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Can bacteria help us improve crops?

Scientists are learning how to influence the complex interactions that plants have with bacteria, pests, nutrients and other components of the phytobiome in hopes of preventing mass starvation

Illustration: pixabay.
Illustration: pixabay.

By Marla Broadfoot, the article is published with the approval of Scientific American Israel and the Ort Israel Network 14.09.2017

  • To meet the global demand for food, scientists are looking for new ways of utilization The phytobium - the complex fabric in which there are interactions between agricultural crops, bacterial populations, the soil, the weather, various living creatures and other environmental factors.
  • Among the promising innovations are seeds coated with a coating of bacteria or fungi capable of deterring pests or promoting growth in another way. The first products of this type are already on the market.
  • Interventions at the level of the phytobiome are not likely to be as hotly contested as genetically engineered seeds, but they too carry risks. In any case, biotechnology alone will not solve the problem of world hunger.

Mercedes Diaz makes her way through the plants in a muddy soybean field, sliding her manicured fingers along the knee-high branches of the dozens of plants growing in the field. She examines the stems, pods and leaves, and in the process enumerates in a whisper several possible diseases of the plant: harmful caterpillars, fungi, white mold. Diaz suddenly suddenly notices a tangle of spotted leaves and calls out: "SDS!" - the initials of "Sudden death syndrome". She plucks one of the leaves and places it in my hand. I turn over the crumpled palm-sized leaf. The surface of the leaf is pierced with holes of various sizes, and around them ugly brownish-yellow spots are visible - the traces of the toxin secreted by the SDS fungi, which spread through the plant, destroying its pods and chewing on its surface, turning the leaf outwards. Sudden death syndrome is one of the main crop killers in the USA. According to reports from the American Soybean Growers Council, the damage caused to farmers due to this in 2014 alone reached more than one and a half million tons of crops that went down the drain. But Diaz is actually passionate about discovering the deadly pests in her soybean field.

Diaz, a plant pathologist, is one of many researchers who are looking for new ways to protect agricultural crops from the dangers lurking in them and dramatically increase productivity. In 2016, her research group coated seeds with thousands of different bacteria and planted them, alongside control plots of untreated seeds, in half a million sites across the Midwest and southern United States. Around these fields, the researchers planted monitoring plots - in which plants of disease-sensitive varieties whose role, similar to that of the famous canary in the coal mines, is to warn of potential damage to the other crops. When Diaz finds sudden death syndrome or other signs of blight in the monitoring plots, but these do not appear in the experimental plots, this may indicate that the bacteria are active, helping to grow healthier and richer crops.

However, on that rainy day in September 2016, Diaz found that both the experimental plots and the control plots escaped the fate of the monitoring plots. The effect of the bacteria was not evident in them - or was it? In fact, it is almost impossible to detect with just a glance an increase in the yield of plots of up to approximately 40 kilos per dunam (when on average, a soybean field yields about 350 kilos per dunam). She will have to wait for the harvest and the analysis of the data to find out whether any of the experimental bacteria actually helped to achieve the goal.

Crop research tends to be slow and trial-and-error, and scientists like Diaz feel they are in a race against time. If agriculture does not change in a revolutionary way during the coming decades, humanity may be left without enough sources of food. The world population is expected to grow from 7.5 billion today to 9.7 billion in 2050. In order to feed the mouths that will be added to it - and to respond to the changing dietary habits, which include more meat - farmers will have to increase food production by about 70%. So according to predictions Food and Agriculture Organization of the United Nations (FAO). This is not a simple task at all, and some worrying trends make it even more complex. The shortage of agricultural land in the world is getting worse, partly as a result of the processes ofurbanization וClimate change. According to the FAO reports, the annual output of agricultural crops that provide essential foods has stopped growing. For example, the use of fertilizers has reached a tipping point from which onwards, continuing to fertilize the fields with chemicals may bring more harm than good. And even genetically engineered crops, which were considered both the curse of agriculture and its great promise, did not justify the hopes placed in them and failed to jumpstart food production.

"We need to stop looking for magic solutions," says Jen Leach, a plant pathologist at the University of Colorado. "This is not a problem that any of us can solve on our own, and there will be a need for cooperation between different teams from diverse fields in a way that has not been done so far." Leach and other scientists advocate a more holistic approach, which takes into account the totality of the factors on the agricultural farm - the plants, the soil, the bacteria, the insects and the climate, all together known as phytobium - and the interrelationships between them, which jointly affect Agricultural output. The idea brings to mind the writings of the 19th century naturalists Alfred Russel Wallace and Charles Darwin, who described nature as a vast fabric in which the species living in it are in a constant process of adapting to changes in their living environment.

Take for example the soy plants that Diaz lovingly cultivates. When an insect lands on a soybean plant leaf, the plant may respond by excreting volatile chemicals through its roots and these substances, in turn, change the composition of the soil's bacterial population. These bacteria can activate an array of genes in nearby plants, which will alert them to an impending attack and allow them to prepare for it. However, these essential defenses for the plant's survival are sensitive to various environmental factors, and may be damaged, for example, by climate change. Topathogens There are amazing sophisticated ways of their own. They can leap over the surface of a leaf, as if shot from a cannon barrel, "catch a ride" on air currents and fly from field to field and even from continent to continent. and certain varieties ofmicroorganisms Chicken raisers can affect the weather and cause showers of rain and hail with which they return to earth from the clouds.

In view of the predictions according to which the world population is expected to grow from 7.5 billion people today to 9.7 billion people in 2050, farmers will have to increase food production by about 70%.

Scientists have been aware of this complexity for hundreds of years, but only recently has technological progress allowed them to map this complex interaction in order to develop systematic and sustainable solutions in the field of agriculture. Using methods to determine the genetic sequence, scientists can locate all the bacteria found in the soil, including rare strains and even problematic strains that cannot be grown under laboratory conditions. They are able to follow communities of bacteria as they move in space and time, following an increase in fertilization levels, for example, or a decrease in temperatures. They are able to document the interrelationships that exist between bacteria, plants and other organisms and try to decipher the effect of the chemical communication between them, on the agricultural output and the robustness of the crops.

In the future, a farmer will be able to go out into the field on a tractor equipped with special dedicated equipment and perform a comprehensive survey of the bacterial population in the field as well as other measurements accepted inprecision agriculture” – such as measurements of moisture levels and the content of nutrients in the soil. These factors, along with agricultural yield data from previous years, information regarding potential pests and pathogens, and predictions regarding expected weather trends will be taken into account in order to evaluate the optimal combination between seeds, nutrients, chemicals and bacteria that may yield record crops.

The movement to realize this vision began to take shape only recently. Last year, a group of scientists from various fields of knowledge published an ambitious plan for a revolution in the agriculture of the future, titled Phytobiomes: A Roadmap for Research and Translation. With the publication of this road map, the academic journal was also published Phytobiomes, and a project was launched for cooperation between industry and academia called Phytobiomes Alliance, where more than a dozen bodies are members - some of which were established not long ago, such as Bioconsortia וindigo, and others, well-known names in the arena, such as the company Monsanto, Diaz's employer. Over the past few years, these companies have invested considerable sums in promoting research and development in this field in an effort to secure their market share Biological agriculture The global one, whose business turnover is expected to reach 10 billion dollars by 2020.

The initiators of the transformation see the soil under our feet - and the extensive fabric of the population of microorganisms that reside in it - as an essential factor for the success of the initiative. Soil-dwelling bacteria and fungi can help plants grow and thrive, deal with arthritis conditions, strengthen immune responses and ward off pests and diseases. Farmers have been aware of some of these insights since the end of the 19th century, when they started treating their pea and bean plots using Rhizobium bacteria, which enrich the soil with nitrogen. Today, dozens of products are offered for sale on the market based on the population of bacteria - The microbiome - that in the ground, and many others are under development. The Monsanto company, in collaboration with the company Novozymes, which is based in Denmark, is investing considerable sums of money in the bacteria-coated seeds under development as part of the large-scale research in which Diaz is taking part. Other researchers are trying different approaches, such as changing the genome of crop plants in a way that will attract beneficial bacteria to them, or changing the communication between pests and plants in a way that will allow the plants to detect threats and respond to them in a better way. Considering the complexity of the phytobium, it seems that there is no limit to the number of ways in which it is possible to influence the processes that occur between the plant and its environment. The same is true for the chances of reaching a dead end. The challenge is to find an effective solution in time and to prevent it mass starvation.

Impressions from the world below the surface of the earth

An hour's drive from St. Louis, the cornfields look withered and faded in the mid-September sunlight. The soy plots are painted in shades of avocado green and harvest gold. I accompany Diaz and her colleagues on a journey to an uncontrolled site on the outskirts of the town of Stonington, Illinois. As I step into a puddle, I hold a copy of the field map showing where thousands of germ-coated seeds have been sown. The bacteria were grown in containers containing liquids enriched with proteins and other nutrients. The seeds were wrapped in the bacterial mantle in huge stainless steel bowls, and frozen until the time of sowing. When the seeds germinate, the bacteria that surround them come to life, but what happens next depends on the many factors that make up the phytobiome.

I follow Diaz into the maze of corn plants. She points to some corn cobs in the monitoring plot covered in pink mold, with moth aphids swarming around them. Plants are not equipped with a real immune system, but they have developed their own methods of repelling harmful insects. Some plants thicken their cell walls and thus prevent intruders from penetrating through them, while other plants secrete toxic chemicals through their roots or on them and thus keep pests away. Nicotine, caffeine and even tannin, which gives red wines their sharpness, are all products of the plant's defense mechanisms.

During hundreds of years of improving varieties through hybridization and decades of improvement in genetic engineering, attempts were made to improve the plant's defense mechanisms and at the same time, to give it other useful properties with the aim of increasing agricultural productivity. For example, more than half of the corn crops grown in the US contain a gene taken from a harmful insect-killing bacterium called Bacillus thuringiensis, or Bt, which allows the corn plant to destroy beetle larvae. Scientists are now looking for other phytobium-related properties that may contribute to plant health. In studies conducted on the subject, it was found that plants invest about 30% of their energy to attract beneficial bacteria and reject unwanted bacteria. Jeffrey Dangle, who studies plant biology at the University of North Carolina at Chapel Hill, is exploring ways to change the plant's genome in order to nurture the bacterial family that surrounds it. he Revealed Recently, a gene that affects the communities of bacteria living in and around the roots of the plant and spurs them to increase the absorption of phosphorus (phosphate) from the soil - a nutrient whose sources are dwindling.

Other research dealing with phytobium focuses on insect resistance. Normally, plants can detect pests operating in their environment based on the presence of special chemicals response provoking In the saliva of insects that chew the plant. Gary Felton, dealing withInsect research at the University of Pennsylvania, and his colleagues discovered that certain species of beetles and caterpillars can mask these secret-revealing molecules by spitting their gut bacteria onto the plant's leaves, thus tricking it into reacting as if it were soaking in a bath of bacteria and not about to fall prey to destructive pests. The mistaken reaction of the plant - a reaction to the presence of bacteria - damages the plant's ability to defend itself against the harmful insects. Platon recently showed that feeding the beetles a certain type of bacteria changes their microbiome enough to take away their ability to fool the plant (see box).

The methods described here, which shape the dialogue between plants, pests and soil dwellers of various kinds, can bring about, all together or each of them separately, the next green revolution. But even before the vision is realized, we have to take care of the experimental crops, monitor them and collect and process huge amounts of data.

corn field Photography: Richard Hurd.
corn field Photo: Richard Hurd.

In the late summer of 2016, a fleet of harvesters was deployed in fields from Louisiana, through Minnesota and North Carolina to Nebraska, to collect the harvest from the experimental plots of corn and soybeans planted by BioAg Alliance, as the partnership between Monsanto and Novozymes is called. Data from the giant compressors are streamed in real time to Monsanto's data center in St. Louis as well as to Novozymes' facilities in the research park. Research Triangle Park in North Carolina. The scientists at both sites are known to sit for hours, glued to the computer screens, as they monitor the data coming from the fields. "It's like watching a horse race in slow motion," says Scott Schacher, head of the biotechnology data strategy group at Monsanto.

The teams processing the data realized that too much importance should not be attached to the first results coming from the field. The raw data can be misleading, since they do not take into account factors that may give a particular bacterium an initial advantage or rather leave it behind in the race. The microbiome in the soil can vary from plot to plot, even in the same field. The weather can create names: early rains can wash away the bacterial coating from the seeds, and a few years ago, the hurricane "Joaquin" left destruction in thousands of plots planted by the partnership. Apart from yield data from half a million sites, the team of scientists collects data from 50 different measurements conducted on each of the soil samples from each site. And to these are added other data relating to phytobium, so that in the end terabytes of data are accumulated that are "a celebration or a nightmare for statisticians," as Shacher says.

Even if a more extensive sharing of information between scientists engaged in crop research, the private industrial sector, academia and government is guaranteed, it will not be enough, and biotechnological innovation alone will not solve the problem of world hunger. Success in the task will also require political commitment to the issue.

Shaker pulls up a map of the USA on the computer monitor in his office. The map is decorated with red and green dots, like a Christmas tree: the green dots indicate bacteria that contributed to an increase in productivity, while the red ones indicate bacteria that resulted in a decrease in productivity. They represent the results for 2016 in five corn fields. Shaker and his staff can analyze and present the data according to the characteristics of the soil and environmental conditions, the weather and stress conditions due to pests and diseases. They can focus on sites where high levels of SDS—the syndrome Diaz discovered in her soybean field—were measured to see if they could identify any bacteria that excelled in those conditions.

The team implements a "field first" strategy, that is, it skips the usual phase of experiments in the greenhouse and tests its candidates directly in the field. Because of this, the researchers have no idea which bacteria, if any, will give the plant an advantage. In 2014, the first year the field experiment was conducted, research team members sowed seeds coated with bacterial spores that included 500 different strains. 90% of the bacteria failed the experiment. In 2015, 2,000 bacteria were recruited for the race, including bacteria that successfully met the task in the first year of the experiment. At the end of the experiment, only a handful of the original competitors reached the finish line, and next to them, several hundred of the new ones. In 2016, another group of 2,000 varieties was selected to participate in the experiment, including the outstanding ones in the previous round and a group of new recruits. After three years of experiments, only one bacterium from the first round - and several hundred from the other rounds - remained in the race. The team members are not looking for one-time outstandings - they are interested in "Triple Crown" winners whose performance is consistent, year after year, in several fields.

Dangerous business?

The use of natural bacteria - which are taken from agricultural land, grown in the laboratory and returned to the field - may appear to be a risk-free course and devoid of controversies such as those that provoke genetically modified organisms (GMOs). However, some disturbing questions arise in this context. Interfering with the bacterial environment may affect the taste of crops, just as the composition of the soil affects the taste of wine. A bacterium that increases productivity may have pathogenic properties that are harmful to human health. Long-term application of Probiotics In plants, it may disrupt the natural dynamics in the soil, accelerate the reproduction of certain microorganisms and cause the extinction of others. There is also a risk that the bacterial coating, like many other active substances used in the field, will peel off the seeds in one part and contaminate plants in another part.

According to Shaker, BioAg Alliance invests a lot of effort to prevent such problems. The bacterial strains candidate for the experiment undergo a series of tests before being transferred to the field. In addition, individual genomic sequencing of each bacterium is performed to ensure that it does not carry pathogens similar to those known to cause disease in humans, and additional tests are conducted to assess whether the bacterium may be toxic to its environment or spread to other crops. Shaker and his staff consult regularly with representatives of the US Department of Agriculture, and it is these representatives who decide whether permission is required to use a certain strain of bacteria in a field experiment. Organisms that perform beneficial functions like nitrogen fixation או making phosphates soluble are generally approved for use in these experiments. Other varieties that perform more dangerous functions, such as destroying fungi or other bacteria, require a more rigorous and lengthy approval process.

But what worries those engaged in agricultural research even more than that new strains of bacteria may take over or spread to other crops, is the possibility that the bacteria will not survive long enough in the field to have an effect and carry out their mission, says Gwyn Beatty, who studies plant diseases at the University of Iowa, who participated in drafting the Phytobiomes Roadmap. A teaspoon of soil sample contains about 50 billion bacteria - a mixed group of up to 10,000 different strains. The researchers can add millions of bacteria of a certain strain to the soil without it having any effect. "If [from time to time] one person is added to the population of New York City, most of the people added will not make any difference to the city," says Beatty. "A similar thing happens in the bacterial community. Adding organisms may only rarely have any effect, and that's actually what's most frustrating.” (A similar challenge is faced, unsuccessfully, by the probiotics industry intended for humans. Probiotics are supposed to balance the population of bacteria in the intestines, which number trillions of bacteria. Its products - the powders, pills and drinks of all kinds - are marketed as miracle cures for the treatment of many diseases, from diarrhea to depression, but there are few studies only point to some measureable effectiveness of these products.)

However, Monsanto's activities arouse serious concerns among large sections of the public, and more than once the company has been accused of risking public health, trampling on the rights of farmers, and controlling it as a monopoly in the food supply market. The giant corporation that dominates the agriculture industry drew sharp criticism in the 90s when it launched a new line of genetically engineered crops. Since then, two opposing narratives have developed: one, according to which the company develops seeds that double the yield and provide a large-scale solution to food shortages; and the other, according to which the company's products pollute the agricultural lands and cause cancer. Last year completed US National Academy of Sciences A thorough examination, probably the most thorough and comprehensive examination ever conducted on the subject of genetically engineered creatures, and found that none of the narratives are true. From the summary report published by the academy, it appears that genetically modified crops are no less safe to eat than normal crops, but "there is no evidence" that genetically modified creatures increase productivity.

The main benefit of genetically modified soybeans, cotton and corn, the report said, is "positive economic outcomes enjoyed by producers who have adopted these crops." When I asked for the company's response to these not at all impressive findings, a Monsanto representative admitted that the company no longer emphasizes in its sales promotion campaigns its part in feeding the world's hungry mouths, and instead, it highlights the assistance it provides to farmers so that they can obtain the best possible crops at the lowest costs. The company's sales turnover in 2016 reached a total of $13.5 billion, and about $10 billion of that came from seeds, many of which are genetically engineered and improved. The progress in this field in the last two decades has contributed to a decrease in the costs borne by farmers and has generated profits for the industry, but has not provided an answer to the growing and pressing need for food.

Tomorrow's crops

The seeds sown today in the fields of the USA are not at all similar to the seeds sown by the ancestors of today's farmers. Today, the seeds carry at least 14 different genetically engineered traits, added on top of each other. These "stacks", as they are called in the industry, are often supplemented by several other products that may improve and increase yield, including fertilizers, herbicides and, more recently, also products produced from biological sources, such as the BioAg Alliance's bacterial seed coats. However, not much is still known about what is needed to ensure healthy crops - and scientists in academia and government bodies, as well as in the agricultural industry, are all trying to find an answer to the question.

Despite the considerable progress in the technology of mapping the genetic code, scientists have so far identified only one percent of the bacterial species living in the soil. The turbidity of the soil makes it difficult for scientists to study what is happening below the surface. They are therefore forced to resort to destructive research methods - and to conduct surveys of the population of soil-dwelling bacteria based on soil samples taken from the field, surveys that probably do not accurately reflect the composition of the bacterial population in the field's soil or its activity. This is likened to a giant reaching across the earth to take a sample of the human race. Such a sample might reveal who the human beings that inhabit the earth are, but not how they act or what their interrelationships were before their world was turned upside down.

A few years ago, a team of scientists in Scotland concocted artificial soil that can be seen through, allowing researchers to observe communities of bacteria living in or around plant roots. Elizabeth Shank, a microbiologist in Chapel Hill, used this transparent artificial soil to study the signals that the bacteria send off. The range of action of these chemical messages ranges from the lethal - 70% of the antibiotic drugs are produced from chemical substances that the bacteria use to kill each other - to the beneficial - certain bacteria send chemical signals to bring together members of their species to create Biofilm which allows them to stick together to the surface of the plant's roots. In November 2016, Shank presented her research at the Phytobium Symposium held in Santa Fe, New Mexico. She described how staining various bacterial materials with fluorescent markers allows her to track the chemical messages that communities of bacteria send to each other in response to events such as planting seeds, rising temperatures, or invading pathogens.

Her innovative research may yield handsome profits. Or maybe not. Many academics, like Shank, sign agreements with commercial companies that grant them permission to use their discoveries or, alternatively, establish their own start-up companies. The economic arena is flooded with many new entities, collaborations and mergers, including the acquisition of Monsanto by in Iyar in September 2016 for $66 billion. The US government also joined the game. The Agriculture Lawthat the American Congress in 2014 allocated 200 million dollars for the establishment of the American Food and Agriculture Research Agency (FACT), with the aim of encouraging collaborations between academia and industry in the fields of agriculture and food. In July 2016, the FFAR Foundation convened a group of experts for a brainstorming meeting that dealt with the question of how to get the most benefit from the phytobium.

Kelly Eversole, executive director of the Phytobiomes Alliance, says that while academia, government and industry may share similar goals, their methods are not always aligned. Commercial companies, which are obliged to generate profits for their investors, are characterized by a short-term approach motivated by economic considerations of profit and loss. But "without Basic research And in the absence of long-term infrastructure, we may be hurt," says Eversole. On the other hand, the industry has at its disposal resources that botany professors can only dream of: a few days after the brainstorming event organized by the FFAR Foundation, Shaker appeared, as a representative of Monsanto, at a conference of American Phytopathological Society – An annual meeting of more than 1,500 phytopathology experts. When Schacher presented the map of field trials conducted by the BioAg Alliance partnership, Linda Kinkel, a plant disease research specialist at the University of Minnesota, reacted with astonishment. "If they really collect data on the populations of soil-dwelling bacteria from 500,000 sites, that's more than all of us manage to collect together." And the question is, said another Kinkel with concern, "how many scientific insights lie there that will never come to our attention?"

Leveraging the phytobium to improve crops will require a comprehensive integration of information from different sources and fields of knowledge, but not all parties concerned are willing to cooperate and disclose the information they have. Farmers are afraid, for privacy reasons, to allow outsiders access to the data they collect in their fields. The BioAg Alliance partnership occasionally passes on scraps of information to its colleagues in academia, but according to Shaker, it is unable to share with them all the data it has because the partner companies, Monsanto and Novozymes, must "protect their competitive advantage." This year the partnership launched its first product, a microbial seed coat based on fungi living in the soil of corn fields. In field experiments it was found that these mushrooms contributed to increasing the yield by an average of 0.08 tons per acre. According to predictions, this product could be used to increase agricultural productivity on more than 22 million dunams of agricultural land worldwide.

This is a start, but there is still a long way to go to meet the growing needs of the planet. Even if a more extensive sharing of information between scientists engaged in crop research is guaranteed, it will not be enough, and biotechnological innovation alone will not solve the problem of world hunger. For this it is necessary to address not only the problem of food supply, but also the problem of loss of food and the waste of food, and in dealing with a series of challenges, starting withdistribution of food and its distribution, including in situations of war, political conflicts, Income inequality and climate change. Fred Gould, a scientist who studies insects at the University of North Carolina, and who led the survey conducted by the American National Academy of Sciences on the subject of genetically modified organisms, warns that even if scientists succeed in doubling food production in some way, it will not necessarily be the right thing to do, since intensive exploitation of The resources may leave desolate land that will not be suitable for agricultural cultivation in the future. Gold also says that solutions, to the extent that they are found, must prove themselves in the field. "As extensive and comprehensive as the knowledge we have, its application depends to a large extent on the environmental conditions, that it will be necessary to manipulate [the phytobiome] on each individual farm," says Gold. "In the practical test, when things come to implementation in the field, some of these ideas are not feasible." In the end, the challenge of controlling and managing the processes occurring in the phytobium will likely be just one of the challenges of the next agricultural revolution. Success in the task will also require political commitment to the issue and a lot of luck. All in all, by 2050 there will be only 32 annual crop cycles left.

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