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Pine Bacteria Getting a Closer Look From Scientists

March 30, 2016

Professor Carolin Frank

Professor Carolin Frank

Professor Carolin Frank’s research into the nitrogen-fixing properties of bacteria inside the needles of some high-elevation pine trees is the topic of a new paper in the journal New Phytologist. Frank, with the School of Natural Sciences, won a $1.6 million, four-year grant from the National Science Foundation (NSF) in 2014 for her work on foliar endophytes.Evidence for Foliar Endophytic Nitrogen Fixation in a Widely Distributed Subalpine Conifer” is the first publication to come from that research. 

Some old-growth coniferous forests have more nitrogen in their soils and vegetation than can be explained by known sources, Frank and her colleagues explain in the paper. That limits researchers’ ability to understand and predict carbon and nitrogen cycling across about 15 percent of the Earth’s surface.

In the past few years, Frank discovered a novel symbiosis between pines and the bacteria inside their needles. She and her collaborators, including UC Merced postdoctoral researcher Andrew Moyes and project scientist Lara Kueppers, demonstrated that the enzyme responsible for fixation of atmospheric nitrogen, called nitrogenase, is active inside the needles.

That was a surprise because only bacteria associated with a few forest plants, such as legumes and alders, and free-living bacteria in soil were known to do this.

However, Frank and her colleagues still need to figure out which species of bacteria fix the nitrogen, and if they transfer it to the plants.

The researchers are using DNA probes in hopes of finding a match and being able to identify the microbes.

Frank’s discovery and the subsequent research could help solve an ecological mystery: Where does all the nitrogen in forests come from? The endophytes could be one source.

A better understanding of the microbes that fix nitrogen inside non-legume plants could help reduce fertilizer use and improve forecasts about climate change.

Frank studies limber pines. The trees are slow growing, but can live 1,000 years or more. They are commonly found from Alberta, Canada, to New Mexico, including eastern California, between 2,800 and 12,500 feet in elevation.

She has new undergraduate and graduate students in her lab who are excited to get out into the field and start sampling.

We’re going to work in Yosemite to see if the microbe community changes with the seasons,” Frank said.

She’s working with Kueppers and Jennifer Pett-Ridge, researchers with the Sierra Nevada Research Institute and the Lawrence Livermore National Laboratory, respectively. They plan to learn what’s going on with the bacteria at the sub-cellular level through stable-isotope microscopy.

We don’t know what these bacteria need — we can’t see them and we can’t grow them in the lab,” Frank said. “The bacteria that we can grow, we know a lot about. But there is a huge diversity of bacteria and the functions they perform, and we don’t know a lot about that. We don’t even know how they get into the pine needles. There are many mysteries in microbiology.”

Leaf bacteria fertilize trees, researchers claim

Science Magazine, May 2015

Elizabeth Pennisi

F1.largeOne of the fastest growing trees, poplars, may rely on tiny microbes in their leaves to fuel their growth. For more than a decade, a lone researcher has been building a case for nitrogen fixation by bacteria living in poplar leaves. There have been many claims of nitrogen fixation in plants outside nodules where it was known to occur for more than a century. Newly reported experiments involving rice grown on nitrogen-poor soil and poplar cuttings put in air with heavy nitrogen should help convince the skeptics. In addition, another researcher finds evidence of nitrogen fixation in the needles of limber pine and Englemann spruce. If these bacteria prove to be widespread, they could be used to boost crop production on marginal soils.


Mapping Genomes of Pine Bacteria Yields Unexpected Results

April 29, 2015

A grove of Scots pine trees

UC Merced Professor Carolin Frank is helping figure out how a certain bacteria helps promote healthy tree growth by studying the bacteria’s genome sequence.

In the new paper, published in the open-access journal mBio, Frank and research colleagues in Finland said their discoveries could have practical applications in agriculture and forestry by stimulating plant growth.

While trying to grow pine tree cells in petri dishes, the Finnish researchers couldn’t get rid of the Methylobacterium extorquens microbe. They were surprised to find the bacterium collecting inside the tree’s cells, especially around the nuclei.

And they found that inoculating the pine seedlings with the bacteria made the little trees grow faster, suggesting the bacteria are beneficial. That made Frank want to unveil the mechanisms behind the host-microbe interaction.

She and her colleagues were thrown another curveball when they found that some of the bacteria’s genes look more like eukaryotic than bacterial genes.

Plants are eukaryotes, and it is possible the bacterium makes these proteins so they can work with the plant’s machinery for protein synthesis, affecting plant growth from within the cells themselves, Frank said. Instead of producing plant hormones like some endophytes do, the microbes seem to transfer growth-supporting proteins into the tree cells’ nuclei.

We usually don’t think about endophytic bacteria as intracellular, but it might be that we just haven’t looked enough,” she said. “I like to get a new perspective on questions, and maybe we just need to look from all the different angles.”

Now that the researchers have found this novel niche for endophytes, they will sequence other bacteria they’ve found in the Scots pine stem cells and study the symbiosis between the trees and their bacteria.

The genome sequencing was completed at the Department of Energy’s Joint Genome Institute in Walnut Creek, where UC Merced researchers are forging numerous collaborations. Frank said graduate students can apply to work on summer projects there, as well, giving them a unique opportunity.

This isn’t Frank’s first foray into tree endophytes. She works on a bacterial inventory in Colorado and California conifers with fellow Sierra Nevada Research Institute researcher Lara Kueppers. She’s also trying to get a better understanding of the microbes that fix nitrogen inside plants, which could help reduce fertilizer use and improve forecasts about climate change.

Frank, a computational biologist, started out researching bacterial pathogens in humans and animals in Sweden, where she’s from.

It’s funny, because Finland and Sweden are covered with conifers, but I didn’t start studying trees until I came here,” Frank said.


Pine Needle Bacteria Earn Professor Second NSF Grant of the Year

September 22, 2014

Professor Carolin Frank will collect $1.6 million over the next four years to continue researching the nitrogen-fixing bacteria that live in pine needles and to work with the Sierra Foothill Charter School, which she helped found.

The National Science Foundation (NSF) selected Frank, with theSchool of Natural Sciences, and collaborators Lara Kueppers, Jennifer Pett-Ridge and Tanja Woyke at the Department of Energy National labs in Berkeley and Livermore, for its 4-year-old Dimensions of Biodiversity Award, designed to help fill gaps in understanding the many species of plants and animals on Earth.

The NSF is distributing $23 million among 12 biodiversity projects this year.

Scientists funded by the Dimensions of Biodiversity program integrate genetic, taxonomic and functional approaches in their study and exploration.

This is huge,” Frank said. “It will allow me and my collaborators to work on this fascinating problem for the next few years. UC Merced is a great place to be doing interdisciplinary team science.”

In contrast to traditional biodiversity research that focuses on one taxonomic group or ecosystem, Dimensions of Biodiversity integrates multiple aspects into research projects.

The program links functional, genetic and phylogenetic/taxonomic dimensions of biodiversity, offering opportunities to make rapid advances in understanding the generation, maintenance and loss of biodiversity.

This year’s portfolio of projects will accelerate our understanding of biodiversity across disciplines and across scales of time and space,” said Penny Firth, director of NSF’s Division of Environmental Biology. “Through this program, we’re witnessing a transformation in our ability to bridge scientific approaches and perspectives.”

The research will fill in gaps in biodiversity knowledge, Firth said. It also has the potential for significant effects on agriculture, fuel, manufacturing and health.

Dimensions of Biodiversity scientists are working to stem the tide of species losses around the world.

In the past few years, Frank and her graduate student Alyssa Carrell, who defended her Ph.D. this summer, discovered a novel symbiosis between pines and the bacteria inside their needles. Recently, Frank, Kueppers and postdoctoral fellow Andrew Moyes demonstrated that the bacteria, or endophytes, appear to fix atmospheric nitrogen.

That’s surprising because until now, only bacteria associated with a few forest plants, such as legumes and alders, and free-living bacteria in soil were known to do this. Nitrogen is critical to plant growth and development, but our understanding of the nitrogen budget is incomplete.

Frank’s discovery could help solve an ecological mystery: Where does all the nitrogen in forests come from?

There’s more nitrogen in there than there should be, and these endophytes could be a previously ‘hidden’ source,” Frank said.

That could have huge implications for ecosystems and climate.

A better understanding of the microbes that fix nitrogen inside plants could help reduce fertilizer use and improve forecasts about climate change.

The grant will allow Frank to study the limber pine across its range, from Canada to New Mexico and Colorado to California. A teacher from the charter school will work with the researchers, too, and take what he or she learns back to the classroom. Frank will also help develop some curriculum for grade-school students, focused on environmental microbes.

Frank said she appreciates the opportunities the new grant affords.

There hasn’t really been a way to study most microbes in the environment until recently, when DNA sequencing technology became good enough to sequence lots of bacterial DNA from the environment and discover who’s there,” she said. “The grant will allow us to study this symbiosis further and identify the specific bacteria that fix nitrogen.”

This is her second NSF grant this year. In the spring, she won a $150,000 Early-concept Grant for Exploratory Research (EAGER) award that supports exploratory work in its early stages on untested, but potentially transformative, research ideas or approaches.

I have an undergraduate degree in engineering and a Ph.D. in molecular evolution, and was never trained in any one discipline. I tend to see connections among disciplines,” said Frank, who, as a graduate student at the University of Uppsala, Sweden, trained herself both as a computational and experimental biologist. “I think the interdisciplinary approach has great potential – that’s how we discovered this symbiosis – but sometimes I have wondered if the system is set up to fund that type of research, so this is very exciting!”

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