Monday, October 28, 2013

Bizarre purple shiny mat in Kilauea cave is a new species of cyanobacteria

Cyanobacteria, which have sometimes confusingly and inaccurately been called blue-green algae, are cool critters.

To find a new species to science, in a genus that is only represented by one other species in the world, is cooler still.

And to find it in a hot, 100-year-old volcanic cave on active Kilauea volcano, well, that's so cool it's downright polar.

University of Hawai`i researchers are reporting they found the primitive life form on a film of biological material growing on the rock wall of a Kilauea cave a few hundred feet from Halema`um a`u. To get into it, they had to back feet first through a small entrance into the cave, whose floor radiated heat at 90 degrees Celsius or 190 degrees Fahrenheit.

(Image: The cyanobacteria mat on Kilauea cave wall. Photo courtesy Stuart Donachie, UH.)

They found a glistening purple mat of moist stuff, growing in very low light on the cave wall. When they ran its genetics, they found it fits in a genus of cyanobacteria that wasn’t described until 1974 and has only one other species in it. That one was found in Switzerland on limestone rock, while this one was on basalt. And genetic work showed the two had diverged from each other 280 million years ago.

Why should we care about cyanobacteria? We wouldn’t exist without them. They are largely responsible for much of the oxygen in our atmosphere. Some varieties fix nitrogen, creating nutrients for plants.

They are some of the earliest life forms ever identified on Earth. They’re different from many others in that their cells have no nucleus, making them procaryotes like bacteria. By contrast, humans and other animals, insects, fungi and all plants are eucaryotes: they have their genetic material encased in nuclei within their cells.

“Cyanobacteria are among the most diverse and successful microbes on Earth. As pioneers of oxygenic photosynthesis they permanently changed Earth's atmosphere by emitting gaseous diatomic oxygen, paving the way for the evolution of aerobic metabolism,” says a paper in the journal PLOS One, “Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawai'i.” 

The paper’s authors are Jimmy H. W. Saw, Michael Schatz, Mark V. Brown, Dennis D. Kunkel, Jamie S. Foster, Harry Shick, Stephanie Christensen, Shaobin Hou, Xuehua Wan, and Stuart P. Donachie.

As the article title suggests, they’re proposing naming the new species Gloeobacter kilaueensis sp. nov. (sp. nov. simply stands for “new species.”)

A colony of these new cyanobacteria is purple in color, and smooth and shiny. It has a gel or mucous-looking surface, said co-author Stuart Donachie. He said it’s a unique discovery.

"It’s a great find because both species represent an entire taxonomic order distinct from the other 7,500 known cyanobacteria species. They lack the photosynthetic membranes that are found in all those 7,500 species, which means they are also the most primitive known cyanobacteria,” said Donachie an associate professor in the Department of Microbiology at the University of Hawai`i’s College of Natural Sciences.

So how did this cyanobacterium get into a hot, young Kilauea cave?

“That’s a question we get asked all the time. It is a question we could not answer and have not answered,” Donachie said. 

The most likely answer, he figures, is that it blew in on the wind. And not from a Switzerland colony. 

That suggests there are, somewhere on the planet, other, undiscovered cyanobacteria colonies in the Gloeobacter genus, one of which was the source for Gloeobacter kilaueensis.

 © Jan TenBruggencate 2013

Friday, October 18, 2013

Kaua`i Council's GMO bill, a review.

The Kaua`i County Council this week passed a groundbreaking piece of legislation, regulating both pesticides and genetically modified crops.

Whether you support or oppose the bill, and whether it is rejected in court or not, it represents a significant legislative event. 

Its key features are an aggressive disclosure policy targeted at big farmers, significant buffer zones, and the call for a study of the environmental and health impacts of big ag—specifically big ag that uses both genetically modified crops and any kinds of pesticides. 

The bill has taken a circuitous route to the form that is now being considered for signature or veto by Mayor Bernard Carvalho. 

Here are key provisions of the document approved by an exhausted Kaua`i County Council, driven by a drumbeat of chants of “Pass The Bill!,” after 3 a.m. on October 15, 2013. 

1.      Any farm that uses more than 5 pounds or 15 gallons of a restricted use pesticide (the kind that require you be a certified pesticide applicator), must disclose the use of all pesticides of any kind during the following year. Warning signs must be posted at the site of pesticide use 24 hours ahead of time and during and after the application. Farms must also post all such pesticide notifications at a central area for workers.

2.      Farms must, before applying pesticides, personally notify neighbors within 1,500 feet of the farm’s property lines. That includes anyone who lives, works, keeps bees or who occupies the property, legally or otherwise. These “Good Neighbor Courtesy Notices” can be sent by phone, text or email. Such messages need to be sent weekly or more often as necessary.
3.      Similar messages are also required to be made available weekly to everyone else on the island, through reports to the county that will be posted online. The weekly after-use reports are to include what pesticide is being used including its trade name and EPA registration number, on what day, at what time, on what field, over what acreage, during what wind conditions. Maps of pesticide application locations are to be provided.

4.      Farmers must also provide an emergency hotline to provide to medical personnel details of pesticide use when there is a documented medical need.

5.      Farms that grow genetically modified crops must file annual reports with the county and state, and those reports are to be posted for the public online. Annual reports are to describe the genetically modified crop being grown, where it is grown and when it was first planted there.

6.      The farms that use 5 pounds or 15 gallons of restricted use pesticides must establish 500-foot no-grow zones around care homes, medical facilities, residential houses, and schools. There’s 250-foot buffer around parks, 100 feet along roads (unless signs are posted), and 100 feet along shorelines or streams

7.      A two-part environmental and public health impact study will be outlined by a fact-finding group within 12 months, which will then oversee the conducting of the study by a professional consultant, which has an 18-month deadline. The study is to look into impacts from big agriculture uses of both genetically modified crops and pesticides.

The 2.5-year total for the study may seem generous, but it took the United States from the 1940s, when scientists began expressing concern about DDT, until the 1970s, to ban DDT. Various neonicotinoid insecticides began being marketed in the 1980s and 1990s, but it took until this year, 2013, before significant numbers of studies prompted European restrictions on their use.
In each case, 30 years for a single pesticide or class of pesticides.

An optimistic Kaua`i County Council hopes that on Kaua`i, the problems of  pesticides as well as genetically modified organisms can be identified and regulations recommended—in 30 months.

© Jan TenBruggencate 2013

Thursday, October 10, 2013

UH researchers test more sophisticated fish tracking.

You can radio tag a bird or a mammal to track their movements with GPS, but the technology doesn’t work so well under water.

Researchers have overcome this with satellite tags that report locations when whales or seals or turtles come to the surface. And there are tags that automatically release and float to the surface, where they can report their positions.
(Image: Map of fish tracking stations at Palmyra Atoll. Credit: UH Mānoa.)
But tracking a fish that stays down in the water can be a problem, so researchers have adopted sound waves as their tracking systems.
One solution has been acoustic monitoring, since sound travels well in the water. It works this way: you set up an array of precisely located listening devices on the reef. Then you attach small noisemakers to fish, and the sounds collected on the listening devices give you a sense of when fish are present and which microphone they’re closest to.
New research is fine-tuning the information.
“Previous methods were not formulated with the fish, ocean and acoustics in mind. They therefore do not exploit all available information, such as the biology of the fish limiting its range of possible movement.” Martin W. Pedersen, a UH Mānoa postdoctoral fellow.
Pedersen and Kevin C. Weng, manager of the Pelagic Fisheries Research Program at the University of Hawai‘i at Mānoa, published their new fish tracking model in the scientific journal Methods in Ecology and Evolution.
Pedersen and Weng’s new state-space model for estimating individual fish movement is two-part—one part that models the fish behavior, and one that models the detection of that behavior.
The system uses data on fish behavior, along with information on where fish are detected and where they are not detected to help pin down their precise locations.
“Knowing where the fish is not located actually tells you a lot about where it is located, and with our new method, we are able to utilize that information and achieve a better accuracy,” Pedersen said.
Their tracking model was tested in remote Palmyra Atoll, far to the south of Hawai`i, where 51 underwater observation stations were established. They were able to create maps that helped show where the fish were and how they moved.
“It helps us to better understand how they feed, breed and rest,” Weng said.  “Ultimately, more accurate movement information will help us to conserve these species.”
© Jan TenBruggencate 2013

Citation:  Pedersen, M. W., Weng, K. C. (2013), Estimating individual animal movement from observation networks. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12086