Genetics sheds light on frog fungus.

Genes shine light on mystery frog fungus

By ABC Science Online's Dani Cooper

Posted Tue Aug 7, 2007 6:31pm AEST

Scientists have uncovered genetic markers of a deadly fungus that is wiping out frog populations worldwide.

Researchers will now use them to pinpoint where on the globe the killer micro-organism originated.

Lead researcher Dr Jess Morgan, an Australian scientist from the Queensland Department of Primary Industries, says evidence has emerged that the frog-killing fungus Batrachochytrium dendrobatidis reproduces sexually and may be creating resistant spores, which can survive for a decade.

The international research findings, published in the journal Proceedings of the National Academy of Sciences, suggests the pathogen will be harder to eliminate.

Dr Morgan, who was a post-doctoral fellow at the University of California, Berkeley at the time of the study, says little is known about the fungus.

She says it was only identified in 1998 after a wave of frog population extinctions worldwide from chytridiomycosis, a disease caused by the fungus.

Scientists believe the fungus kills by attacking the frog's ability to absorb water through its skin, causing it to dehydrate to death.

But they still do not know exactly how the pathogen has spread around the globe.

In the paper, Dr Morgan says the team used genetic analysis of a well-studied population of mountain yellow-leg frogs in California's Sierra Nevada to determine whether the fungus was endemic or had been recently introduced.

Dr Morgan says of six sites studied, four were dominated by a single genetic make-up or genotype, suggesting the fungus had been recently introduced and spread through clonal reproduction.

But she says at two sites evidence of recombination was found with multiple genotypes present.

This indicates for the first time that the fungus reproduces sexually and may be producing resistant spores.

Dr Morgan says the presence of resistant spores helps explain the global spread of the disease and means the fungus can survive for long periods in areas where the frog population has been vastly reduced.

But it also means any attempts to reintroduce frog populations at sites of local extinction are likely to fail as the spores will re-infect the frogs.

Reintroduction

Dr Morgan says of 10 attempts at reintroducing frogs in the Sierra Nevada during the past four years, seven have failed and three are ongoing.

She says resistant spores help spread the fungus as they are easily transported in dirt on tyres and shoes, and can hitchhike on birds and other wildlife.

Dr Morgan says during the study researchers isolated 15 marker genes for the fungus, which will now be used in a worldwide hunt to track the geographic origin of the killer fungus.

"The next thing in terms of genetics is to find out where this is coming from," she said.

"The area which is most likely the origin will not be suffering a decline in frog population. We are looking for a healthy population of frogs.

"If we can look at the frogs and find out how they are living with the disease then maybe we can [help] our frogs."

Dr Morgan says the study also found some frogs within one species are resistant to the disease and could survive a mass mortality.

"It could be the frogs and the fungus are evolving to be able to live together," she said.

But she says more research is needed on the factors, either physical or environmental, behind this phenomenon.

Energy and gold among the SliMEs

Clean fuel research deal agreed by BP and Synthetic Genomics
15.jun.07
Biofuel Review
Synthetic Genomics Inc., a privately-held company dedicated to commercializing synthetic genomic processes and naturally occurring processes for alternative energy solutions, has announced a significant, long-term research and development deal with BP.
The deal between BP and Synthetic Genomics is centered on developing biological conversion processes for subsurface hydrocarbons that could lead to cleaner energy production and improved recovery rates. As part of the agreement, BP has also made an equity investment in Synthetic Genomics.
Microbes are key components in sustaining and maintaining life on Earth, and genomics is leading to an enhanced understanding of these organisms. In the first phase of the BP/Synthetic Genomics program, the research will focus on gaining a better understanding of microbial communities in various hydrocarbon formations such as oil, natural gas, coal and shale. Synthetic Genomics, which was founded by genome pioneer J Craig Venter, Ph.D., will use its expertise in environmental DNA sequencing and microbial cell culturing to produce the first comprehensive genomic study of microbial populations living in these environments. Once the basic science research phases are complete, BP and Synthetic Genomics will seek to jointly commercialize the technologies developed.
“We believe that one of the most promising solutions to producing cleaner fuels will be found through genomic-driven advances,” said Dr. Venter. “Through our research collaboration with BP, we will achieve a new and better understanding of the subsurface hydrocarbon bioconversion process which we are confident will yield substantial cleaner energy sources.”
The overall goal of Synthetic Genomics is to discover and/or design new genomes that will code for new types of cells with desired properties for bioenergy or specific chemical production. In this project, Synthetic Genomics scientists hope to better understand hydrocarbon metabolism by sequencing the genomes and culturing the cells of the naturally occurring microbes that thrive in subsurface hydrocarbons.
Tony Meggs, Group Vice President of Technology at BP, adds: “This collaboration is an exciting development that could lead to an unprecedented understanding of the microbial activity in the subsurface; and eventually to the development of more environmentally-friendly and efficient energy production and recovery techniques.”

Q and A on BACs and Metagenomics. Why large inserts?

Question from student (edited):

I am reviewing the Soil Metagenome paper that we reviewed in class (Rondon et al., 2000, Appl. Environ. Microbiol. 66: 2541-2547), and have a written note claiming that there are two important reasons to clone large DNA fragments into the BAC vectors. I can only think of one reason, which is that many soil microbes produce important bioactive compounds, and genes required for production along with regulatory genes are often clustered in one continuous segment on the chromosome called an operon. A large fragment of DNA inserted into BAC plasmid would increase the likelihood that the entire operon included. Is this correct, and is there another reason why having large DNA fragments in the BAC plasmids is important?

Answer:

Yes, you are correct, and yes, there is another reason. Large inserts mean that each clone (Escherichia coli clone line) is likely to contain genes encoding for multiple activities that may be of interest. This means that fewer clones need to be maintained than if the inserts were smaller, i.e., the same amount of metagenomic information is maintained in fewer clones (or more metagenomic information can be maintain in any given number of clone lines). Using screening assays for different activities, the same amount of metagenomic material can therefore be interrogated for the presence of specific activities while manipulating fewer cultures.

A question of cycles of oxidation in mineral leaching.

Question from student (edited):

Regarding acid mine drainage, does the oxidation of sulfides to H2SO4 result in the release of the metal ions which get leached out (eg, the release of Fe2+ from FeS2)? Does the H2SO4 that is produced cause the leaching out of other metals from their ores because of its acidic nature? Can the microorganisms also oxidise the S2- in the FeS2 in addition to oxidising the Fe2+ that is produced from this reaction?

Answer (from Pundit's Environmental Expert Jan Pundit):

Initially, the H2SO4 formed by microorganisms helps to solubilise metals released from the ores. They oxidise the S2- (in the metal sulfides) to produce the H2SO4, which helps to stabilise Fe2+ (which oxidises in air under neutral or alkaline conditions), and keeps Fe3+ in solution, which would otherwise react with water to produce ferric oxy-hydroxides (rust) at neutral and alkaline pH. Once the system is acidic, and there is a high concentration of Fe3+, then the propagation cycle becomes important. There is direct chemical oxidation of the sulfides in the ores, by Fe3+, to produce more H2SO4, and releasing more (reduced) metal ions, and the Fe3+ is chemically reduced to Fe2+. The bacteria are now important for the biological reoxidation of Fe2+ to Fe3+, which is required to keep the chemical oxidation going.

Using microbes to mine copper.

The Escondida copper mine in Chile- the worlds largest copper mine. Photo BHP Billiton Group from here.

Thomas Barton has recently written a great book - The Australian Miracle: An Innovative Nation Revisited (Picador 2006) - which has many interesting things to say about commercial and technological innovation in Australia.

It has an interesting discussion of the use of bacteria to extract copper in the following passage (pages 223-4):

For many years, people in Australia have talked about the need to shift from an economy based on the production of physical goods to an economy based on the production of knowledge. This idea is so commonplace that it is difficult to imagine anyone interested in Australian technological and economic competitiveness not taking it up.

What does it mean, though? When most people hear this recommendation, they usually imagine it means that Australia needs to shift out of mining, agriculture and other traditional sources of wealth, and into design, computer programming, biotechnology and the arts.

In actuality, though, what the shift might imply is quite the opposite.

One of Australia's biggest biotechnology companies is now BHP Billiton, the mining giant. Little known to the outside world, the company has a biotech laboratory with around eighty employees whose main job is to develop the use of bacteria for minerals leaching. The group specialises in identifying bugs in hot springs and other extreme environments, and then breeds them up so that they become efficient at breaking down intractable ores. Furthermore, unlike a good number of other biotech companies, BHP Billiton is actually putting its products to work.

As part of a one-billion-dollar exercise at Escondida in Chile - the world's largest copper mine - the company is currently bioleaching a heap of ore that stretches across nine square kilometres. Biomining, for the first time in human history, is a reality.