The purpose of the travel was for Sarah Cooper to attend and present her research paper at the 6th Congress of European Microbiologists (FEMS Federation of European Microbiological Societies), Maastricht, the Netherlands. This conference is one of the leading meetings of its kind and brings together approximately 3000 microbiologists from around the world. As part of my communication strategy this congress provided the perfect opportunity to disseminate my research to the wider scientific community and it was a privilege to present my PhD findings at such a renowned congress. It is a biennial conference, therefore limited opportunity to attend this conference within researcher candidature. It is important that research results be presented as soon as possible and attending this congress enabled the researcher to do so.

Both the conference abstract can be found on page four of this report along with a copy of the given presentation.

Gin stands are responsible for the removal of fibre from the seed. Seed fingers are an important part of the gin stand and are used to control the seed roll load. Yet mechanically the seed fingers are undeveloped in terms of their control and ability to be set. Until now seed fingers were set manually by the ginner who typically selects and then fixes a mechanical setting. This setting have been then not routinely adjusted because of the inconvenience in stopping the gin stand to make adjustments. Bagshaw (2012) in his research presented constant variations in seed roll density and the forces exerted on the roll box casing across the length of the seed roll. His research showed seed roll density could change significantly many times over a one minute period as material in the seed roll is charged and discharged. It was assumed that development of an automated seed finger system that has the capability to constantly self-adjust would improve distribution of forces on the seed fingers.

The principal aim of this project is to pilot a system for remote identification of cotton pests using mobile technology, wireless microscopes and the Pestpoint software developed by the Plant Biosecurity CRC(PBCRC).

Currently, pest identification is largely done in an adhoc manner. A person who finds a pest may either identify it themselves or ask for an opinion from an experienced peer or peers, or in a difficult case, consult an expert. Most people, (consultants, specialists, growers, extension officers) have networks of peers and expert contacts who they consult in such cases. But in most cases, whether a person identifies a pest themselves or consults peers or experts, the identification is not recorded or if it is, it is only accessible to an individual or within an agency. Moreover, the inconvenience and logistics of handling and transporting pest specimens may often deter people from even seeking an identification. So in the current system, we fail to record valuable pest information and have limited options for identifying and diagnosing pest problems.

The PBCRC has developed a system that attempts to overcome both of these problems. We know that many pests can be identified from images and we now have wireless microscopes and cameras in mobile devices that can capture high quality, high magnification images in the field. We also have powerful software (Pestpoint) and internet connectivity that can be used to create communication networks so that people can share pest images and seek assistance for identifying pests. Pestpoint allows people to create virtual networks with their peer groups and to share, discuss, capture, store and retrieve their pest information for future reference – all from their mobile device.

Improved methods of assessing crop nutrient status in early season cotton will allow growers to remediate their crops and improve fertilizer management practices. By optimising the nutrition of cotton crops, growers can avoid nutritional stresses that can reduce the economic viability of commercial cotton growing. Monitoring nutrient status of individual cotton crops will allow precise fertilizer recommendations to be formulated. Soil and plant tissue tests have been available to the industry for many years but this technology has not been widely accepted because of the time consumed in sampling procedures, cost, inexperience in interpreting analytical results and variations in laboratory procedures and reporting of results. Growers often use soil testing as their only indication of crop nutrition requirements. Plant tissue testing offers a better indication of crop nutrition than soil testing, but it has not been adopted in commercial cotton production. NIR technology has the potential to facilitate and reduce the costs of nutrient analysis of cotton plant material. Similarly, development of the SPAD chlorophyll meter to allow in-field assessment of crop N nutrition will reduce response time for making N fertilizer management decisions.

Cropping systems experiments are currently being used to evaluate the sustainability of various cotton systems. An important component is the inclusion of legume crops for grain or green manuring. This assists in maintaining desirable levels of soil organic matter, with improved soil quality, soil N reserves and availability of other plant nutrients. Legume cropping provides direct economic benefits to growers through reduced N fertilizer requirement and indirect long-term benefits through enhanced sustainability achieved by remediation of soil chemical and physical properties. Management practices which reduce reliance on chemical fertilizers and which conserve and improve our soil resources are environmentally responsible and ecologically sound.

'Biodiversity' refers to the diversity of genes, species, ecosystems and ecoregions. Like other

sectors in the Australian economy, the cotton industry has a duty of care to ensure its

environmental sustainability, including conserving and enhancing the biodiversity upon which

it depends and minimising negative environmental impacts. Australia ratified the United

Nations Convention on BiologicaI Diversity, in June 1992. The Convention noted the global

loss of biodiversity as a result of human activities, identified the need to conserve biodiversity

in viable areas of natural or restored habitat, and recognised the need to mitigate the processes

that most threaten biodiversity. Subsequent Commonwealth and State legislation and policies

have given effect to the Convention.

Biodiversity is important for ecosystem (life support), ethical, aesthetic and cultural and

economic reasons. The challenge is to balance utilisation of biodiversity on the one hand with

its conservation to ensure that present and future human welfare is not compromised. This is

not easy due to the value judgements and diversity of private and public interests involved, as

well as the incomplete nature of the science of biodiversity and its poor predictive power for

decision making. This report aims to revioew the literature of past and current cotton-funded research and is limited to

Queensland and New South Wales cotton growing areas.

An automatic flow analyser was purchased to analyse nitrate, phosphate, chloride and sulfate. The monies for the instrument were a combination of CRDC, Australian Cotton CRC and University of Sydney funding.

Many of the cotton resourced projects involve the analysis of anions such as Nitrate (NO3-), Ammonium (NH4+), Phosphate (PO43-), Chloride (Cl-) and Sulfate (SO42-) in soil extractions or water samples. This is particular true for all projects interested in soil fertility, soil salinity and water quality. The analysis of these anions is cumbersome, and involves several wet chemistry steps. The current procedure is to outsource the nitrate and Phosphate analysis. The analyses from these outsourcing companies however are mainly aimed at soil fertility parameters. The instruments used for the automated analysis, the flow injection analysers, are not only capable of measuring nitrate and phosphate but can in fact analyse several anions in solution. In particular we are interested in analysing chloride and sulfate, since these anions are most important in terms of soil salinity and water quality.

The instrument has been purchased last March and has since been going through an installation and testing phase. The instrument is currently capable of analysing up to 100 samples per hour of nitrate, ammonium, phosphate and chloride in soil and plant extracts and waters. We are currently at the end of the testing phase and are drawing up a plan for operation and costing of sample analysis. This costing will be based solely on technical assistance, chemical costs and replacement of instrument parts. The analysis of sulphate would still have to be developed and therefore will take some time.

The intended use of the instrument is to support cotton funded and other projects within the University of Sydney. In addition we will be able to analyse samples for researchers on cotton funded projects outside the University of Sydney on a cost recovery basis.

Pesticides provide essential protection in the production of many agricultural commodities. However, increasing pesticide use as a result of increased production has led to community concern about the social and environmental impacts of pesticide residues. Of particular concern is the contamination of irrigation run-off and drainage water, agricultural soils and horticultural products.

Pesticide residues in soil have been detoxified by introducing and/or encouraging the growth of microorganisms capable of detoxifying the residues on site – a technology known as bioremediation. This method of bioremediation is based on traditional composting techniques and relies on microbial growth to metabolise the toxicants. The detoxification process is generally slow, taking weeks to months to accomplish. Furthermore, the methodology is not suited to the generally low aeration and nutrient content of contaminated water. However, the microorganisms capable of breaking down toxicants in contaminated soil can be sources of enzymes capable of detoxifying pesticide residues in such a low aeration, low nutrient medium. The application of such enzymes is particularly suited to pesticide-contaminated water in that they can achieve rapid remediation without the addition of nutrients or aeration.

The problem of pesticide contamination of water needs to be addressed prior to its release into the waterways. CSIRO Entomology, in conjunction with Orica Australia Pty Ltd. and CSIRO Molecular Science, has successfully developed enzyme-based bioremediation technologies for detoxifying pesticides in contaminated water prior to its release off-farm. For example, an organophosphate degrading enzyme has proven to be an effective and powerful tool for the rapid degradation of pesticide residues in agricultural and rinsate water. In a recent field trial, methyl parathion levels in 80,000 L of fast flowing run-off water in cotton farm drainage channels were reduced by 90% in less than ten minutes. This is a low concentration/high volume source of pesticide-contaminated water that also contains high levels of silt and other particulate matter. In a second field trial, enzyme treatment of rinsate from the washdown of pesticide spray equipment achieved a reduction in methyl parathion concentration of 90% in 10 minutes, and 99% after 1 hour. In contrast to the run-off water in the first trial, this rinsate is a high concentration/low volume source that also contains organic solvents. The application range of the technology has been broadened further to include diazinon detoxification in spent sheep-dip liquor, and the treatment of methyl parathion residues on the surface of leafy green vegetables. In a recent laboratory trial, the concentration of diazinon was reduced from 4.7 parts per million to below 1 part per billion (99.98% reduction), within 1 hour. In the trial involving leafy green vegetables, residues on the surface of baby bok choy were reduced by up to 95%. Given the complex nature of the surface of bok choy, this trial further demonstrated the utility of the enzyme technology.

Our research currently focuses on several major insecticide classes including organophosphates, carbamates, synthetic pyrethroids and the organochlorine, endosulfan. This project centres around the isolation of enzymes that degrade the toxic metabolite of endosulfan, endosulfan sulfate. As a result of this project we have isolated a bacterium that degrades endosulfan sulfate. This bacterial strain was isolated by providing endosulfan sulfate as the only source of sulfur to a soil microbial population. Sulfur is an essential component of living matter. Therefore only bacteria that could release the sulfur from endosulfan could survive. Removal of sulfur from endosulfan sulfate results in substantial detoxification. The enzyme responsible for this activity was cloned and characterised. The feasibility of conducting field trials of this enzyme in irrigation run-off was assessed in collaboration with our commercial partner, Orica Australia Limited. The requirement of co-factors for activity meant that alternative, more stable co-factors would need to be found, or another (non-co-factor requiring) gene / enzyme system isolated.

Gossypolis a naturally occurring sesquiterpene chemical and a product of secondary metabolism unique to cotton species. Gossypol is important to the cotton plant because it provides a degree of natural resistance against pests and diseases. Gossypolis the end product of just one branch of sesquiterpene biosynthesis in cotton, with other branches leading to the antibacterial phytoalexins of the Iacinilene group, and the important pest protection chemicals of the heliocides. It and its derivatives are stored in the gossypol glands spread throughout the plant as well as being induced in other tissues when the plants are attacked by disease organisms. Unfortunately gossypol is toxic to humans and monogastric animals, and cottonseed products must undergo expensive post-harvest treatments to remove the high levels of gossypol from oil and meal before consumption. The ideal cotton plant would possess high levels of gossypol in the plant and negligible levels in the seed. This is a characteristic already present in the native Australian cotton species, Gossypium sturtianum, however has proven exceedingly difficult to introgress this trait into cultivated species by traditional breeding methods. Genetic engineering offers another way of producing this phenotype if we have a clear understanding of the enzymes and genes responsible for gossypol production. This project aimed to clone some of the important genes in gossypol biosynthesis and use them in transgenic plants to specifically reduce gossypol production in cotton seeds.

The 14th International Symposium on Plant Lipids was held from 23-28 July 2000 in Cardiff, UK. This is a biennial gathering of international research groups working on the structure, metabolism and molecular biology of plant lipids. Nearly 300 delegates from 31 countries participated in the conference. At the conference,the delegates discussed the most recent advances of our knowledge about a wide range of research fields in plant lipids, including fatty acid and lipid biosynthesis and catabolism, lipid analysis, roles of lipids in membrane functions, cell signalling, and applications of modern molecular techniques in genetic engineering of oilseeds.

The project was established in response to grower support to promote the adoption of new technologies into sound management practices in the Balonne rivers irrigation area, St George to Dirranbandi. As part of the Cotton CRC extension program it involved the development of a framework of regional trials/demonstrations (in liaison with researchers) as part of a group adoption process to facilitate better communication between farmers, advisers and researchers from government and agribusiness.

The Industry Development Extension Officer would co-ordinate demonstration trials, take a

role in information transfer with the region's growers associations and assist grower direct

and respond to gaps in the current research base as well as adapt existing technology to local needs.

The adoption of new technologies, AWM, IPM and BMP play a large role in meeting the cotton industry's objectives of maintaining and promoting the most sustainable and profitable practices, for benefit of the industry as a whole and the communities/areas where cotton is grown.

In earlier times much research was left on the shelf by growers because of the perception that it was not applicable in their situation or locality. Many growers carry out on-farm trials and demonstrations to help them fine tune management. An extension officer takes a role as an intermediary enabling this on farm trial and demonstration work to continue on a co-ordinated basis as well as ensuring the latest research is incorporated into these trials.