This project aims to investigate the cause of and differences in the levels of GHG emissions during sequences of crops and fallows.

CSIRO is involved in environmental research into atmospheric and climate changes associated with human activity. Green house gases (GHG’s - N2O, CO2 and CH4) contribute to climate change by altering the solar radiation balance of the earth. In Australia, current research indicates that cotton crops are over-fertilised by an average of ~50 kg N ha-1 which leads to a potentially high N2O emission. Emissions of GHG’s have been monitored from cotton systems with Professor Peter Grace in the past, but these measurements were only short term. To adequately assess the contribution of irrigated cotton rotation’s to the GHG emission long term measurements that encompass the complete rotation are required. This will help improve the fundamental understanding of the processes (soil denitrification) and practices (fertiliser rate, rotation) that contribute to GHG emissions in irrigated cropping systems, encompassing the full crop rotation, to develop better management practices that mitigate GHG emissions.

“Diseases of Cotton X” aimed to increase sustainability of the Australian cotton

industry through comprehensive disease surveillance. Continued collaborative

research, communication and education will enable better understanding of pathogen

biology and ultimately improve integrated disease management strategies. The three

year project resulted in several outcomes with direct consequences for the cotton

industry.

Important outcomes for the Diseases of Cotton X project include: incorporating

surveillance for exotic diseases into the biannual disease surveys has increased the

industries preparedness to deal with biosecurity threats of exotic diseases through

early detection. Evaluating existing and novel fungicide treatments each season

ensures growers have access to the latest information on seed treatments available.

This information helps the industry to make decisions on seed treatments in order to

decrease seedling mortality.

National diagnostic protocols have been developed for Texas root rot and

Hypervirulent bacterial blight and are currently being reviewed by DAFF. These

protocols will aid the industry in rapid diagnosis using standard procedures should

an incursion occur.

Australia capacity to screen for exotic races of bacterial blight has been re-established

through the importation of 10 differential cotton lines in 2012. The lines included:

Acala 44, Stoneville 20, Mebane B-1, Gregg, Empire B4, Stoneville 2B-S9, 1-10B, 20-3,

101-102B and DPxP4. The importation of these differential cotton lines has increased

Australia’s preparedness to diagnose exotic strains of bacterial blight in cotton.

The “Symptoms of diseases and disorders of cotton in Australia” was updated in 2012,

titled “Cotton Symptoms Guide – the guide to symptoms of diseases and

disorders in Australian cotton”. The pathology unit worked in collaboration with

Steve Allen (CSD) and the extension staff from Cotton Delivery and Development

Team, particularly Susan Maas. Updated images were supplied and many drafts of

the book were reviewed. The industry benefits from having an excellent resource full

of images, a symptoms key, looks like section and information on how to send a

sample for confirmation.

The network known as PathWAY was developed by the principal researcher to enable disease enquiries to industry staff from growers and consultants to be

captured and quantified as they occur. In the twelve months it has been running,

PathWAY has documented over 50 enquiries. This collaborative network links

cotton professionals from across agencies and borders and consists of pathologists,

virologists, researchers, extension, consultants and funding body representatives.

The network has facilitated a co-ordinated approach to enquiries resulting in faster

responses to disease issues.

For many in the agriculture industry around the world, an issue of significant concern is the sourcing of staff with the required skill set to assist in managing the operation of their farm businesses. In an environment of technological advancement, demographic shifts, urban- rural disconnect and increasing size, farm businesses struggle to access an appropriately trained and skilled workforce from which to source labour to fill the increasingly multifaceted roles on farm. In particular, the industry has a ‘missing middle’, with a dearth of talent to fill middle management roles that assist in both the decision-making process and the implementing of on farm operations.

This report investigates existing programs based in industry, education and privately, that assist in a person’s development towards a career in farm management. Globally, many programs exist in this field. However, what this report aims to do is examine the potential links between these programs and initiatives. By doing so, the objective is to develop a career path that begins at a primary school age and allows individuals to develop an appreciation of agriculture, make a head start in an agricultural career and develop knowledge with an emphasis on tying that knowledge to experience, to ensure the skills and abilities built up have an applied nature and are ‘paddock ready’.

Whilst not all the findings of this report may be directly applicable at farm level, it’s aim is to provide a viewpoint that can provide industry with a bigger picture on the pathway required to bring more people into agriculture. What this report suggests is that by supporting and advocating for curriculum-based programs in the classroom, more children from a broader range of backgrounds can be introduced to agricultural whilst learning their Science, Technology, Engineering and Mathematics (STEM) subjects. It also suggests that by supporting school-based traineeships and apprenticeships, those who are inclined towards agriculture can be given a head start. In turn, by helping to establish and utilise links between vocational and tertiary education institutions, agriculture can further up skill its workforce and importantly keep all participants engaged in further learning.

The resolution of this issue is as multifaceted as the skills requirement of the ‘missing middle’. What it is important is the creation of a pathway that engages the next generation of farm managers at a young age and sets them on a trajectory towards a career in

agriculture and farm management that will allow them to enjoy professional and personal development, provide the opportunity to build a career in agriculture without necessarily coming from a farming background and to allow the agriculture industry to further build its capacity and not be hamstrung by a lack of human capital.

The native budworm Helicoverpa punctigera is an important pest of field crops in Australia alongside the cotton bollworm Helicoverpa armigera, and both share a number of host plants. H. punctigera moths are known to migrate into cropping regions, from inland Queensland, Western Australia and South Australia but multi-year weather perturbations such as the Millennial drought may have reduced migration from drought-stricken areas in inland Queensland. Resistance management in Bt cotton may be at risk from reduced migration as migrants dilute any resistance genes that might be present in H. punctigera that have been exposed to Bt toxins. In southeast Australia H. punctigera appears to be becoming more abundant later in the cotton growing season, and thus, the overwintering ecology of H. punctigera needs to be re-examined.

Laboratory studies were conducted under a range of temperature and photoperiods to determine under what conditions diapause occurs in H. punctigera, and to compare the results with similar published studies. At 25°C the least amount of diapause was induced at 14L:10D, and the highest percentage of diapause at 12L:12D. Temperatures of 19°C or cooler produced the highest percentages of diapause, even under a summer 14L:10D photoperiod. At a 12L:12D photoperiod the highest percentages of diapause were induced at temperatures below 19°C. Larvae and pupae moved from 25°C to 19°C showed an increase in diapause levels while larvae moved from 19°C to 25°C did not. A statistical model was created from my data, showing the significant effects of temperature, photoperiod, and photoperiod:temperature interaction on diapause induction.

Field studies were conducted at various sites in the cropping region of Namoi Valley in NSW and in inland Queensland to study overwintering behaviour of H. punctigera In the Namoi Valley, larvae seeded in emergence cages suffered heavy mortality and in only one of the three years was it possible to collect diapausing H. punctigera pupae. All pupae extracted from the Namoi Valley field site “Drayton” were in diapause, and pupae exposed to 25°C resumed normal development while those exposed to 19°C maintained diapause.

Field studies in Inland Queensland were more successful and emergence timing data combined with temperature probe data suggested that winter diapause does not occur in Inland Queensland on sand dunes with light vegetation, but can occur on floodplains with heavy soils and dense vegetation cover. The timing of emergence within inland Queensland appeared to coincide with pheromone trap catches of H. punctigera in the Namoi Valley, potentially providing evidence that some of these inland moths migrate into cropping regions upon emergence in spring.

Temperature probe data in winter and spring were useful in relating field conditions to the laboratory studies. Potentially lethally cold temperatures were present in the Namoi Valley and lethally hot temperatures could occur in some habitats in inland Queensland. Extremes of external temperature were ameliorated by being 10cm below the surface, but daily minimum and maximum temperatures were low enough to induce diapause in much of the population in the floodplain soils at “Monkira” in inland Queensland.

Preliminary laboratory studies on summer diapause indicated the presence of a potential summer diapause in pupae. In 17-31% of pupae arrested development was detected through observation of eyespot movement and the length of pupal duration at temperatures of 31-35°C. A potential reproductive diapause/quiescence was also detected in adults exposed to 32°C, defined by a 73% failure of females to mate, compared to 21% not mating at 25°C.

Possible long term changes in the vegetation of inland Queensland, potentially affecting the importance of immigration and local overwintering in the dynamics of H. punctigera populations in cropping areas, were investigated by examining a largely unpublished collection of survey results dating back to the late 1980s. Historical subjective scorings of the amount of green host plant vegetation with remotely sensed data were correlated against MODIS EVI satellite data using a statistical model. There were large variations in herbaceous vegetation ratings in floodplains during the pre-drought period. Major floods and associated rainfall in 1994 and 2000 have been correlated with high vegetation scores in the floodplains and Acacia shrublands, and lower values corresponded with minor floods or no floods. Post- drought vegetation scores have not yet reached the same high levels as in pre-drought years even though significant flooding occurred in 2010 and 2011. Acacia shrublands have had a downward trend in vegetation scores since the 1990s and have been relatively low post-drought, with the exception of 2011. Sandy deserts regions have shown little change in average vegetation scores before and after the drought, with lower vegetation cover being reflected by lower vegetation ratings even after periods of increased rainfall. Very low vegetation scores are rare in the desert, which may reflect the ability of herbaceous vegetation in sandy soils to respond to small falls of rain. Examination of the survey database showed that the relative abundances of key host plants of H. punctigera have changed after the 2000-2009 drought. Overall, the presence of daisies has declined following the drought, especially in Acacia shrubland regions, and while some other hosts have increased in abundance, host plants capable of supporting large numbers of H. punctigera have generally declined. In particular, Rhodanthe floribunda, a host capable of supporting many larvae, has decreased greatly in Acacia shrublands, floodplains and sandy desert habitats.

The purpose of this travel sponsorship was to attend and present the researchers findings 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 the researchers communication strategy this congress provided the perfect opportunity to disseminate the research to the wider scientific community and it was a privilege to present PhD findings at such a renowned congress. It is a biennial conference.

The congress had a number of sessions, which covered current topics and issues relating to microorganisms. It provided new concepts and ideas that have contributed to the research being conducted in my project. Topics ranged from microbial genetics, hyphal structure and growth, to interactions in soil microbiomes and biofilms and ecosystem resilience. Of particular interest were a number of presentations, one on chitinase production by fungi, a discussion of the genomic flexibility of Verticillium dahliae, one on siderophores and trace element availability, a presentation on fungal highways and bacterial movement.

The plant-fungal pathogens plenary lecture included discussions on the production of chitinases by fungal root pathogens and discussed the control and induction of chitinase production. This presentation provided valuable information that assisted in the development of a medium that induces the production of chitinases by the Trichoderma isolates in my project.

Another valuable aspect of the conference was some of the research being done on the same microorganisms that involved current work with, Verticillium dahliae, Aspergillus fumigatus or in the same genera as with Fusarium solani. In these projects they often applied different techniques and used different fields of science to investigate these microorganisms. Alternatively, they applied different approaches to similar questions, this provided a different, wider perspective and a way of thinking about and analysing these microbes. An example of this was the work being done in the project entitled ‘Plant-microbiome interactions in the heavy metal polluted environments’. The mobilization of trace elements, in particular, the work on the mechanisms of siderophore production and other secondary metabolites is genetic based (mine involves plate assays). What they are doing could easily be used for to assist or enhance and maybe a better way to do it in the future. Another study ‘Pathogenomics of Verticillium wilt diseases’ introduced genomic flexibility a characteristic of Verticillium dahliae that enables it to escape host immunity whilst maintaining its aggressiveness. The researcher believes this was a really interesting study and something that should definitely be addressed when looking at disease control for this pathogen.

The concept of ‘fungal highways’ was discussed by a number of presenters; this is where bacteria use fungal hyphae as a way to move around the soil and plant roots. This may be something to consider when bacterial bio-inoculations are being applied to soil. It provides a mechanism for a non-motile bacterial inoculant to disperse in the soil. It could be that when some of the bacterial agents identified in my study are used they need a mechanism to disperse through the soil in order to work more effectively. Fungal highways may be the biologically sustainable way to achieve this.

iv

Abstract

Whereas the use of gypsum for the amelioration of sodic soils under dryland and

irrigated agricultural systems has been relatively well studied, experiments investigating lime

as a sodicity ameliorant have shown little success. This lack of success, and the use of lime as

a pH buffer, has caused it to be largely disregarded as useful for sodicity amelioration. Thus,

due to the extensive evidence for gypsum use as a sodicity ameliorant and the general

disregard of lime as an ameliorant, lime/gypsum combinations have only been given cursory

consideration, especially under irrigation. This study is principally concerned with addressing

the efficacy of lime and gypsum use for amelioration of sodic soils in the Lachlan and

Macquarie Valleys of NSW. However, there is an apparent lack of knowledge encompassing

the issue of sodicity and perhaps soil health in general. For this reason, it was necessary to

undertake an investigation into landholders’ soil health management education and the

impediments associated with implementing a soil health program in the Lachlan and

Macquarie Valleys.In order to assess the efficacy of lime and gypsum use for sodicity amelioration, four

field-based experimental sites were obtained, two in the Lachlan Valley (near Hillston, NSW)

and two in the Macquarie Valley (one near Trangie, NSW, and the other near Warren, NSW).

The soils form the Lachlan Valley were described as a Brown Vertosol and a Red Dermosol,

with pH 8.0–9.0, electrolyte concentration (EC) ranging from 0.30 to 3.50 dS.m-1 and

exchangeable sodium percentage (ESP) between 10 and 38%. The soils from the Maquarie

Valley were described as a Brown Vertosol and a Brown Dermosol, with pH 6.5–8.0, EC

ranging from 0.20 to 0.30 dS.m-1 and ESP between 6 and 12%. Full-field, replicated

experimental-strips were treated with L0G0 (Lime 0 t.ha-1 and Gypsum 0 t.ha-1), L2.5G0,

L0G2.5, L2.5G2.5, L2.5G5, L5G2.5 and L5G5 at each site. Due to insufficient rainfall and

unsecured irrigation water, only the Lachlan Valley soils were subject to irrigation; the

Macquarie Valley soils were subject to a dryland agricultural system.The study of the dryland agricultural system shows, through pH/EC relationships, that

EC is maintained at higher levels than the control where lime is applied, or where gypsum is

applied alone after 2.5 years. Furthermore, the increases in EC due to lime generally result in

a significant relationship between EC and aggregate stability. There is possibility of a

synergistic ameliorative effect between lime and gypsum on soil sodicity levels, although this

is not directly measured.

For the irrigated agricultural system, it is observed that gypsum is the primary means of

amelioration through Ca2+ exchange after 6 months, although these effects did not persist to2.5 years. The EC effect of gypsum is not observed after 6 months or 2.5 years post-gypsum

application and approximately 12.85 ML.ha-1 of infiltrating irrigation-water/rain. The results

of this work show that the use of lime and gypsum in combination and alone is not necessarily

viable for broadacre irrigated agriculture on two Lachlan Valley soils with pH >8.0.As it is apparent that the rate of gypsum dissolution is too high under the irrigated

system studied, gypsum was combined with chicken manure/wheat straw compost (CMWSC)

in order to investigate the potential of creating a slow release source of calcium (Ca2+). A

leaching column experiment was conducted using a Brown Vertosol treated with C0G0

(CWMSC 0 t.ha-1, gypsum 5 t.ha-1), C0G5, C5G0, C5G5, C144G0, and C144G5. Columns

were irrigated every two weeks for 14 weeks (6.5 ML.ha-1 of irrigation water in total). The

application of gypsum alone was shown to be comparable to the C5G5 treated soil, although

the C5G5 treated soil retained more Ca2+ and leached less Ca2+. Rapid decrease in soil

electrolyte level was evident in all treated soils. The results of this study indicate that gypsumenhanced

CMWSC is more effective in ameliorating sodicity than the use of gypsum alone,

due to a greater retention of exchangeable Ca2+.Despite mounting scientific evidence for the credibility of certain soil health

management strategies such as those in this work, farmers remain hesitant to implement

structured management plans and strategies. Hence, an investigation of the proportion of

Lachlan and Macquarie Valley landholders who implement a structured soil health program

was undertaken with focus on the impediments associated with the adoption of such

programs. Non-parametric analysis of a mail-based survey supported with content analysis of

landholder comments, suggests that the overall attitude towards soil health management is

positive, although soil health management programs are often inconsistent, unstructured, or

ad-hoc. Landholder knowledge of sodicity was found to be low, although landholders’ do not

believe that education is an impediment to program adoption. This research highlights that

ongoing communication between landholders, agronomists, extension agencies and scientists

is shown to be vital in the adoption of soil health management programs. While the initial

investment in soil health management is perceived as an impediment, landholders indicate

that production longevity and long-term financial gain are achievable.

n September 2006 the Namoi Catchment Management Authority (Namoi CMA) and

the Cotton Catchment Communities Cooperative Research Centre (Cotton CRC)

signed an umbrella agreement which would see them operate a partnership project

within the Namoi Catchment. Cotton Australia and the Cotton Cooperative Research

and Development (CRDC) were also brought in as partners of the project titled,

Schedule 1.2 'Supporting the adoption of Best Management Practice (BMP) in the

Cotton Industry in the Namoi Catchment'.The purpose of the prQject was to support the delivery and implementation of the

Australian Cotton Industry BMP program, in particular the Land and Water

Management Module in the Namoi Catchment and to foster better natural resource

management outcomes for the Namoi Catchment through the integration of the

principles of the Cotton BMP program and Namoi CMA catchment and management

targets defined in the Catchment Action Plan.The prQject employed a Cotton BMP Officer through the Cotton CRC and prqject

activities undertaken by the Officer during this prQject included property planning,

extension of on-farm best practice, workshops aimed at up skilling land managers and

increased communication between natural resource management bodies and industries

within the Namoi Catchment.

Expectations for industries to manage resources in a sustainable manner raise the question of how industries can demonstrate their sustainability credentials. This thesis reviews the question of sustainability monitoring and reporting in relation to the Australian cotton industry. Principals of sustainability reporting in business and agriculture were reviewed. A set of

sustainability indicators has been developed and economic, environmental and social data

compiled. A specific analysis of the cotton industry’s environmental management system, the

Cotton Best Management Practices program was completed to investigate its potential to track

and report farm management practice change over a 10 year period.

Key economic sustainability indicators include (Chapter 3): production area, yield, quality, gross

value, profitability and regional economic activity. Very good economic data is available about

the cotton industry, although it is not readily accessible for all stakeholders.

Key environmental sustainability indicators (Chapter 4) include soil, water, pesticide and

transgenic crop trait stewardship, biodiversity and greenhouse emissions. The cotton industry

has good data sets available from case studies and research reports for environmental

indicators. However, these generally give a ‘point in time’ picture rather than a long term trend

and are rarely industry wide. They are also often associated with the best producers, rather

than the “average” producer. There are very few data sets that can be used to track changes

over long periods of time. The BMP analysis showed it has great potential for monitoring long

term trends, which should be supplemented with some targeted and repeated surveys as

needed.

Key social sustainability indicators (Chapter 5) include education levels, demographics,

employment, health, community attitudes, social capital, research and development and

compliance with the law. There exists reasonable data relating to social indicators. This was an

unexpected finding as the gathering of social data is usually considered difficult for

sustainability reporting. A major gap is employment data, which is not well quantified either

for farms or the local service industries.

The analysis of the Cotton Best Management Practices (BMP) program farm practice audit

criteria for the 10 years between 1999 and 2008 shows that it is possible to identify and

quantify how cotton growers have implemented changes to a wide range of their farm

management practices (Chapter 6).

A preliminary water balance was carried out for the Maules Creek catchment to assist in the establishment of an appropriate conceptual model for the aquifer-river system. Interactions between streams in the Maules Creek catchment and the underlying aquifer were assessed and the available data on stream flow, groundwater abstractions and surface diversions was assembled. Estimates of evapotranspiration and crop-water use have been assembled and the areas under irrigation defined. The results of this study have implications for understanding the impacts of groundwater abstraction, such as more intermittent stream flow due to enhanced stream fed aquifer recharge, and for estimating the sustainable extraction of groundwater from the regional aquifer.

This project demonstrates one approach to coordinating and analysing hydrogeological data to help

with the evaluation of catchment water management issues. The methodologies presented in this

report are not intended to replace existing approaches to coordinating hydrogeological data being

used by NSW state government water management departments. Rather the applications presented

complement.

Four software programs are used for this project: MS Access, ArcGIS, Mathematica and FEFLOW.

MS Access (http://office.microsoft.com/en-au/default.aspx) is used to coordinate the data from the

NSW Water Information Pinneena Groundwater Works CD, which is the primary data set for the

bore construction details and the standing water level measurements. This information is combined

with other continuously recorded climatic data from the Bureau of Meteorology and the Pinneena

Continuous Flow CD into a single MS Access database.

ArcGIS (http://www.esri.com/software/arcgis/index.html) is used to coordinate all the 2D spatial

information. Important information in this database includes the digital elevation model (DEM),

geological maps, soil maps, landuse maps and the stream network.

Mathematica (Wolfram Research, Inc., 2008, http://www.wolfram.com/) is used for the plotting and

analysis of the hydrograph data, for constructing the 3D conceptual site model of the catchment

hydrogeology, populating the FEFLOW (www.dhigroup.com) mesh, and the post processing of the

modelled groundwater hydrographs. The Mathematica notebooks developed for this project have

been coordinated under the name Crystallize. These notebooks are to be placed in the public

domain. To use the Mathematica notebooks requires the purchasing of a Mathematica license. The

hydrograph analysis applications described in this report could all be used on the web by running

the applications using Wolfram webMathematica3 (http://www.wolfram.com/).This would make

the information on the Pinneena CDs accessible to anyone in a visual format.

Only a few representative data analysis applications are presented, because there are numerous

aspects to coordinating the data for a catchment, and approaches to analysing the data are open

ended. The components that are presented demonstrate working with the databases, the workflow

for key aspects of constructing a conceptual 3D geological model of a catchment, and pre and post

processing information when using FEFLOW for the catchment water balance modelling.

A copy of the MS Access database, ArcGIS database, all the Crystallize notebooks (Mathematica

.nb files), supporting Excel files and a MS Word document version of the notebooks are located on

the accompanying USB memory stick. Below, the contents of the USB memory stick are described

in more detail.

This project sought to verify whether the Mein-Larson variant of the Green-Ampt infiltration equation could work for time-varying application rates using real-world moving sprinkler systems. This required laboratory testing of sprinkler equipment, computer modelling and field trials to verify the modelling. Field measurements of surface runoff were problematic, however, and ultimately no conclusive position could be arrived at.