PhD. and MSc. (Biotechn.) projects in the Microbes and Heavy Metal Laboratory

PhD. and MSc. (Biotechn.) projects in the Microbes and Heavy Metal Laboratory

School of Biological Sciences

Department: Molecular and Cellular Biology, Microbes and Heavy Metal Laboratory (MHMG, Waite Campus), shared with

CSIRO Land and Water – Environmental Contaminant Mitigation and Technologies (ECMR)

Lab Head / Supervisor: 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.

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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 real-time 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 nano-particulate 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 thiosulfate-producing) 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 bio-precipitation 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

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  1. Pingback: New PhD and MSc projects available! | The man with the gold bug

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