SCHOOL OF
BIOLOGICAL SCIENCES
Honors Projects
School of Biological Sciences
Department:
Lab Head /
Supervisor:
Molecular and Cellular Biology, Microbes and Heavy Metal Laboratory (MHMG,
Waite Campus), shared with CSIRO Land and Water – Environmental
Contaminant Mitigation and Technologies (ECMR)
Dr Frank Reith (Microbes and Heavy Metal Group (MHMG) group leader)
Dr Anu Kumar (CSIRO Land and Water, ECMR group leader)
Laboratory:
Microbes and Heavy Metal Laboratory, Waite
Campus
Research Focus:
The Microbes and Heavy Metal Group (MHMG)
Our research is focussed on understanding how heavy metals, in particular the noble
metals gold and platinum, are cycled through the environment. Hence, the group works
at the nexus between fundamental process understanding and biomedical and
biomining applications. One area of particular interest is understanding the cellular
processes of metal toxicity, resistance and their link to biomineralisation. We also study
how these metals affect micro- and microbiota as well as in situ microbial communities.
Another focus lies on metal mobility, transport and precipitation in current and past
environments The fundamental processes understanding created in a range of projects
is used to develop tools for industry, e.g., biosensors and bioindicators for mineral
exploration as well as bio-processing applications for sustainable mining. To achieve this
our approach has always been highly multidisciplinary with techniques from (and
publications in) the fields of geomicrobiology, (meta)genomics, microbial ecology,
proteomics, engineering, micro-analyses, geochemistry, geology and synchrotron
science.
For further information please visit:
http://www.adelaide.edu.au/directory/frank.reith
https://goldsamples.wordpress.com/
Project Outlines:
Project 1 – A Biosensor for gold
Supervisors: Frank Reith, John Bruning, Florian Weiland and Peter Hoffman
Gold is one of Australia’s most important commodities and was worth 13 billion dollars
in exports in 2013. Worldwide demand for gold is increasing, because of its proven
safety in times of crises. Australia is among the world’s four biggest Au-producing
nation and features highly prospective terrains that are extensively regolith-covered.
In spite of the progress achieved using geochemical and geophysical techniques,
exploration for new gold deposits is technically challenging, thus the discovery of new
deposits is extremely rare. Thus, new field- and laboratory-based techniques need to be
developed that will complement existing technologies and provide additional
information to narrow-down targeting during exploration. To make the industry more
productive and ensure its sustainability, improvements in the processing of Au-ores are
also required. An in-line tool to quantify gold in processing solutions and provide realtime monitoring of gold concentrations, will inform the ore processing workflow,
opening the way to real-time plant optimisation to improve gold recovery and minimize
costs. In 2012, this group succeeded in developing and testing a whole-cell biosensor
specifically for gold detection. However, this prototype utilises whole cell technology
that requires a sophisticated laboratory setup. To develop a field-based technique the
cells need to be stripped away, so that only the gold binding protein remains. Early in
2013, during an ARC Linkage project, we succeeded in identifying the actual gold binding
target protein in C. metallidurans CH34, which provides the foundation of the protein
biosensor for gold to be developed here. Currently, the University of Adelaide is
applying for a provisional patent for this application. This we hope will lead to an
AMIRA/ARC funded project, after some of the claims in the patent application have
been substantiated with additional data.
As part of this the next steps towards development of the biosensor need to be
undertaken, these are:
1. Purification of the gold binding protein and synthesis of a protein crystal. To
obtain the structure of the protein and be able quantitative assess of gold
binding capacity.
2. Assessment of the protein-based biosensor response. To inform sensor design
and future testing protocols, how the biosensor response is related to
bioavailable gold and which chemical gold species give the best biosensor
response needs to be established.
3. Test gold extraction methods to find a procedure that works efficiently with a
protein-based biosensor. As biosensors quantify the analyte in solution, a major
consideration for the implementation of a gold biosensor in field application is
the dissolution of the gold from the exploration sample, e.g. soil, sediment or
rock. Hence, a suitable method for the extraction of gold from the sampling
medium needs to be developed.
Project 2 – Gold nano-particles – Healthy Blessing or Environmental Curse?
Understanding fundamental aspects of gold ecotoxicology
Supervisors: Frank Reith and Anu Kumar
Gold nanoparticles and -complexes have stained glass and tiles in churches and temples
around the world for many centuries. Now researchers are discovering ever new
applications for these forms of gold, including their widespread application in cancer
treatments, drug delivery systems, photo-reactive sensors and probes and for
nanochip/nanobot design. Due to their high stability, ability to enter cells and high
catalytic capabilities differently sized, differently shaped and capped (i.e., stabilized in
solution) are widely manufactured and now ubiquitous in anthropogenic environments.
Gold nano-particles resulting from biomineralisation by bacteria, algae, fungi and higher
plants are important vectors of gold mobility in natural environments, e.g., around gold
deposits. Particles commonly end up in the streams and/or sewage systems, with
concentrations of 10s of mg kg-1 of gold been reported in sewage sludge from major
cities around the world, including Melbourne. The sludge is often recycled as biosolid
fertiliser, yet nobody understands the effects of the high concentrations of nanoparticulate and complexed gold on the aquatic and terrestrial micro- and macro-fauna
and –flora.
Previous research has shown that gold complexes are highly toxic (with toxicity levels
similar to silver and mercury) to micro- and macro-organisms. In many environments
mobile gold complexes are transformed biogenically to mobile nano-particulate gold.
Gold nano-particles have been reported to induce strong toxic effect to micro- and
marcobiota, other studies suggest them to have little effect, yet studies agree that there
is likely a link to speciation/particle sizes and the ligands/capping agents used.
Therefore, with the rapid growth of gold-complex/nanoparticles-based technologies,
there is a need to understand the fundamental effects and interactions of these forms
of gold with aquatic and terrestrial biota.
To develop the knowledge required to guide risk assessment and management practices
for sustainable future in Australia, CSIRO’s leading ecotoxicologist Dr. A. Kumar and the
University of Adelaide’s expert on (bio)geochemical gold cycling Dr. F. Reith (also an
academic visitor in CSIRO Land and Water) have establish a strategic research
collaboration in the proposed project will answer a range of key-problem and set the
baseline for further investigations, hence we will:
1. determine toxicity levels of a range of gold complexes and gold nano-particles
using world-class ecotoxicological approaches developed by Kumar’s group.
2. assess the effect of gold toxicity on offspring of affected organisms as well as
effects occurring along the aquatic food chain.
3. assess size and distribution of nano-particles gold in environmental samples and
model organisms using single particle-(SP)-ICP-MS, TEM and synchrotron
approaches developed by Reith’s group.
Project 3 - Understanding gold formation – A pathway to sustainable ore processing
Supervisors: Frank Reith and Gordon Southam
In this project we take a whole system approach to the exploration, mining and
processing of ‘problematic’ gold (Au) ores. A detail understanding of the processes that
control the (bio)-geochemistry and mineralogy of Au in ores from primary hydrothermal
ore formation, to remobilization and weathering, mining and ore processing, evolution
in the tailings leading to eventual reprocessing of these tailings, forms the basis on
which to improve existing mining and processing technology. This will lead to the
development of new processing method using microbial agents. Taking advantage of
recent advances in electron microscopy and spectroscopic techniques, we aim to
provide detailed insights into Au speciation in ores as well as processes resulting in Au
remobilisation/reprecipitation in ores and tailings. These insights will be used to
pinpoint causes for processing difficulties of problematic Au ores. A particular focus on
the role of microorganisms in Au cycling aims to identity naturally occurring organisms
that can be used to develop novel microbially-based processing solutions. This is timely
because of the coming to age of metagenomic methods and recent advances our
understanding of the fundamental role that microorganisms play in Au cycling. Low
recovery rates from our target ores often result from Au being locked in minute
inclusions within the sulfide matrix (refractory Au). Such ores require cyanide leaching
and/or roasting, introducing potential large-scale environmental hazards. Hence, we
seek innovative and environmentally sustainable solutions using microbial processes for
Au solubilisation and precipitation that allow high recovery rates from low-grade ores or
reprocessing of existing tailings.
1. Assessment of microbial biosolubilisation of Au in different types of ore systems
i) Discovery, isolation and characterisation of new strains of bacteria from ‘extreme’
environments that may display novel biochemical pathways for Au solubilisation.
ii) Enrichment of new strains of gold solubilising (e.g. cyanide- and thiosulfateproducing) organisms from soils, mine sites, waste rock piles, hydrothermal systems
and Au grains.
iii) Assessment of newly isolated and known cyanide- and thiosulfate-producing
bacteria and bacterial consortia for the biosolubilisation of different types of Au ore.
iv) Characterisation of kinetics and optimal conditions of biosolubilisation, such as
microbial thiosulfate and cyanide-production, using batch- and column-leach
experiments coupled with (HPLC)-ICP-MS to assess concentration and speciation of
mobilized Au.
2. Assessment of microbial bioprecipiation of Au for technical applications in different
types of ore systems
i) Identification of suitable bacterial strains for bioprecipitation
ii) Characterization of mechanisms, kinetics and optimal recovery conditions of bioprecipitation in metallophillic and other extremophile bacteria.
iii) Investigation of direct coupling of Au solubilisation and precipitation.
Project 4 – Novel microbial communities in extreme environments
Supervisors: Frank Reith and Angelica Rea
Biomining is increasingly utilized in metal mining operations in Western Australia, Chile,
Indonesia, Mexico and other parts of the world. However, many ore beneficiation
processes are conducted under extreme conditions (e.g. hypersaline, highly acidic and
thermophilic conditions), which are above the threshold of many common
microorganisms documented to effectively perform biomineralization and mobilization
of the prospective metals. Thus, the search for extremophiles such as halophiles,
acidophiles and thermophiles is underway to develop ideal microbial consortia in
biomining operations. Organisms with the ability to withstand moderately thermophilic,
highly acidic and hypersaline condition are possibly the best candidates to be used for
the sustainable bioprocessing of ores, however few suitable species/communities have
been described. In addition, one promising advantage of utilizing a halophilic organism
in mining operation is the decrease in utilizing freshwater sources by tapping saltwater
or recycled water systems. A detailed survey of the salt-tolerant organisms in the waters
of Western Australia has been conducted by Rea et al., (2014) to screen for candidate
halophiles. However, no study has been conducted to look at the diversity of
microorganisms in hypersaline lake, water and soil systems of South Australia and the
Philippines, in particular those found as endophytes and gold-associated
microorganisms. Thus, this research will be conducted to compare the microbial
population in the extremophilic (hypersaline, moderately thermophilic and acidophilic)
environments of South Australia and Philippines to improve the understanding of
microbial populations and functions present in under theses environment.
Sampling sites covers hypersaline systems, e.g., impounded salt evaporation ponds,
natural salt pans and extremophilic environments in South Australia and Pangasinan,
Philippines. Samples will be collected at three sampling points per collection site. Across
all sites 90 samples of well characterised acid sulfate soil, water & gold/mineral grains
and 10 samples of halophyte leaf will be collected and sent frozen to the laboratory. All
samples will be used to survey and screen for eubacteria, archaea and fungi. Fungal
endophytes will be cultured following the protocol of Xing et al. (2011) and will be
identified by ITS DNA Sequencing. Microorganisms will be isolated by traditional
microbiological technique from collected samples. Optimization of culture condition and
identification of isolated species by means of molecular and morphological characters
will then be done. Thus, the following objectives are set-out for this collaborative work:
 Utilize Next Generation Sequencing Technology to compare the microbial
communities in extremophilic environments of the arid and tropical regions of
South Australia and Philippines, respectively.
 Isolate, identify and characterize microbial population in extremophilic
environment of South Australia and Philippines
 Perform genomics sequencing of potential microorganisms for biomining to
search for candidate genes involved in various metabolic pathways and
physiological functions