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Plants prepackage beneficial microbes in their seeds

Plants have a symbiotic relationship with certain bacteria. These ‘commensal’ bacteria help the pants extract nutrients and defend against invaders — an important step in preventing pathogens from contaminating fruits and vegetables. Now, scientists have discovered that plants may package their commensal bacteria inside of seeds; thus ensuring that sprouting plants are colonized from the beginning. The researchers, from the University of Notre Dame, presented their findings at the 5th ASM Conference on Beneficial Microbes.

Plants play host to a wide variety of bacteria; the plant microbiome. Just as in humans, the plant microbiome is shaped by the types of bacteria that successfully colonize the plant’s ecosystem. Most of these bacteria are symbiotic, drawing from and providing for the plant in ways such as nitrogen-fixing and leaf-protection. Pathogenic bacteria may also colonize a plant. Pathogens can include viruses and bacteria that damage the plant itself or bacteria like the Shiga-toxin producing E. coli O104:H4. In 2011, Germany, France and the Netherlands experienced an outbreak of E. coli that was ultimately traced to the consumption of contaminated sprouts, which was thought to be caused by feral pigs in the growing area. Such opportunistic contamination is hard to guard against as most growing takes place in open, outdoor spaces with little opportunity for control.

The hypothesis behind this research is that the best way to defend against pathogenic contamination is with a healthy microbiome colonized by bacteria provide protection from invasive pathogens. Just as with babies, early colonization is crucial to establishing a beneficial microbiome. The researchers, led by Dr. Shaun Lee, looked inside sterilized mung beans and were able to isolate a unique strain of Bacillus pumilus that provides the bean with enhanced microbial protection.

“This was a genuine curiosity that my colleague and I had about whether commensal bacteria could be found in various plant sources, including seed supplies” said Dr. Lee. “The fact that we could isolate and grow a bacterium that was packaged inside a seed was quite surprising.”

The researchers first sterilized and tested the outer portion of a sealed, whole seed. When that was determined to be sterile, they sampled and plated the interior of the seeds and placed them in bacterial agar, which they incubated. What they found was the new strain of Bacillus pumilus, a unique, highly motile Gram-positive bacterium capable of colonizing the mung bean plant without causing any harm. Genome sequencing revealed that the isolated B. pumilus contained three unique gene clusters for the production of antimicrobial peptide compounds known as bacteriocins.

Dr. Lee and his colleagues theorize that their findings could have a wide impact, both on our understanding of plants and in creating food-safe antimicrobials. The finding that plant seeds can be pre-colonized may be an important mechanism by which a beneficial plant microbiome is established and sustained. Moreover, the team is now isolating and studying the bacteriocins, which Dr. Lee says “have tremendous potential.”

Story Source:

The above story is based on materials provided by American Society for Microbiology. Note: Materials may be edited for content and length.

Agriculture and Food News — ScienceDaily

Rotation-resistant rootworms owe their success to gut microbes

June 24, 2013 — Researchers say they now know what allows some Western corn rootworms to survive crop rotation, a farming practice that once effectively managed the rootworm pests. The answer to the decades-long mystery of rotation-resistant rootworms lies — in large part — in the rootworm gut, the team reports.

The findings appear in the Proceedings of the National Academy of Sciences.

Differences in the relative abundance of certain bacterial species in the rootworm gut help the adult rootworm beetles feed on soybean leaves and tolerate the plant’s defenses a little better, the researchers report. This boost in digestive finesse allows rotation-resistant beetles to survive long enough to lay their eggs in soybean fields. Their larvae emerge the following spring and feast on the roots of newly planted corn.

“These insects, they have only one generation per year,” said University of Illinois entomology department senior scientist Manfredo Seufferheld, who led the study. “And yet within a period of about 20 years in Illinois they became resistant to crop rotation. What allowed this insect to adapt so fast? These bacteria, perhaps.”

Controlling rootworms is an expensive concern faced by all Midwest corn growers, said study co-author Joseph Spencer, an insect behaviorist at the Illinois Natural History Survey (part of the Prairie Research Institute at the U. of I.). Yield losses, the use of insecticides and corn hybrids engineered to express rootworm-killing toxins in their tissues cost U.S. growers at least $ 1 billion a year.

In a 2012 study, Seufferheld, Spencer and their colleagues reported that rotation-resistant rootworm beetles were better able than their nonresistant counterparts to tolerate the defensive chemicals produced in soybeans leaves. This allowed the beetles to feed more and survive longer on soybean plants. The researchers found that levels of key digestive enzymes differed significantly between the rotation-resistant and nonresistant rootworms, but differences in the expression of the genes encoding these enzymes did not fully explain the rotation-resistant beetles’ advantage. Seufferheld and his colleagues thought that microbes in the rootworms’ guts might be helping them better tolerate life in a soybean field.

To test this hypothesis, graduate student Chia-Ching Chu analyzed the population of microbes living in the guts of rootworm beetles collected from seven sites across the Midwest. Some of these sites (including Piper City, Ill.) are hot spots of rotation-resistance and others (in Nebraska and northwest Missouri, for example) lack evidence of rotation-resistant rootworms.

Chu found significant and consistent differences in the relative abundance of various types of bacteria in the guts of rotation-resistant and nonresistant rootworms (see graphic). These differences corresponded to differing activity levels of digestive enzymes in their guts and to their ability to tolerate soybean plant defenses.

The researchers found other parallels between the composition of gut microbes and the life history of the rootworms. The beetles’ gut microbial structure corresponded to the insects’ level of activity (rotation-resistant rootworms are usually more active), and also paralleled — in a graduated fashion — the plant diversity of the landscapes they inhabited. (Rotation-resistant rootworms are most abundant in regions where rotated corn and soybean fields are the dominant components of the agricultural landscape.)

To determine whether the microbes were in fact giving the rotation-resistant beetles an advantage, the researchers dosed the beetles with antibiotics. Low-level exposure to antibiotics had no effect on any of the beetles, but at higher doses the rotation-resistant beetles’ survival time on soybean leaves fell to that of the nonresistant beetles. Antibiotics also lowered the activity of digestive enzymes in the rotation-resistant beetles’ guts to that of their nonresistant counterparts.

The message of the research, Seufferheld said, is that the gut microbes are not just passive residents of the rootworm gut.

“They are very active players in the adaptation of the insect,” he said. “The microbial community acts as a versatile multicellular organ.”

“It’s not just the rootworm that we have to worry about,” Spencer said. “There’s really this whole conspiracy between the rootworm and its co-conspirators in the gut that can respond fairly quickly, relatively speaking, to the assaults that they face.”

The research team also included former postdoctoral researcher Jorge Zavala (now a professor at the University of Buenos Aires) and graduate student Matias Curzi.

ScienceDaily: Agriculture and Food News

Rotation-resistant rootworms owe their success to gut microbes

June 24, 2013 — Researchers say they now know what allows some Western corn rootworms to survive crop rotation, a farming practice that once effectively managed the rootworm pests. The answer to the decades-long mystery of rotation-resistant rootworms lies — in large part — in the rootworm gut, the team reports.

The findings appear in the Proceedings of the National Academy of Sciences.

Differences in the relative abundance of certain bacterial species in the rootworm gut help the adult rootworm beetles feed on soybean leaves and tolerate the plant’s defenses a little better, the researchers report. This boost in digestive finesse allows rotation-resistant beetles to survive long enough to lay their eggs in soybean fields. Their larvae emerge the following spring and feast on the roots of newly planted corn.

“These insects, they have only one generation per year,” said University of Illinois entomology department senior scientist Manfredo Seufferheld, who led the study. “And yet within a period of about 20 years in Illinois they became resistant to crop rotation. What allowed this insect to adapt so fast? These bacteria, perhaps.”

Controlling rootworms is an expensive concern faced by all Midwest corn growers, said study co-author Joseph Spencer, an insect behaviorist at the Illinois Natural History Survey (part of the Prairie Research Institute at the U. of I.). Yield losses, the use of insecticides and corn hybrids engineered to express rootworm-killing toxins in their tissues cost U.S. growers at least $ 1 billion a year.

In a 2012 study, Seufferheld, Spencer and their colleagues reported that rotation-resistant rootworm beetles were better able than their nonresistant counterparts to tolerate the defensive chemicals produced in soybeans leaves. This allowed the beetles to feed more and survive longer on soybean plants. The researchers found that levels of key digestive enzymes differed significantly between the rotation-resistant and nonresistant rootworms, but differences in the expression of the genes encoding these enzymes did not fully explain the rotation-resistant beetles’ advantage. Seufferheld and his colleagues thought that microbes in the rootworms’ guts might be helping them better tolerate life in a soybean field.

To test this hypothesis, graduate student Chia-Ching Chu analyzed the population of microbes living in the guts of rootworm beetles collected from seven sites across the Midwest. Some of these sites (including Piper City, Ill.) are hot spots of rotation-resistance and others (in Nebraska and northwest Missouri, for example) lack evidence of rotation-resistant rootworms.

Chu found significant and consistent differences in the relative abundance of various types of bacteria in the guts of rotation-resistant and nonresistant rootworms (see graphic). These differences corresponded to differing activity levels of digestive enzymes in their guts and to their ability to tolerate soybean plant defenses.

The researchers found other parallels between the composition of gut microbes and the life history of the rootworms. The beetles’ gut microbial structure corresponded to the insects’ level of activity (rotation-resistant rootworms are usually more active), and also paralleled — in a graduated fashion — the plant diversity of the landscapes they inhabited. (Rotation-resistant rootworms are most abundant in regions where rotated corn and soybean fields are the dominant components of the agricultural landscape.)

To determine whether the microbes were in fact giving the rotation-resistant beetles an advantage, the researchers dosed the beetles with antibiotics. Low-level exposure to antibiotics had no effect on any of the beetles, but at higher doses the rotation-resistant beetles’ survival time on soybean leaves fell to that of the nonresistant beetles. Antibiotics also lowered the activity of digestive enzymes in the rotation-resistant beetles’ guts to that of their nonresistant counterparts.

The message of the research, Seufferheld said, is that the gut microbes are not just passive residents of the rootworm gut.

“They are very active players in the adaptation of the insect,” he said. “The microbial community acts as a versatile multicellular organ.”

“It’s not just the rootworm that we have to worry about,” Spencer said. “There’s really this whole conspiracy between the rootworm and its co-conspirators in the gut that can respond fairly quickly, relatively speaking, to the assaults that they face.”

The research team also included former postdoctoral researcher Jorge Zavala (now a professor at the University of Buenos Aires) and graduate student Matias Curzi.

ScienceDaily: Agriculture and Food News

Taking Aim at Microbes on Farm Good Strategy for Food Safety

Just because you can’t see something with the naked eye doesn’t mean it isn’t there.

While that statement certainly doesn’t qualify as rocket science, it is, nevertheless, an important message to heed when it comes to microscopic beings such as harmful bacteria, viruses and parasites that can make animals and people sick.

In a report, “What if we could see germs?” Phil Durst, dairy and beef extension educator at Michigan State University, shares that message with livestock owners as he fine-tunes the focus on harmful microbes, among them E. coli O157:H7, Salmonella, Campylobacter, and Cryptosporidium — all of which can infect animals and people alike.

“Just because we can’t see them doesn’t mean we should manage our livestock as though they aren’t there,” he told Food Safety News. And, while his report focuses on animal health, Durst said it also pertains to food safety.

“Healthy animals are an important step toward food safety,” he said. “With healthy animals, you have limited spread and introduction of pathogens. Ultimately, that has to have an impact on food safety.”

In his report, Durst asks these questions: “What if we could see the invisible on farms? What if we could see pathogens that are shed by animals, get tracked by people, are transferred with other materials, take up residence in pens, and, ultimately, infect another animal? What would we do differently?”

These are important questions for livestock farmers to ask themselves, states the report, referring to the results of research conducted by a team at the University of Pennsylvania School of Veterinary Medicine. In this project (reported in the Journal of Dairy Science, Sept. 2013), a team of researchers, led by soil scientist J.D. Toth, selected 13 dairy farms, varying in size from 41 to 275 cows, in southeast and south-central Pennsylvania. They went in search of five animal-borne pathogens on these farms: E. coli O157:H7, Salmonella enterica, Campylobacter jejuni, Mycobacterium avium, ssp. paratuberculosis (MAP) and Cryptosporidium parvum — many of which can cause foodborne diseases in humans.

Looking for these pathogens in samples of fresh and stored manure, bedding, field soil, stream water and milk filters, they discovered that, on all but one dairy, they could isolate one of these pathogens, and, on 7 of the 13 dairies, they could isolate multiple pathogens.

Of special concern when it comes to food safety, E. coli O157:H7 was found in half of the positive samples and on six of the 13 farms.

And, while Salmonella, Campylobacter and Cryptosporidium were found on fewer farms, at least one of these pathogens was isolated from samples taken from six of the 13 farms.

The researchers also looked for, and found, positive samples of a bacterium that causes a serious cattle disease known as Johne’s Disease on 10 farms and from 20 of the 46 positive samples.

Bottom line, the results of this research project revealed that harmful pathogens on farms can be spread not only to other animals, but also potentially to people.

“This may have serious consequences as E. coli O157:H7 has caused fatalities among infected people,” states the report.

Dairy cows that have been culled from a herd are an important source of ground beef. According to the Cattlemen’s Beef Board, culled dairy cows make up approximately 18 percent, or about 2.1 billion pounds, of the ground beef (sometimes steaks) produced each year in the United States.

Referring to the research project, Durst warns that “to the extent that these farms are typical, it likely means that bacteria and viruses that cause disease are probably present on your farm” — even if you can’t see them.

Durst also warns that “not seeing pathogens” can lead livestock farmers to act as though they don’t exist. With that in mind, he makes it a point to warn farmers that “it makes more sense for us to assume that the pathogens are there.”

He said that even though the farms in the research project were small farms — “almost idyllic” — the researchers still found pathogens there.

“We portray small farms as being healthy, but there can always be a sick animal that can spread pathogens,” he said. “Ultimately, this will have an impact on food safety.”

Daniel Grooms, a professor at the College of Veterinary Medicine at Michigan State University, agreed with Durst that some food-safety problems do start on the farm.

Grooms also teaches classes in a food-safety master’s program, with one of his specialties being pre-harvest food safety.

“If we could see [the pathogens], it would make it easier to control them,” he said, referring to the pathogens that can cause food-safety problems when the animals are milked or butchered. “Any time you have something you can see, it’s easier to convince people about the need to control it.”

He compares the incentive to controlling something you can’t see to controlling something that you can see — an oil leak in your tractor, for example. You know you can’t very well ignore it, and you also know you need to fix what’s causing it. Yet something that you can’t see can be ignored — until, of course, an animal or person gets sick.

When it comes to the dangerous form of E. coli, Grooms said it can be in animals that are perfectly healthy and showing no overt signs of harboring the bacteria. And, he pointed out that that’s true in the case of some other zoonotic diseases as well.

According to the Centers for Disease Control and Prevention, zoonotic diseases are contagious diseases spread between animals and humans. They can be caused by bacteria, viruses, parasites and fungi that are carried by animals and insects. Some examples that have to do with food safety are E. coli and Salmonella, which can end up in an animal’s meat or milk.

Although pasteurization kills pathogens in milk, in the case of raw milk, which isn’t pasteurized, the pathogens can be present in the milk if it has been contaminated by fecal material. And, while the pathogens might be in a cow’s digestive tract and not its meat, those pathogens can contaminate the meat when the animal is butchered.

Grooms also pointed out that whenever you have to use antibiotics to treat a sick animal, a food-safety risk is introduced, both because of possible residues in the animal’s meat or milk and also because of the possibility of antibiotic resistance.

“When we reduce the need of having to treat animals with antibiotics, we reduce some of the food-safety risks,” he said. But he also pointed out that, even with good management systems, there will be times animals will get sick and need to be treated with antibiotics.

“But if we can prevent pathogens like Salmonella from coming onto the farm (from the introduction of sick animals from other farms), we’d never have to treat the animals for that,” he said.

Even so, Grooms emphasized that, while you can reduce pathogens on a farm, you’re never going to eliminate them altogether. “But you can manage them,” he said. “We can do things to help reduce the risk of pathogens being present on a farm that could be a food-safety risk.”

Toth, who led the University of Pennsylvania research team, said that, as a soil scientist, he had been researching pathogen survival on farms.

The research team found that Salmonella can survive for more than a year in field soil and that E. coli can survive at least three months in the soil. There’s always a risk of these being transported off or onto a farm when new animals are brought in or shipped off of a farm, he said.

He said that, even though there are more risks of pathogens spreading from animal to animal or from animal to people on large farms simply because more cows are congregated together, he also said that most large farms have veterinarians on board who serve as “another set of eyes.”

Taking a broader view, he said that farmers are typically good stewards of their animals because it’s in their interest to reduce pathogens on the farm.

Taking aim at pathogens

Durst’s report includes five ways that farmers can reduce the spread of pathogens, which he refers to as “what we cannot see.” The recommendations, developed by Michigan State University Extension, outline steps livestock farmers can take to reduce exposure of pathogens.

This approach — preventing instead of reacting to problems — is similar to the approach embodied in the Food Safety Modernization Act, which primarily covers produce. Another similarity is that one of the act’s proposed rules focuses on on-farm practices.

Here are the five recommendations:

  • Practice biosecurity between farms. Whether you visit another farm or someone comes on your farm after being on another farm, boots and coveralls should be clean and sanitized, tires should be free from manure and any materials (feed, for example) should be free of manure.

“Let’s face it,” states the report, “the carelessness of people, including professionals, leads to transfer of pathogens between farms.”

  • Practice biosecurity within your farm. Keeping different groups of animals separated is the best chance we have to keep pathogens from being transferred between groups. Protect calves from exposure to pathogens shed from cows. Clean boots and clothes, clean equipment and feed are key when working with calves. Isolation and separation from older animals need to be maintained.

Toth found a higher prevalence of pathogens in maternity pen bedding than in calf bedding, which leads to the conclusion that removing calves quickly from the maternity pen reduces the risk of infection.

  • Practice good hygiene on farms. In the University of Pennsylvania study, 73 percent of the stored manure samples were positive for at least one of the five target pathogens, and half of the fresh manure samples were positive. Cleanliness helps reduce exposure to pathogens.
  • Practice personal hygiene. Some of the diseases that cattle can carry can also infect people. It is important that you and your employees who work on the farm practice good personal hygiene. Healthy employees are critical to farm function. Consider providing employees with both training about biohazards and with tools (hand-washing stations, disposable gloves, coveralls, etc.) that actually make a difference in the spread of disease agents.
  • Protect your animals. Vaccination is an important tool that can boost  the protection of animals, but it is not a perfect tool. The vaccine must be handled well, administered to animals that will respond and, in some cases, boostered to strengthen the immune response. As important as vaccination is, it only covers specific pathogens. In addition, we need to feed four quarts of colostrum within two hours of birth, pasteurize milk for calves, reduce stresses, reduce overcrowding and isolate new arrivals.

But Durst emphasizes that these five steps, while extremely helpful, are not the silver bullet.

“We’d have to say that bacteria is not on the farm at all, which would be impossible, so these five steps are not enough in themselves,” he said. “But they are certainly good steps farmers could take to reduce pathogens on their farms.”

He concludes the report by warning livestock farmers that they consistently need to take steps to reduce risk by considering how diseases may be spread, and, by doing that, they’ll be protecting their cattle.

“This must be the concern of everyone working on and for the dairy,” he said. “Let’s open our eyes to the work that needs to be done.”

The whole picture

Durst said his report calls attention to research showing potential problems on farms. But he also said that while farmers do take many of these steps, it’s not always done on a consistent basis “because sometimes we rush.”

“In the rush to get there, we take shortcuts,” he said.

Referring specifically to the important part employees play, he said that some farms provide lunchrooms and places where the workers can clean up before eating, which lowers their risk to exposure through food, which could be contaminated if they don’t have resources such as this.

Some farms also provide work clothing and laundry services.

“The greatest benefit of this,” Durst said, “is that it helps the farm to have healthy employees who won’t spread the pathogens on the farm or somewhere else.”

He also said larger farms tend to have lunch rooms, lockers, and showers.

“It’s an investment that’s spread over more employees,” he said. “Healthy employees are an important part of managing pathogens on a farm.”

Grooms would agree, pointing out that practicing good pathogen control should be a culture throughout the operation — that it’s important for everyone to be ever diligent to reduce the concentration of pathogens anywhere they might be. Cleaning the maternal pens but not the calf pens, for example, leaves a hole in the overall goal of managing pathogens.

“We need to look at this holistically,” he said. “It should be a culture throughout the operation. It’s important for everyone, including the employees, to understand this.”

But when asked if he could foresee the day that dairies and beef operations would be required to take steps such as those recommended by Michigan State University,  he said that regulations, for the most part, are market-driven.

“But that may happen over time,” he said.

Toth, meanwhile, also gives a thumbs-up to the Michigan State University recommendations.

“Any way that you can break the transmission of pathogens is good for animal health and good for food safety,” he said.

Food Safety News

Microbes facilitate the persistence, spread of invasive plant species by changing soil chemistry

Sep. 26, 2013 — Invasive species are among the world’s greatest threats to native species and biodiversity. Once invasive plants become established, they can alter soil chemistry and shift nutrient cycling in an ecosystem. This can have important impacts not only on plant composition, diversity, and succession within a community, but also in the cycling of critical elements like carbon and nitrogen on a larger, potentially even global, scale. Clearly, both native and exotic plants form intimate relationships with bacteria in the soil that facilitate the extraction and conversion of elements to biologically usable forms. Yet an unanswered question with regard to plant invasions remains: could the changes in soil biogeochemistry be due to an advantage that invasive plants get from interacting with their microbiome?

When alien species invade and take over communities, they may not come alone — many plant species are host to a whole suite of microorganisms that not only live in plant cells, but also in the soil surrounding the plants’ roots. These microbes form close, often mutualistic, associations with their plant hosts. Some convert atmospheric nitrogen into bioavailable forms that are then exchanged for carbon from the plant. Bioavailable nitrogen is frequently limiting in soils, yet many invaded ecosystems have more carbon and nitrogen in plant tissues and soils compared with systems dominated by native plants. Since changes in the soil nitrogen cycle are driven by microbes, could bacteria associated with invasive species not only be responsible for the observed changes in soil nutrient concentrations, but also for enabling the continued growth and persistence of the invader species?

These were the kinds of questions that started percolating for Marnie Rout (University of North Texas Health Science Center) after she drove by a remnant tallgrass prairie in North Central Texas as a beginning graduate student. She was particularly struck by the obvious and drastic changes the native prairie was undergoing due to the invasion of an exotic grass.

“It literally looked like someone had drawn a line down the field,” Rout explained. “On one side was the native prairie, the other side had this towering monoculture of invasive Sorghum. The plant looked like it was invading in a military fashion, forming this distinct line that was clearly visible.”

Subsequent literature searches led to the discovery that sugar cane, an agriculturally important crop, is a nitrogen fixer that contains bacterial endophytes, and Rout became curious if the microbes she and her colleague Tom Chrzanowski (The University of Texas Arlington) discovered in invasive Sorghum might be providing similar benefits to this invasive plant.

Rout combined forces with colleagues from The University of Montana, The University of Texas Arlington, and University of Washington to investigate whether the differences in soil nutrient concentrations found in an invaded prairie could be due to metabolic processes of the bacterial microbiome associated with the invasive grass, and to determine whether these microbial agents facilitate the perpetuation and spread of this invasive grass. They published their findings in a Special Section in the American Journal of Botany on Rhizosphere Interactions: The Root Biome.

“Things attributed to plant-plant interactions like competition and facilitation are likely under more microbial regulation than we have been giving them credit,” Rout commented. “Studying disruptions to ecosystems like those seen in plant invasions provides a window into something — specifically the process of co-evolution — that we normally don’t get to observe in a single human lifetime.”

Indeed, the alarming rate — almost 0.5 meters a year — at which the invasive grass Sorghum halepense has invaded the tallgrass prairie, formerly dominated by the native little bluestem (Schizachyrium scoparium), over the last 25 years, and the complete dominance of that invasive was the ideal situation in which Rout could test her ideas.

Rout and colleagues first confirmed that the invaded soils of the prairie did indeed have higher levels of nitrogen, phosphorous, and iron-derived chemicals compared with the non-invaded prairie soils still dominated by native plants. They then tested whether the interactions between the dominant invasive grass and the soil biota could be responsible for the observed changes in the soil nutrient concentrations.

By isolating five bacterial strains of endophytes found inside S. halepense rhizomes (subterranean stems used for storage and vegetative reproduction) and growing them in the lab in different mixtures of substrates, the authors determined that these microbes were able to fix and mobilize nitrogen, phosphorus, and iron. All three are important elements associated with plant growth; however, some were produced in excess of what would be needed for plant growth. Indeed, perhaps somewhat alarmingly, the amount of iron that was produced reached levels that are toxic to many crops — and may even inhibit establishment of native species.

Furthermore, the authors were able to show that not only can this invasive plant acquire microbes from the environment, but that it is also capable of passing them on to the next generation via seeds. Using a sophisticated series of intricate experiments involving growing seedlings from surface sterilized seeds in nitrogen- deprived or nitrogen-augmented soils and slurries with different suites of soil microbes, Rout and colleagues showed that these microbes enabled the grass to produce 5-fold increases in rhizomes, a primary mechanism driving invasions of this species.

These findings give us a new understanding of how an invasive plant can acquisition soil biota to its own advantage, altering the environment and changing the ecosystem in the process. By acquiring soil bacteria, S. halepense increases the bioavailable nitrogen and phosphorus in the soil, and has increased rhizome production and aboveground biomass, which in turn facilitates its spread and establishment. Moreover, these changes to the soil chemistry not only increase the competitive edge of this invasive species, but also can inhibit or eliminate the existing native species.

“This research shows that macro-scale observations, such as plant trait expression, and ecosystem functions like nutrient cycling, are more intimately connected to micro-scale influences than we might expect,” summarizes Rout.

Rout’s fascination with bacterial endophytes continues; she is currently exploring them from a genetic perspective to better understand the complex communication between the microbiome and the plant.

“With the growing human population and concerns for meeting the global food crisis in the coming decades, invasive plants and their microbiomes might turn out to be useful for enhancing crop yields.”

“The root microbiome is as important to plant health and agricultural productivity,” she concludes, “as the human microbiome is to human health.”

ScienceDaily: Agriculture and Food News

The secret life of underground microbes: Plant root microbiomes rule the world

Sep. 18, 2013 — We often ignore what we cannot see, and yet organisms below the soil’s surface play a vital role in plant functions and ecosystem well-being. These microbes can influence a plant’s genetic structure, its health, and its interactions with other plants. A new series of articles in a Special Section in the American Journal of Botany on Rhizosphere Interactions: The Root Microbiome explores how root microbiomes influence plants across multiple scales — from cellular, bacterial, and whole plant levels to community and ecosystem levels.

Plants are teeming with microbial organisms; not only are they in plant cells, but they are also found in between the cells (intercellular spaces) and in a small layer of soil surrounding plant roots. This area of soil, the rhizosphere, is an especially important zone of activity as it contains microbes that are intricately involved in the molecular, genetic, and ecological components of a plant, and it also influences plant community composition and soil health. The importance of this “unseen majority” led Marnie Rout (University of North Texas Health Science Center) and Darlene Southworth (Southern Oregon University) to gather together a series of works highlighting some of the significant advances that have been made in the last decade in understanding the integrative and far-reaching impacts plant root microbiomes have not only on the organisms themselves, but globally as well.

“Until recently,” Rout commented, “the microbiome had been easy to ignore in plant science because soil was considered a ‘black box’ for so long. But microbial research approaches and molecular techniques are illuminating this unknown — essentially, shining light on the microbiome.”

By bringing together works by a diverse set of authors in this special section, Rout and Southworth’s intentions are to illustrate the wide spectrum of impacts that microbiomes have on plant performance, and they emphasize that these interactions transcend several scales, from genes to ecosystems.

“Microbiomes play a significant role in the health of their hosts, and microbiome community composition can inform us about the spectrum of healthy-to-diseased host state,” said Rout.

Indeed, the papers in this section demonstrate that the microbiome is metabolically diverse and communicates through the rhizosphere, which enables the microbiome to serve as a genomic reservoir for plants and other microbes. The papers also highlight the complex communication exchange that occurs between plants and their microbiomes.

For example, a paper in the special section by Gilberto Curlango-Rivera and associates found that the cell layer that is sloughed off by the roots of certain cotton cultivars and released into the rhizosphere may function as a defense mechanism, serving as a layer of immunity to the plant, similar to that of white blood cells in animals.

“Understanding how the microbiome can regulate plant performance could have enormous implications for many of the world’s most pressing problems, such as utilizing marginal lands and fragile ecosystems to meet the food demands of a growing global population, minimizing losses of land and biodiversity due to plant invasions, or mitigating impacts of climate change on plant communities,” states Rout.

For example, another paper in this special section, by Drora Kaplan and associates suggests that harvesting growth-promoting bacteria from plants found in harsh or dry climates, such as deserts, could help with crop production in currently stressed regions or in areas likely to be affected by global climate changes.

Rout and Southworth emphasize in the introduction that in order to better understand the intricate and complex impacts microbes have on many levels, from molecular to global, it is critical to understand that the plant microbiome is an integrated genome of the plant, and that it has profound influences on plant genetics, function, ecology, and communities. Interactions between plants and their microbial communities are dynamic — plants can manipulate the microbiome to their advantage (such as defense), and microbiomes can influence which plants survive in certain habitats (such as facilitating invasive species).

“It is my goal for readers to recognize that the plant does not stop at the roots,” summarizes Rout. “I think the sustainability of microbes as residents on the planet should inspire everyone to reach a deeper understanding of microbiome influence on the part of the world that we can readily perceive.”

ScienceDaily: Agriculture and Food News

Panda poop microbes could make biofuels of the future

Sep. 10, 2013 — Unlikely as it may sound, giant pandas Ya Ya and Le Le in the Memphis Zoo are making contributions toward shifting production of biofuels away from corn and other food crops and toward corn cobs, stalks and other non-food plant material.

Scientists presented an update today on efforts to mine Ya Ya and Le Le’s assets for substances that could do so during the 246th National Meeting & Exposition of the American Chemical Society (ACS). And if things work out, giant pandas Er Shun and Da Mao in the Toronto Zoo will be joining the quest by making their own contributions.

“The giant pandas are contributing their feces,” explained Ashli Brown, Ph.D., who heads the research. “We have discovered microbes in panda feces might actually be a solution to the search for sustainable new sources of energy. It’s amazing that here we have an endangered species that’s almost gone from the planet, yet there’s still so much we have yet to learn from it. That underscores the importance of saving endangered and threatened animals.”

Brown and her students, based at Mississippi State University, now have identified more than 40 microbes living in the guts of giant pandas at the Memphis Zoo that could make biofuel production from plant waste easier and cheaper. That research, Brown added, also may provide important new information for keeping giant pandas healthy.

Ethanol made from corn is the most common alternative fuel in the U.S. However, it has fostered concerns that wide use of corn, soybeans and other food crops for fuel production may raise food prices or lead to shortages of food.

Brown pointed out that corn stalks, corn cobs and other plant material not used for food production would be better sources of ethanol. However, that currently requires special processing to break down the tough lignocellulose material in plant waste and other crops, such as switchgrass, grown specifically for ethanol production. Breaking down this material is costly and requires a pretreatment step using heat and high pressure or acids. Brown and other scientists are looking for bacteria that are highly efficient in breaking down lignocellulose and freeing up the material that can be fermented into ethanol.

Bacteria in giant panda digestive tracts are prime candidates. Not only do pandas digest a diet of bamboo, but have a short digestive tract that requires bacteria with unusually potent enzymes for breaking down lignocellulose. “The time from eating to defecation is comparatively short in the panda, so their microbes have to be very efficient to get nutritional value out of the bamboo,” Brown said. “And efficiency is key when it comes to biofuel production — that’s why we focused on the microbes in the giant panda.”

Working with scientists at the University of Wisconsin-Madison, Brown’s team identified bacteria that break down lignocellulose into simple sugars, which can be fermented into bioethanol. They also found bacteria that can take those sugars and transform them into oils and fats for biodiesel production. Brown said that either the bacteria themselves or the enzymes in them that actually do the work could be part of the industrial process.

“These studies also help us learn more about this endangered animal’s digestive system and the microbes that live in it, which is important because most of the diseases pandas get affect their guts,” said Brown. “Understanding the relationships between the microbes and the pandas, as well as how they get their energy and nutrition, is extremely important from a conservation standpoint, as fewer than 2,500 giant pandas are left in the wild and only 200 are in captivity.”

Additional plans include expanding the work to include samples from red pandas at the Memphis Zoo, which also eat bamboo. Brown and colleagues also are forging a collaboration to get samples of feces from giant pandas that arrived in the Toronto Zoo earlier in 2013.

The scientists acknowledged funding from the Memphis Zoological Society, in addition to past funding from the Mississippi Corn Promotion Board, the U.S. Department of Energy and Southeastern Research Center at Mississippi State.

ScienceDaily: Agriculture and Food News

Why crop rotation works: Change in crop species causes shift in soil microbes

July 18, 2013 — Crop rotation has been used since Roman times to improve plant nutrition and to control the spread of disease. A new study to be published in Nature’s The ISME Journal reveals the profound effect it has on enriching soil with bacteria, fungi and protozoa.

“Changing the crop species massively changes the content of microbes in the soil, which in turn helps the plant to acquire nutrients, regulate growth and protect itself against pests and diseases, boosting yield,” said Professor Philip Poole from the John Innes Centre.

Soil was collected from a field near Norwich and planted with wheat, oats and peas. After growing wheat, it remained largely unchanged and the microbes in it were mostly bacteria. However, growing oat and pea in the same sample caused a huge shift towards protozoa and nematode worms. Soil grown with peas was highly enriched for fungi.

“The soil around the roots was similar before and after growing wheat, but peas and oats re-set of the diversity of microbes,” said Professor Poole.

All organisms on our planet can be divided between prokaryotes (which include bacteria) and eukaryotes (which include humans, plants and animals as well as fungi). After only four weeks of growth, the soil surrounding wheat contained about 3% eukaryotes. This went up to 12-15% for oat and pea. The change of balance is likely to be even more marked in the field where crops are grown for months rather than weeks.

Analysis has previously relied on amplifying DNA samples. This limits scientists to analysing one taxonomic group at a time such as bacteria. It also means that everything present in that group is analysed rather than what is playing an active role. Every gram of soil contains over 50,000 species of bacteria so the task is enormous.

There are relatively fewer actively expressed genes, or RNA. It is now possible to sequence RNA across kingdoms so a full snapshot can be taken of the active bacteria, fungi, protozoa and other microbes in the soil. The research was carried out in collaboration with the University of East Anglia and The Genome Analysis Centre on Norwich Research Park.

“By sequencing RNA, we can look at the big picture of active microbes in the soil,” said PhD student Tom Turner from the John Innes Centre.

“This also allows us to work out what they are doing there, including how they might be helping the plants out.”

“Our work helps explain the experience of farmers in the field,” said Professor Poole.

“The best seed needs to be combined with the best agronomic practices to get the full potential benefits.”

“While continued planting of one species in monoculture pulls the soil in one direction, rotating to a different one benefits soil health.”

Seeds can be inoculated with bacteria before planting out, just like humans taking a dose of friendly bacteria. But this does not achieve the diversity or quantity of microbes found in this study.

The scientists also grew an oat variety unable to produce normal levels of avenacin, a compound that protects roots from fungal pathogens. They expected the soil to contain higher levels of fungi as a result, but instead found it contained a greater diversity of other eukaryotes such as protozoa.

The findings of the study could be used to develop plant varieties that encourage beneficial microbes in the soil. John Innes Centre scientists are already investigating the possibility of engineering cereal crops able to associate with the nitrogen-fixing bacteria normally associated with peas.

“Small changes in plant genotype can have complex and unexpected effects on soil microbes surrounding the roots,” said Professor Poole.

“Scientists, breeders and farmers can make the most of these effects not only with what they grow but how they grow it.”

ScienceDaily: Agriculture and Food News

Why crop rotation works: Change in crop species causes shift in soil microbes

July 18, 2013 — Crop rotation has been used since Roman times to improve plant nutrition and to control the spread of disease. A new study to be published in Nature’s The ISME Journal reveals the profound effect it has on enriching soil with bacteria, fungi and protozoa.

“Changing the crop species massively changes the content of microbes in the soil, which in turn helps the plant to acquire nutrients, regulate growth and protect itself against pests and diseases, boosting yield,” said Professor Philip Poole from the John Innes Centre.

Soil was collected from a field near Norwich and planted with wheat, oats and peas. After growing wheat, it remained largely unchanged and the microbes in it were mostly bacteria. However, growing oat and pea in the same sample caused a huge shift towards protozoa and nematode worms. Soil grown with peas was highly enriched for fungi.

“The soil around the roots was similar before and after growing wheat, but peas and oats re-set of the diversity of microbes,” said Professor Poole.

All organisms on our planet can be divided between prokaryotes (which include bacteria) and eukaryotes (which include humans, plants and animals as well as fungi). After only four weeks of growth, the soil surrounding wheat contained about 3% eukaryotes. This went up to 12-15% for oat and pea. The change of balance is likely to be even more marked in the field where crops are grown for months rather than weeks.

Analysis has previously relied on amplifying DNA samples. This limits scientists to analysing one taxonomic group at a time such as bacteria. It also means that everything present in that group is analysed rather than what is playing an active role. Every gram of soil contains over 50,000 species of bacteria so the task is enormous.

There are relatively fewer actively expressed genes, or RNA. It is now possible to sequence RNA across kingdoms so a full snapshot can be taken of the active bacteria, fungi, protozoa and other microbes in the soil. The research was carried out in collaboration with the University of East Anglia and The Genome Analysis Centre on Norwich Research Park.

“By sequencing RNA, we can look at the big picture of active microbes in the soil,” said PhD student Tom Turner from the John Innes Centre.

“This also allows us to work out what they are doing there, including how they might be helping the plants out.”

“Our work helps explain the experience of farmers in the field,” said Professor Poole.

“The best seed needs to be combined with the best agronomic practices to get the full potential benefits.”

“While continued planting of one species in monoculture pulls the soil in one direction, rotating to a different one benefits soil health.”

Seeds can be inoculated with bacteria before planting out, just like humans taking a dose of friendly bacteria. But this does not achieve the diversity or quantity of microbes found in this study.

The scientists also grew an oat variety unable to produce normal levels of avenacin, a compound that protects roots from fungal pathogens. They expected the soil to contain higher levels of fungi as a result, but instead found it contained a greater diversity of other eukaryotes such as protozoa.

The findings of the study could be used to develop plant varieties that encourage beneficial microbes in the soil. John Innes Centre scientists are already investigating the possibility of engineering cereal crops able to associate with the nitrogen-fixing bacteria normally associated with peas.

“Small changes in plant genotype can have complex and unexpected effects on soil microbes surrounding the roots,” said Professor Poole.

“Scientists, breeders and farmers can make the most of these effects not only with what they grow but how they grow it.”

ScienceDaily: Agriculture and Food News