Developing ‘sniffer’ bugs and pig face to save our soils

Posted on December 4, 2013

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New tricks for old organisms: Ms Wiltshire, foreground, and Ms Bereza-Malcolm in their microbiology lab.

In our increasingly industrialised world good farmland is fast becoming a limited resource.  To help remedy that, La Trobe scientists are harnessing two of nature’s most common life forms – bacteria and plants – to track down toxic contamination and clean up the soils we have polluted.

Lara Bereza-Malcolm is training harmless bacteria as ‘sniffer dogs’ to identify dangerous and toxic environmental compounds like arsenic, cadmium, lead and mercury.

And colleague Jen Wiltshire is trying to put more muscle into the common creeper pig face, modifying the way it interacts with soil microbes, to boost its ability to clean up heavy metal pollution.

Not just a pretty pig face: this plant has potential to help clean up toxic waste – and take mining in whole new a new direction.

Green  biotechnology…

The two doctoral scholars – part of the University’s Research Focus Area dealing with securing food, water and the environment – say the best solution lies in such new ‘green biotechnology’.

No chemical or biological process known so far, they point out, can degrade heavy metals. Contaminated soil has to be removed and washed, which is expensive and environmentally destructive.

Heavy metals can be highly mobile in soil. They spread in the water table and into biological systems where they accumulate in the food chain, causing diseases of the kidney, liver, blood, brain, miscarriages and even cancer.

Recently the two researchers spoke about their work on the ABC Radio Science Show and at the Victorian graduate and postgraduate ecology and environmental science conference, which they helped organise on the Melbourne Campus.

Both work in La Trobe’s Environmental Microbiology research lab led by Dr Ashley Franks, which develops biological sensors, electric bacteria and environment microbial processes to create environmentally friendly solutions for modern problems. The lab is also a member of the University’s interdisciplinary Biodiversity, Ecology and Evolution Group, BEEG@L.

… in many colours

Bacteria showing red and green flourescence in response to different toxins   (Lara Bereza-Malcolm)

Bacteria fluorescing red and green in response to different toxins (Lara Bereza-Malcolm)

Ms Bereza-Malcolm says bacteria usually get bad press. ‘Most are not harmful to humans. They sustain life through carbon and nitrogen cycles and by removing toxic compounds from the soil. And they can live in the most extreme environments.’

‘Bacteria need to detect change in their environment to survive, including fluctuations in temperature and toxins.

They do this by reacting to stimuli they detect through programmed genetic responses’ she says. ’Due to this, bacteria can make excellent biological sensors.’

Ms Bereza-Malcolm plans to tap into that response and reprogram it so that when the bacteria find a toxic target they will emit a fluorescent signal.  ‘I am designing bacteria that will glow in different colours in response to arsenic, cadmium or mercury in sub-soil on land and at the bottom of the ocean.’

Testing kit for specific compounds

She says such microbial-based biosensors can then be incorporated into a testing kit for specific compounds in their environment.

‘Today’s treasure trove of genetic information can be used by synthetic biologists to create new biological pathways which allow bacteria to perform specific tasks.  Ready-to-assemble DNA sequences with specific functions are available in modules known as bio-bricks. These allow us to design microbes with specialised functions.’

Ms Bereza-Malcolm likens programming bacteria to programming a computer. ‘Rapid detection and response is essential if we want to stop harmful chemicals contaminating our food chain.’

Environmental Microbiology lab members:  Dr Ashley Franks with, from left, Ms Sanja Aracic,  Ms Bereza Malcolm and Ms Wiltshire

Environmental Microbiology lab members: Dr Ashley Franks with, from left, Ms Sanja Aracic, Ms Bereza Malcolm and Ms Wiltshire

Exploiting plant’s own strategy

Ms Wiltshire says plants and their interaction with soil microbes offers a great way to clean up heavy metal pollution.

Toxic heavy metals include arsenic, cadmium, lead, mercury, as well as trace elements like zinc, copper, or nickel. They are required for biological systems, but become toxic at high levels.

Her research exploits the very thing that makes heavy metals such a problem in the first place – their ability to move into biological systems.

Ms Wiltshire is studying special plants known as heavy metal hyper-accumulators. Focusing mainly on pig face, she also plans to explore larger tropical plants.

‘These plants can not only withstand the toxic effects of heavy metals, but are able to remove them from the soil and store them in their lea ves at concentrations that would be deadly to a normal plant,’ she says.

Quest for economic viability

‘I’m also examining whether we can take advantage of heavy metal accumulation in another way. Maybe we can use these plants to recover valuable metals, like gold, and recycle them – a process known as phytomining.

‘The problem’, she says, ‘is that these plants are not efficient enough at extracting the metals from the soil. I’m working to understand how microbes that live on and around the roots can be used to improve metal accumulation by the plant.’

Root section from a cadmium hyper-accumulating plant:  hot spots for plant-microbe interactions that can influence heavy metal uptake from the environment. (Jen Wiltshire)

Root section from a cadmium hyper-accumulating plant: hot spots for plant-microbe interactions that can influence heavy metal uptake from the environment. (Jen Wiltshire)

So far Ms Wiltshire has isolated twelve microbes with increased resistance to heavy metals in the root zone of pig face. ‘I have found that these microbes exhibit a range of characteristics that can help promote plant growth.’

‘Ultimately the question I am working on is: could the right combination of microbes make phytoremediation an economically viable strategy for saving our soils?’ – Ernest Raetz