Enormous array of bacteria discovered on common bird; could have agricultural implications

A microbiology professor and an ornithology professor have discovered that one of North America's most common migratory birds – the Dark-eyed Junco – carries on its feathers a remarkable diversity of plant bacteria, the greatest ever found on wild birds. And while many of these bacteria may be harmful to plants, the bacteria could also be of great benefit. 

And while many of these bacteria may be harmful to plants, the bacteria could also be of great benefit.
That's what Schneegurt and Rogers, researchers from two different disciplines with one common goal, are working to determine.
"Some of the bacteria we find are beneficial to plants. Some are harmful to plants," Schneegurt says. "How does that balance work out for the plants? That's not clear."
But what is clear is the importance of this research.
Wild birds interact with the environment, contacting soils and plants with their feathers. Those feathers filter the air, gathering particles of soil and plant matter. Because microbes are everywhere in nature, feathers naturally carry a diverse community of microbes. And as for Juncos specifically, these migratory birds can fly 200 or more miles a night, making them highly capable of spreading bacteria over large swaths of land.
Pathogens are notoriously costly for agriculture, so the benefits of preventing possible diseases or, conversely, identifying helpful bacteria, are vital.
"The Juncos are probably good guys in all of this," Rogers says. "It may be that they're spreading pathogens, but theoretically it's possible that they're also beneficial instead of just being negative."
Possible commercial applications
Much of Schneegurt and Rogers' research work was conducted at the WSU Biological Field Station, Ninnescah Reserve. They hope to secure further funding for their project.
Their next step is to test the isolates they've captured on plants such as tomatoes, potatoes, wheat, oat and rye to see if they have qualities of beneficial bacteria or those of pathogens.
A potential benefit may be bacteria that produce growth-encouraging hormones. Another possibility would be bacteria that actually inhibit fungi which are trying to damage the plant.
The pair have also found many isolates that actually degrade bird feathers. Not good for the birds, but of possible interest to biotechnology companies. Schneegurt says these bacteria could be used to break down enzymes in laundry detergent, as well as other industrial and potential medical uses.
"This is where the basic description of natural phenomenon -- in this case communities on bird feathers -- can lead to commercial applications," he says.
An innovative approach
Rogers and Schneegurt weren't planning on conducting a study of this scale on Junco bacteria. Last year they were reviewing WSU grad student John "Wes" Dille's thesis, which described the microbial community on Junco feathers.
"We weren't looking for this," Schneegurt says. "We were originally looking to simply describe the community of bacteria found on the bird feathers. It's serendipity."
He and Rogers thought previous work of the scientific community on feather bacteria wasn't as complete as it could be.
"I said, 'I think we could do a better job,' and as it turns out, we did," Schneegurt says.
Why is that? In large part, they say, because of their ability to put their unique skills and knowledge together for this study.
"Here we have a professional long-term ornithologist and a professional long-term microbiologist putting our major backgrounds together to make a major discovery," Rogers says.
Schneegurt says hearing someone else's perspective will inevitably result in better work.
"If you listen to the same guys all the time, you only know what they know," he says. "Iinteractions lead to things you would never imagine happening. That's where real innovation comes from."

This story is taken from Science Daily

Extra DNA creates cucumber with all female flowers

A new study identifies the gene duplication that causes cucumber varieties produce only female flowers -- a high-yeild variety. The researchers discovered the extra DNA by screening genome sequences from a core collection of 115 different cucumber lines. 

The study, led by Zhangjun Fei of the Boyce Thompson Institute at Cornell University, and Sanwen Huang of the Chinese Academy of Agricultural Sciences, in Beijing, appeared recently in The Plant Cell.
Dutch breeders take advantage of "gyneoecious" varieties that produce only female flowers. When grown in nutrient-rich, soil-free greenhouses they produce a cucumber from each flower, greatly increasing the yield over "monoecious" varieties that produce both types of flowers. The female flowers must be fertilized by pollen from a male flower, but by controlling the sex ratio, growers can greatly increase their harvest.
"If you compare the greenhouse production in the Netherlands, which uses plants with female flowers, to China, where they use monoecious plants and normal agricultural practices, the production in the Netherlands is about 15 times greater than in China," said Fei. He explained that farmers in China do not plant gynoecious cucumbers because the nutrition in the soil is not sufficient for fruits to develop at each flower.
Though researchers have known since the 1960s that there was a genetic cause for all-female flower-bearing plants, the exact location and sequence of the responsible segment of DNA was previously unknown.
The researchers discovered the extra DNA by screening genome sequences from a core collection of 115 different cucumber lines. They looked for changes called structural variations--large regions of the genome that are missing, added, reversed or duplicated. They generated a map of the 26,778 different structural variations that they found, some of which are associated with cucumber domestication. The analyses show that collectively, these structural variations affect more than 1,600 genes in the cucumber genome.
"It turns out that we found this one specific structural variation that is a duplication of about 30,000 bases. The duplication was highly correlated with gynoecy," said Fei. "For female flowered-plants, there's a lot of potential for agricultural production."
The study builds off of previous work by Fei, Huang and colleagues, who collaborated in sequencing the initial cucumber genome and later published a paper that identified single base differences called SNPs, between multiple cucumber lines.

This story is taken from Science Daily

Bee warned: Study finds pesticides threaten native pollinators

A new study of New York state apple orchards finds that pesticides harm wild bees, and fungicides labeled 'safe for bees' also indirectly may threaten native pollinators. 

The research, published June 3 in Proceedings of the Royal Society B, finds the negative effects of pesticides on wild bees lessens in proportion to the amount of natural areas near orchards.
Thirty-five percent of global food production benefits from insect pollinators, and U.S. farmers have relied exclusively on European honeybees, whose populations have been in decline for decades due to colony collapse disorder.
"Because production of our most nutritious foods, including many fruits, vegetables and even oils, rely on animal pollination, there is an intimate tie between pollinator and human well-being," said Mia Park, an assistant professor at the University of North Dakota and the paper's first author, who worked on the study as a Cornell entomology graduate student. Co-authors include professor Bryan Danforth and associate professor John Losey, both in entomology.
"With honeybee numbers in decline, relying on wild pollinators and encouraging the services they provide seem very important," Park said.
The researchers studied 19 New York state apple orchards over two years, 2011 and 2012. They determined the health of bee populations by analyzing the numbers of wild bees and honeybees and the number of species for each orchard. They also created an index of pesticide use from low to high use, then quantified the amount of natural areas that surrounded each orchard.
"We found there is a negative response of the whole bee community to increasing pesticide use," Park said, adding that fungicides also are contributing to the problem.
The effects of pesticides on wild bees were strongest in the generation that followed pesticide exposure, Park said, possibly suggesting pesticides affect reproduction or offspring. Park said her research only looked at one generation to the next, and more study is needed. The study found no effect of pesticides on honeybees, but European honeybee hives are brought in to an orchard for short periods during blossoming then removed. In addition, growers are careful not to spray while honeybees are in the area. "Honeybees may have shown a response if they were allowed to stay," Park said.
"Our studies of wild bees in apple orchards are showing how important wild bees are for apple pollination in the eastern U.S.," said Danforth. With more than 20,000 known bee species, native bees are abundant and diverse in many agricultural habitats, and likely pollinate watermelons, squashes, blueberries and other orchard crops, he said.

This story is taken from Science Daily

Researchers edit plant DNA using mechanism evolved in bacteria

Researchers have used a gene editing tool known as CRISPR/Cas to modify the genome of a tree species for the first time. Their research opens the door to more rapid and reliable gene editing of plants. By mutating specific genes in Populus -- a genus of deciduous trees that includes poplar, aspen and cottonwood -- the researchers reduced the concentrations of two naturally occurring plant polymers. 

By mutating specific genes in Populus -- a genus of deciduous trees that includes poplar, aspen and cottonwood -- the researchers reduced the concentrations of two naturally occurring plant polymers. One is called lignin, which traps sugars and starches used for biofuel production inside the tree's sturdy cell walls. The other is known as condensed tannin, and its presence in leaves and barks of the tree deters feeding by ruminants, such as deer, cattle, goats and sheep.
"CRISPR is a relatively new technology, but it could improve our ability to produce novel varieties of food crops, animal feeds and biofuel feedstocks," said the study's lead researcher C.J. Tsai, a Georgia Research Alliance Eminent Scholar in UGA's Warnell School of Forestry and Natural Resources and department of genetics. "Compared to some other gene editing techniques, this is incredibly simple, cost-effective and highly efficient, and it could serve as the foundation for a new era of discovery in plant genetics."
CRISPR technology is derived from a defense mechanism evolved by bacteria and other single-celled organisms. When a bacterium is attacked by an invader like a virus, it captures some of the virus's DNA, chops it up into pieces and incorporates a segment of the viral DNA into its own genome.
As the bacterium experiences more threats, it accumulates a bank of past infections in a special part of its genetic code called CRISPRs -- short for clustered regularly interspaced short palindromic repeats -- which act as a kind of immune system to protect against future invasions.
"This is a mechanism that evolved naturally, but we can borrow the bacteria's gene-cutting abilities and use it to edit very specific genes in all kinds of organisms, including plants and animals," said Tsai, who is also director of UGA's Plant Center. "It's like using a pair of scissors with GPS tracking to locate and snip out tiny bits of DNA -- enough to nullify the gene you don't want, while leaving everything else unchanged."
Tsai credits her collaborator Thomas Jacobs, a former doctoral student in UGA's Institute of Plant Breeding, Genetics and Genomics, who adapted the CRISPR system for plant genome editing.
"Tom was a student in my class a few years back, and we were testing some of the gene silencing systems he developed for soybean in poplars," Tsai said. "It was a side project, also involving Xiaohong Zhou, a visiting doctoral student from Nanjing Forestry University, to test the new CRISPR system, and its high efficiency exceeded all of our expectations."
Every single poplar plant Zhou produced from the lignin-gene-targeting experiment had red-colored wood. Red stem is a known side effect of lignin modification found in natural mutants of maize, sorghum and pine, Tsai explained, so the researchers knew the CRISPR system worked when they saw the telltale red stems on their Populus plants.
"I was blown away by the results," Jacobs said. "This is one of the highest efficiencies ever reported, even in mouse and other animal models where the technology has been more extensively tested."
The modified Populus plants contained about 20 percent less lignin and 50 percent less condensed tannins than wild trees.
"We thought we knew what genes control lignin and condensed tannin production, and we did target the right genes, but the work showed us that there are other genes with overlapping roles," Tsai said. "The CRISPR system can now guide researchers seeking to identify these previously unknown gene family members."

This story is taken from Science Daily

How dividing cells end up the same size

A new study shows that how much a cell grows before it splits into two depends on its initial size. The finding goes against recent publications suggesting cells always add the same amount of mass, with some random fluctuations, before beginning division. 

A new study appearing June 3 in Nature shows that a cell's initial size determines how much it will grow before it splits into two.
This finding goes against recent publications suggesting cells always add the same amount of mass, with some random fluctuations, before beginning division.
"It's like students going through college," said Lingchong You, the Paul Ruffin Scarborough Associate Professor of Engineering in the Department of Biomedical Engineering and the Center for Genomic and Computational Biology at Duke. "If they're not prepared, they take five or six years to graduate rather than taking more classes and overburdening themselves."
It all began with explainable oscillations. The team was looking at how genes on circular pieces of DNA called plasmids segregate when cells divide by tagging the genes with different fluorescent colors.
"We noticed oscillations in the expression of these colors in about 30 percent of the cells," You said. "And that's weird because we knew the genes involved aren't regulated, so this was incredibly baffling to us. We were very surprised."
The project was initiated by two former Duke graduate students, Yu Tanouchi and Anand Pai, now postdoctoral scientists at Stanford University and UC-San Francisco, respectively. The team was using a "mother machine," invented by Suckjoon Jun at UC-San Diego, to watch the division patterns of individual cells over many generations.
The device places individual cells -- in this case E. coli bacteria -- at the closed end of very small tubes. As each trapped cell grows and divides, its daughter cells are forced up the tube, where they are eventually swept away by a stream of nutrients.
The setup allows researchers to watch hundreds of cells go through divisions over dozens of generations and was key in seeing the baffling oscillations.
"Most studies take the average of many cells or many generations, which would make it impossible to see these oscillations," explained You. "That's why the single-cell analysis was critical, because these oscillations occur over many cell cycles with varying periods."
While trying to trace the origin of the genetic oscillations, You and his team were even more surprised to discover that the initial cell size also oscillated over multiple generations. After spending months trying to find the reason for the oscillations, Yu looked at correlations of different growth metrics like cell size at division, speed of growth and time to division.
And the results were a strikingly simple linear relationship, revealing that a cell's initial size determines how much biomass it would add before beginning cell division.
You and his colleagues then checked their findings against computer models. By using the same linear relationships and throwing in random fluctuations, they were able to recreate the oscillations in size in 30 to 40 percent of their virtual cell lines, just like in their experimental data.
Although the group does not know how the cells determine how long to grow based on their initial size, the computer models fit their experimental data precisely. But whether or not others in their field will be convinced is yet to be seen.
"During the review period of our paper, there were two experimental papers published in high-impact journals providing evidence for the 'adder model' (or the 'incremental model'), which is that when cells divide, they add a constant biomass on average," said You. "But the data are the data, and in our data we don't see this. The two models are very similar, but they have completely different implications for how cells maintain their uniform size. It will be interesting to see how people respond to our paper."

This story is taken from Science Daily

Cause or consequence? Scientists help to settle an epigenetic debate

Using the flowering plant Arabidopsis thaliana as a model for their research, scientists have been trying to understand how organisms 'remember' past events at the cellular level. 

Using the flowering plant Arabidopsis thaliana as a model for their research, Professor Martin Howard, Professor Caroline Dean and members of their labs, have been trying to understand how organisms 'remember' past events at the cellular level.
Previous work showed that expression of a gene called FLC -- a 'brake' to stop plants flowering until after winter -- is repressed by cold exposure. Furthermore, the amount of repression is epigenetically 'remembered' after winter to permit flowering at the appropriate time. In many organisms, DNA is packaged around histone proteins to make a structure called chromatin. Intriguingly, the level of FLC repression is correlated with the level of cold-induced chemical modifications to the histones at the FLC gene, added by a protein complex called Polycomb Repressive Complex 2.
But are these histone modifications or other local features of the chromatin the cause of epigenetic memory, or are they a consequence of memory stored elsewhere? The findings of a new study published in the journal eLife provide compelling evidence that has helped to settle this long-standing debate.
Professor Martin Howard explains: "We engineered plant cells to contain two distinguishable copies of FLC -- when one copy of the gene is expressed it generates a protein that glows red; when the other copy is expressed a yellow fluorescent protein is made. If epigenetic memory was inherited via the action of proteins freely diffusing inside a cell, then these proteins would affect both copies of FLC equally. As a result, either both copies of the gene would be expressed, leading to cells glowing red and yellow, or both copies of the gene would be repressed, giving cells that don't glow at all."
However, in these experiments, which were carried out by PhD student Scott Berry, cells glowing only red, or only yellow, were also observed, and this pattern of expression was epigenetically inherited through many cell divisions.
Professor Howard said: "The fact that two FLC copies in the same cell can have different heritable expression states shows that it is the local chromatin which must hold the epigenetic information passed from parent to daughter cells."
Although a flowering plant was used as the 'vehicle' to demonstrate these findings, epigenetic memory involving the Polycomb Repressive Complex can be found in many other organisms too. In particular, misregulation of Polycomb has been implicated in human cancers, thus these findings could have wide implications.

This story is taken from Science Daily

Feeding caterpillars make leaves shine

Scientists have succeeded in visualizing the immediate wound or herbivory responses in plants. They used Arabidopsis thaliana plants that produce a special protein which breaks down after the binding of calcium ions and emits free energy in the form of light. Visualization revealed that calcium signals occur systemically and wander from attacked to neighboring leaves. 

Calcium is a universal intracellular messenger. In plants, many physiological processes are mediated by calcium ions, especially responses to abiotic and biotic stresses, such as feeding caterpillars. These trigger the activation of a number of defense mechanisms. If a leaf is attacked by an insect, the wound signal which emanates from the affected leaf is transmitted to other, unattacked leaves. In order to visualize this signal, the scientists performed experiments with transgenic Arabidopsis plants which were genetically modified to express a protein in the cytosol, the liquid inside the cells, which breaks down and releases light energy after it has bound calcium ions. The emitted light energy correlates with the respective concentrations of calcium ions. In this way, intracellular changes of calcium levels can be determined directly. Moreover, these processes can be made visible in the plants by applying a highly sensitive camera system which uses charge-coupled devices (CCD). "It is very impressive to see how every bite of a caterpillar makes certain leaf areas shine. The immediate reaction of the plants is clearly visible," says Victoria Kiep, who carried out most of the experimental work together with Jyothilakshmi Vadassery.
It was very important for the researchers to show that the calcium signal is a systemic process, rather than a local one, as it wanders from the attacked leaf to neighboring leaves within a few minutes to trigger the subsequent defense responses. "We succeeded in visualizing the dynamic signal processing of intracellular calcium as a secondary messenger which is elicited by insect feeding and transmitted systemically to unattacked areas of the plant," Axel Mithöfer, the leader of the project group "Physiology of Plant Defense" in the Department of Bioorganic Chemistry, summarizes the results of the study.
How calcium signals are elicited in different and separate areas of plants is not yet fully understood. However, the scientists speculate that electric signals which are transmitted via the vascular system of plants, so-called vascular bundles, play an important role. There are no important differences between calcium signals which are elicited by mechanical wounding and those which are triggered by feeding caterpillars. Surprisingly, the application of larval oral secretions inhibited the transduction of calcium signals to neighboring leaves in the experiment. Of general importance for systemic calcium signaling is the wounding of the vascular system of the leaf, which is also responsible for the internal transport of water and nutrients in the plant.
Further experiments are planned in order to find out which kind of wounding triggers the systemic calcium signal, for example, whether a similar wound response is elicited by aphids and spider mites, as these insects puncture the plant tissue to suck the plant sap and damage the tissue only slightly. The scientists would like to investigate how signal transduction is achieved in grasses whose vascular bundles are structured differently in comparison to Arabidopsis which belongs to the Brassicaceae family. They are also interested in determining the operating distance of calcium signals in general and would like to answer the question whether the signals can be transmitted to the plant roots.
This study demonstrates that calcium signals, which are necessary for eliciting plant defense responses, and their spatial and temporal expansion can be visualized. Moreover, the scientists showed that calcium signaling can be studied directly in intact plants in different physiological and ecological contexts, which helps to better understand its role as a secondary messenger in plants.

This story is taken from Science Daily

A first in tree research: European trees planted in China to identify potentially invasive species in our forests

The expansion of international trade, rapid transport, increasing sales of decorative plants and agricultural goods, and global warming are all factors that contribute to the unintentional introduction and survival of organisms, fungi and insects in new geographical zones far from their region of origin. European scientists worked with colleagues in China to study the ability of Chinese insect and fungal pathogens to colonize European trees. 

Most of the exotic species which attack plants in Europe now come from Asia. INRA scientists, together with teams from the Academy of Sciences in Beijing and the Forestry University in Zhejiang have devised a new method for detecting potential invaders in their region of origin before they are introduced on another continent. European sentinel trees were planted in China for four years, and during this period, the ability of Chinese insect and fungal pathogens to colonize these trees was studied. Two articles in PLoS ONE present the results of this study, including those dealing with insects, published online on 20 May 2015.
The expansion of international trade, rapid transport, increasing sales of decorative plants and agricultural goods, and global warming are all factors which contribute to the unintentional introduction and survival of organisms, fungi and insects in new geographical zones far from their region of origin. Often, these organisms do no damage in their country of origin thanks to the presence of natural enemies or resistance in their hosts. Though only a small fraction of accidentally introduced species become invasive, the financial costs to the agriculture and forestry industries are significant and risks to human health (via the tiger mosquito, for example) and biodiversity (e.g. Asian wasps, Asian long-horned beetle) can result.
An original experiment
INRA scientists planted seven species of European trees: five broadleaved (hornbeam, beech and three species of oak) and two conifer (cypress and pine) at two sites in China (one near Beijing and another in Fuyang, Hangzhou). One hundred trees of each species, initially measuring about 1.5 metres, were planted at each site in adjoining lots of 25 plants each. In total, 400 trees were planted at the Beijing site and 700 at the Fuyang site. Between 2007 and 2011, researchers regularly monitored the colonization of these trees by Chinese insects and fungi closely.
Over the course of this four-year period, every two weeks at Fuyang and monthly at the Beijing site, each tree was examined to identify and count adult insects and larvae and any damage found. The insects were then collected. Different types of damage to foliage, buds, branches or trunks were noted and photographed. Using reared insects, researchers then tried to link each type of damage to the insects present, and larvae and adult insects were kept for taxonomic and genetic identification.
104 insect species, 38 of which are potentially invasive
In total, 104 insect species were observed on the new host trees. Some simply ate the leaves of the trees on an occasional basis, but 38 species caused multiple colonisations -- on the sessile oak, primarily -- and demonstrated that at least six species could produce larval development on European trees. These 38 species are considered to be potentially invasive if they are introduced in Europe. Surprisingly, most of these species appear to be originally linked to agriculture and fruit trees rather than neighbouring forest trees.
A maximal rate of colonization took three years. As such, nearly all the trees survived the first year. After that, the mortality rate was significantly high at both sites, though important differences were noted between varieties. After three years of testing, only 99 of the 400 trees planted at the Beijing site were still alive: all but four of the conifers were dead but half of the oaks survived. At the Fuyang site, after being planted two years, the sessile oak was the only variety with a survival rate of nearly 50%.
Additional results on the colonisation of these European trees by fungal pathogens native to China were recently published in the same journal by a consortium of scientists from INRA, Viterbo University in Italy and the Academy of Sciences in China (Vettraino et al. PloS One 10(3): e0120571).
The sentinel tree method appears to be promising, and its possible use in other contexts is being examined within the framework of GLOBAL WARMING, an EU COST project. One major stumbling block is the difficulty of identifying insects, particularly at the larva stage, and pathogens using standard methods. This could be solved by developing molecular databases.

This story is taken from Science Daily

Move over Arabidopsis, there's a new model plant in town

Biological nitrogen fixation provides a free way for plants to alter and absorb the nutrient. Legumes like soybeans fix nitrogen due to the symbiosis with bacteria in the soil through development of nodules on their roots, but since grasses like corn and rice don't form this specialized structures that relationship has been trickier to explore. Researchers have now shown the grass Setaria viridis received 100 percent of its nitrogen from the bacteria Azospirillum brasilense.

Less dependence on nitrogen could start with a simple type of grass, Setaria viridis, and its relationship with bacteria. The plant promises to lay groundwork for scientists exploring the relationship between crops and the fixing nitrogen bacteria that provide them the nitrogen amount plants need daily.
'In science sometimes you have to believe because we often work with such small microorganisms and DNA that you cannot see,' said Fernanda Amaral, co-author and MU postdoctoral fellow at Bond Life Sciences Center. 'Before this research no one had actually proved such evidence that nitrogen excreted by bacteria could be incorporated into plants like this.'
Biological nitrogen fixation -- where diazotrophic bacteria fix atmospheric nitrogen and convert it to ammonium -- provides a free way for plants to alter and absorb the nutrient. Farmers have long known that legumes like soybean fix nitrogen due to the symbiosis with bacteria in the soil through development of nodules on their roots, but since grasses like corn and rice don't form this specialized structures that relationship has been trickier to explore.
Yet in fact, this team's experiments showed the grass Setaria viridis received 100 percent of its nitrogen needs from the bacteria Azospirillum brasilense when associated with plant root surfaces.
'I believed in these bacteria's ability, but I was really surprised that the amount of nitrogen fixed by the bacteria was 100 percent,' Amaral said. 'That's really cool, and that nitrogen can make so much of a difference in the plant.'
Worldwide farmers used more than 100 million tons of nitrogen on fields in 2011, according to the United Nations Food and Agriculture Organization. In the same year, the U.S. alone produced and imported more than $37 billion in nitrogen.
This grass can serve as a simple model for research, standing in for grass relatives such as corn, rice and sugarcane to explore a similar relationship in those crops. This research, 'Robust biological nitrogen fixation in a model grass-bacterial association,' was published in the March 2015 issue of the Plant Journal.
Proving that this grass actually uses nitrogen excreted from the bacteria took some clever experiments, a global collaboration and a nuclear reactor.
MU researchers in the lab of Gary Stacey, a Bond LSC investigator, partnered with scientists in Brazil and at Brookhaven National Laboratory in New York to find a robust plant model system.
They screened more than 30 genotypes of Setaria viridis grass, looking for a strong nitrogen fixing response when colonized with three different bacteria strains. They germinated the seeds in Petri dishes and inoculated those three days after germination with a bacterial solution. Then plants were transplanted into soil containing no nutrients. By eliminating nitrogen in the soil, the scientists were able to make sure that the bacteria was the only source of nitrogen for plant.
The team settled on Azospirillum brasilense bacteria, which has been used commercially in South America to improve crop plant growth. It colonizes the surface of the roots and showed the greatest amount of plant growth when associated with plant roots.
Proving that the bacteria truly fixed the nitrogen used by the plant, required exposing plants to radioactive isotopes at Brookhaven National Laboratory. That began with Nitrogen 13, an unstable radio isotope that showed exactly where and how quickly this nutrient was taken up from the bacteria.
'Nitrogen 13 is really sensitive matter with a half-life of less than 10 minutes, and we first thought there wouldn't be that much nitrogen fixed by the plant,' Amaral said. 'We administered Nitrogen 13 only on the roots, quickly scanned the samples and calculated how much of the nitrogen the plants assimilated based on the decay analysis of the tracer.'
This experiment, paired with several others, showed that this model grass truly incorporated the nitrogen released by the bacteria and metabolizes it in several components.
But why does a type of grass that doesn't produce food matter so much?
The answer is time and simplicity.
'Corn is really good at responding to bacterial inoculation, but it's very big and takes a long time to produce seeds and also the genome is complex,' said Beverly Agtuca, an MU Ph.D. student who worked on the study. 'Setaria viridis is a small plant that can produce a lot of seeds faster, has a pretty simple genome and can serve as a model for research.'
That makes it perfect to explore how the plant actually uses its bacterial partners, and labs around the world are already using this plant model for research.
For the Stacey lab, the next step is to pinpoint the gene in the model grass that makes this possible.
'We want to identify the genes responsible for the interaction between plant and bacteria and meanly the ones involved with the nitrogen uptake,' Fernanda said. 'We hope that will allow us to improve plant growth based on the gene to further study. We believe that our findings can stimulate others studies at this area, which seems to be a promise plant friendly way to apply for promoting a sustainable agriculture, especially to crop systems including bioenergy grass.'

This  story is taken from Science Daily

New method may eliminate antibiotic use in livestock

An animal scientist has developed an antibiotic-free method to protect animals raised for food against common infections. The innovation comes as growing public concern about antibiotic resistance has induced McDonald's, Tyson Foods and other industry giants to announce major cuts in antibiotic use in meat production. About 80 percent of antibiotics in the United States are used by farmers, because they both protect against disease and accelerate weight gain in many farm animals. 

The innovation comes as growing public concern about antibiotic resistance has induced McDonald's, Tyson Foods and other industry giants to announce major cuts in antibiotic use in meat production. About 80 percent of antibiotics in the United States are used by farmers, because they both protect against disease and accelerate weight gain in many farm animals.
The overuse of antibiotics in agriculture and medicine has created a public health crisis of drug-resistant infections, such as multidrug resistant staphylococcus aureus (MRSA) and "flesh-eating bacteria."
"You really can't control the bugs forever; they will always evolve a way to defeat your drugs," says Mark Cook, a professor of animal science and entrepreneur.
Cook's current work focuses on a fundamental immune "off switch" called Interleukin 10 or IL-10, manipulated by bacteria and many other pathogens to defeat the immune system during infection. He and animal science associate researcher Jordan Sand have learned to disable this switch inside the intestine, the site of major farm animal infections such as the diarrheal disease coccidiosis.
Cook vaccinates laying hens to create antibodies to IL-10. The hens put the antibody in eggs that are then sprayed on the feed of the animals he wants to protect. The antibody neutralizes the IL-10 off-switch in those animals, allowing their immune systems to better fight disease.
In experiments with 300,000 chickens, those that ate the antibody-bearing material were fully protected against coccidiosis.
Smaller tests with larger animals also show promise. Dan Schaefer, a professor of animal science, and his graduate research assistant, Mitch Schaefer, halved the rate of bovine respiratory disease in beef steers by feeding them the IL-10 antibody for 14 days.
"That's a very enticing early result," Dan Schaefer says. "Bovine respiratory disease is the number one health risk for feeder cattle coming into a confinement situation." He is planning a larger trial in collaboration with colleagues at other universities.
In a test in newborn dairy calves, Sheila McGuirk, a professor of medical sciences at the School of Veterinary Medicine, found less than half as much respiratory disease among calves that ate the antibody for 10 days compared to those that did not. The treated calves also showed less shedding of Cryptosporidium parvum, a protozoa that causes diarrhea, although the trend was not statistically significant.
"These diseases cause long-term reproduction, production and growth impairments in livestock," says McGuirk. "The affected animals are suboptimal in health, performance and profitability. To have something affordable, safe and nonantibiotic that controls these very important diseases is absolutely awesome. We are eager to study this further."
In the past few years, scientists have learned that a large group of pathogens -- including bacteria, single- and multicelled parasites, protozoa, even certain viruses -- make a chemical called macrophage migratory inhibition factor, or MIF, which activates the IL-10 mechanism to shut down the host animal's immune system. "This apparently arose deep in the evolutionary past, and it's wholesale piracy of the immune system," says Sand.
"People have manipulated the immune system for decades, but we are doing it in the gut. Nobody has done that before," Cook says.
Cook and Sand, who have been working on the IL-10 system since 2011, are forming Ab E Discovery LLC to commercialize their research. One of the four patents they have filed through the Wisconsin Alumni Research Foundation has just been granted, and WARF has awarded a $100,000 Accelerator Program grant to the inventors to pursue the antibiotic-replacement technology.
Cook previously founded Isomark LLC, which is developing a technology for early detection of infection in human breath.
The benefits of reducing farm usage of antibiotics should extend to workers' families and the wider population. Significantly more people working in conventional chicken farms carry multidrug-resistant pathogens than those who work in antibiotic-free farms, Sand notes.
A nonantibiotic method to prevent pathogens from shutting down the immune system seems far less conducive to resistance than the current routine feeding of antibiotics, Cook says. "We are not focused on the pathogens. We are focused on what they are trying to do to the immune system. We are getting encouraging data from dairy and beef. We have conducted experiments involving 300,000 chickens in commercial farms, half receiving the product. We know it works. The market is interested, and now it's a matter of making a product."
 

This story is taken from Science Daily

Food or fuel? How about both?

In the United States, federal mandates to produce more renewable fuels, especially biofuels, have led to a growing debate: Should fuel or food grow on arable land? Recent research found encouraging, sustainable results when growing Camelina sativa with soybean in the Midwest. 

Russ Gesch, a plant physiologist with the USDA Soil Conservation Research Lab in Morris, Minnesota, found encouraging results when growing Camelina sativa with soybean in the Midwest.
Camelina is a member of the mustard family and an emerging biofuel crop. It is well suited as a cover crop in the Midwest. "Finding any annual crop that will survive the [Midwest] winters is pretty difficult," says Gesch, "but winter camelina does that and it has a short enough growing season to allow farmers to grow a second crop after it during the summer."
Additionally, in the upper Midwest, soils need to retain enough rainwater for multiple crops in one growing season. Gesch and his colleagues measured water use of two systems of dual-cropping using camelina and soybean. They compared it with a more typical soybean field at the Swan Lake Research Farm near Morris, MN.
First, researchers planted camelina at the end of September. From there growing methods differed. In double-cropping, soybean enters the field after the camelina harvest in June or July. Relay-cropping, however, overlaps the crops' time. Soybeans grow between rows of camelina in April or May before the camelina plants mature and flower.
The benefits were numerous. Relay-cropping actually used less water than double-cropping the two plants. Camelina plants have shallow roots and a short growing season, which means they don't use much water. "Other cover crops, like rye, use a lot more water than does camelina," says Gesch.
Conveniently, the extra water use during dual-cropping takes place in the spring. "We tend to have an excess of moisture in the soil in the spring from the melting snow pack," says Gesch. Growing camelina as a winter cover crop can help farmers take advantage of spring's extra moisture.
Gesch points out the need for more water use does mean camelina dual-cropping may not be the best option in all areas. "As you get further west and precipitation drops off and soils get lighter with lower water-holding capacity, crop yields may start to go down," says Gesch.
Growing camelina as a winter cover crop can also have other benefits, according to Gesch. "We had greater soybean yields with the relay-cropping system than when double cropping," says Gesch, referencing a previous study. The earlier planting date during relay cropping allows for a longer growing season and contributes to the higher yield, according to Gesch.
In addition, camelina plants flower early in the spring, providing a vital food source for pollinators, like bees, when little else is available to them. As a cover crop, camelina may also help prevent erosion and build soil carbon content. Gesch and his colleagues are working to measure these ecological benefits of dual-cropping.
"We wanted to find alternative crops that could be integrated into the Midwestern corn/soybean cropping system in a sustainable way that also makes economic sense for farmers," says Gesch.
In camelina, they may have found just such a plant. Gesch's study was recently published in Agronomy Journal.

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Walnut twig beetle's origin, spread revealed in genetic studies

Even though the walnut twig beetle is likely native to Arizona, California, and New Mexico, it has become an invasive pest to economically and ecologically important walnut trees throughout much of the Western and into the Eastern United States. Through genetic testing, researchers have characterized the beetle's geographic distribution and range expansion. 

 

These researchers examined genetic variation in WTB samples from 62 counties in 13 states representing the beetle's current range and concluded that WTB descends from two geographically distinct genetic lineages in the Southwest. The most genetic diversity within these two lineages occurred in WTB populations in Western New Mexico and the Madrean Sky Island region of Arizona and New Mexico, where WTB is believed to be native. In areas where WTB has become invasive, researchers found evidence of hybridization of the two genetic lineages. Hybridization did not occur in areas where WTB is believed to be native.
"The discovery of two genetic lineages for walnut twig beetle is exciting because it implies that this pest may in fact be two species, one that has invaded many parts of the United States and one that is still largely resident to the foothill and mountain canyons of the desert Southwest," says Steven Seybold, PSW research entomologist.
WTB carries the Geosmithia morbida fungus and causes damage to walnut trees when it excavates under bark to feed and lay eggs, and, in the process, inoculates the tree with the fungus. The result is Thousand Cankers Disease (TCD), so named because of the numerous cankers that form and cut off nutrient flow. Infected trees experience dieback of branches and may be killed in as few as three years. TCD is a threat to walnut in most of the western United States and, since 2010, has been detected in seven eastern states.
TCD and its spread may be due to the beetle's relatively recent range expansion to areas where walnut species (particularly eastern black walnut) did not co-evolve with WTB or the fungus. Researchers are concerned about the strong possibility for new associations among walnut trees and other twig beetles and fungi that exist in walnut's range that could result in similar diseases devastating to walnut.
Walnut trees and fruit are an incredibly valuable resource worldwide. "California produces over $1 billion dollars in edible nuts each year, and the value of the eastern black walnut growing stock east of the Mississippi is in the neighborhood of $500 billion. The five species of native black walnut trees and butternut trees are also important ecological components of riparian corridors across the United States where they provide a key food source for wildlife," explains Seybold.
Researchers conducted a similar study on the genetic variation of G. morbida and published a companion paper in 2014. The findings from this research can inform policies to prevent the introduction of agricultural and forest pests during global trade.

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Scientists see a natural place for 'rewilded' plants in organic farming

One key element of organic agriculture is that it rejects unpredictable technologies, such as genetic engineering. But what if adding a gene from undomesticated plants to bring back a natural trait isn't unpredictable? Researchers present a case for using precise genetic engineering technologies to 'rewild' crops in a way that would make organic farming more efficient, and thus more profitable. 

The concept behind "rewilding" is that grocery-brand fruits and vegetables have been made weak by generations of breeding for traits that yield the best harvest, and so a way to toughen them up would be to add genes found in their wild cousins, which are less bountiful but more resilient to pests, drought, and other challenges.
"The corn we eat does not live in nature anymore," says senior author Michael Palmgren, a plant and environmental scientist at University of Copenhagen. "It's like how we turned a wolf into a poodle. During breeding you select for specific characteristics, but then you risk losing others because you're not selecting for them. If you wanted to strengthen a dog, you would breed it with a wolf."
Theoretically, corn-strengthening mutations could occur naturally through long-term breeding programs, and so the question for debate is whether hastening the process through genetic engineering, ethically and legally, would be able to benefit organic farmers who are not allowed to use the pesticides, weed-killers, and fertilizers that define conventional agriculture.
While no "rewilded" crops have yet been created by inserting a trait, a 2014 Nature Biotechnology paper (10.1038/nbt.2969) showed that it is possible to make bread wheat crop resistant to mildew by removing DNA from three locations, thereby allowing offspring of this plant to pass on this benefit. This product could have been made through traditional breeding, so it challenges the unpredictability that is currently associated with genetic engineering.
"In current legislations, a plant is considered natural if it's mutated by chemicals and radiation--that happens in nature," Palmgren says. "If you can make a precise mutation that has the same effect and you don't introduce new material, then this type of plant should also be an exception."
He specifically collaborated with ethicists and legal experts to determine that yes, this type of precise "rewilding" is in accordance with values of organic agriculture. They believe that, at least outside of the European Union where there are fewer restrictions on genetically modified organisms (GMOs), it would be legally compatible to introduce this technology without labeling the plants as GMOs.
"Originally, when the whole idea of transgenic plants came up--that you can take a gene from a bacteria or a fish and put it in a corn--we as plant scientists were excited about the technology and didn't understand the objections," Palmgren says. "This is a new program, and I've learned to have discussions and debates with people in other fields from the beginning so that we do not repeat past mistakes that affected public opinion."

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Public raises alarm about ineffectiveness of some Montagu's harrier conservation measures

A citizen science program reveals the protection measures for the Montagu's harrier in the cereal crop season in France to be ineffective if nests are not protected to decrease predation after harvesting. A new study proposes fencing off the nests as a way of mitigating the damage and optimizing conservation efforts in different areas. 

Over the last decade there has been an explosion in the so-called citizen science programs, in which people (without a scientific background) voluntarily gather useful information for research programs.
A study published in the Journal of Applied Ecology, for which the scientist Beatriz Arroyo from the Hunting Resources Research Institute has collaborated with researchers from the University of Helsinki (Finland) and the National Centre for Scientific Research (CNRS) (France), presents an example of the use of citizen science to evaluate and optimize the effectiveness of conservation programs.
The scientists used data gathered over six years by a volunteer protection program of the Montagu's harrier (Circus pygargus) across France (more than 1,000 nests a year). This fair-sized bird of prey is linked to cereal crops (wheat and barley) and lives in large open and treeless spaces.
"An average of 500 people a year work as volunteers in France on this objective. They have to look for nests and once located, search for the owner of this land and convince them to put up a fence or protect the nest without a fence when the crop is being harvested (depending on what they decide), then monitor the nest and pass this information on (nest details, fledglings, etc.) to a regional coordinator," Arroyo explains.
The study shows that the productivity of the nests which are protected only during the crop harvest is strongly reduced by predation after the harvest, except where the nests are temporarily protected by a fence.
"The fence helps to decrease the predation post harvest, as uncut wheat in a 'sea' of stubble is easily detected by predators. Each fence costs between 10 and 15 euros, and can be reused for other nests the following year," notes the expert. This significant labour force is, in any case, limited and distributed irregularly given that it depends on the number of volunteers that there are in each area.
The scientists combined the information on the density of Montagu's harriers such as, for example, the proportion that would fail to thrive in the absence of conservation measures, and the availability of volunteers, to map the potential benefits for the species (estimate of chicks saved per km2) if the most effective measure was applied. According to the study, the areas of greatest potential benefit are not necessarily those where there are most volunteers.
"The areas which would benefit more from an increase in the conservation are in the north-eastern France, above all those in Champagne-Ardenne, Lorraine and France-Comté. We chose France for the study because this citizen involvement has been in place there for years, but nobody had evaluated the implications of what is being done or if this effort could be optimized," says Arroyo.
An unsuitable solution for partridges or bustards
This specific example of how to protect nests in crops could be extrapolated to other harrier species in other areas. However, it could not be applied to other ground-nesting birds, such as partridges or bustards that also die during harvesting, because they would suffer stress from having a fenced-in nest.
"The main conclusion is that the impact of the conservation programs would increase exponentially if efforts were concentrated in areas where the imbalance between potential benefits and availability of volunteers is greater," stresses the researcher.
The study also highlights the importance of citizen science in obtaining large-scale data, which can be used to obtain management recommendations based on scientific evidence, in an adaptive management framework.

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Team pinpoints genes that make plant stem cells, revealing origin of beefsteak tomatoes

A team of scientists has identified a set of genes that control stem cell production in the tomato. Mutations in these genes explain the origin of mammoth beefsteak tomatoes. More importantly, the research suggests how breeders can optimize fruit size in potentially any fruit-bearing crop. 

In its original, wild form the tomato plant produces tiny, berry-sized fruits. Yet among the first tomatoes brought to Europe from Mexico by conquistador Hernan Cortez in the early 16th century were the huge beefsteaks. Producing fruits that often weigh in at over a pound, this variety has long been understood to be a freak of nature, but only now do we know how it came to be.
The secret of the beefsteak tomato, CSHL Associate Professor Zachary Lippman and colleagues show, has to do with the number of stem cells in the plant's growing tip, called the meristem. Specifically, the team traced an abnormal proliferation of stem cells to a naturally occurring mutation that arose hundreds of years ago in a gene called CLAVATA3. Selection for this rare mutant by plant cultivators is the reason we have beefsteak tomatoes today.
In plants, like animals, stem cells give rise to the diversity of specialized cell types that comprise all tissues and organs. But too many stem cells can be a problem. In people, too many stem cells can lead to cancer. Similarly, when stem cell production goes unchecked in plants, growth becomes imbalanced and irregular, threatening survival.
The finely tuned balance of stem cell production in plants is controlled by genes that have opposite activities. Specifically, a gene known as WUSCHEL promotes stem cell formation, whereas CLAVATA genes inhibit stem cell production. Several genes in the CLAVATA family encode for receptor proteins that sit on the surface of plant cells -- the equivalent of locks -- as well as a series of proteins that dock at these receptors -- the equivalent of keys. When a CLAVATA key is made and fits in a CLAVATA lock, a signal is sent inside the cell that tells WUSCHEL to slow down. Critically, this prevents WUSCHEL from making too many stem cells.
It is therefore no surprise that when CLAVATA genes are mutated, the plant makes too many stem cells in the meristem. However, in the newly reported experiments, Lippman's team examined never before studied mutant tomato plants, three of which contained faulty genes encoding enzymes that add sugar molecules to proteins. How was this discovery relevant to plant stem cells? Lippman's experiments revealed that the enzymes, called arabinosyltransfersases (ATs), add sugar molecules called arabinoses to CLAVATA3 -- one of the CLAVATA keys. Remarkably, these sugars are required for the key to fit a CLAVATA lock.
The team's important discovery: changing the number of sugars attached to the CLAVATA3 key can change the number of stem cells. Three sugars is normal, and produces normal growth. But when the one or more sugars on the CLAVATA3 key are missing, the key no longer fits properly in the lock. WUSCHEL therefore sends its signal to make new stem cells, but that message is not accompanied by a "stop" signal. There is abnormal growth; the plant's fruit becomes extremely large. Revisiting the original beefsteak tomato variety, Lippman and collaborator Esther van der Knaap at Ohio State University found that the secret of the beefsteak is that not enough of the CLAVATA3 key is made in the meristem. The result is too many stem cells and giant fruits.
The research more broadly shows that there is a continuum of growth possibilities in the tomato plant, and in other plants -- since the CLAVATA pathway is highly conserved in evolution and exists in all plants. By adjusting the number of sugars on CLAVATA keys, and through other mutations affecting components of the pathway, Lippman and colleagues show it is possible to fine-tune growth in ways that could allow breeders to customize fruit size.

This story is taken from Science Daily

Study uses farm data to aid in slowing evolution of herbicide-resistant weeds

Although researchers and industry personnel have made recommendations to slow the evolution of herbicide-resistant weeds, an understanding of the patterns and causes of the resistance has been limited. A recently published study looking at glyphosate-resistant waterhemp is providing valuable evidence that points to management practices as the driving force behind herbicide resistance, and that herbicide mixing, as opposed to herbicide rotation, is the most effective tool in managing resistance

Diversifying the herbicide mechanisms of action (MOAs) has been recommended to stop the spread of herbicide-resistant weeds. MOAs refer to the biochemical interaction that affects or disrupts the target site in the weed. Two common methods of diversifying MOAs involve rotating herbicides--from season to season or within the same season--or by using a mix of herbicides in the same tank. The question has been which of these methods is the most effective.
A recently published study by weed scientists at the University of Illinois and USDA-ARS, looking at glyphosate-resistant waterhemp, is providing valuable evidence that points to management practices as the driving force behind herbicide resistance, and that herbicide mixing, as opposed to herbicide rotation, is the most effective tool in managing resistance.
Pat Tranel, a U of I weed scientist and a co-author on the study, said this is not the first time researchers have presented evidence that herbicide rotation is not the best resistance management strategy. "This paper is valuable because these conclusions were obtained doing our experiment in a more 'real-life' fashion," Tranel said. "This study confirmed previous conclusions that farmers should use herbicide mixing rather than rotation."
During the study, the researchers evaluated glyphosate-resistance incidents, as well as landscape, soil, weed, and farm-management data from 105 central Illinois grain farms, including almost 500 site-years of herbicide application records. Having this data, collected between 2004 and 2010, helped the researchers identify relationships between past herbicide use and current glyphosate-resistance occurrences.
Tranel said when glyphosate-resistant waterhemp was first reported in Illinois in 2006, researchers working at the site saw some fields that were infested with waterhemp, but adjacent fields that were free of the weed.
"We asked, 'what is different between these two fields? Is it what the farmers are doing?' We asked a retail applicator to let us review all the management practices data from 100 fields--50 that have resistant waterhemp and 50 that don't," Tranel said.
"We took the results of what farmers have already done, and asked what is different in the fields that have resistance versus the ones that don't," he added.
After collecting the management data, sampling waterhemp from the fields, and screening seeds from the field for resistance back in their greenhouses, the researchers analyzed that data for management factors most associated with resistance. Overall the researchers examined 66 variables related to environment, soil, landscape, weed community, and weed management.
"We looked at every factor we could think of in terms of management and landscape," Tranel said. "We found that it was management factors that are the most important. It doesn't matter whether you're next to a water course that might bring in new seed, what the waterhemp density of your field is, etc. It's what you did in your field that matters.
"That's what's encouraging," he added. "It's not inevitable that if your field is next to a water course, for example, you will have resistance."
Aaron Hager, a U of I weed scientist and co-author on the study, explained that the occurrence of glyphosate-resistant waterhemp was greatest in fields where glyphosate had been used in over 75 percent of the seasons included in the analysis, where fewer MOAs were used each year, and where herbicide rotation occurred annually. "Simply rotating herbicide MOAs actually increased the frequency of resistance," he said.
On the other hand, Tranel said that the farmers who were using multiple herbicides per application were least likely to have resistance. "When using an average of 2.5 MOAs per application, you are 83 times less likely to have resistance compared to if you used only 1.5 MOAs per application," he explained.
"That's pretty amazing that adding one additional mode of action in your tank reduces your chances of resistance by that much," Tranel added.
Hager pointed out that this strategy will work only if each component of the tank mixture is effective against the target species. "Effective, long-term weed management will require even more diverse management practices," he added.
Another piece of good news for farmers is that the researchers did not find an association of proximity between neighboring fields and resistance. "The good thing is not only does management matter, it's what you do in your own field that matters. Even if a neighbor's resistance moves, it's at a small frequency. If you're doing the right thing it will stay at a small frequency," Tranel said.
Although there may be some concerns with herbicide mixing, Tranel said it is still the best tool to manage resistance. One concern is the greater expense and environmental load of using multiple herbicides.
Another concern is using the correct mix of herbicides in the tank. Particularly as waterhemp becomes resistant to other herbicides, such as PPO inhibitors, mixing glyphosate and a PPO inhibitor, is not going to be a good management strategy if there is already resistance to a PPO inhibitor, Tranel explained.
"As we have new tools coming like 2,4-D and dicamba-tolerant soybeans, some people may think 'I'll throw in 2,4-D with glyphosate, because that's using two modes of actions,' but if you already have glyphosate resistance then you are not really using two effective modes of action," he added.
"We don't say that mixing is the end-all solution. What we saw from this study if success for farmers is measured by lack of resistance or lower frequency, then successful farmers use multiple herbicides per application."

This story is taken from Science Daily