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Position Details

Job Title: CSIRO Undergraduate Vacation Scholarships – Agriculture

Reference No: 2261

Classification: CSOF1.1

Stipend: $1462.77 per fortnight

Location: Please refer to the List of Projects at the end of this document

Tenure: 8 to 12 weeks from November 2015 to February 2016

Role Purpose: The 2015/16 Vacation Scholarship Program is designed to provide students with the opportunity to work on real-world problems in a leading R&D organisation.

Participation in the Vacation Scholarship Program has influenced previous scholarship holders in their choice of further study and future career options. Many have gone on to pursue a PhD in CSIRO or to build a successful research career within CSIRO, a university or industry.

Project Description:

Please refer to the list of Projects on the following pages of this document. If you require further information please contact the person listed as the contact for the project.

How to Apply: Please apply for this position online at www.csiro.au/careers

You will be required to:

1. select your top 2 research projects in order of preference;2. submit a resume which includes:

the reasons why the research project/s you have selected are of interest to you; and how your previous skills/knowledge and experience meets the project requirements;

an outline your longer-term career aspirations and detail how this program will help you achieve them; and

using the project numbers listed below, list in order of preference, all of the projects you are interested in.

3. upload your academic results.

Referees: Please ensure that your resume includes the name and contact details of your academic supervisor and at least one other referee (work or university).

If you experience difficulties applying online call 1300 984 220 and someone will be able to assist you. Outside business hours please email: [email protected].

Please do not email your application. Applications received via this method may not be considered.

Sponsored by:

mailto:[email protected]


http://www.csiro.au/careers

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Project No. Project Title & Description (see the following pages for more information)AG01 Spatial modelling of population genetic diversity against habitat suitability in a widely dispersed tree

species to characterise local adaptation across the genome.Project DescriptionThe project will use bioinformatics and spatial modelling to identify genomic regions that have been important for adaptation of Red gum to environmental conditions across the landscape. This information will be applied to predict population responses to future climate which will have implications for ecological restoration and plantation forestry.

AG02 Deciphering plant-pathogen interactions. Project DescriptionPathogens secrete effector proteins into host plants, which target plant proteins and modify fundamental plant processes to facilitate infection. This project aims to identify the plant pathways targeted by an effector isolated from the fungal pathogen powdery mildew.

AG03 Digital growth analysis using 3D reconstruction of crops Project DescriptionDetermine the growth of different crops in the field using state of the art field phenotyping tools such as laser scanner (LiDAR) and 3D reconstruction.

AG04 Regulation of fructan synthesis in wheat.Project DescriptionFructans play a crucial role under abiotic stress conditions to increase yield in wheat. Role of fructan synthesis and its regulation in wheat roots will be studied in this project

AG05 Identify energy efficient roots to increase our future wheat production. Project DescriptionWheat roots are hidden from our view and so we know little about them, yet they are responsible for supplying the plant with water and nutrition essential for growth. This project will explore the anatomy of old and new wheats grown in the laboratory and in the paddock, and apply aspects of plant anatomy, physiology, microscopy, image analysis and statistics in pursuing future food security by investigating the hidden half of the plant.

AG06 How can we better grow super oil producing plants? Project DescriptionCSIRO has managed to create plants that can be harvested for oil in their leaves. This project will investigate how high oil accumulation will affect plant photosynthesis and growth.

AG07 Investigating the development of silverleaf whitefly on cotton genotypes.Project DescriptionSilverleaf whitefly is an important pest of cotton plants. The student will study the development of whitefly adult and nymphs in different cotton genotypes by performing experiments in glasshouse and laboratory conditions.

AG08 Signalling and the secretome – do secretory processes regulate short- and long-distance signalling? Project DescriptionTransport of signals through plants depends on regulation of short- and long-distance pathways. This project will investigate secretome mutants to identify effects on transport within plants.

AG09 RFID tracking of range use in laying hens fed insects.Project DescriptionRFID technology will be used to measure the range use of free-range laying hens with and without a novel insect food supplement on the range. This project will be the first to assess the behaviour and welfare of individual hens in response to this high protein supplement to make recommendations to Australian laying hen industry.

AG10 Development of breeding programs for an Angus cattle breederProject DescriptionIn an environment where technologies and product requirements constantly change, it can be difficult for cattle breeders to choose a direction for their breeding program to remain profitable in the long term. The project simulates in collaboration with an Angus breeder scenarios for cattle breeding programs, and the economic analysis of different options will provide the breeder with objective criteria to assess his breeding objective and consider other options that increase profitability.

Project No. Project Title & Description (see the following pages for more information)AG11 Functional annotation of the ruminant specific microRNA 2284 family in the gastrointestinal tract

Project DescriptionGenes of the large microRNA-2284 family are present in all ruminants and not in any non-ruminant studied, but their functions are unclear. We found some members of the mir-2284 family specifically expressed in sheep rumen, thus intend to further explore their functions in the gastrointestinal system using bioinformatic approaches.

AG12 Linking vertical distribution of microorganisms in soil with carbon stability Project DescriptionThis project will explore how soil microbial abundance is associated with stability of C at various soil depths under different agricultural management practices.

AG13 Better use of scarce fertiliser resources: how do roots capture P in soil?Project DescriptionPasture legumes with more phosphorus-efficient roots will reduce Australia’s heavy reliance on phosphorus fertiliser. This project will analyse how legume roots explore nutrient patches in soil to achieve high P uptake efficiency.

AG14 A landscape investigation of the dynamics of avirulence genes in populations of Leptosphaeria maculans exposed to different host resistance genes.Project DescriptionThe fungal pathogen Leptosphaeria maculans is a major disease of canola in Australia and worldwide. Host resistance is an important tool to control fungal diseases, but L. maculans has the ability to rapidly break down resistance in its host plant. This project will use molecular techniques to investigate changes in the pathogen population in response to the use of canola cultivars with different resistance genes

AG15 Testing endophytes of cereal crops for their plant growth promoting capabilities Project DescriptionbonnSymbiosis with recently-discovered endophytes (bacteria and actinobacteria) may offer a way to increase crop production. Endophytes that have previously been isolated from different plant types will be grown in the laboratory, their DNA will be tested for the presence of genes conferring nitrogen fixation ability and stress tolerance, and the nitrogen fixation capability of the endophytes will be measured.

AG16 A first simulation analysis to inform the use of nitrification inhibitors to reduce nitrogen losses in sugarcane systems. Project DescriptionThe Australian sugarcane industry is interested in trialling enhanced efficiency nitrogen fertilisers (controlled release fertilisers and nitrification inhibitors) to optimise timing of nitrogen supply to the crop and reduce environmental losses that may affect the Great Barrier Reef. This project will use simulation analysis with the APSIM agro-ecosystem model to understand the timing of nitrogen losses from sugarcane systems, and to explore the possible effectiveness of nitrification-inhibiting chemicals in reducing N losses.

AG17 Impact of extreme climate events on agricultural productivity & profitability Project Description• An opportunity to develop skills in advanced applied statistic and biophysical modelling• An opportunity to engage in research on emerging issues of global change and agricultural productivity & profitability

AG18 Impact of soil amendments on root growth and soil respirationProject DescriptionThis project will assess the response of plant roots and the soil microbial community to novel soil biological amendments. The work will use image scanning and analysis (WinRHIZO) to characterise root responses and a microplate assays (Microresp) to quantify soil respiration (CO2).

AG19 Developing an image analysis tool for aquaculture researchProject DescriptionThe project offers the opportunity to develop an image analysis tool for characterising the morphology of Atlantic salmon eggs, a character that is important for salmon breeding. The student will digitise microscope slides, and develop the image analysis workflow and algorithms to consistently identify and parameterise egg morphology.

Project Number

Vacation Scholarships Project Details

AG01 Project Title

Spatial modelling of population genetic diversity against habitat suitability in a widely dispersed tree species to characterise local adaptation across the genome.

Project Description

The project will use bioinformatics and spatial modelling to identify genomic regions that have been important for adaptation of Red gum to environmental conditions across the landscape. This information will be applied to predict population responses to future climate which will have implications for ecological restoration and plantation forestry.

Understanding how plant populations adapt to their natural environment can help inform industry and conservation. The competing forces of selection and genetic drift determine the distribution of genetic diversity among natural populations. By investigating the frequency of single nucleotide polymorphism (SNP) alleles among natural populations with respect to their environment we can begin to characterise the genetic loci linked to important adaptive traits. Patterns of local adaptation may represent past or present climates and potentially indicate adaptive capacity under future climates. Peripheral areas of the current range of species may exhibit the kind of selective pressures that the species will experience under future scenarios across the majority of the range. These areas may harbour beneficial variants that could inform ecological restoration efforts, as well as aiding development of climate adapted material for commercial production. The River Red Gum (Eucalyptus c. camaldulensis) is an iconic Australian species that is endemic to the Murray-Darling Basin (1 x 106 km2) – which generates 39% of the national income derived from agricultural production. Red gum is an important riparian tree that is a foundation species in many ecosystems including ecologically threatened communities. The species is widely distributed and therefore a good model for studying local adaptation. Its distribution in the landscape is likely to have been shaped by local adaptation of growth and physiology traits in response to environmental drivers such as drought and water-stress.

The project will attempt to characterise single nucleotide polymorphism (SNP) variants in a genome-wide data set of E. c. camaldulensis. By focusing on population-level diversity we aim to identify genes responsible for variation in adaptive traits reflecting variation in localised conditions across the heterogeneous range. Whole Genome Sequencing has already been completed for 14 populations (10 individuals per population) of E. c. camaldulensis that span the range of the subspecies (750,000-1,000,000 km2). High-resolution environmental datasets (9-arc secs; 270m cell size) are also available. The student will use bioinformatic methods to identify population-level SNP variation in this data set. They will then apply spatial modelling methods to model habitat suitability among red gum populations based on occurrence records. The student will subsequently apply similar methods to identify which loci are associated with environmental factors that shape the species distribution across the landscape. Depending on progress, the student may also use E. c. camaldulensis physiological data and preform tests of correlation between ‘adaptive’ SNPs and trait data.

Project Duties/Tasks

Learn and apply bioinformatic methods to identify genetic variation at the population-level from a large genomic dataset.

Learn and apply ecological niche modelling methods integrating high-resolution environmental data in ArcGIS, to determine areas of high and low

environmental variation across the species range and likely environmental drivers acting as selective gradients in this species.

Learn and perform correlative modelling using the MaxEnt software with genome-wide SNP and high-resolution environmental data sets to identify genomic regions that may have been important for species adaptation.

Possibly test whether regions are associated with adaptive trait data.

Compare the results against past-present-future environmental projections and make interpretations on the consequences of local adaptation for different populations’ capacity to respond to climate change.

Undertake a one day fieldtrip to Gundagai to observe natural populations along the Murrumbidgee River.

Prepare a written project report, and a presentation to a symposium in Canberra

Relevant Fields of Study

Genomics and bioinformatics

Population genomics

Landscape genomics

Ecology

Biogeography

Geographic Information Systems

Location: Black Mountain, Canberra

Contact: Rohan Mellick via email [email protected]

AG02 Project TitleDeciphering plant-pathogen interactions

Project DescriptionPathogens secrete effector proteins into host plants, which target plant proteins and modify fundamental plant processes to facilitate infection. This project aims to identify the plant pathways targeted by an effector isolated from the fungal pathogen powdery mildew. Pathogens secrete a plethora of proteins, called effectors, into the cells of host plants during the infection process. Effectors cause the re-programming of a diverse array of plant processes, such as defence responses and nutrient transport, to ensure the parasite can survive. Identifying the plant pathways targeted by the pathogen provides an invaluable insight the plant-pathogen interaction, and thereby into potential targets for novel methods of pathogen control. This project involves the cloning of an effector from the grapevine powdery mildew pathogen, Erysiphe necator. To identify plant proteins that interact with the effector, a yeast two-hybrid screen will be performed. The effector will be used as a “bait” to screen a library of “prey” proteins generated from grapevine tissue infected with powdery mildew. The plant-pathogen protein interactions that are identified in the yeast assay will then be tested in plant cells, using bimolecular fluorescence complementation.



Design primers and clone the effector from powdery mildew infected grapevine leaf tissue.

Perform a yeast two-hybrid screen and to identify putative interactions between the effector and plant proteins.

Clone target plant proteins into vectors required for bimolecular fluorescence complementation (BiFC). Bombard the DNA into onion cells and perform fluorescence microscopy.


Relevant Fields of Study Molecular biology

Location: Waite Campus (Wine Innovation West), S.A.Contact: Dr. Laura Davies on (08) 8303 8608 or email [email protected]

AG03 Project Title

Digital growth analysis using 3D reconstruction of crops

Project Description

Determine the growth of different crops in the field using state of the art field phenotyping tools such as laser scanner (LiDAR) and 3D reconstruction.

The goal of the project is to analyse a series of datasets where LiDAR scans were performed over a number of crops (mainly wheat and canola) in a multi-temporal way. The data will be extracted and compared with field validation data obtained by destructive sampling.

This project will familiarise the student with the state of the art digital growth analysis tools developed at the High Resolution Plant Phenomics Centre (HRPPC) for measuring crop growth in the field. In this project the student will be embedded in a multidisciplinary team. By the end of the program the student will have excellent exposure and experience in big-data analysis and data handling tools.

Plant Phenotyping is a research area that is rapidly expanding today linking upscale research efforts in field agronomy, physiology and plant breeding, and finer scale research in plant genomics. This area presents a wide range of exciting opportunities for future research.


Process digital growth data from HRPPC field platforms such as Phenomobile

Validate digital growth data against destructively sampled field data

Statistical analysis of the data using R or Python. Become familiar with big-data processing and analysis tools.



Agriculture Science, Computer Science, Machine vision, Statistics


Contact: Jose Jimenez-Berni phone on (02) 6246 5420 or email [email protected]

AG04 Project Title




Regulation of fructan synthesis in wheat Project Description

Project Description

Fructans play a crucial role under abiotic stress conditions to increase yield in wheat. Role of fructan synthesis and its regulation in wheat roots will be studied in this project.

Fructans are polysaccharides that can protect the plants from adverse environmental conditions. Our previous study identified a transcription factor and its overexpression enhanced fructan accumulation in leaves and stems, and also increased grain yield in transgenic plants under water-limited conditions. Fructans in the roots may also be important during stress, however the regulation of fructan synthesis in roots is currently unknown. To study the role of fructan in wheat roots under stress conditions, we plan to grow low and high fructan accumulating wheat lines in liquid media with stress inducible chemicals. After treatment, the fructan levels will be determined, and also the expression of fructan synthetic genes will be analysed through quantitative real-time PCR in the roots. Overall, this study may help to deduce a role and mechanism of fructan regulation in the wheat roots. (There will not be any field work in this study)

Project Duties/Tasks Grow low and high fructan accumulation genotypes under stress conditions Gene expression analysis fructan synthetic pathway genes and its regulators Determination of fructan level in the roots Prepare a written report and present results at a public symposium


Plant Molecular Biology

Location: St Lucia, Brisbane, Qld

Contact: Sundaravelpandian Kalaipandian on (07) 3214 2606 or email [email protected]

AG05 Project Title

Identify energy efficient roots to increase our future wheat production.

Project Description

Wheat roots are hidden from our view and so we know little about them, yet they are responsible for supplying the plant with water and nutrition essential for growth. This project will explore the anatomy of old and new wheats grown in the laboratory and in the paddock, and apply aspects of plant anatomy, physiology, microscopy, image analysis and statistics in pursuing future food security by investigating the hidden half of the plant.

Great progress has been made in understanding the parts of the plant we can see. We now understand what changes have been made to above-ground parts of plants to improve food production. But we know little about what has happened to the roots to improve food production and we know little about whether we can improve the roots to grow better crops. In this Project you will investigate how we may be able to develop plants with more efficient root systems. We have evidence that the structural anatomy of roots can strongly influence the yield, the basis of food production. Thus, root anatomical traits will be investigated in wheat. You will determine the variation in root between old and new wheats and you will also investigate the extent to which root anatomical traits are altered by their growth conditions.Old and new wheats will be grown in pouches, hydroponics, and soil filled tubes in the glasshouse, and at the experimental farm with different management regimes.


Statistical principles will be used to optimise the design of these experiments. The roots of young plants will be sampled, cross-sectioned, and imaged on a microscope. Using image analysis software the size of the root, vasculature, and cell will be measured. The heritability of the traits (i.e. how uniform the results in different wheat types were in different experiments) and the best technique for selecting the favourable types will be determined.


Establishing plant growth experiments in the growth chamber, glasshouse, and field.

Microscopy, including sample preparation and image analysis.

Statistical design and analysis.


Plant Biology, Plant Physiology, Plant Biotechnology


Contact: Anton Wasson phone on (02) 6246 4739 or email [email protected]

AG06 Project Title

How can we better grow super oil producing plants?

Project Description

CSIRO has managed to create plants that can be harvested for oil in their leaves. This project will investigate how high oil accumulation will affect plant photosynthesis and growth.

The supply of plant oils will not meet the world demand within the next 30 years. In the context of a future variable climate, less arable land and water scarcity the production of oil in plant tissue other than seed presents the greatest opportunity to increase oil production per unit area. At CSIRO, we have managed to increase leaf oil levels to almost 15% of the plant dry mass. However, the consequences of excess oil on plant physiology and performance are unknown. In this project we will study how photosynthesis responds in plants were carbon resources are diverted into oil. The experiments will include measurements of leaf photosynthesis, studies of plant growth, and leaf anatomy, and quantification of pigments and nitrogen in plants accumulating leaf oil grown under controlled-environment conditions.


Grow and maintain plants in PC2 environment

Perform non-invasive phenotyping and estimate photosynthesis

Process tissue sample for biochemical analyses



Agriculture Science, Plant Biology, Biochemistry


Contact: Gonzalo M. Estavillo phone on (02) 6246 5548 or email [email protected]

AG07 Project Title



Investigating the development of silverleaf whitefly on cotton genotypes.

Project Description

Silverleaf whitefly is an important pest of cotton plants. The student will study the development of whitefly adult and nymphs in different cotton genotypes by performing experiments in glasshouse and laboratory conditions.

The project proposes preliminary work for the development of fast and effective screening techniques that would allow breeding for host plant resistance to silverleaf whitefly (SLW) in cotton. The experiments in this project will study the development of SLW in different cotton genotypes and environments. The population development of both adult and immature SLW will be followed in the plants (or in leaf discs in the laboratory experiments) over several weeks. Some morphological plant and leaf traits, such as leaf hairiness and shape, will also be assessed in the studied genotypes and environments. The data will be analysed and the results interpreted in the context of determining the best conditions to screen a large number of cotton genotypes for SLW resistance.


SLW life-history study under glasshouse and laboratory conditions

Data analysis and interpretation of experimental results



Entomology

Plant breeding

Integrated pest management

Location: Myall vale (Narrabri)

Contact: Dr. Carlos Trapero phone on (02) 6799 2453 or email [email protected]

AG08 Project Title

Signalling and the secretome – do secretory processes regulate short- and long-distance signalling?

Project Description

Transport of signals through plants depends on regulation of short- and long-distance pathways. This project will investigate secretome mutants to identify effects on transport within plants.

Many signals travel through plants to coordinate their growth and responses to external signals. Until recently, we thought that larger signalling molecules – proteins, peptides, and RNA, move from cell-to-cell exclusively via small cytoplasmic channels (plasmodesmata). They then move via these channels into the vascular system (phloem) to spread through the plant.

Exciting new work identified an unsuspected role for elements of the secretory system in cell-to-cell and long-distance signalling. It is unclear how this system would coexist with transport mechanisms via plasmodesmata or the phloem, but one possibility is that the secretory system has a direct role in regulating plasmodesmata. This project will assess whether mutants lacking elements of the secretory pathway also show differences in cell-to-cell and long-distance transport. Transport will be tested using tracer dye analogues of known signals applied to the secretory mutants,


and in wildtype plants treated with inhibitors of secretory activities.


Grow a range of secretory mutants in the growth room, analyse phenotypes.

Microscopy, including sample preparation and image analysis.

Quantify dye transport in mutants and in wildtype plants treated with inhibitors


Plant biology, Plant biotechnology, Plant physiology


Contact: Rosemary White by phone on (02) 6246 5475 or email [email protected]

AG09 Project TitleRFID tracking of range use in laying hens fed insectsProject DescriptionRFID technology will be used to measure the range use of free-range laying hens with and without a novel insect food supplement on the range. This project will be the first to assess the behaviour and welfare of individual hens in response to this high protein supplement to make recommendations to Australian laying hen industry.

Range access in laying hens can lead to a reduction in formulated feed intake with increasing time spent outdoors. Hens may be underweight and welfare can be compromised. Supplying insects on the range is a possible method of increasing protein intake as well as providing enrichment. Using RFID technology and video footage, this project will assess changes in range use of hens with or without insect supplements and possible aggression and competition for the valued food resource. Individual hen range-use will be RFID-recorded for 2 weeks prior to insect supplementation, then 2 weeks and 4 weeks following the commencement of insect supplementation (in 4 of 8 pens). Video recordings of behaviour on the range will be made 1 week prior and 1 week following commencement of insect supplementation. Basic Welfare Quality® health assessments on each hen will be made 1 week prior and 4 weeks following commencement of insect supplementation.

Project Duties/Tasks Learn how to use the RFID system and collect the tracking data for individual

hens. Learn how to do correctly handle hens and do basic health assessments using the Welfare Quality® scoring system

Set up video recording and learn video-decoding techniques for analysing hen behaviour on the range

Run all RFID data through the specialised software program and complete statistical analyses on all behavioural and welfare data

Preparation of a written project report, and a presentation to a symposium in Canberra

Relevant Fields of Study Animal science Veterinary science

Location: Chiswick and Laureldale Poultry Facility (UNE)

Contact: Dana Campbell on (02) 6776 1347 or email [email protected]



AG10 Project Title

Development of breeding programs for an Angus cattle breeder

Project Description

In an environment where technologies and product requirements constantly change, it can be difficult for cattle breeders to choose a direction for their breeding program to remain profitable in the long term. The project simulates in collaboration with an Angus breeder scenarios for cattle breeding programs, and the economic analysis of different options will provide the breeder with objective criteria to assess his breeding objective and consider other options that increase profitability.

With the emergence of novel traits and novel measurement technology, it is of important to the economics of the inclusion these options in breeding programs to demonstrate and communicate to industry to achieve application and impact.

The project involves the interaction with an Angus Breeder to understand the specifics of their operation and their current selection index. This information is used to model the breeders operation as a base scenario breeding program. Building on the base scenario, the inclusion of a novel trait in the existing selection index will be investigated and different options of testing and recording structures evaluated.

The project will provide the student with an understanding of the Angus industry, selection index theory and economic modelling of a breeding program. The interaction with a breeder is a unique opportunity for the student to comprehend the relevance of an understanding of the industry and a challenge to communicate a scientific topic with industry.

Project Duties/Tasks Develop an understanding of selection index theory Liaise with an Angus breeder, plan and gather information about his breeding

operation Model a number of scenarios of an Angus breeding program in ZPLAN and R Preparation of a written project report, and a presentation to a symposium in

CanberraRelevant Fields of Study

Agricultural science with an interest in Animal Breeding and Genetics and computer based modelling work, problem solving and a high level of motivation to learn

An understanding of matrix algebra is desirable, but not essential

Location: Armidale, NSW

Contact: Dr Sonja Dominik on (02) 67761376 or email [email protected]

AG11 Project Title

Functional annotation of the ruminant specific microRNA 2284 family in the gastrointestinal tract

Project Description

Genes of the large microRNA-2284 family are present in all ruminants and not in any non-ruminant studied, but their functions are unclear. We found some members of the mir-2284 family specifically expressed in sheep rumen, thus intend to further explore their functions in the gastrointestinal system using bioinformatic approaches.

Sheep and cattle are successful herbivores due to the additional stomach, namely, rumen that acts to mix plant-feed and bacteria to produce nutrients. Rumen has a


tough surface, constructed by the proteins that form the outmost layers of the skin. These proteins are made by a contiguous group of genes located in the epidermal differentiation complex (EDC) region. So what signals order this group of genes to make the different proteins forming rumen or skin surface?

MicroRNAs are important gene regulators and the MIR-2284 family is active in sheep and cattle. We showed that two MIR-2284 members, one located in the EDC region, are specifically expressed in the rumen. However, their biological function is unclear. We aim to implement human microRNA functional prediction tools in cattle and sheep to search for the targets of the MIR-2284 family. This will improve our understanding of the control of rumen epithelium development.

Project Duties/Tasks Annotation of sheep and cattle MIR-2284 families Implement human microRNA function computational prediction tools for the

analysis of sheep and cattle data Perform functional prediction analyses of MIR2284 in sheep and cattle and

combine the results in different species Preparation of a written project report, and a presentation to a symposium in

Canberra

Relevant Fields of Study Genomics Molecular biology Genetics Bioinformatics Computational biology

Location: St. Lucia, Qld

Contact: Ruidong Xiang on (07) 3214 2253 or email [email protected]

AG12 Project Title

Linking vertical distribution of microorganisms in soil with carbon stability

Project Description

This project will explore how soil microbial abundance is associated with stability of C at various soil depths under different agricultural management practices.

Soils constitute the largest reservoir of terrestrial carbon (C) and over half of the total C pool remains below 50 cm depth. Agricultural soils have high potential for sequestering C and mitigating climate change, but it is important to know how management practices affect the formation and stabilization of soil C; for example with the retention of stubble in cropping systems. Our group recently showed that addition of inorganic nutrient enhances the formation of stable C in soil from incorporated residue, with evidence of an interaction with depth. However, how this stability of C associates with the activity and abundance of soil microorganisms within the soil profile is not known. Soil microorganisms play a pivotal role in the soil C cycle by breaking down of plant residues and transforming/mineralizing soil organic matter. However, little is known about how abundances of key microbial groups change with soil depth. Using soil analyses and quantitative PCR for microbial analysis, this project will explore:

How C stability changes with soil depth in relation to management of crop residues.

Whether the abundances of fungi, bacteria and archaea are linked to C stability at


various soil depths under different management practices.


Extraction of soil DNA

Measurement of stable soil C pools using laboratory protocols

Quantification of archaeal, bacterial and fungal genes by quantitative PCR.



Agronomy, Microbiology and Ecology

Location: Crace, ACT

Contact: Samiran Banerjee phone on (02) 6246 4863 or email [email protected]

AG13 Project Title

Better use of scarce fertiliser resources: how do roots capture P in soil?

Project DescriptionPasture legumes with more phosphorus-efficient roots will reduce Australia’s heavy reliance on phosphorus fertiliser. This project will analyse how legume roots explore nutrient patches in soil to achieve high P uptake efficiency.

Phosphorus (P) fertilisers are fundamentally important for Australian agriculture because most Australian soils are P deficient and fertiliser must be applied to ensure high production. P also underpins global food security but the world has only about 300-400 years supply of the high-grade phosphate rock reserves from which P fertilisers are made. Presently, the cost of P-fertiliser is rising rapidly. Globally, it is recognised that greater efforts must be made to use P resources more efficiently.

Our reliance on P can be reduced by developing agricultural plants with long, fine roots and long root hairs that can explore soil more effectively.

In this project you will investigate how plants adjust their root morphology to capture P. The work will focus on subterranean clover, a key pasture legume used across southern Australia. The work aims to identify traits for breeding more P efficient pasture legumes.

Project Duties/Tasks Review literature on how roots respond to localised concentrations of

nutrients in soil Conduct and harvest controlled environment experiment examining response

of plants to patches of P Assess root morphology using root scanning technologies. Analyse data

Prepare a written report and present results at a public symposium


Agricultural Science Science or equivalent


Contact: Rebecca.Haling@csiro

mailto:Rebecca.Haling@csiro


AG14 Project TitleA landscape investigation of the dynamics of avirulence genes in populations of Leptosphaeria maculans exposed to different host resistance genes

Project DescriptionThe fungal pathogen Leptosphaeria maculans is a major disease of canola in Australia and worldwide. Host resistance is an important tool to control fungal diseases, but L. maculans has the ability to rapidly break down resistance in its host plant. This project will use molecular techniques to investigate changes in the pathogen population in response to the use of canola cultivars with different resistance genes.

Leptosphaeria maculans (blackleg) is the major pathogen of canola in Australia. Genetic resistance is an inexpensive and effective control strategy to minimise disease impacts on crop yield and many Australian canola cultivars currently rely on major resistance genes for protection from blackleg. These genes confer resistance when they recognize and directly interact with a corresponding ‘avirulence’ gene in the pathogen. However L. maculans has the capacity to rapidly evolve and overcome this resistance via genetic changes at avirulence loci. In this project we aim to assess temporal changes in the frequency of avirulence genes in response to deployment of cultivars with different host resistance genes in a commercial cropping situation. Single spore isolates from historical collections will be cultured and molecular techniques used to identify the presence of characterised avirulence genes. Single spore isolates will also be collected from stubble collected from paddocks on a farm known to contain different resistance genes.

Project Duties/Tasks Collect single spore isolates and population samples of L. maculans from

stubble, and grow in culture to harvest mycelium Perform PCR techniques to characterise avirulence genes frequencies in

populations and single spore isolates Phenotype a sub-set of isolates for virulence Prepare of a written project report, and a presentation to a symposium in

Canberra

Relevant Fields of Study Evolutionary biology Molecular biology Plant biology

Location: Crace and Black Mountain, ACT

Contact: Susan Sprague on (02) 6246 5387 or email [email protected]

AG15 Project Title

Testing endophytes of cereal crops for their plant growth promoting capabilities

Project Description

bonnSymbiosis with recently-discovered endophytes (bacteria and actinobacteria) may offer a way to increase crop production. Endophytes that have previously been isolated from different plant types will be grown in the laboratory, their DNA will be tested for the presence of genes conferring nitrogen fixation ability and stress tolerance, and the nitrogen fixation capability of the endophytes will be measured.

Plants have beneficial associations with microorganisms both internally and externally. Unlike rhizosphere microorganisms, endophytes, which colonize the interior parts of plants without damaging the host, escape competence and environmental stresses and so they are considered better suited to provide benefits to crop production in the field. Endophytic microorganisms can help plant growth and


health through improved nutrition (nifH gene) and/or stress tolerance (acdS gene). Within CSIRO a variety of bacterial and actinobacterial endophytes have been isolated and tested for their plant growth promoting abilities using bioassays only; their genetic potential in terms of beneficial capabilities is not known. This project proposes to acquire basic but critical information that can greatly benefit one of the main objectives of the Integrated Agricultural Systems program to ‘develop farming systems that deliver improvements in agricultural productivity’.


Grow actinobacteria and bacterial cultures (approximately 100) in the laboratory (2-4 weeks).

Extract DNA and test the isolates for the presence of nifH gene and acdS gene and positive isolates sequenced.

Test the nifH positive cultures for nitrogenase enzyme activity using acetylene reduction activity.



Microbiology and molecular biology

Location: Waite campus (Adelaide)

Contact: Gupta Vadakattu phone (08) 8303 8579 or email [email protected]

AG16 Project Title

A first simulation analysis to inform the use of nitrification inhibitors to reduce nitrogen losses in sugarcane systems.

Project Description

The Australian sugarcane industry is interested in trialling enhanced efficiency nitrogen fertilisers (controlled release fertilisers and nitrification inhibitors) to optimise timing of nitrogen supply to the crop and reduce environmental losses that may affect the Great Barrier Reef. This project will use simulation analysis with the APSIM agro-ecosystem model to understand the timing of nitrogen losses from sugarcane systems, and to explore the possible effectiveness of nitrification-inhibiting chemicals in reducing N losses.

The Australian sugarcane industry is interested in trialling enhanced efficiency nitrogen (N) fertilisers (controlled release fertilisers and nitrification inhibitors) to optimise the timing of N supply to the crop and reduce environmental losses of N that can affect the Great Barrier Reef. The effectiveness of nitrification inhibitors to reduce N losses depends on the timing of these losses relative to the timing of crop N uptake and the longevity of inhibitor action. This first simulation analysis will explore the system’s interactions to characterise the timing of N losses for a select number of locations. This will then be linked to preliminary, conceptual model of the action of nitrification inhibitors to provide a first indication of the drivers that determine their effectiveness. The project complements a larger project on the role of controlled release fertilisers in sugarcane and will inform future directions for modelling and experimental trialling of nitrification inhibitors.


Familiarisation with APSIM using online training materials

Adapt an existing APSIM-Sugarcane simulation and analyse the output to


characterise timing of N losses.

Building on the simulations of Task 2, incorporate a simplified, conceptual model mimicking basic nitrification inhibitor action to explore its effectiveness in reducing N losses.



Soil Science, Agricultural Systems Science or Engineering

(mathematical skills to the level of high school Mathematical Methods or higher)


Contact: Kirsten Verburg by phone on (02) 6246 5954 or email [email protected]

AG17 Project Title

Impact of extreme climate events on agricultural productivity & profitability

Project Description• An opportunity to develop skills in advanced applied statistic and biophysical

modelling

• An opportunity to engage in research on emerging issues of global change and agricultural productivity & profitability

Extreme climate events (drought, frost and heat waves) endanger the resilience of agricultural systems. To understand their importance in a changing climate, we need to analyse historical trends in the frequency of extreme events; estimate what might happen in the future; and we also need to be able to analyse the way in which extreme events might interact with other changes in the climate to affect agricultural productivity. In this project, a student will use statistical and biophysical modelling to explore these questions. The historical frequency and intensity of extreme events will be analysed using time series techniques and associations between extreme events and historical crop production will be sought. The student will then evaluate existing agricultural simulation models to ask whether they can capture the effects of future extreme climate events on agricultural production. This work will be an opportunity for a summer research student to explore emerging climate related issues, do statistical analysis on a real problem and become familiar with biophysical modelling techniques.


Identification and time series analysis of historical extreme events of frost, heat, and drought in selected sites (1-2 sites),

Analyse historical production data to identify the impact of historical extreme events on agricultural productivity

Modelling the impact of extreme climate events in agriculture for 2030 (1-2 wheat farm and 1 livestock enterprise)




Agriculture, natural resources, climatology, ecology, agro- climatology, environmental science. Some prior training in statistics will be needed.


Contact: Dr. Afshin Ghahramani phone on (02) 6246 4892 or email [email protected]

AG18 Project TitleImpact of soil amendments on root growth and soil respiration

Project DescriptionThis project will assess the response of plant roots and the soil microbial community to novel soil biological amendments. The work will use image scanning and analysis (WinRHIZO) to characterise root responses and a microplate assays (Microresp) to quantify soil respiration (CO2).There are a growing number alternative organic and biological soil amendments available to farmers. Compared to mineral fertilisers these amendments are proposed to support more sustainable management practices through building soil organic matter and improving soil health. These amendments have the potential to alter the input of carbon to soil (e.g. root production, exudates) and its rate of turnover (e.g. soil respiration). However, there is relatively little information as to the impact of different types of amendment on these parameters. This laboratory based project will address these research gaps and provide a learning opportunity that includes germination assays, image based determination of root length and diameter, and colourimetric microplate determination of soil respiration. There will be opportunity to visit a South Australian field site trialling the amendments (GRDC funded project) and to discuss how rapid laboratory based assays can be used to support field scale work.

Project Duties/Tasks Prepare and score germination assay and recover root materials Collect digital images of root samples and use WinRHIZO software to

determine length and diameter Prepare and conduct microplate colourimetric assay to determine soil

respiration, including calculation of standard curve Collate data and use ANOVA analysis to determine significant impacts Preparation of a written project report, and a presentation to a symposium in

Canberra


Soil science Plant physiology Agricultural sciences Agronomy

Location: Waite Campus, SAContact: Lynne Macdonald on (08) 8273 8111 or [email protected]

AG19 Project Title



Developing an image analysis tool for aquaculture research

Project Description

The project offers the opportunity to develop an image analysis tool for characterising the morphology of Atlantic salmon eggs, a character that is important for salmon breeding. The student will digitise microscope slides, and develop the image analysis workflow and algorithms to consistently identify and parameterise egg morphology.

Contemporary Aquaculture research is bringing together genetics with environmental and management factors (GxExM) to predict performance of animals and breeding programs. The experiment and sampling aspects of this research is increasingly automated, producing larger and larger datasets. Tools are now needed to automate processing of these large datasets. This project offers the opportunity to develop an image analysis tool for characterising the morphology of a large set of Atlantic salmon eggs preserved on slides. The tool will enable researchers to understand why salmon from different family perform better under certain environmental conditions such as hypoxia. The student will also have the opportunity to work with researchers to draft a manuscript on the technique of the study.


Capture image data from prepared slides

Develop and validate image processing algorithms to parametrise egg morphology from images obtained from the historical slides.

Batch run the algorithm over the selection of slides

Work with a fish physiologist to draft a paper on the analysis technique and morphometric results.



Computer science or engineering

Location: Hobart, TAS

Contact: Sarah Andrewartha phone on (03) 6232 5208 or email [email protected]


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