeon pea,

to give an indication of species composition. Excluded are collections from maize and

sorghum.

% Parasitism is the percentage of eggs from all crops supplied to the Bt resistance

monitoring program that were parasitised by Trichogramma spp.

Fusarium oxysporum f.sp. vasinfectum (Fov) was first identified in Australia in 1993, and as

since become one of the most significant threats to the country's thriving cotton industry. The

interaction between a unique Australian biotype of Fov and cotton hosts with varying

susceptibilities to Fusarium wilt was studied. This research described the infection process an

associated host defence mechanisms of two commercial cotton varieties after inoculation with

Fov, and quantified their subsequent accumulation of antimicrobial terpenoids.

A rapid, reliable glasshouse bioassay that correlated with field resistance was developed for the

study of Fusarium wilt of cotton. Detailed observations of the infection process obtained through

light microscopy were used to formulate the disease cycle of Australian Fusarium wilt of cotton.

Using pathogen growth assays, varietal differences in root exudates and vascular tissues in the

cotton hosts were documented. Root diffusate from the most susceptible cotton variety to

Fusarium wilt, Siokra 1- 4, contained a lipophilic compound that promoted the germination of Fov

microconidia. On the other hand, a lipophilic compound present in diffusate from the least

susceptible variety, Sicot 189, inhibited the growth of Fov germ tubes.

A bioassay using inoculated whole plants showed that Fov colonisation of the vascular tissues of

Sicot 189 was restricted after 3 days. The basis for this inhibition was investigated further using

light and transmission electron microscopy. Infection induced the reorganisation of contact cells

in host vascular tissue, including an increase in cytoplasmic content and the partitioning of

vacuoles, which was concurrent with the accumulation of materials in adjacent vessel lumens, via

pits. Histochemical analysis indicated these globular materials secreted into the vessels were

terpenoids. These structural and terpenoid responses in Siokra 1-4 and SiCot 189 were similar,

however, they were more intense and rapid in the latter, less susceptible variety. The responses in

Sicot 189 also corresponded to the time period that pathogen inhibition was observed. Thus, a

correlation was demonstrated between the rapid and intense induction of both structural and

biochemical responses with decreased susceptibility to Fusarium wilt. Detailed HPLC analysis of

vascular tissues confirmed that terpenoids accumulated more rapidly and at higher concentrations

in the less susceptible cotton variety. These findings provided strong evidence for the involvement

of antimicrobial terpenoids in the determination of Fusarium wilt susceptibility of Australian

cotton varieties.

This work represents the most complete survey to date of the interaction of Australian biotypes of

Fov with cotton. These insights can contribute to future cotton breeding efforts and cultural

management of Fusarium wilt in the field. Thus, each part of this study has advanced

complementary facets of our understanding of Fov, and has provided a framework from which

future studies on phytoalexins and other putative cotton defences can be studied.

) used to support pesticide management decisions at the catchment-scale can deliver environmental protection while retaining farm production benefits. Presently, ERA’s in Australia are typically performed to evaluate farm-scale ecological impacts from pesticides. However, as pesticide exposure in rivers is usually a result of the activities of more than one farmer affected by spatially and temporally explicit factors such as climate, hydrology, geomorphology and land uses, a catchment-scale pesticide management approach seems a logical progression. The aim of this thesis was to investigate the potential effectiveness of applying ERA adapted to the catchment-scale as a pesticide management tool for agricultural catchments.

Initially, a catchment-based ERA of diuron, prometryn and endosulfan use in the Gwydir River catchment, NSW, Australia, was used to identify possible aquatic exposure sites. The classic phases of problem formulation, analysis and risk characterisation were established. The problem formulation phase identified hazard concerns and established assessment endpoints specific for areas that were considered to have high (95% of species protected 95% of the time) or lower (90% of species protected 95% of the time) ecological value. The analysis phase identified that the likely exposure sources of diuron, prometryn and endosulfan in the reaches of the Gwydir River catchment were agriculture, characterised using available ecotoxicology and regulatory exposure monitoring information using continuous probability distributions.

The characterisation of risk involved comparing distributions of exposure and ecotoxicity as species sensitivity distributions (SSDs) to estimate the probabilities that the endpoints were being exceeded (Solomon et al., 2000). With the exception of prometryn, significant risk from diuron (maximum risk = 8.95%) and endosulfan (maximum risk = 7.86%) exposure was found to occur in some reaches of the Gwydir River catchment. These areas, considered as “hot spots”, predominated where intensive agricultural production was most prevalent.

An uncertainty evaluation identified a number of information shortfalls in this ERA. These gaps included permanency of ecological effect resulting from pulse exposures, conservative risk estimation that was based on exposure data from a sampling regime targeted when chemical use and rainfall were more prevalent, and, for the purpose of supporting risk management, identification of specific areas in the catchment contributing chemical loads in areas of concern. These uncertainties led to the need for further research.

The consideration of organism recovery under a pulse exposure scenario likely to be observed in the Gwydir River catchment was investigated in a laboratory toxicity study. This study tested the potential for two duckweed species (Lemna minor and L. gibba) to recover from a seven day diuron pulse. The duckweed species were exposed to a range of diuron concentrations (0.3-200 μg L-1) for seven days, and placed in to clean growth media for a further seven days to simulate a recovery phase.

Exposure toxicity and recovery were evaluated through plant and frond counts, and wet and dry weights. The inhibition of growth was used as the toxicity metric by comparing growth response with control (0 μg L-1) populations. Significant growth inhibition of L. minor (EC50 = 34.9 and 52.8 μg L-1 for dry weight and frond count, respectively) and L. gibba (EC50 = 50.3 and 47.6 μg L-1 dry weight and frond count, respectively) was observed at the end of the seven day exposure. By the end of the seven day recovery phase, growth inhibition compared to the controls were shown to decline for a range of treatment exposure concentrations to the point that inhibition was not significantly different from the control for both L. minor (50 and 100 μg L-1, for dry weightand frond count, respectively) and L. gibba (200 and 50 μg L-1, for dry weight and frond count, respectively). With reference to the literature, growth inhibition was determined to be in response to photosynthesis inhibition (Haynes et al., 2000; Fai et al., 2007). Population recovery for treatment concentrations greater that observed in the Gwydir River catchment suggested was a clear reversal of this effect. It was concluded that both L. minor and L. gibba could sufficiently recover from a prolonged exposure event, suggesting the possibility of keystone aquatic plants and algae resilience to diuron exposure occurring in the Gwydir River catchment.

To clarify the risk characterisation uncertainty of diuron in the Gwydir River catchment, a spatial exposure modelling framework was required. A modelling procedure with the capacity to provide a daily time series exposure concentration pointing to catchment areas contributing to chemical load was selected. This framework involved combining two models, a chemical fate model (Pesticide Root Zone Model, PRZM) and a chemical routing model (Riverine Water Quality model, RIVWQ). The inputs to these models were obtained and processed from readily accessible databases and/or literature. Required inputs included soil, land use and weather station information; characteristic agronomic practices for different land uses and their respective label application rates. In accordance with the chemical labels all maximum application rates were used for the respective land uses of cotton, wheat, chickpea, canola and pasture in the simulations. To account for the full range of in season applications two scenarios were required to be run. Specifically, pre- (i.e. chemical incorporated in the top 4 cm of soil) and post-emergence (chemical applied directly to the surface) were simulated for cotton.

The simulation results showed that under the post-emergence application regime the highest chemical loading for streams was predicted. This was the result of chemical being more readily available at the surface to be entrained in runoff. It was found that the post-emergence application scenario reflected more closely the peak concentration magnitude and timing observed in the monitoring data. However, when compared with monitoring data, the model framework was unable to predict peak exposure concentrations on precisely the same dates. This indicated a degree of error in the model predictions, an outcome likely to be the result of uncertainties in the model inputs, especially with respect to pesticide applications, timing and crop rotation scenarios. However, the modelling framework did perform in a way that was consistent with chemical fate and fugacity principles. Subsequently, from these different scenarios, the sub-catchments contributing chemical loads were able to be identified, potential pulse durations were characterised as were their probabilities of re-occurrence, with the longest pulse exceeding the toxicity threshold lasting 6-9 days. It was concluded that this approach to estimating exposure at the sub-catchment level could be a useful tool for catchment management, devising and directing risk management strategies associated with monitoring. However, this will require further calibration and validation for effective use as a risk management tool.

The outputs of this thesis are suggested to provide justification for further development of catchment-based ERA strategies in Australia. These would include site specific chemical loading,employ probabilistic risk characterisation and account for ecosystem biodiversity value and resilience. This strategy would take ERA in Australia from the top-down approach now taken by national regulators to a bottom-up alternative, inclusive of catchment managers

operating at the local level interacting directly with stakeholders. Pesticide exposure concerns identified through an ERA should then be addressed through the implementation of a management strategy. This strategy would utilise outputs from spatial modelling supported by monitoring, as a basis for directing management to areas of a catchment where it is most needed. The thesis concludes that managing pesticide exposure in agricultural catchments with more informed ERA can provide a sounder basis for pesticide use in crop production coexisting with ecosystem protection.

Globally, natural wetlands are under threat from water resource development

reflecting the need to support a growing population. In the Border Rivers Catchment

in Queensland, Australia, a large irrigation industry coupled with a highly variable

flow regime has necessitated the building of large on-farm water storages and often

associated destruction or isolation of their natural counterparts. With the decline in

abundance of natural wetlands, the presence of these storages on the floodplain has

raised the question of their suitability as alternative aquatic habitat. This project

aimed to investigate the diversity of storages and the structure and function of the

aquatic assemblages they support compared with nearby natural wetlands. These

results were then used to recommend best management practice for optimising both

diversity and ecosystem function in storages.

Initially the physical variety of water storages in the Border Rivers Catchment was

described and their morphology and hydrology compared to that of natural wetlands.

Storages and natural wetlands formed two distinct groups based on morphology.

Storages tended to be large, deep structures with a more regular shape, while natural

wetlands were irregular and shallow with large perimeters. Although there was a

degree of variability amongst storage sites, most fell into one group and were

considered to be a ‘typical’ storage in this region.

Storages primarily function as water supplies and their associated management makes

them mostly unsuitable as ‘replacement’ wetlands. However, given the large numbers

of storages across the catchment, if managed effectively, they may provide an

additional source of aquatic habitat and help maintain regional biodiversity. To

maximise the biodiversity of storages it will be essential to reduce the morphological

homogeneity of storages across the landscape and increase habitat diversity within

storages. In the future, improved design of new storages and alterations to existing

storages and their management could help overcome this problem of low diversity of

habitat.

As a group, storages in the Border Rivers Catchment are still fundamentally different

to natural waterbodies, with storages being a mostly homogeneous group. If we are to

sustain the aquatic biodiversity in the Border Rivers Catchment and other similar

irrigation regions it will be necessary to preserve the spatial and temporal variation in

habitat evident in natural wetlands.

The purpose of this Final Report is to provide you with information regarding the participants, Ben Stephens, perspective of the development of his personal skills and understanding in relation to leadership, while undertaking the Australian Rural Leadership Program. While drafting the Final Report, the ALRP participant is encouraged to reflect on their experiences on the Program and to consider how these have influenced their understanding of leadership, of themselves, of their work and their role in their industry, and of rural Australia. Final Report for Ben Stephens is attached.

The three day Field to Fabric course was extensive and detailed, with a diverse range of

participants. It was an advantage to have people coming from all aspects of the cotton

industry as they provided a variety of knowledge and experience and contributed to well

rounded discussion sessions.

It was also a great advantage to be able to observe machinery and processes in action

once we were given the theoretical sessions. The staff made our question and observation

time worth while and we were able to spend extensive periods in the processing areas.

The course met all of my expectations and high lighted other issues in the cotton industry.

I have gained a good understanding of the processing aspects of cotton and have gained

an insight into the need for good quality fibre for this process. I have also learned about

the essential characteristics of quality fibre and the activities that can impact on these

characteristics particularly at a farm and gin level.

An excellent snapshot of the current global perspective of the cotton industry was

presented and included information on marketing, Australian markets and our

competitors.

I would recommend this course to all members of our industry for its comprehensive

coverage of the cotton industry and because it not only highlights where improvements

need to be made to ensure high quality Australian cotton and why, it also provides

suggestions on how improvements can be made.

In June-July 2007, five Year 12 students from all around Australia were given a once in a

lifetime opportunity to travel to Russia for a scientific study tour hosted by the All-Russian

Youth Aerospace Society, following their participation in the National Youth Science Forum

(NYSF) in January. The tour combined a week trekking near Kununurra in North Western

Australia and two weeks exploring Russia.

The purpose of the tour was to represent Australia, experience a country

and culture totally differento our own, and observe the science and

technology behind the space program of a major world player. There was

also a major emphasis on developing leadership, teamwork and time

management skills. Being placed into an environment outside our comfort

zone, we were all tested individually, resulting in us, ultimately,

becoming a stronger group within Australia's aspiring future scientists

and leaders.

The Russian Scientific Study_Tour 2007

We were all given the task of fundraising $5, 500 as a contribution to our

travels, and we each had to juggle our already hectic Year 12 lives in

order to do so. Despite very stressful and sometimes difficult moments for

both us and our families, we all managed to reach this target. Our success

would not have been possible were it not for the help and support of our

fantastic families, schools. sponsors, individual mentors and the Rotary

Clubs of Australia.

In 1996, a set of guidelines called the “Australian Cotton Industry Best Management Program”, or Cotton BMP for short was developed. This program is a voluntary, self regulated approach to the protection of resources, associated with cotton production and environmental management. Cotton BMP is a cornerstone model for the industry and during it’s evolution, it has lead the way for other industries in terns of assessing environmental risk. Cotton BMP accreditation is awarded to the property not the individual. This lack of recognition for the individual within the BMP accreditation process has lead to the development of this project.

This project is a strategic step towards building on this successful model for Queensland cotton producers. The project investigates how the Cotton BMP Assessment manual aligns to competencies within the Australian Training Framework. The results clearly showed alignment at various levels to 19 training competencies from the Business Management, Rural Production and Land Conservation training packages.

A skills mapping report was produced and ten units of competencies from this report were selected to form a Diploma of Agriculture. The Diploma of Agriculture has given rise to the concept of a Certified BMP Farm Manager. To the Cotton Industry, this title represents acknowledgement for an individual’s skill set developed by successfully achieving BMP accreditation for their farm.

A series of assessment sheets were then developed for the purpose of conducting ‘Recognition of Prior Learning’ (RPL) interviews on BMP accredited properties. Four pilot properties were tested with all four participants being awarded the Diploma of Agriculture within the BMP context. This was completed under stringent selection criteria which showed proof of skills and was conducted by an external Registered Training Organisation (RTO). The second stage of the project was to investigate ways to use this information to build a training framework around the Cotton BMP program. Discussions with industry have commenced and the industry endorsement of the certified BMP Farm manager is the first step being investigated.

Overall this ‘Targeted Industry Initiative’ project has developed strategic information that will assist industry in developing both a training culture and increased adoption of RPL assessments. Both aspects will benefit farm managers and owners in Queensland and the rest of the cotton industry.

Key Outcomes

1. The project has made significant steps towards the industry developing a national training framework

2. It has developed a linkage between the cotton BMP document and the national training competencies which paves the way for future training to be aligned to both the industry’s environmental stewardship guidelines and units of competencies that are formal qualifications. That is, all courses in the future that are developed from the BMP documentation now have a mapped link to national training packages.

3. Value adds to BMP by potentially rewarding the individual and offering another incentive to undertake BMP accreditation

4. Creates an opportunity for recognition of prior learning to be adopted within the industry.

Geographical factors are defining the extreme variability in climate and water supply in Australia and, in the past, this was used as a rationale for the construction of large irrigation projects to deliver water to rural, urban, and industrial users. During this ‘expansionary’ phase of Australia’s water use sector, the cost of augmenting supply was relatively low and environmental considerations were secondary to the development imperative. As a result, water resources became over-allocated for extractive uses spurred on by consistent underpricing of water, which indicated a failure to reflect the true cost of water supply. As Australia’s water economy entered a ‘mature’ phase, it was no longer possible to increase supply cheaply as the most easily accessible water resources had already been captured. This was followed by widespread environmental degradation manifested in the Murray- Darling Basin, the nation’s largest river basin which hosts much of Australia’s agricultural production. Consequently, the focus shifted towards demand management, leading to a myriad of regulation aimed at increasing the allocative efficiency of scarce water resources. Towards this end, substantial government funding was injected into the various initiatives throughout the water reform process. Despite the on-going government activities in the area of water reform, the understanding of the actual economic impact and environmental outcomes of various water policies in practice remains limited. In the absence of such understanding, the effectiveness of various government water initiatives is ambiguous and inevitably compromised. The present study addresses this knowledge gap by establishing a method for evaluating the economic and environmental outcomes of environmentally-oriented polices that affect irrigated industries in a catchment. The method is based on an integrated biophysical and economic modelling approach, which enables spatial relationships to be captured accurately allowing a more realistic analysis. Information generated from a computer based biophysical simulation model form the basis of an economic optimization model with constraints pertaining to environmental targets and water supply limits. The economic model consists of a linear programming and dynamic programming component, and involves the optimisation of resource use from a catchment manager’s perspective, seeking to achieve efficient resource use but at the same time conform to given environmental objectives. This two-stage modelling process was required to determine the optimal intra-seasonal and inter-seasonal water allocation, given various catchment environmental targets. The interdisciplinary approach enables the economic and ecological outcomes of the catchment management policies to be simulated and assessed at a spatially explicit scale, due to the link to Geographical Information Systems (GIS) in the biophysical model. The overall objective was to create a decision-making framework that could be used to determine the least-cost means of meeting environmental targets and resource constraints. The solutions to the analysis are directly applicable to the case study, the Mooki catchment in northern New South Wales (NSW), but with an adaptable framework that can be applied to other catchments. Specific objectives include an evaluation of the possibility of using alternative irrigation systems, as well as an evaluation of the benefits that can be realised by establishing water market, in the light of environmentally-oriented catchment policies for the case study. The economic cost of achieving environmental targets pertaining to environmental flow requirements and salinity reduction, in the form of end-of-valley salinity targets, was explicitly calculated through the economic model. While salinity targets have been set for NSW catchments, the practicality of such targets is in question, given the substantial reductions in water allocation to irrigation activities, which is one of the key contributors to deep-drainage. An additional objective in this study was therefore to investigate the value of having deep drainage targets. A further consideration is the effect of “external agents” in the form of government plans to buyback entitlements from irrigation districts, or the possibility of significant water rights purchases from mining industries. The implications of external water market entrants on the regional agricultural industry were examined. Some conclusions and recommendations drawn from the results of this thesis are as follows:

• Alternative irrigation systems, including pivot and drip irrigation, are beneficial to irrigators in the Mooki basin, improving their water use efficiency and productivity. Pivot irrigation systems were shown to be the optimal system for most of the catchment, while drip irrigation systems are less economically viable due to the high cost of investment. Significantly, the viability of these irrigation systems is reliant on the security of water supply. It has been demonstrated that where groundwater is used in conjunction with pivot or drip, profit is consistently higher compared to where surface water is used. This relates to the uncertainty of river flow in an ephemeral system, which result in irregular irrigation water availability and, consequently, lower crop yields. To encourage investment in water efficient technologies, it is important there are ample and secure water supplies. Considering the recent cuts in groundwater entitlements in the Mooki basin, and the prospect of future reductions in both surface and ground water rights, irrigators in the region may be reluctant to make the investment. This is especially the case where the capital requirement for water efficient technologies is substantial. It reiterates the importance of secure water rights and clear policy implications for future supplies.

• It was found that the initial area-based water licensing led to an inefficient distribution of water amongst irrigators, and that a fully functional water market would enhance basin profitability since water is shifted to higher value uses in the downstream-most region of the Mooki. This leads to an efficient outcome, as irrigation areas contract and leaves more land available for conservation purposes. The presence of a water market also augments the value of irrigation technologies, leading to a shift away from tradition furrow irrigation towards pivot irrigation systems. In this light, it would be more effective for government funding to be used in promoting water trade than subsidising the cost of irrigation technologies.

• The opportunity costs of meeting environmental flow and salinity reduction targets are also reduced where water efficient technologies and water trading are utilised. However, where these environmental targets are stringent, the economic burden will be substantial even if water trading or irrigation technologies are used. Where a significant reallocation of water for environmental flows or reduction in salinity is envisaged, the resulting opportunity costs should ideally be justified by the environmental benefits that are generated.

• A dual-instrument, simultaneously managing water use and deep drainage through separate instruments, is unnecessary. Surface water caps alone provide sufficient

Insects can respond to selection pressure by mobilising new defence mechanisms. In contrast to recessive resistance mechanisms based on rare target site mutations in receptor proteins, leading to extreme resistance to high B. thuringiensis (Bt) toxin concentrations, we observed a “hidden” inducible immune and metabolic tolerance in field derived laboratory populations of H. armigera to Cry1Ac and Cry2Ab toxins, with potential to cause ecological and economic problems in cotton production. Given that offspring from insects surviving in the field are tolerant of Bt but do not exhibit resistance to Cry1Ac and Cry2Ab due to target site mutations, it is likely that other mechanism(s) is assisting larvae to survive on certain parts of the plants or late in the season when toxin expression is low. Importantly for cotton bollworm management, we have the following three main outcomes:

1) Tolerance in H. armigera larvae is induced by gut-derived toxins (both Cry1Ac and Cry2Ab) and creates sub-populations of insects that show significant levels of tolerance without displaying mutational changes in a major resistance gene locus. Instead, the tolerant phenotype is caused by differential regulation of immune and metabolic activities (larval induction), and is transmitted to offspring by an epigenetic mechanism showing a maternal effect (embryonic induction). While the epigenetic contribution to incremental increases in tolerance is prominent under low to medium selection pressure, other resistance mechanisms that are transmitted genetically may predominate over time with incremental increase in toxin exposure.

2) Testing gene expression in tolerant and susceptible neonate larvae indicates that a range of genes are expressed significantly differently (both higher and lower expression) in tolerant insects compared to susceptible control. Although some of these differentially expressed genes are important key receptor, putative immune and catalytic genes, most of the differentially regulated genes (up to 190 fold) are unknown in function. By understanding these highly altered unknown genes, it is likely we will gain an understanding of the tolerance mechanism and able to develop management options to specially counter tolerance buildup. Further, significant differential regulation of key receptor genes opens up avenues for further research that may lead to establish monitoring tool to detect inducible tolerance and/or resistance in the field.

3) There appears to be significant developmental penalties under laboratory selection, as evidenced by lowered larval weights and increased developmental times. However, once the populations were kept at constant toxin levels, the developmental penalties slowly diminished over subsequent generations. This could indicate possible genotype selection of allelic combinations of multi-gene functions that reduce developmental penalties. This may in long term provide tolerant populations with the adaptive potential to acquire resistance mechanisms that are genetically transmitted and involve target site mutations in important resistance genes. Our findings have practical significance for adapting pest management protocols to counter inducible tolerance, particularly the importance of susceptible females in blocking this form of resistance.

Lastly, laboratory selected H. armigera (25 generations selected with Cry1Ac, 63 fold resistance) are able to complete their larval development on transgenic cotton expressing Cry1Ac and produced fertile adults (Akhurst et al., 2003). Therefore, whether incremental increases in tolerance can support selection for target site mutations in key receptors allowing insect larvae to survive on Bt-plants is another key issue that requires investigation.