Black root rot caused by Thielaviopsis basicola has become a major seedling disease in cotton soils since 1989. The role of seedling pathogens has become increasingly evident in the establishment and early growth of cotton. It is now clear that seedling disease has complex aetiology, many potential pathogens and environmental factors contribute to reduced seedling growth and development. This project set out to examine two aspects with a view to reducing seedling disease: (1) develop measures of diversity of microbes in soils and correlate them with soil health esp in relation to seedling disease, and (2) determine the impact of land management and microbial diversity on the development of seedling disease, especially black root rot (BRR) which is caused by the fungus Thielaviopsis basicola.

The effect of P and AMF on cotton yield and yield components of cotton Honours thesis The soils of the Ord River Irrigation area (ORIA) are extremely old and naturally low in available Phosphorus. The production of cotton in the area requires the application of fertilisers to provide a profitable yield. The P requirement for cotton has been studied extensively with critical limits of P reported to range from 5 to 12 mg/kg with Phosphorus availability declining as soil pH increases. An optimum of 80 kg/ha of double superphosphate (17.5% P) was required on virgin soil to meet the nutrition requirements of a dry season cotton crop grown in the ORIA. Breaking down the yield into yield components helped to provide an understanding of which components contributed most to the increase in yield. The increase in lint yield is primarily attributed to bolls/m2 and to a lesser extent by lint/boll. Percentage fruit retention contributed most to the increase in bolls/m2 and lint/seed contributed most to the increase in lint/boll. The number of fruiting sites and seeds/boll do not contribute much to the increase bolls/m2 and lint/boll, respectively. P was the most significant treatment in the glasshouse study. Plants which had P applied had higher P uptake and dry weights. AMF did not contribute to growth or P uptake in the glasshouse study.

The effects of rotation crops and stubble management on soil quality, carbon sequestration, deep drainage, nutrient leaching, yield and profitability of succeeding cotton in irrigated and dryland Vertosols was studied from 2005 to 2008 in seven irrigated experiments (near Ashley via Moree, Narrabri and ACRI in NSW and Goondiwindi in Queensland), and one dryland experiment in Queensland (Brigalow in the Darling Downs). Key management issues considered were tillage systems, rotation crops and stubble management, sowing cotton into standing wheat and vetch stubble, in particular.

Within the overall aim of the project there were three key objectives pertaining to cropping systems in Vertosol-based cotton farming systems:

- Determine the effects of sowing cotton into standing wheat and vetch stubble on soil and water quality and conservation. Find solutions to management problems associated with in situ mulch in furrow-irrigated Vertosols.

- Compare cotton-wheat and cotton-vetch rotations in terms of soil quality, water conservation and long-term cotton production.

- Determine efficacy of organic and inorganic amendments in stubble-mulched irrigated

and dryland Vertosols.

Measurements taken in all experiments were: soil physical and chemical properties (e.g. soil organic matter, plastic limit, soil structure, exchangeable Ca, Mg, K and Na, ESP, pH, electrical conductivity). Profile water content to 1.2 m, crop growth, , nitrate-N, cotton lint yield and fibre quality were also measured. Economic returns in irrigated sites at ACRI and Ashley were evaluated by comparing seasonal and cumulative gross margins. Spatial and temporal deep drainage (with the chloride mass balance model) and nutrient leaching were measured at ACRI, and drainage at Narrabri and Ashley. Investigations were also conducted at ACRI into soil and cotton crop management practices and machinery which could overcome problems associated with sowing cotton into standing rotation crop stubble.

Sowing cotton into standing wheat stubble facilitated drainage and leaching of salts, and

water conservation through rainfall harvesting. Leaching of nutrients such as nitrates was also higher. Due to drought during 2006 and 2007, winter rotation crop growth was poor, and consequently carbon sequestration did not differ significantly from control treatments. Under restricted water availability and on a whole-farm basis minimum-tilled cotton-wheat was more profitable than continuous cotton, whereas with unlimited water or on an individual field basis the reverse was true. In comparison with infrequent irrigation (10-14 day interval), frequent irrigation (7-10 day interval) doubled cotton lint yield and profitability (measured as gross margins), and improved fibre quality. Growers would, therefore, be better off reducing the area of cotton sown and giving it sufficient water rather than reducing irrigation frequency over a larger area. Within soil layers in the cotton root zone, drainage with frequent irrigation was greater than that with infrequent irrigation. Drainage out of the crop root zone was, however, similar under both irrigation frequencies and may be related to differing drainage pathways.

Vetch in a cotton-wheat-vetch sequence responded positively in terms of growth and N

fixation to phosphate fertiliser whereas in a cotton-vetch sequence it did not. N fixation by vetch in the former rotation was also higher due to a longer growth period (sown in Late- February vs. later May) and wetter soil profile at sowing (sown into fallow vs. sowing immediately after cotton). Wheat grain yield and quality was improved by including vetch in the rotation (i.e. cotton-wheat-vetch) relative to cotton-wheat rotations. Cotton yield was highest when a wheat crop was included in the rotation. However, in comparison with cottonwheat where stubble was incorporated, the cotton-wheat (standing stubble)-vetch sequence required less N fertiliser (due to N fixation by the vetch) and irrigation water (due to better 5 subsoil water storage and presumably, reduction of evaporation by the in situ mulch). Under restricted water availability and on a whole-farm basis, profitability was in the order of cotton-wheat-vetch > cotton-wheat > cotton-winter fallow-cotton > cotton-vetch-cotton. Adding vetch to a cotton-wheat rotation is more profitable but adding vetch to a continuous cotton rotation is less profitable. The “Mulch Manager”, a machinery attachment which is able to kill vetch while minimising herbicide application rates and trafficking was developed.The amount of C added to soil C stocks by the roots of Bollgard II-Roundup Ready Flex varieties was less than that added by non-Bollgard II varieties. Above-ground stress such as insect pressure also reduced cotton root growth and C addition to soil, whereas minimum tillage and wheat rotation crops increased them. In comparison with above-ground dry matter, however, contribution by cotton root material to soil C stocks is small.

Sowing corn in rotation with cotton increased concentrations of the light carbon fraction but not total soil carbon. A close relationship was present between the light carbon reaction and microbial activity. Microbial activity and hence, nutrient cycling may be improved by including corn as rotation crop. Including vetch in a cotton-corn rotation increased SOC and exchangeable K, and decreased exchangeable Na concentrations.

Furrow soil in continuous cotton systems sown with minimum tillage had lower pH and

higher SOC than that under conventional tillage. In comparison with non-wheel-tracked

furrows, EC1:5 and geometric mean diameter of aggregates were higher in wheel-tracked

furrows, and plastic limit lower. Differences were small between conventionally-tilled and

minimum-tilled furrows, and between wheel-tracked and non-wheel-tracked furrows. Large inter- and small intra-seasonal changes also occurred with respect to soil physical and chemical properties in furrows. Interactions between surface soil factors in furrows may not, therefore, play a major role in influencing water application efficiency and infiltration within a season. Inter-seasonal differences could, however, affect hydrological processes.

In a K-deficient dryland Vertosol with high subsoil salinity and sodicity, only application of cattle manure (16 t FW/ha) resulted in a sustained improvement in soil quality, whereas gypsum and inorganic fertilisers had no effect.

Between 2005 and 2008, training was provided for two postgraduate students, and one

honours student. During the same period, 6 journal articles, 5 conference papers and 12 cotton industry and extension publications were published by project research and technical staff. A total of 21 public presentations were given by project and associated staff.

Key outcomes included:

- identifying cotton-wheat-vetch with in-situ stubble mulching as one which can reduce

cotton’s N fertiliser and irrigation water requirements while maintaining yields;

- identifying the practice of irrigating with treated sewage effluent as potentially risky to

soil health;

- determining that increasing complexity of cropping systems (i.e. sowing rotation crops)

under conditions of restricted water availability can improve whole farm profitability;

- identifying carbon sequestering management practices such as minimum tillage, vetch

rotation crops and manure application

- identifying corn as a rotation crop which could facilitate nutrient cycling;

- Identifying manure as a soil amendment which could alleviate K deficiency.

In 2001 a scoping study (phase I) was commissioned to determine and prioritise the weed issues of cropping systems with dryland cotton. The main findings were that the weed flora was diverse, cropping systems complex, and weeds had a major financial and economical impact. Phase II 'Best weed management strategies for dryland cropping systems with cotton' focused on improved management of the key weeds, bladder ketmia, sowthistle, fleabane, barnyard grass and liverseed grass.In Phase III 'Improving management of summer weeds in dryland cropping systems with cotton', more information on the seed-bank dynamics of key weeds was gained in six pot and field studies. The studies found that these characteristics differed between species, and even climate in the case of bladder ketmia. Species such as sowthistle, fleabane and barnyard grass emerged predominately from the surface soil. Sweet summer grass was also in this category but also had a significant proportion emerging from 5 cm depth. Bladder ketmia in central Queensland emerged mainly from the top 2 cm, whereas in southern Queensland it emerged mainly from 5 cm. Liverseed grass had its highest emergence from 5 cm below the surface. In all cases the persistence of seed increased with increasing soil depth. Fleabane was also found to be sensitive to soil type with no seedlings emerging in the self-mulching black vertisol soil. A strategic tillage trial showed that burial of fleabane seed, using a disc or chisel plough, to a depth of greater than 2 cm can significantly reduce subsequent fleabane emergence. In contrast, tillage increased barnyard grass emergence and tended to decrease persistence. This research showed that weed management plans can not be blanketed across all weed species, rather they need to be targeted for each main weed species.This project has also resulted in an increased knowledge of how to manage fleabane from the eight experiments; one in wheat, two in sorghum, one in cotton and three in fallow on double knock. For summer crops, the best option is to apply a highly effective fallow treatment prior to sowing the crops. For winter crops, the strategy is the integration of competitive crops, residual herbicide followed by a knockdown to control survivors. This project explored further the usefulness of the double knock tactic for weed control and preventing seed set. Two field and one pot experiments have shown that this tactic was highly effective for fleabane control. Paraquat products provided good control when followed by glyphosate. When 2, 4-D was added in a tank mix with glyphosate and followed by paraquat products, 99-100% control was achieved in all cases. The ideal follow-up times for paraquat products after glyphosate were 5-7 days. The preferred follow-up times for 2, 4-D after glyphosate were on the same day and one day later. The pot trial, which compared a population from a cropping field with previous glyphosate exposure and a population from a non-cropping area with no previous glyphosate herbicide exposure, showed that the pervious herbicide exposure affected the response of fleabane to herbicidal control measures. The web-based brochure on managing fleabane has been updated.Knowledge on management of summer grasses and safe use of residual herbicides was derived from eight field and pot experiments. Residual grass and broadleaf weed control was excellent with atrazine pre-plant and at-planting treatments, provided rain was received within a short interval after application. Highly effective fallow treatments (cultivation and double knock), not only gave excellent grass control in the fallow, also gave very good control in the following cotton. In the five re-cropping experiments, there were no adverse impacts on cotton from atrazine, metolachlor, metsulfuron and chlorsulfuron residues following use in previous sorghum, wheat and fallows. However, imazapic residues did reduce cotton growth.The development of strategies to reduce the heavy reliance on glyphosate in our cropping systems, and therefore minimise the risk of glyphosate resistance development, was a key factor in the research undertaken. This work included identifying suitable tactics for summer grass control, such as double knock with glyphosate followed by paraquat and tillage. Research on fleabane also concentrated on minimising emergence through tillage, and applying the double knock tactic. Our studies have shown that these strategies can be used to prevent seed set with the goal of driving down the seed bank. Utilisation of the strategies will also reduce the reliance on glyphosate, and therefore reduce the risk of glyphosate resistance developing in our cropping systems.Information from this research, including ecological and management data were collected from an additional eight paddock monitoring sites, was also incorporated into the Weeds CRC seed bank model &quote;Weed Seed Wizard&quote;, which will be able to predict the impact of different management options on weed populations in cotton and grain farming systems. Extensive communication activities were undertaken throughout this project to ensure adoption of the new strategies for improved weed management and reduced risk for glyphosate resistance.

The aims of the project were to determine the effect of selected management practices on

carbon sequestration, soil quality and hydrology, crop agronomy and profitability in irrigated

and dryland Vertosols using a combination of field and laboratory experiments, and desktop

studies. Management practices were tillage systems, rotation crops, soil amendments,

irrigation and stubble management. Measurements included environmental variables such as

soil quality, carbon storage and sequestration, greenhouse gas emissions, deep drainage and

soil water storage, and agronomic variables such as above- and below-ground crop growth

and cotton lint yield. Economic returns in irrigated sites at ACRI were evaluated by

comparing seasonal and cumulative gross margins. Partial life cycle analyses of greenhouse

gas emissions were made using a desktop approach. The “Mulch Manager”, a machinery

attachment which was able to kill vetch while reducing herbicide application rates and

trafficking was completed and assessed.

In general, SOC stocks in the 0-60 cm depth ranged between 50 and 70 t/ha. Legumes,

although contributing large amounts of carbon to the soil were unable to retain it because their low C/N ratio facilitated rapid microbial decomposition. Carbon inputs of C4 crops such as sorghum and corn were much larger than those of C3 crops such as wheat. A major proportion of that carbon came from their root systems. Increasing water availability and reducing tillage improved root growth. SOC sequestration rates were generally negative or neutral, except where a stressed soil (disease, sodicity, salinity) was in the process of recovering.

Estimates of carbon inputs, based on above-ground and root dry matter, together with measured sequestration rates indicated that large losses of carbon were occurring, probably due to a combination of accelerated erosion, runoff and microbial decomposition. SOC storage was positively related to dry matter inputs, average maximum temperature, soil aeration and water availability but was negatively associated with N fertiliser inputs. Except for temperature, the other variables can be manipulated by cotton growers. Average maximum temperature and soil organic carbon in the 0-60 cm depth had a curvilinear relationship. The temperature optima were higher in the Namoi valley (27-28 oC) than in the Macquarie (25.5 oC). Farming practises that could reduce emissions include eliminating inversion tillage, minimising use of groundwater, sowing winter crops in rotation with cotton, reducing/optimising mineral N fertiliser rates, substituting a legume an thus, fixed N for mineral N fertiliser. Long-term cropping-related K depletion may be minimised by regular application of cattle manure. Gypsum application did not improve subsoil structure under dryland conditions, probably because of the erratic rainfall pattern.

Water losses through drainage can be reduced and soil water storage increased (i.e. water

conservation improved) by including a wheat crop in the rotation with in situ stubble retention under less frequent irrigation. Management systems that conserve all rainfall received in situ, thereby reducing irrigation water requirements can contribute greatly to the sustainability of irrigated cropping. Deep drainage in cropped plots under normal or low rainfall conditions was many times higher than that in fallow plots, and reflects the higher water inputs in the former. When rainfall was frequent and no irrigation was required, drainage was higher under fallow, with fallow length being positively correlated to drainage. A model was developed that used rainfall and potential evaporation to estimate soil evaporation from beds where stubble was either incorporated or retained in situ. A model that used EM38 measurements, soil water storage and sodicity (ESP) was able to accurately estimate chloride in non-saline soils. These values could then be used to estimate drainage using chloride mass balance models.

Cotton yields and gross margin/ML were generally higher when wheat was included in the

rotation with highest values occurring on permanent beds. Amendments such as gypsum or

manure did not improve crop yields under dryland conditions, even though soil quality was

improved. Including vetch in the rotation did not result in sufficient improvements in cotton

yield to compensate for the increase in production costs. In years of plentiful water (or when

crop area is the limiting factor) reducing water application rates on a continuous cotton crop

was a false economy.

Cotton lint yields, in general, were positively related to water and N inputs, soil aeration in

some sites and average annual daily maximum temperature in cooler or poorly-drained sites

but were lowered by higher average annual daily minimum temperature. In a sodic soil, a high frequency of the tillage practices intended to aerate the soil may have caused yield decreases, presumably due to exposure of more sodic soils. Depth and frequency of tillage, average annual maximum and minimum temperature, N and SOC directly affected WUE of cotton. Except for SOC, which had no effect, all of the above variables directly affected NUE of cotton, particularly N fertiliser rate, which was negatively related, and legumes, which were positively related. The relative importance of individual variable differed among sites for yield, WUE and NUE.

The “Mulch manager” reduced use of herbicides, decreased labour, lowered risk to operators

and had a lower carbon footprint. In comparison to spraying with an 8-row boom sprayer,

depth of compaction was more when this 4-row implement was used, although the former

resulted in more intense and shallower compaction.

Between 2008 and 2011, two postgraduate students, two honours student and a visiting fellow from Pakistan were hosted by the project. Project outputs were: 7 journal articles, 11

conference papers and 5 cotton industry and extension. A total of 16 public presentations were given by project and associated staff.

Key outcomes included:

• Identifying soil and crop management practices, and climatic variables that had direct

impacts on soil carbon stocks, yield, water and nitrogen use efficiency in irrigated cotton

soils.

• Quantifying rainfall harvested, and associated drainage and evaporation, and thus, water

saved by retaining rotation crop stubble as in situ mulch.

• Identifying practices that could reduce carbon footprint of cotton farming systems with

life cycle analysis.

• A machinery attachment for managing prostrate cover crops bed-furrow systems.

• Simplified field methods to estimate soil evaporation and deep drainage.

• A whole-farm model of profitability for cotton farming systems that can be used as an

analytical research tool

This study was carried out in afield trial on black clay soils in the Macintyre cotton growing region during a 2005/2006 cotton season and future improvements on this experiment may see significant results that will give us a better understanding of the K and B effects on cotton development, which may lead to improvements in agronomic practices.

The study will was the first stage of a process aimed at assisting the industry and its communities to manage change effectively. The industry will benefit from a better understanding of the factors affecting the economic and social condition of cotton communities, the change processes in those communities, and the means by which these factors and changes might be managed. In the discussion of possible socio-economic topics at the 'Industry and Community' meeting at UNE in April 2005, a strong consensus emerged that a necessary component of research in this area would be to select indicators that could be used to track the economic and social condition of cotton communities over the life of the CRC and beyond. Such indicators could have a variety of uses, including:helping the industry to monitor its influence on the rest of the community; helping the community to monitor its influence on the industry; helping stakeholders in both community and industry to understand the changes they were undergoing; and helping both industry and community manage these changes and interactions. The Main Project Aims were to:scope the selection of socio-economic indicators for cotton catchment communities engage stakeholders in those communities in the identification of issues relevant to the sustainability of their livelihoods engage stakeholders in the definition of indicators relevant to their communities. The report of the study will serve as a basis for addressing some of the specific questions posed in the Cotton Catchment Communities Prospectus.

Water remains a key issue for the cotton industry, with improving water use efficiency a priority. Relatively water research has focussed on the plant and its interaction with the soil and climate. Currently deficit irrigation and many different row configurations are used in the cotton industry without accurate knowledge of how these irrigation regimes affect root development. Water deficit and irrigation can influence cotton plants root systems: dryland cotton has deeper roots than fully irrigated crops and the timing of first irrigation can be used to encourage good root development. These affects are important in overall plant responses to moisture stress.

A thesis submitted in the form of two papers for fulfilment of the requirements for the degree of Bachelor (Land and Water Science) Faculty of Agriculture, Food and Natural Resources The University of Sydney

The primary purpose of DAQ 122C was to investigate alternative pest management options under central Queensland conditions with a view to supporting and expanding the role of area wide management. The project accomplished of a broad suite of research spanning the use of assassin bugs as applied biological control agents through to investigating the potential of using attract and kill technology (Magnet®) for the management of Helicoverpa and Bt resistance.

The threat of ascochyta leaf blight disease gaining a foot-hold within the CQ chickpea industry provided an impetus to re-investigate alternative legume options for spring trap cropping. Field peas (cvs Alma or Glenroy) were found to be the most effective legume for Helicoverpa trap cropping and were unique in that the majority of eggs laid on it perished due to dislodgement from the waxy foliage making it a partially self-maintaining trap crop. The adoption of field peas for spring trap cropping circumvents any problems associated with chickpea leaf blight disease.

The use of refuges to augment natural enemies in cotton was investigated, with niger identified as being attractive to the broadest range of natural enemies. However, the use of refuges was found to be a inconsistent method for augmenting natural enemies commonly associated with cotton systems. The patterns of natural enemy abundance observed in the refuge treatments were probably more closely associated with variations within the surrounding environment than any in-field modifications to vegetative biodiversity via the provision of refuges. These results suggest that the key to reliably predicting and augmenting endemic populations of natural enemies within cotton farming systems may potentially exist in developing a more refined understanding of the interactions that occur between beneficial species and the broader natural environment.

The assassin bug, Pristhesancus plagipennis was demonstrated to be an effective biological control agent for Helicoverpa and mirids in conventional cotton. Assassin bugs were found to be innately tolerant of Steward®, Admiral®, Tracer®, Regent® and Affirm®, as well as NPV and Bt biopesticides. The compatibility of these products with assassin bugs in the field is highly desirable and our experiments demonstrated that the strategic integration of these insecticides with releases of assassin bugs provided effective pest management with 50% less insecticide whilst maximising crop yield. Should assassin bugs become commercially available in the future, significant potential exists utilise them within a low spray IPM program for conventional cotton.

Population dynamic studies demonstrated that Silver Leaf Whitefly, Bemisia tabaci Biotype (B) has become a regular pest of cotton within the Dawson Valley, infesting crops each year during late November and December and peaking in abundance during February. Sampling has also determined that native Eretmocerous parasitoids have become well established with their increased abundance correlating with a reduction in regional whitefly populations on cotton. Mean parasitism rates recorded in cotton have risen from 15% in 2003 to 87% in 2005 whilst applications of Insect Growth Regulators (IGRs) for whitefly control have decreased from 40% to <5% of fields over the same period. The reduction in IGR use constitutes savings of $100 per hectare not treated. Our data suggest that it is imperative to ensure the compatibility of pest management practices with whitefly parasitoid conservation and that this consideration will continue to influence future pest management research.

DAQ122C identified the potential for using Magnet® as a regional moth busting tool for targeting last generation Helicoverpa emerging from Bollgard® fields. Such an approach could supersede the requirement for summer trap cropping as part of the CQ Bt resistance management strategy and will be the focus for future research. Refinement of the current Bt resistance management strategy is of critical importance to ensuring the prolonged viability of pesticide reducing transgenic technologies.

Best pest management practices and novel research outcomes were promoted to CQ cotton growers throughout DAQ122C via several interactive field days each season and the provision of significant technical support and input for three IPM short courses conducted in the Dawson Valley and Central Highlands regions of CQ.