Unraveling Environmental Issues with Genetics

Posted on December 20, 2012

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The tiny western flowered thrip is an insect as translucent as ale that looks like a cross between a grasshopper and a maggot.  But its small parenthesis-like size doesn’t fool farmers. It’s costing them millions of dollars as the bug chomps its way through hundreds of thousands of acres of fruits, vegetables and flowers in Southern and Western United States.

And it’s just not a United States scourge. Because it has been resistant to every kind of pesticide thrown at it, the thrip causes more than $1 billion in tomato losses globally.

Now scientists are turning to a new strategy in hope of finding the bug’s weakness—its genes.

Researchers at the University of Kansas are using a process called RNA interference, RNAi, that’s been widely used in biomedical science to quell expression of certain genes like those in measles, influenza and cancer to disarm the thrip.

The researchers are not alone.  Investigators are marrying two branches of science—environmental science and genomics—in an attempt to solve some of today’s most pressing environmental issues: from droughts in Africa, to weed and pest infestation in the Southeastern United States and Canada to harmful algal blooms on Long Island.  For scientists in Africa success in creating drought resistant rice could feed millions while failure means facing an unproductive season for local farmers in the drought-stricken Horn of Africa.

“Ecological genomics came about through determination to see whether the techniques and approaches of medical genomics could be extrapolated to situations of nature,” said Martin Feder, geneticist at The University of Chicago and a co-pioneer in the field.

Genomics first arose in the 1980s when a technique called polymerase chain reaction, PCR, was invented by the biochemist and avid surfer, Kerry Mullis.  The application produced millions of copies of DNA sequences and enabled a scientist to sequence any gene. The Human Genome Project was the first major breakthrough. It took 10 years to sequence the human genome in 2000.

That historic accomplishment was a gateway to answering scores of potential questions about human disease.  But it wasn’t until 2003 that Feder and Thomas Mitchell-Olds of Duke University coined the name of another emerging field in Nature Reviews Genetics:evolutionary and ecological functional genomics. Their goal was to explain diversity and variation in organisms and their populations.

This time grasslands, forests and bodies of water would be the laboratories and billions of organisms would be the potential subjects of experiments that took place in a dynamic, real-time environment.

“What ecogenomics allows us to do is clearly confront the cells and ask what are you doing at this time? Are you using organic matter? Do you care that there’s no nitrogen around? Do you use phosphorus?  Does it matter to you?” said Sonya Dyhrman, Associate Scientist in Massachusetts at Woods Hole Oceanographic Institution and co-author of the brown tide genome project.

“Instead of having to infer from the environment,” Dyhrman added, “we can directly [profile] the cells and that is hugely powerful and that’s something we couldn’t do and tell before we had these ecogenomic approaches and tools.”

New cheaper and faster technology is creating new opportunities.  Today, scientists can sequence the thrip genome for $1,000 in one day and assemble it in several months to a year.  Researchers are predicting they will have sequencing machine within 10 years in their own laboratories, some even predict that the technology to sequence genomes will become as portable as a laptop or iPhone and cost less than $5,000—that was until last month when Oxford Nanopore Technologies Ltd. unveiled a $1,000 genome sequencer the size of a USB for doctors and scientists to use outside the labs.

“There is now, no technological barrier for an ecological genomicist scientist to take and sequence the genome of anything they want,” Feder said.

Applying the new technology, 13 scientists from the University of British Columbia and Alberta University sequenced the genomes of a pine tree, beetle and fungus.  For over a decade, the tale of the menacing mountain pine beetle in British Columbia, Canada has been all too familiar: a forest epidemic devours the native lodgepole pine trees as the beetle transmits a blue stain fungus.

Already, the beetles have killed off more than 44 million acres of pine trees in British Columbia and have cost the province $884 million since 2001 to mitigate its impacts on forestry, according to the Ministry of Forests, Lands and Natural Resources Operations.  The Canadian government and other agencies funded lead researcher Joerg Bohlmann and his team $7.8 million to find a solution.

After the genome sequencing, researchers identified an enzyme in the beetle that can disarm the toxins the pine tree releases to defend itself against the fungus.  Now the researchers are applying an RNAi technique in the lab to suppress the enzymes produced by the beetle.  Administering an aerosol treatment would be one approach to eradicating the epidemic in the natural environment.

Another pest, cogongrass, is a toxic weed that has invaded 73 countries and more than 1.5 million acres in southeastern United States.  A. Millie Burrell at Texas A&M University’s department of Horticultural Sciences has been studying the invasive species.  Burrell is also part of a multi-state task force consisting of forestry professionals and state and federal management specialists and landowners trying to prevent the expansion of cogongrass.

The weed, which isn’t native to the United States, is displacing native plants and fertile soil for farmers. Some states are so economically-depressed, they can’t afford to even apply herbicides.  But even if they do it, it might not make a difference.

“Throwing herbicide is millions of dollars wasted,” Burrell said.

In the summer of 2011, Burrell and her collaborators began studying the genetic varieties of cogongrass and received a grant from United States Department of Agriculture-National Institute of Food and Agriculture, USDA-NIFA, to study biological control plants and insects that can keep the cogongrass in check.

Burrell found that the weed spread through aggressive underground growth.  Burrell’s USDA collaborators will initiate international exploration for potential biological controls like insects that target cogongrass with the same genetics as those found in the U.S. and rear those insects in quarantine in the U.S. before introducing them into the environment to ensure they don’t attack crops.

“If the potential controls pass that set of tests and prove to eat only cogongrass, then testing to determine if the bio-control can survive in its new environment and effectively control the species will be undertaken,” said Burrell.  “The testing is extremely stringent.”

In West Africa, where rice is a food staple, Michell-Olds collaborated on developing drought resistant rice with the Africa Rice Center’s lead researcher, Marie-Noelle Ndjiondjop.   Ndjiondjop identifies resistant genes and crosses them in rice plants to create a superior drought-resistant plant.

“In Africa, drought is the most important issue impacting rice production,” Michell-Olds said. Irrigation from outside sources is not a practical option for poor farmers because it’s scant in parts of Africa.

But the project has been challenging and demonstrates some of the limitations of ecogenomics.

For example, the work involved crossing the African rice, which was drought resistant, with an Asian rice that had high yield but poor resistance, in an effort to grow rice that was both resistant and produced a high yield.  But yields have been disappointing. The high-yielding strain of rice is also the most stressed during drought and sterility is higher in the hybrid rice, according to West Africa Rice Development Association.

Jack Schultz, Professor and Director of Bond Life Sciences Center at the University of Missouri, says that understanding the genetic makeup doesn’t necessarily solve everything.

“When we come to natural environments, first there’s an incredible array of things to study…every organism is unique and every environment is unique,” Feder said. “They don’t have a standard condition.”

On Long Island, scientists from the School of Marine and Atmospheric Sciences have been using genomics in a challenging natural environment: underneath. For years, researchers have had few clues as to what caused an infamous brown tide that nearly destroyed a once robust shellfish industry.  Since the brown tide first appeared in the 1980s, the population of hard clams and bay scallops has declined by 99 percent.

Christopher Gobler, a marine biologist and director of the Stony Brook Southampton Coastal and Estuarine Research Program, assembled a team of researchers to look at the genome and found that the algae thrive in low levels of light and high levels of organic nitrogen, which provides evidence as to how they’re surviving in natural conditions.

“Stepping back, it’s clear that the reasons we have high levels of organic nitrogen is that there’s a lot of high levels of nitrogen system entering the land, many cases primarily from septic tanks and cesspools,” Gobler said. “So the idea being if we can reduce the amount of nitrogen from land coming to these bays we can reduce the intensity of all algal blooms and increase levels of light and reduce levels of organic nitrogen and make the estuaries less habitable for [brown tide].”

Although federal and state-run agencies and other institutions have successfully reduced nitrogen discharge by 25 percent, and the current the level of nitrogen in local bays at 10 milligrams per liter of water is safe for drinking, the levels remain too high to eradicate the algal blooms. Based on Gobler’s research, officials need to reduce the levels another 95.5 percent to meet the requirements to destroy algal growth.  Reaching that goal would mean installing expensive septic systems. The project is not currently on the priority list of the New York State Department of Environmental Conservation.

This year, the scientists received a $3.7 million grant to begin restoration of Shinnecock Bay, a major waterway in the area.  The project seeks to reduce the harmful algal bloom, by planting eelgrass beds and shellfish in an effort to make it more habitable again for the organisms and bring back the fisheries.

But not everyone is sure the restoration efforts will be enough.  Jackie Collier, a Stony Brook co-author of the brown tide paper, finds that analyzing the algae genes at various stages of growth might better give the scientists crucial clues.

“Best studies come from ecologists who can address ecologically relevant traits and collaboration between geneticists and molecular biologists focused on addressing molecular mechanisms that can adapt to certain environments,” said Jill Anderson, an evolutionary ecologist and a former student of Michell-Olds at Duke University.

As for the voracious thrips, The Bill and Melinda Gates Foundation has come to the rescue and funded an RNAi-delivering technology developed at Swansea University.  The lead microbial geneticist, Paul Dyson, said, the RNAi is carried through the insects own bacteria and could be a non-chemical pesticide that safely targets the thrips only.

Plant pathologist and postdoctoral student Ismael Badillo-Vargas from Kansas State University, studied the thrips’ proteins and found most of the proteins in the infected thrips were involved in promoting the virus that caused crops to wilt and spot.  Badillo-Vargas is now targeting the part of the gene that produces those proteins by artificially feeding the thrips RNAi that will subdue the number of viral proteins produced.

He said it might take his team several more months before they determine if the experiment will be successful.

“From there it will take quite some time before this can be used in the field,” Badillo-Vargas said, “because it would be delivered using crossbreed plants and those take time to be made and then undergo a lot of regulations.”

If the team is successful at targeting the genes with the artificial diet, they expect the process to be patented.

“We’re living in a unique time that’s empowering scientists,” said Burrell.  “With genomics you can apply something that’s safer because you have more information. 

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