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:
How to Apply:
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.
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: csirocareers@csiro.au.
Please do not email your application. Applications received via this method
may not be considered.
Sponsored by:
Project No.
AG01
AG02
AG03
AG04
AG05
AG06
AG07
AG08
AG09
AG10
Project Title & Description (see the following pages for more information)
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.
Deciphering plant-pathogen interactions.
Project Description
Pathogens 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.
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.
Regulation of fructan synthesis in wheat.
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
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.
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.
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.
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.
RFID tracking of range use in laying hens fed insects.
Project Description
RFID 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.
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.
Project No.
AG11
AG12
AG13
AG14
AG15
AG16
AG17
AG18
AG19
Project Title & Description (see the following pages for more information)
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.
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.
Better use of scarce fertiliser resources: how do roots capture P in soil?
Project Description
Pasture 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.
A landscape investigation of the dynamics of avirulence genes in populations of Leptosphaeria
maculans exposed to different host resistance genes.
Project Description
The 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
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.
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.
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
Impact of soil amendments on root growth and soil respiration
Project Description
This 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).
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.
Project
Number
AG01
Vacation Scholarships Project Details
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 populationlevel 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 (750,0001,000,000 km2). High-resolution environmental datasets (9-arc secs; 270m cell size)
are also available. The student will use bioinformatic methods to identify populationlevel 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 highresolution 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 Rohan.Mellick@csiro.au
AG02
Project Title
Deciphering plant-pathogen interactions
Project Description
Pathogens 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.
Project Duties/Tasks

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.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Molecular biology
Location: Waite Campus (Wine Innovation West), S.A.
Contact: Dr. Laura Davies on (08) 8303 8608 or email laura.davies@csiro.au
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.
Project Duties/Tasks

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 bigdata processing and analysis tools.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Agriculture Science, Computer Science, Machine vision, Statistics
Location: Black Mountain, Canberra
Contact: Jose Jimenez-Berni phone on (02) 6246 5420 or email jose.jimenezberni@csiro.au
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
Relevant Fields of Study

Plant Molecular Biology
Location: St Lucia, Brisbane, Qld
Contact: Sundaravelpandian Kalaipandian on (07) 3214 2606 or email
sundar.kalaipandian@csiro.au
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.
Project Duties/Tasks

Establishing plant growth experiments in the growth chamber, glasshouse,
and field.

Microscopy, including sample preparation and image analysis.

Statistical design and analysis.
Relevant Fields of Study

Plant Biology, Plant Physiology, Plant Biotechnology
Location: Black Mountain, Canberra
Contact: Anton Wasson phone on (02) 6246 4739 or email anton.wasson@csiro.au
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.
Project Duties/Tasks

Grow and maintain plants in PC2 environment

Perform non-invasive phenotyping and estimate photosynthesis

Process tissue sample for biochemical analyses

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Agriculture Science, Plant Biology, Biochemistry
Location: Black Mountain, Canberra
Contact: Gonzalo M. Estavillo phone on (02) 6246 5548 or email
gonzalo.estavillo@csiro.au
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.
Project Duties/Tasks

SLW life-history study under glasshouse and laboratory conditions

Data analysis and interpretation of experimental results

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Entomology

Plant breeding

Integrated pest management
Location: Myall vale (Narrabri)
Contact: Dr. Carlos Trapero phone on (02) 6799 2453 or email
carlos.trapero@csiro.au
AG08
Project Title
Signalling and the secretome – do secretory processes regulate short- and longdistance 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.
Project Duties/Tasks

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
Relevant Fields of Study

Plant biology, Plant biotechnology, Plant physiology
Location: Black Mountain, Canberra
Contact: Rosemary White by phone on (02) 6246 5475 or email
rosemary.white@csiro.au
AG09
Project Title
RFID tracking of range use in laying hens fed insects
Project Description
RFID 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 dana.campbell@csiro.au
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
Canberra
Relevant 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 sonja.dominik@csiro.au
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 ruidongx.xiang@csiro.au
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.
Project Duties/Tasks

Extraction of soil DNA

Measurement of stable soil C pools using laboratory protocols

Quantification of archaeal, bacterial and fungal genes by quantitative PCR.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Agronomy, Microbiology and Ecology
Location: Crace, ACT
Contact: Samiran Banerjee phone on (02) 6246 4863 or email
samiran.banerjee@csiro.au
AG13
Project Title
Better use of scarce fertiliser resources: how do roots capture P in soil?
Project Description
Pasture 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
Relevant Fields of Study

Agricultural Science

Science or equivalent
Location: Black Mountain, Canberra
Contact: Rebecca.Haling@csiro
AG14
Project Title
A landscape investigation of the dynamics of avirulence genes in populations of
Leptosphaeria maculans exposed to different host resistance genes
Project Description
The 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 Susan.sprague@csiro.au
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’.
Project Duties/Tasks

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.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Microbiology and molecular biology
Location: Waite campus (Adelaide)
Contact: Gupta Vadakattu phone (08) 8303 8579 or email
Gupta.Vadakattu@csiro.au
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.
Project Duties/Tasks

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.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Soil Science, Agricultural Systems Science or Engineering

(mathematical skills to the level of high school Mathematical Methods or
higher)
Location: Black Mountain, Canberra
Contact: Kirsten Verburg by phone on (02) 6246 5954 or email
kirsten.verburg@csiro.au
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.
Project Duties/Tasks

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)

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Agriculture, natural resources, climatology, ecology, agro- climatology,
environmental science. Some prior training in statistics will be needed.
Location: Black Mountain, Canberra
Contact: Dr. Afshin Ghahramani phone on (02) 6246 4892 or email
af.ghahramani@csiro.au
AG18
Project Title
Impact of soil amendments on root growth and soil respiration
Project Description
This 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
Relevant Fields of Study

Soil science

Plant physiology

Agricultural sciences

Agronomy
Location: Waite Campus, SA
Contact: Lynne Macdonald on (08) 8273 8111 or lynne.macdonald@csiro.au
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.
Project Duties/Tasks

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.

Prepare a written project report, and a presentation to a symposium in
Canberra
Relevant Fields of Study

Computer science or engineering
Location: Hobart, TAS
Contact: Sarah Andrewartha phone on (03) 6232 5208 or email
sarah.andrewartha@csiro.au