tagging along with a carbon atom

As any student of soil science will tell you, soil is not just dirt under your feet. Soil is so multifunctional that there are soil health advocates who sound like they must belong to some soil fan club. Healthy soil nourishes plants, nourishes humans, fights disease, fights drought, fights flooding, and recently soil has taken on another role — fighting climate change. In the wake of the 2015 Paris Climate Agreement, André Leu, president of the International Federation of Organic Agriculture Movements, spoke excitedly about the prospects for reversing climate change. Not slowing ‒ reversing. In response to the gloomy prediction of continued global temperature rise from carbon dioxide already emitted into the atmosphere, Leu advocates building up the organic matter in the soil through more conscientious agricultural practices. He calculates that if adopted on a global scale, such practices could draw down enough carbon from the atmosphere to bring the carbon dioxide concentration to pre-industrial levels in just 57 years, possibly sooner. Soil organic matter, the stuff that darkens soil brown to black, the stuff that is the basis for plant nutrition, disease resistance, drought resistance, etc., etc., provides a service that was not even conceivable a few decades ago.

The question then becomes, how does one build soil organic matter? Organic farmers have been working on this issue from the beginning of the organic movement and have made incorporation of manure and plant residues one of their central practices for achieving this goal. However, what became apparent from the work of researchers like Dr. Hollis Waldon was that microbes would then break down the added organic matter and exhale it as carbon dioxide back into the atmosphere, leaving little to no accumulation of organic matter in the soil. This season’s organic amendments have to be replaced come next season.

One method that has succeeded in increasing organic matter is no-till farming. In no-till, the tillage is replaced by herbicides or organic practices to manage weeds, and herbicides or crimping to terminate cover crops, and thus quantities of plant residue are left on the field. Most importantly, when the soil is not opened up, the microbes are deprived of oxygen and are slow to make use of the fuel in the organic matter. How does the organic matter get into the soil? How much organic matter might be contributed by the roots versus the aboveground portions of the plant, its “shoot”? How long does this season’s organic matter last in the soil? Is there a way to figure out where the carbon from the plant ends up after the plant dies?

There is. Researchers can essentially mark the carbon in carbon dioxide, feed it into the plant’s leaves, and detect it in plant residue and the environment afterward. This is done using rare variants of carbon. A well known carbon variant is carbon fourteen, abbreviated 14C, the same type of carbon at the heart of radiocarbon dating. The number 14 signifies that it has fourteen neutrons in the nucleus rather than the usual twelve, and this makes it radioactive. In carefully controlled laboratory experiments a researcher can use chemical compounds made with radioactive 14C in biological systems to discern with high sensitivity how the compounds move and where they end up, using techniques for detecting radioactivity. For open field experiments, though, researchers take advantage of a lesser known carbon variant, 13C. Its thirteen neutrons make its nucleus stable, so it can be handled without so much as gloves.

The non-radioactive 13C atoms are detected using a machine known as the mass spectrometer. The researcher takes a sample and burns it to turn the carbon back into carbon dioxide. The mass spectrometer gives the carbon dioxide molecules a charge and then shoots them through a magnetic field, which makes them curve toward a detector as they pass. A sample’s carbon dioxide will always contain a mix of regular and 13C. The extra neutron makes 13C heavier than the regular carbon, and that causes a carbon dioxide molecule made from it to travel slightly farther along the detector than an ordinary carbon dioxide molecule. The researcher records the proportion of heavy versus regular carbon in the various samples, and then with the appropriate bookkeeping determines exactly how much of the carbon dioxide that was originally applied has ended up in the samples of interest.

Dr. Emily Austin fed carbon dioxide containing extra 13C into a rye cover crop and followed it into the soil organic matter. She addressed the question of whether it is roots or shoots that contribute to organic matter accumulation by giving the 13C-enriched carbon dioxide to half of her cover crop patches and leaving the others open to the atmosphere. At termination, when she cut down the shoots, she switched the 13C shoots with the untreated ones. At that point, any 13C that was in the soil from which the 13C shoots were removed could only have come from the roots, and any in the plain-air patches that received 13C shoots would have to be from those shoots.

And the answer is, soil organic matter comes mainly from the roots. After five months ‒ the end of the summer corn-growing season ‒ there was four times as much organic matter from the roots and from the carbon that they had given off into the soil around them than there was from the shoots, and after a year there was seven times. By comparison, at the time that the shoots were first cut the roots had 1/6 less carbon than the shoots.

This result is consistent with the idea that lack of oxygen slows the breakdown of organic matter. Chopped leaves and stems sitting on top of the soil in this no-till system are exposed to oxygen and get broken down quickly by microbes, while buried roots are relatively protected. There is more to the story, though. Dr. Kris Nichols and other researchers who specialize in the beneficial fungi that live in roots claim that these fungi fill the soil with a sticky protein known as glomalin and that this glomalin is the source of recalcitrant organic matter, the organic matter that is hard to break down. With 13C flowing into the rye roots and their associated fungal partners, Dr. Austin was in a position to look for evidence of this claim.

Dr. Austin further processed soil samples from the experiment and extracted organic matter that had differing degrees of protectedness ‒ the unprotected free bits, the stickier stuff tucked away inside tiny clumps of mineral particles, and the small metabolites that form an intimate coating on the clay particles. She also chloroform-fumigated soil samples to extract total microbial biomass, that is, all the living fungi and bacteria. She then shot all these organic matter extracts through the mass spectrometer. The story that emerged from this finer analysis is that only about 2/3 of the carbon atoms that move into the roots are retained to build root tissue. The other third are sent directly to the soil. Growing root tips release carbon-rich mucilage that feeds microbes and coats soil particles. Slender short-lived root hairs and threads of fungi work their way into tiny aggregates of soil particles where they are relatively protected and deposit their carbon. Soil microbes incorporate the carbon into their cells within hours, and these cells turn over rapidly and release the transformed carbon into the soil, further contributing to the clumping and the coating of the particles. The organic matter that coats the clay particles is protected from degradation by the way it is bound to the mineral surface, suggesting that while the protein glomalin may play a role in binding aggregates together, it is not the only source of persistent organic matter. The shoots can enter the same pathway of transformation, but only at a later stage of breakdown.

What does this mean in practical terms? Dr. Austin’s focus is the loss of organic matter from farmland when the leftover stalks and leaves of a corn crop are hauled off for bioenergy. If the shoots of the corn account for a small fraction of the organic matter that builds up in soil, then the removal of a major portion of them can be fully compensated using the cover crop. Dr. Amélie Gaudin investigates the feasibility of increasing soil organic matter in fields where the shoots are grazed by livestock. Glomalin researcher Dr. Nichols insists that every field should have something growing on it at all times. In fact, at the end of Dr. Austin’s project, after a second corn crop, the amount of 13C detectable in the soil from the original cover crop had fallen to a very low level, and the difference in the relative contributions of root and shoot were negligible. Cover crops have to be used every year in order to build up soil organic matter and sequester carbon out of the atmosphere over the long term.

If soil organic matter buildup can play such a key role in pulling carbon dioxide out of the atmosphere, climate activists sometimes ask how to convince farmers to take on such a burden. One incentive is direct government payments to farmers who switch to methods that capture carbon dioxide, such as California’s Healthy Soils Program. However, increasing soil organic matter is in the farmer’s self-interest. One of the functions of soil organic matter is to increase the soil’s water holding capacity, and another is to decrease its erodibility. These are exactly the advantages a farmer needs to face a future of harsher droughts and bigger storms. Soil organic matter not only fights climate change, it helps farmers weather its effects. Soil organic matter lives up to the hype. Time to join the club.

cultivating community

To the uninitiated, the term “urban farming” may seem like something of a contradiction. The typical image of a farm might include a tractor, long rows of crops, clouds of dust drifting past a rickety barn, while the image of an urban landscape is that of entombed earth under austere buildings and roads, with the occasional manicured park. The combined term may evoke a community garden, or perhaps a legacy parcel of land on the fringe that has not yet succumbed to the march of concrete. What is not obvious from the term urban farming is that it is as much a political act as a means of providing food.

The California EcoFarm Conference has in recent years begun increasing its commitment to equity with its convocation of a Diversity Advisory Group. In 2019 the Conference featured as a keynote speaker urban farmer Karen Washington of Rise and Root Farm in New York, and showcased as successful organic farmers Chanowk (pronounced can-oak) and Judith Yisrael of Yisrael Family Farm in Sacramento. In addition to their plenary talks, these invitees participated in workshops dealing with equity and urban farming.

Rise and Root Farm is in upstate New York, but Bronx resident Karen Washington also participated in the urban community garden movement starting in the 1980s. She set the scene for the history lesson by evoking neighborhoods where buildings had been bulldozed in the wake of white flight during New York City’s fiscal crisis of the 1970s. The resulting open spaces became magnets for trash, not from the residents but from outsiders who dumped their loads in the dark of night, including tires and even automobiles. It was the residents who undertook the cleanup of vacant properties, only to find an endless supply of trash poised to fill the void. The advent of the community gardens was first and foremost a means of holding space that residents had cleaned up.

Gardening, however, is a fraught subject among African-Americans in the northern states. The history of slavery and Jim Crow has tainted their view of working with the earth, and many turn their back on planting and weeding in order to feel that they have moved ahead. Ms. Washington turns that historically based aversion on its head by pointing out to the members of her community that before slavery Africans were farmers. The reason that Africans were so crucial to agriculture in the humid southern US was not that they were mere laborers, but that they had the knowledge to farm in such a climate. Africans had domesticated rice independently, using an indigenous African species, and American plantation owners had to learn rice production from the Africans over whom they claimed ownership. Africans brought seeds with them from the old world. African-American families passed on the knowledge of medicinal herbs down through the generations. Today African-American urban gardeners can tap into a source of pride by learning the deeper history that has been kept from them.

With gardens beautifying the neighborhoods of New York, the community members felt that they had done a service to their city. Mayor Rudolph Giuliani took notice, but not in a good way. Seeing the opportunity to turn a profit off the volunteer labor of poor and minority people, Giuliani moved to auction off the land underneath hundreds of community gardens throughout the city. Thanks to the organizing that underlay the community garden movement, communities from all five boroughs sprang into action with a campaign of resistance that culminated in a lawsuit by Attorney General Eliot Spitzer blocking the sale and transferring the gardens to the Parks Department. That battle was won. Nevertheless, capital continues to test new schemes to dispossess the people.

Chanowk Yisrael had the epiphany to leave his IT job and harness his love of gardening to empower his community in the ‘hood. Starting out as a family operation, the Yisraels did not have to disabuse their fellow African-Americans of the notion that growing food was slave labor. Instead, nature did the recruiting. As urban dwellers spent time in the refuge of the garden, their eyes opened wide, they breathed easier, and their doubts melted away. The Yisraels’ sleight of social alchemy was to make their small farm a multi-use space where residents would be pulled in by community events and would leave as allies.

And allies became crucial for the functioning of the farm. When the Yisraels set up a farm stand they learned that selling garden produce was illegal in Sacramento. With the community at their back they approached City Hall and got the ban lifted. When the Yisraels wanted to set up a community farmers market, they had the foresight to approach community leaders in order to insure buy-in by the community before the market ever opened.

The Yisraels had to confront another legacy of racism, one now identified as food apartheid. African-American neighborhoods suffer from a dearth of grocery stores with fresh produce, a result of decades of social engineering and disinvestment. In their place are liquor stores, fast food joints, and food pantries. These areas have previously been referred to as food deserts, but activists point out that this latter term has been co-opted by the fast food corporations, and ecologists complain that the term does a disservice to deserts. What it meant to the farmers was that the residents did not know how to deal with farm stand produce.

Judith Yisrael had faced one of these knowledge gaps when she married Chanowk and his garden — how to prepare the variety of produce. Through trial and error she persevered, and now she runs edible education classes for the community. A more insidious knowledge gap surfaced when the residents asked why they should pay for the produce. The food pantry model upon which they had become dependent had instilled in them the expectation that food was free. The Yisraels had to educate them on the true cost of producing food, as well as the importance of community self-sufficiency. Non-profits that use their resources to provide free food are making the choice to not fund actual community development. The Yisrael Family Farm by contrast uses its profits to re-invest in the community. The neighbors who buy from the Yisraels are not just consumers, but what Karen Washington would call co-producers.

The inclusion of an equity track at the mostly white EcoFarm Conference allowed for a discussion of the role of white allies. Beth Smoker of the Pesticide Action Network spoke from her experience as a white person supporting communities of color. Sympathetic white people become allies when they ask how they can be supportive rather than imposing their own ideas about how to proceed. They have to be prepared for some discomfort as their understandings are challenged. Being an ally is an action, not a state of mind, and an ally must go out of his or her way to amplify the voices of the oppressed, rather than leaving the targets of oppression to take on the entire battle themselves. Mr. Yisrael recommends that white people who want to be allies read the chapter dedicated to white allyship in Leah Penniman’s book Farming While Black. In the end, white activists cannot transform the food system on their own. They will need to make alliances with African-American, Latino, Asian-American, and Native American communities who are on the front lines of confronting the unsustainable system that profits corporations while exploiting people and the environment.

in sickness

We often treat disease as an exception, a departure from the ordinary state of things. Thanks to public health infrastructure such as sewage treatment, restaurant inspections, and ventilation standards, we live disease-free for long intervals and don’t spend our all waking moments bracing for the cough that could signal misery, isolation, or death. Public health officials admonish us to cover our cough, wash our hands, get vaccinated, in short, to alter our behavior for the active prevention of disease, which is a menace that is always with us. However, not every employer offers sick leave, not every public gathering place supplies tissues, and not every medicine cabinet is stocked with unexpired analgesic, measures that can suddenly become necessary when the the darker side of life inevitably arises.

The situation is similar for agricultural producers. They prepare the soil, select the varieties, do the planting, manage water and fertility, weed, harvest, market the product, pay the workers and the creditors, and more. It would be understandable for them to relegate thoughts of disease to the back of their mind, especially with diseases they have no firsthand experience with. Disease is a chance event, and growers often get lucky. However, they ignore disease prevention at their peril.

Professor Cassandra Swett is a plant pathologist who bemoans the inattention that agronomists give to plant disease. Among other endeavors, Dr. Swett has lent her expertise to the study of deficit irrigation, an emerging practice intended to address water scarcity. The idea is to reduce water inputs only low enough to slightly stress the plants, not to reduce yield. In theory, plants can compensate for a certain amount of environmental stress. However, Dr. Swett’s first question is always about plant disease, and she is quick to point out that stress can often exacerbate disease, or even trigger symptoms in apparently healthy plants. Before she began asking about deficit irrigation and disease, none of the deficit irrigation proponents had considered that question.

Many fruit crops produce better flavor when they receive less than plentiful water. Tomatoes are one example, and thus a logical choice for deficit irrigation trials. Dr. Swett found that at light levels of deficit the plants had more infection with the fungus Fusarium than they would have under conventional water management, while at a greater deficit they had less infection. This finding of an apparently paradoxical result is also reflected in work her lab did with greenhouse poinsettias, where deficit irrigation reduced populations of water molds, but wherever the water mold organism Pythium was present it caused more disease. These are just the initial explorations of disease dynamics under deficit irrigation, but without Dr. Swett’s contribution, agronomists might have made sweeping recommendations that would have saved some growers money while costing other growers in terms of yield.

Dr. Kamyar Aram is a scientist at the Foundation Plant Service of UC Davis, the facility charged with providing virus-free grapevine propagation material to the nurseries that growers depend on for their supply. As part of his public outreach, Dr. Aram receives calls from California growers when their vineyard is overcome with viruses, at a point when little can be done to save production. Dr. Aram laments that growers generally do not regularly scout for virus symptoms and rogue symptomatic vines, that is, rip out infected individuals before the infection can spread and interfere with yields across the entire vineyard, or in terms of the enterprise, let go of underperforming assets before they become toxic across a wider portion of the portfolio.

The grapevine viruses causing the biggest dent in California wine production are the Grapevine Leafroll-associated Virus strain 3 and the Grapevine Red Blotch-associated Virus (“GLRaV-3” and “GRBaV”, following to the conventions of virus nomenclature). Grapevine viruses are transmitted through grafting infected material onto a new plant or through feeding and dispersal by sucking insects, such as mealybugs for GLRaV-3 or the three-cornered alfalfa hopper for GRBaV. Different virus strains presumably arose from an ancestral virus by coevolving in the grapevine population of a locality. Coevolved grapevines may tolerate their local virus, but a globalized grape-growing industry has spread viruses from every part of the grapevine’s native range to all the major wine regions. Such a situation can lead to viral infection of naive vines, mixed infections where viruses have synergistic effects on their host, and trading of virulence genes to create souped-up viruses.

Once a grapevine gets infected with a virus, it stays infected with that virus until the end of its life. Yield can be reduced, sugar production is impaired, and wine quality suffers. Vineyards that catch the eye with stunning red foliage in the fall are showing off virus infection; the vines’ natural fall color is yellow.

Grapevine Leafroll-associated Virus strain 3 is originally from Israel. Some traveler decided it was more important to get his hands on a particular grapevine for his vineyard than to protect the wine industry of an entire region. With the recent invasion of the vine mealybug into California, GLRaV-3 has a more efficient means of transport to move from vineyard to vineyard. The presence of the vine mealybug means that if you are a grape grower, your neighbor’s infected vineyard has become your affair. If your neighbor rips out his infected vineyard and replants, mealybugs can reintroduce virus from his neighbors. And because vine mealybugs can hide out on grapevine roots in certain soil types, a grower’s own soil can be a source of future virus infection.

Dr. Aram posits that growers in the Lodi area of California could eliminate GLRaV-3 for good if they all ripped out their vineyards simultaneously and kept the region grapevine-free for a season, and then re-planted with clean material. As far-fetched as this scenario might sound, it has been done in New Zealand and South Africa. In the US the emphasis on individual prerogative over collective action, codified in the economic system, generally makes thoughts of region-wide cooperative efforts inconceivable. Business as usual insures that GLRaV-3 will continue to be a problem.

Other examples abound. Dr. Honour McCann reminds us that the New Zealand breeders who developed the golden kiwifruit did so without considering the bacterial disease known as Psa that was attacking green kiwifruit across Asia at the time. This oversight caused the disease to spread on susceptible vines into New Zealand, Australia, and Europe, where treatment options are limited, and in some cases amount to an IV bag pumping antibiotic into each vine. An example from my own experience is the way some small growers will buy seeds from the bulk bin at the grocery store for planting. They save money on the purchase price of the seeds, but they don’t realize that unlike commercial seeds for planting, seeds marketed as food are not required to be produced on disease-free soil, they do not receive hot water or other treatments to kill seedborne pathogens, nor are they tested for pathogens. These growers are risking not just this year’s yield, but also the health of the field they plant in.

What should be done? Plant disease is an integral part of agriculture. All people involved in the agricultural system, from germplasm prospectors to breeders to agronomists to seed producers to growers to laborers to consumers should take a moment to inquire about the plant diseases to watch out for in their practices. Asking about plant disease should be as routine as washing your hands. Plant pathologists are standing by to take your call. As the American Phytopathological Society’s popular T-shirt says, “Don’t get caught with your plants down!”

Phytophthora man


Recent Ph.D. graduate Tyler Bourret is a phytophthorologist to watch out for. In his nascent career Dr. Bourret has pushed the boundaries of knowledge about that peculiar group of organisms known as Phytophthora.

Once believed to be a type of fungus, Phytophthora is actually a fungal-like organism descended from algae, a member of a group of organisms known in the vernacular as the water molds. It forms a network of tiny threads like a fungus, but its cell wall is made of cellulose, the same material that makes up plant cell walls, where a true fungus would have a cell wall made of a different material known as chitin. From its waterborne ancestors Phytophtora has inherited a type of spore that propels itself through water using flagella. Furthermore, it is not susceptible to many of the usual fungicides.

The name Phytophthora comes from the Greek, meaning “plant destroyer”. Phytophthora blazed a path of destruction across Europe starting in 1845, when late blight disease, caused by the species dubbed Phytophthora infestans, destroyed potato crops in several northern countries, notably Ireland. P. infestans’ uncharacteristically airborne spores allowed it to spread widely to infect whole fields of potatoes. Nevertheless, while many plant pathologists consider P. infestans as the cause of the so-called Irish Potato Famine, such a reductionist disciplinary view ignores the role of the English overlords, who exported great quantities of food from Ireland while the common people starved.

Since that time scores of other Phytophthora species have been discovered. The pathogenic forms normally cause root rot in annual and perennial crops and in wild plants, unlike the whole-plant-infecting P. infestans. The swimming spores take advantage of water-saturated soil, which can be a result of overwatering, to find a banquet of roots. The non-pathogenic forms live in ponds and streams, where they colonize dead plant matter and are probably what you smell when you get a whiff of stagnant water. The most recent species to grab headlines is Phytophthora ramorum, “Phytopthora of the branches”, cause of sudden oak death. P. ramorum can live in streams, colonize California bay trees without causing symptoms except for burned leaf tips, and then from those leaf tips produce spores that get splashed or blown onto the trunks of susceptible trees, most notably tan oaks, where they produce massive deadly cankers.

Sudden oak death burst onto the scene seemingly out of nowhere. At the same time that it was found devastating California woodlands, it was ravaging the European nursery trade. Only years later was a diversity hotspot of P. ramorum was found in southeast Asia, indicating that region as its native range. Unfortunately this kind of knowledge gap is common regarding Phytophthora. Dr. Bourret and colleagues discovered new species of Phytophthora while monitoring streams for P. ramorum and also while screening native plants from a nursery that were used in a restoration planting. It is not known whether these new species are native or introduced because no coordinated effort has been made to survey Phytophthora in different habitats around the world.

The other gap in knowledge is the virulence of these species in introduced habitats. Phytophthora pluvialis, a North American stream dweller, is now causing epidemics on Monterey pine in New Zealand. Plants or soil coming into the US could carry a strain with the virulence capable of causing the next epidemic of forests or crops, and in an era of rollbacks of government spending and regulations, they may not be discovered before mass plant destruction. In another questionable endeavor, Dr. Soum Sanogo’s lab in New Mexico is experimenting with inoculating the non-pathogenic water-dweller Phytophthora riparia onto chili pepper plants to essentially vaccinate them against Phytophthora root rot. Dr. Bourret points out that every Phytophthora species has all the machinery in its genetic makeup for causing disease in plants, but that the water-dwellers are generally overburdened with this machinery, making them easy targets for the plant innate immune system. The risk is that a water-dweller could lose some of its burdening genes and become a pathogen, as seems to have happened with Phytophthora megasperma.

One of Dr. Bourret’s areas of special fascination is the complex family tree of Phytophthora and its relationship with another set of algae descendants, the downy mildews. Downy mildews are not plant destroyers, but rather parasites that can only survive while their host is living, a condition known as obligate biotrophy. Their spores, still encased in their spore-bearing structures, travel through air and land on leaves to infect. The name comes from the fluff that appears on the underside of leaves when their threadlike growths exit through the leaf stomate pores to send off more spores. Because they are intimately dependent on their host’s cellular processes, they are confined to the single host species that they have co-evolved with. They are divided into twenty different genera based on characteristics such as host type, spore color, and leaf-penetration organ.

Since the turn of the current century, advances in molecular genetics have led to the unexpected finding that downy mildews are actually descendants of Phytophthora. The question then became where the downy mildews fit within the family tree if obligate biotrophy is all but absent in Phytophthora. Dr. Bourret analyzed the sequences of six common genes in over 100 species, including all of the downy mildew genera. His big innovation was to include an unusual species of Phytophthora from nutsedge that exhibits obligate biotrophy and an unnamed New Zealand Phytophthora species that was found infecting leaves of the totara tree, a conifer. He was able to show that the those downy mildews that infect sunflower-family plants are descended from a common ancestor they share with the nutsedge-infecting Phytophthora, and that the downy mildews that infect grasses, mustard-family plants, and others such as spinach descended from a common ancestor they share with the New Zealand leaf-infecting Phytophthora. Of course, with all the evolutionary changes required for a family tree branch to lead to true obligate biotrophy, the branches that lead to powdery mildews stick way out from the main tree.

Another result that popped out of the data is that of the six genes studied, those genes contained within the nucleus indicated some different family relationships among the different species than did the genes maintained outside of the nucleus. This disagreement suggests that sometime in the past there were hybridizations between species, or perhaps some species picked up DNA from the environment. Good science leads to the next set of questions, and Dr. Bourret is on his way to a lifetime of discoveries.

the magic of monoculture

The usual agroecological practices for preventing soilborne disease are well known: crop rotation, addition of organic matter and compost, sanitation of tools and plant materials, promotion of good soil structure, prudent water management, use of resistant varieties. Add to that list an incongruous entry — continuous monoculture. When the same crop gets hammered by the same disease in the same field year after year, once in a while the disease will suddenly disappear for good. This is the phenomenon of suppressive soil, and Daniel Schlatter and colleagues recently summarized the latest research on it.

While continuous monocropping contravenes good agroecological management on many levels, the appearance of disease suppression actually does arise out of agroecological principles. What we call disease is really the interaction between a host, in this case a crop plant, and a pathogenic organism. And whenever an organism is present in a field, it is subject to ecological forces. A field that contains a large population of a single species, whether it be a plant, insect, or microbe, potentially presents a target for another organism. For a plant, the opportunistic organism could be an insect or a fungus. For a microbe responsible for a crop disease, the opportunist could be an antagonist — a sort of armed competitor — or even a hyperparasite.

To be sure, a certain amount of disease suppression can come from enrichment of soil organic matter. Schlatter et al. differentiate this phenomenon as general suppression, the suppression that prudent organic farmers enjoy, whereby most soilborne diseases can cause only the most minimal damage. The other kind of suppression, that which arises from monocropping, is designated as specific suppression, where a specific disease caused by a single organism is the only one affected. Specific suppression can often be introduced into a field by addition of a small amount of already-suppressive soil. In addition, specific suppression requires the continuing presence of the host crop. If the field is rotated to a different crop, the resistance subsides, and it takes a season or more to return when the host crop is re-planted.

General suppression is thought to operate based on high numbers and high diversity of microbes present in the soil. This kind of microbial community insures that organic compounds are quickly broken down and taken up. Among these compounds are the exudates that a root characteristically gives off as it extends through the soil. It is these exudates that trigger pathogens to begin their attack. If the exudates dissipate immediately after release, the root may essentially slip past the pathogens unnoticed.

Regarding specific suppression, the authors of the review examine the mechanisms by presenting three case studies highlighting a continuum of suppression, from completely specific to somewhere between specific and general. The first regards the disease known as take-all of wheat. This disease is caused by a fungus that severely rots the plant’s roots. Certain strains of bacteria suppress the disease, and all of these turn out to produce an antibiotic known by the acronym DAPG. When these strains reach high population levels, the take-all pathogen is completely incapacitated and the disease disappears. The wheat plant’s roots even exude compounds that promote colonization by the DAPG strains. However, the DAPG producers have no effect on other pathogens.

The second case is that of Rhizoctonia bare patch of wheat and sugar beets. There is evidence that the organisms antagonistic to the Rhizoctonia fungus possess a certain amount of cross-antagonism against other pathogens, but the bare-patch-suppressing microbes are the least well characterized of the three case studies.

The third case is that of potato scab, a disease caused by a strain of Streptomyces, a genus of bacteria perhaps better known as the source of the antibiotic streptomycin. Interestingly, the antagonistic organisms are also strains of Streptomyces. It seems that the potato plant’s exudates are a food source for a suite of highly similar organisms, and niche theory predicts that in such a situation the best competitor will win out. In this case, the various strains of Streptomyces boost their competitive abilities in the presence of this limited food source by producing unique antibiotics that kill off their competitors. A casualty of this antibiotic arms race is the strain that causes the scab disease.

This third case of specific suppression is the closest to general suppression, although the mechanism is different from the fast degradation hypothesis. The cocktail of antibiotics pulsing through the soil can serve to eliminate other pathogens besides the bacterial strain responsible for potato scab. In fact, disease-suppressive Streptomyces strains can sometimes be enriched in the soil by incorporation of certain organic amendments, such as rice bran or the mustard family plant wall rocket, the presumption being that a particular type of food will cause the microbes that are able to digest it to fight over it, launching their specialized chemical weaponry as the competition intensifies. Whichever management practice initiates the chemical warfare, once it starts, it may tilt the microbial community composition toward ever stronger competitors, leading to a self re-enforcing dynamic that in some cases leads to lasting suppressiveness even when the original crop or amendment is gone.

Disease suppression has long been a phenomenon that emerged from the black box that is the soil microbiome. New tools for microbiome research are beginning to shed light on the inner workings of that system, and Schlatter and colleagues enumerate some of the methodological considerations for further advances. They also call for additional studies that use the knowledge that has been gained about suppression mechanisms to further our understanding of the agroecological circumstances and the specific management practices that will enhance disease suppression. For instance, will tillage increase or decrease disease-suppressive Streptomyces? Co-author Linda Kinkel invokes niche theory in predicting that no-till might allow the different strains to begin to coexist and to ease up on the competition, while tillage would disrupt any coexistence dynamic and more likely set off a chemical arms race. Would that happen in the real world? In every situation? Only field research, with a boost from microbiomics, will give the answer. For the foreseeable future, though, continuous monoculture remains a questionable bet for sustainable agriculture.

Pierce’s Disease and the microbiome

As if you needed any more evidence that microbiomes matter, wife-and-husband team Caroline Roper and Philippe Rolshausen have given us a microbiome study around the phenomenon of grapevines that escape Pierce’s disease.


Winegrapes as a crop are uniquely susceptible to diseases due to their propagation method.  Existing grape varietals such as Cabernet Sauvignon, Chardonnay, and Zinfandel are relics from the eighteenth century or earlier, kept alive through cuttings that are grafted onto more robust rootstocks.  They cannot be bred for disease resistance due to consumer rejection of hybrid varietals.  In France it is even illegal to breed with traditional grape varietals.  Grapevine pathologists are thus always assured of a job.


Pierce’s disease is caused by the bacterium Xylella fastidiosa, the “hard-to-grow xylem vessel-dweller”, Xf for short.  The bacterium gets injected into the water-conducting vessels of grapevine and other hosts, where it forms a film on the inside of these microscopic channels.  It was thought that the bacteria build up to such high numbers there that they block the flow of water to the leaves and cause scorching.  However Hossein Gouran showed in his Ph.D. research that the bacteria in the film are not the life stage associated with the scorching.  Rather, it is the free-floating stage of the bacteria that induces the actual disease.  These cells that have broken free produce an enzyme that flows up the xylem vessels and attacks the cells in the leaves, causing the scorch symptoms.  This revelation is so new that Roper and Rolshausen do not acknowledge it in the introduction to their study.


Pierce’s disease has long been a minor nuisance in California’s grape-growing regions, showing up on field margins that are near streams.  The native sucking insect known as the blue-green sharpshooter picks up the bacterium in the wild streamside vegetation and then disperses into the nearby grapevines, where it feeds on green stems.  It inserts its mouthparts into the xylem vessels, where it injects the bacterium as part of its feeding behavior.  The leaves on that segment of stem are the ones that show symptoms, but after the leaves drop in the fall and the vine has undergone a chilling period, it can emerge pathogen-free in the spring.


If that were the end of the story, it would be a mere footnote in the litany of diseases of grapevine.  Now, though, the introduction of the much larger glassy-winged sharpshooter from the southeastern US into southern California has given the Xf bacterium the upper hand in that region’s grape industry.  The new insect can inject Xf into the woody tissue of the grapevine, causing a much more devastating infection, and it avoids wild vegetation, instead moving extensively through the region’s orchards and vineyards.  Entire vineyards fail because of Pierce’s disease, and in northern California grape-growing facilities one can find wanted posters showing hideous blowup photos of the glassy-winged sharpshooter.


The real footnote of this disease story is that in vineyards that are ravaged by Pierce’s disease, occasionally there will be a lone grapevine that has escaped the disease.  This surprise cannot be the result of genetic resistance because all the grapevines in the vineyard are clones of centuries-old varietals.  With microbiome research all the rage, Roper and Rolshausen and their research groups asked if there was something about the microbiome of the escaped vines that protects them from Xf.


Serious microbiome research has only become possible with the development of so-called “next-generation” DNA sequencing technologies, new methods of reading off millions of DNA sequences in parallel.  The sequence is the order of the four possible building blocks of DNA, strung together in long strands to form a code that a cell can read for its instructions.  Roper and Rolshausen used one such technology, the Illumina system, where the millions of DNA segments get anchored to a tiny surface for a microscopic light show.  Since a DNA strand is made up of two halves that fit together perfectly, when one half is removed it can be recreated based on the sequence of the other half.  By monitoring the construction of the missing portion, one can determine the sequence of both halves.  Every new DNA building block that the Illumina machine adds generates a tiny flash of light from each anchored segment, with a different color representing each of the four building block types.  The sequence of colors in the series of recorded images corresponds to the sequence of a DNA strand at a particular spot on the surface, and given the millions of sequences recorded, with some computation the entire sample’s DNA sequences can be characterized.


The Illumina technology is useful in microbiome work thanks to DNA barcoding.  There are a few genes that are universal, contributing to a microbe’s basic cell structure and functioning.  In particular, the genes for the ribosome are indispensable, comprising the main part of the machinery for reading the DNA code.  They vary hardly at all from microbe to microbe because the vast majority of possible changes would be lethal.  This consistency makes these genes easy to find in the jumble of DNA.  However, there are segments in the DNA of these genes that do not get used in the ribosome, and therefore are free to mutate without consequence.  Different mutations are carried by different lineages, and the resulting DNA sequences can allow a researcher to distinguish different groups of microbes.


Roper and Rolshausen extracted the sap from symptom-free vines in southern California vineyards ravaged by Pierce’s disease and in northern California hotspots of Pierce’s disease and used ribosome DNA barcodes to compare the sap microbial community to that of the sap from nearby vines that had succumbed.  They looked at both bacteria and fungi, and while some of the fungi they found were interesting, there were too few to pick out a consistent trend between symptomatic and asymptomatic vines.  The bacterial communities were indeed different, although not nearly as rich as the bacterial community of a soil or a human gut, and the researchers mentioned a lot of the bacterial groups found, using the Latin, for anyone who is interested.  The key finding was that asymptomatic vines were low in Xf but had a high level a certain bacterial strain called Pseudomonas, which is known to have biocontrol properties.  Is this the key factor allowing the vines to stay healthy?  More research is needed.


With a strain of bacteria able to protect grapevines from Pierce’s disease, conventional ag research’s aim would be to commercialize the strain, with the hope of allowing private laboratories to make a profit by providing vineyard owners with another specialized input.  The high-margin winegrape-growing corporations would in turn be able to increase profits by extracting higher yields from their centuries-old relics, while any artisanal grower without the means to inject all her vines with a specially formulated bacterial preparation would be economically disadvantaged.  By contrast, the aim of agroecological research would be to seek management techniques that any grower could use that would increase the resistance of the vines to Xf.  This would be in the context of promoting overall agroecosystem health and community benefit.  I would even surmise that if varietals bred for disease resistance were ever to find acceptance, it would be by wine club members dedicated to small agroecologically managed vineyards.  More agroecological research is needed.

resistance gene networks

Plant breeders face a conundrum when it comes to plant diseases. The most powerful disease resistance genes, if not managed well, will quickly become useless.

Plants have an innate immune system that recognizes certain molecules that are typically found on pathogens. When a microbe presenting a typical molecular signature enters a plant, the plant basically bleaches the area using highly reactive oxygen compounds. The plant then activates genes that insure the microbe will not spread. However, successful pathogens overcome the innate immune system using molecules called “effectors” that disable components of the plant’s detection or response system.

The story does not end there, though. Thanks to Darwinian evolution, plant populations can develop resistance to pathogens. A dramatic form of resistance is the so-called R gene, the major resistance gene. If a pathogen possessing a single potent effector arrives, it will run rampant in a population of its host species. However, natural plant populations are typically very diverse. Any individual plant that happens to have an R gene that matches the pathogen’s effector allows it to recognize the effector and turn on its so-called hypersensitive response. Microbes with effectors are considered so dangerous that the plant will go crazy bleaching the point of entry until all cells in the area, pathogen and host, are dead. The result is an inconspicuous dot of dead tissue that shows where a pathogen attempted penetration.

In a natural population, the plant with the R gene will outlive its susceptible neighbors and pass this gene on to its progeny. In agriculture, this type of gene is highly sought by breeders aiming to develop resistant crop lines. A field of plants with the R gene will stand firm against the onslaught of a pathogen, growing robustly and giving their full yield where susceptible plants would turn out stunted, discolored, deformed, or dead.

In a further turn of evolution, however, the pathogen population can include individuals with a novel effector gene that allows them to disable a plant’s R gene and carry out its invasion of the plant’s tissues. These individual pathogens will reproduce thousands of progeny that are able to infect all the resistant plants. The pathogen has broken through the resistance. This is a common event, as a pathogen’s lifestyle depends on infecting plants, and therefore it is built to evolve new effectors quickly.

Another type of resistance is partial resistance, termed QTL, for Quantitative Trait Loci. In this case, instead of a single gene in the plant that acts as a tripwire for the pathogen’s effector, the plant has various traits that make it harder for the pathogen to carry out its lifecycle. Perhaps the plant’s external surface is harder for the pathogen to traverse, or one of the plant’s targeted enzymes is only partially disabled, or the plant produces a metabolite that slows the pathogen’s growth. Any single gene for partial resistance buys the plant only a partial or temporary escape from the ravages of the disease, but if many of these genes are present in an individual, that individual can be as resistant to the pathogen as if it had the appropriate R gene.

As you can imagine, partial resistance genes are more work for plant breeders. The QTL-resistant crop varieties they release must have multiple genes bred into them, or “stacked”. There is an advantage, though, in that the odds of any pathogen individual having enough genetic mutations to overcome all the resistance genes is essentially zero. In fact, breeders could stack multiple R genes in the crop varieties they release as well and enjoy the same odds against breakthrough, but expediency often overrules prudence when disease threatens. Furthermore, if one breeder expends the time and resources to stack R genes while other breeders release varieties with single R genes, the pathogens may break through the single R genes one by one, and the crop line with the stacked R genes may end up with few or just one functioning resistance gene. In that case, the pathogen population may be only one mutation away from breaking through the stack.

Plant pathologists are thus perennially concerned about release of resistance genes in seeds to farmers, but releases are often out of the control of the plant pathology commmunity. The network structure of plant pathologists, breeders, non-profit germplasm repositories, agribusiness corporations, and farmers presents a complex adaptive system where each actor has its own incentives, all of whom interact to produce the dynamics of resistance gene diffusion across the globe, both prudent and expedient. Karen Garrett and her plant pathology and plant breeding colleagues have looked into these dynamics using an epidemiological approach, published recently in Phytopathology.

Garrett et al. examine network structure for four staple crops: cassava, potato, rice, and wheat. The result is four abstract diagrams, evocative respectively of a double spiderweb, the tentacles of a sea anemone, a time-lapse photo of flocks of birds taking flight, and spaghetti with cheese flowing off a plate, all with colorful circles and squares on the periphery and black ones in the center. The central black circles show the centrality of the non-profit International Agricultural Research Centers, the IARCs. The other colors are codes for the continents where the different actors are located. Arrays of black squares represent private multinational companies, clustered near the center for potato and wheat, less obtrusive for cassava and rice.

The dots and squares on the periphery are segregated by color, signifying a dearth of direct connectivity between continents or regions. In terms of resistance gene diffusion, this means that there is no easy way for resistance genes from one continent to be bred into another continent’s crop, potentially leaving some areas without optimum disease protection. However, from the perspective of pathogen evolution, it could be helpful to have different resistance gene profiles in different regions to reduce the likelihood of the emergence of a super-strain able to infect the entire world crop. Also, less movement of the plant material containing the resistance genes means less likelihood of bringing hitchhiking pests and pathogens to new regions.

The reason for the four diagrams’ different arrangements of black squares — representing the international-scale private breeders — is the privileged position of some of their non-profit counterparts, the IARCs. In the case of cassava, a staple in tropical Africa and Latin America, the entire network is small, making the lone black square look rather incongruous and with very few connections. Private corporations seek out crops with the largest markets, and cassava is not one of them. In the case of rice, the authors explain that the international centers have played such a dominant role in the development of major resistance genes toward bacterial blight and rice blast diseases that there has been little profit incentive for the entry of private companies into the network. On the opposite extreme is wheat, for which several multinational corporations have extensive germplasm collections and have highly connected black squares in the network diagram. For potato there are similarly black squares in a more central position, but a closer look also reveals a proliferation of red squares on one side of the abstract anemone, representing a large number of private interests in wealthy Europe.

The abstract diagrams and their underlying analysis is a work in progress. The idea is to provide insight into what-if questions, such as how resilient a network would be if a major hub should disappear, such as the recent abandonment of the seed collection at the International Center for Agricultural Research in the Dry Areas in Aleppo, Syria (the Center was reconstituted in Lebanon and Morocco with backup seeds from the Svalbard vault). This type of change in a network would be unfeasible to test in an experiment, but past performance of the existing networks in terms of R gene diffusion and lag times can provide insights into the robustness of the complex adaptive system, as well as whether the networks themselves can be shaped by institutions embedded within them, e.g. the IARCs.

An observation by the authors is that private breeders tend to weaken the structure of the overall network. Whereas non-profit breeders’ focus is on providing farmers with plant material containing resistance genes, and ideally getting feedback on their performance from the farmers, private breeders have an incentive to hoard crop germplasm resources and release only those resistance genes that will make them a profit. Because of pro-corporate intellectual property laws and the development of biotechnology and hybrid varieties, private breeders are proliferating. The authors point out that private breeders focusing on more profitable markets enjoy a funding advantage for research over the constrained resources of the international research centers, thus allowing them to more quickly coordinate the release of resistant material. Poorer farmers have derived some benefit in the past due to trickle-down effects of resources originally directed at richer farmers.

A response to the privatization trend is the rise of open-source breeding movements, but the authors are unable to evaluate the effect of these efforts on breeding networks. Another shortcoming of the analysis, and of the underlying networks themselves, is the emphasis on staple crops. Traditional agriculture depended on a dizzying diversity of crops that is hard to fathom from the perspective of modern agriculture. This diversity provided an economic resilience to farmers as well as environmental services that benefited the crop plants, both of which have been replaced in modern low-diversity agroecosystems by continuous subsidies, in forms that range from pesticide development to resistance-gene prospecting to famine relief. A research focus on a handful of crops has promoted this low diversity, to the detriment of not just the environment but also human diet. While a big-picture analysis of the diffusion of resistance genes is an improvement over uncoordinated efforts to fight local outbreaks or to make a profit, such analysis must also be viewed as a small piece of the overarching big picture that is agriculture.

another tidbit on legumes

The story of a single rhizobium bacterium making its way into a legume root where it fills a nodule with its nitrogen-fixing brood is not as simple as once thought (see my previous post for background). The soil is full of bacteria, and it should be no surprise that other species get into the nodule along with the nitrogen fixer. Also, given the way that bacteria swap genes, it is little surprise that unusual species get hold of nitrogen-fixing genes, and even nodule-inducing genes. Martínez-Hidalgo & Hirsch have just come out with the latest compilation of the nodule microbiome in the new journal Phytobiomes.

Of course the predominant inhabitants of a nodule are the nitrogen-fixing bacteroids, thanks to the strong control the host plant exerts over the nodule environment. Some of the other inhabitants, though, are also beneficial to the plant. The ways they can help include solubilization of phosphate, production of compounds that solubilize iron, protection against heavy metal toxicity, possession of antifungal activity, and other plant growth promoting attributes. Some companion bacteria produce plant hormones that increase plant growth, although I have not heard a convincing argument as to why a plant is not equally benefited by producing its own hormones. Co-inoculation studies involving nodulating bacteria paired with other nodule inhabitants have shown benefits such as increases in nodule number & weight, plant nitrogen, dry shoot weight, pod weight & number, pathogen resistance, seed weight, and total yield.

Some bacteria with plant growth promoting capabilities have picked up genes for nitrogen fixation or nodule induction the way that bacteria are known for picking up new genes. Bacteria can receive genes from closely related bacteria through conjugation, AKA bacterial sex. Under favorable circumstances they can also take up DNA from dead cells in the environment and incorporate it into their own complement of genes. Nitrogen fixation requires a gene dubbed nif, and the ability to communicate with a plant and negotiate growth of a protective nodule requires another gene, called nod, both of which can only come from a strain that already has such a gene. Heavy-metal-resistant strains of nitrogen-fixing Cupriavidus picked up their nif and nod genes from the related species Burkholderia. A strain of Pseudomonas, a genus more commonly associated with diseases of plants and humans, was discovered nodulating black locust using a nod gene received from the more commonly nodulating bacterial species Mesorhizobium. A strain of Klebsiella, a genus associated with opportunistic infections in humans, was found in nodules of several legume species and was demonstrated to nodulate fava bean in a laboratory setting.

The authors envision widespread co-inoculation of legumes with nodulating bacteria and beneficial companion bacteria. While biological fixation of nitrogen has environmental benefits over industrial fixation, the model of turning scientific discoveries into products has its own downside. Highly capitalized farmers will be able to buy any input that can increase their profit margin, while farmers who are struggling financially will have to cut costs and instead use knowledge and additional labor to substitute for external inputs. Scientific knowledge that can only be accessed by specialized corporations will tend to accrue benefits to those who are already better off. If co-inoculation technology is to benefit those most in need, a system of public production and distribution of inputs would be necessary.

The authors point out that co-inoculation would be particularly helpful in degraded soils. Certainly the restoration of microbial diversity would contribute to restoration of soil to a healthy state. It would be helpful, though, if scientific investigations could zoom out from the reductionist business of characterizing beneficial co-inoculant species and in addition elucidate environmental conditions and management practices that would promote the proliferation of in situ populations of beneficial nodule-inhabiting companion bacteria. Laboratory cultures require time, labor, resources, and paperwork to ship internationally, but knowledge can move around the globe in an instant. The era of purely reductionist science must yield to whole-system perspectives. In this way, basic research, such as molecular microbiome studies, can help reduce economic inequality rather than contribute to it.

so you think you know legumes

It seems I have a fascination with legumes. I was about to pass up the New Phytologist journal’s booth when they handed me a reprint of the recent (2017) review by Sprent, Ardley, and James on legumes. Before I read this article, if you had asked me what a typical legume is I probably would have answered “beans”. However, as the third largest plant family, the legumes present a kaleidescope of forms, most of which are not your garden variety.

The legumes are defined by pods that open up along both edges, labeled by botanists as “loments” or “legumes”. Many legumes host nitrogen-fixing bacteria, but many do not, and not all plants with nitrogen-fixing partners are legumes. In my classes I learned that there were three subfamilies — or maybe four — that were classified according to their flower type. One subfamily was characterized by flowers that are pattered like those of the pea, with a large petal at the top giving the appearance of a bonnet, the other petals forming something like a beak in front of it. An early botanist had the impression of a butterfly when he saw this type of flower and called it papilionoid, and thus the subfamily with this type of flower became the Papilionoideae. A second subfamily had flowers with five more-or-less equal petals, sometimes with “claws”, and with a slight bilateral symmetry, such as those my grad school advisor had studied in the tropics. Her connection to these species left me with certain regard for this group, the Caesalpinioideae, named in honor of another early botanist. The third subfamily had flowers with no petals, only stamens and pistils, that clustered together into fuzzy puffs such as those on an acacia, a group named the Mimosoideae, evoking a certain brunch cocktail. The fourth group designated as a legume subfamily had been recognized as a separate family by the time I learned of it.

Part of the reason that legumes are so successful, and the reason they are important to humans, is their ability to harbor specialized bacteria that turn nitrogen gas into nitrogen fertilizer, a process known as nitrogen fixing. The bacteria benefit from this arrangement because they are fed and protected inside the legume roots, while the legume gets millions of tiny internal fertilizer factories. In another one of my classes I was taught how the plant sends a chemical signal into the soil that attracts the bacteria. The bacteria respond with their own chemical signal, causing the plant root hair to curl around a single bacterium and open up a narrow tube, called an infection thread, for the bacterium to enter. The bacterium travels into the main part of the root, where it multiplies as the plant builds a nodule around it. The plant releases the bacteria into a specialized compartment, where they become nitrogen-fixing zombies called bacteroids that have lost the ability to divide, often becoming unable to live in the soil again once the root dies and the nodule breaks open.

Sprent, Ardley, and James have updated my understanding of legumes and nodulating bacteria. The agricultural legumes we are familiar with, especially those grown in temperate zones, are biased toward European and Middle Eastern species such as alfalfa, clover, vetch, and peas, which have been exported around the world. In other parts of the world, by contrast, legumes are often trees or shrubs. The textbook infection-thread story is just one mode of nodulation. In some legume species the infection thread does not end up anywhere, becoming a “fixation thread” as the bacteroids start performing their nitrogen fixation inside the tube. In other legume species the bacteria enter through the root epidermis, and no infection thread is formed. This is the mode in the lineage that includes Scotch broom, rooibos, sunnhemp, and lupine, the latter being noteworthy for its wraparound nodules. Finally, some legume species allow bacteria to enter through cracks. A semi-aquatic West African Sesbania species grows nodules in this way — on its stem.

The previous classification scheme has been overturned, as evidence from DNA has shown that the Mimosoideae are actually a branch of the Caesalpinioideae. Furthermore, some members of the Papilionoideae have perfectly radially symmetric petals, giving the impression of a hibiscus flower. All of the African “acacias” are now placed in separate genera (sing. genus) from the Australian genus Acacia. And even though I had an image of caesalpinioids as tropical trees, the genus Chamaecrista includes temperate zone species and annuals, such as partridge pea, a North American native used for forage.

Another principle I learned from classes was that a species of nodulating bacteria is specific to a legume host genus. The specificity may be very strict — soybean will not nodulate in North America unless the soil is inoculated with the bacterium Bradyrhizobium japonicum. This trend does indeed hold widely across the legumes, particularly those widely exported European/Middle Eastern species. However, among Mimosa species, it is soil factors that determine the symbiotic bacterial species. Sometimes when a legume plant genus is distributed between different continents, its various member species adapt to whichever class of nodulating bacteria is present on the respective continent. There are also legume species that are “promiscuous”, such as the common bean, that can nodulate with bacteria belonging to the distantly related classes.

One mechanism for host-bacteria specificity seems to be a result of evolutionary arms race dynamics. The species of legumes in the European/Middle Eastern group produce a suite of antimicrobial-like molecules that regulate the process of turning free-living bacteria into highly efficient and subservient bacteroids. Each bacterial species, for its part, produces a unique enzyme that neutralizes a range of these regulatory molecules. On the one hand, the enzyme can allow the bacterium to multiply more successfully in the plant and get away with fixing less nitrogen. On the other hand, the particular set of regulatory molecules that the enzyme neutralizes will determine which hosts it can exist within.

Another factoid from the classroom is that some legumes are capable of producing potent toxins. A lecturer told of an acquaintance who cooked and ate scarlet runner bean roots and had to have his stomach pumped. Someone else became ill from munching on a single raw scarlet runner bean while working in her garden. Raw kidney beans can cause nausea with the ingestions of single-digit quantities. Consider, though, the southwest Australian leguminous shrub genus Gastrolobium, which produces fluoroacetate, a cell respiration inhibitor so toxic as to eliminate a sheep after just a few bites. Evidently the endemic legumes of this area share an unusual class of toxins that are not alkaloids and do not incorporate nitrogen atoms at all. Perhaps this attribute is related to their adaptation to low-phosphate soils, phosphate being crucial in most legumes for the nitrogen fixation process.

Some lineages of nodulating bacteria have given rise to well known pathogens. Agrobacterium, associated with crown gall, was revealed to be part of the genus Rhizobium. Agrobacterium uses a small circle of DNA separate from the main chromosome to carry its infection genes, just as nodulating Rhizobium species use a separate DNA circle for their nodulating genes. Another genus, Burkholderia, is known for several pathogenic species causing blights and spots on crops and ornamentals, and only fairly recently was discovered to include nodulating species found in South American mimosoids and South African papilionoids.

The different classes and genera of nodulating bacteria are often associated with particular environments. For instance, Burkholderia species prefer acidic soils and higher altitudes, whereas in higher-nutrient soils they are outcompeted by other species of nodulating bacteria. Other genera are associated with seasonally dry acidic soils or with alkaline soils. The genus Cupriavidus is known for heavy metal tolerance. However, strains of Rhizobium can be found in many environments.

A couple more factoids: Although the soybean, Glycine max, is native to China, oddly the genus Glycine is most diverse in Australia. And aside from providing nitrogen, nodulation may be beneficial in other ways, such as improved water use efficiency. I wonder how this benefit would figure into Ford Denison’s analysis of “cheater” strains. Myriad other factoids are presented in the review that only a legume researcher could love. If you know what “mirbelioid” means, you are the target audience. The value of knowing the full diversity of the legumes, according to the authors, is to help in the search for legumes adapted to extreme conditions for use in agriculture under a changing climate. I would also add that new agricultural legumes would be useful if they have resistance to diseases of today’s set of forage and green manure legumes.

So what is a typical legume? The legume genus Astragalus, made up of herbs and small shrubs, the milkvetches and locoweeds, contains something like 2,500 species, the most of any plant genus, but it is hardly representative of the legume family. I would have to say that this is another instance of a short question with a long answer.

the kids are alright

So organic is the new conventional.‭ ‬So voting with your dollars will not challenge the neoliberal order.‭ ‬What,‭ ‬then,‭ ‬is the path to sustainable agriculture‭? ‬Connor Fitzmaurice and Brian Gareau got down into the weeds‭ ‬–‭ ‬literally‭ ‬–‭ ‬in search of possible answers,‭ ‬and they present hope and direction in their book Organic Futures.‭ ‬In what‭ ‬reads like an extended response to Julie Guthman‭’‬s political economy analysis of organic agriculture,‭ ‬Fitzmaurice and Gareau give us a cultural anthropology study of some of the people who are forging an alternative to Big Organic.

Organic farming has gone from an alternative agriculture movement to a big business,‭ ‬with big growers hewing to the letter of the law while‭ ‬disregarding environmental,‭ ‬economic,‭ ‬and social sustainability. Yet‭ ‬there are still organic practitioners who reject the profit motive and seek to live out the values of the original movement.‭ ‬These are small,‭ ‬predominantly younger farmers who rotate crops,‭ ‬grow a diversity of cultivars,‭ ‬plant hedgerows,‭ ‬sell locally,‭ ‬and even question the USDA list of allowed chemicals.‭ ‬They are subject to the supremacy of market forces that‭ ‬constrain us all,‭ ‬but they have carved out their own space where they can put at least some of their ideals into practice.‭ ‬It is this tension between the structural and the personal that Fitzmaurice and Gareau explore with their ethnographic portrait of one small New England organic farm.

Regarding the very idea of a New England farm, an idea that might induce images of stubborn old-timers eking out a pitiful yield on rocky soil during a two-month growing season, Fitzmaurice and Gareau point out that New England farming is actually quite productive, with yields comparing favorably to those in the rest of the US, but that the fractured landscape is not conducive to the kind of big agribusiness that dominates in places like the Midwest and California. The farmers are younger, reviving the region’s agriculture after farming there came to seem unfeasible after Agriculture Secretary Earl Butz’s admonition to get big or get out. They are generally white and college-educated, a demographic that also includes a significant proportion of the farm workers there. They take advantage of a niche market where proximity to consumers and face-to-face interactions are valued.

The‭ ‬concept that Fitzmaurice and Gareau‭ ‬emphasize is that of matches.‭ ‬As small organic growers negotiate the demands of running a business with their concern for environment and community,‭ ‬they undertake many smaller negotiations with people and practices.‭ ‬When conscientious neighbors volunteer to help fill CSA boxes and get free produce as a gift of gratitude,‭ ‬that is a match.‭ ‬When‭ ‬a local restaurant appreciates the quality of the farm‭’‬s produce and makes a standing commitment to purchase part of the harvest,‭ ‬and in turn the farm gears part of its production to meet the needs of the restaurant,‭ ‬that is a match.‭ ‬When the farmer hires an‭ ‬environmental studies major with a vision of agricultural sustainability to work as a laborer,‭ ‬and then treats that laborer as a‭ ‬human being‭ ‬and a‭ ‬participant,‭ ‬that is a match.‭ ‬When the farmer uses a microbial preparation on the tomatoes to fight late blight in a wet year instead of turning to the more toxic — but organically permitted — copper spray alternative,‭ ‬that is a match.‭ ‬And when the farming couple rents out the cottage on their idyllic property to‭ ‬draw a substantial portion of their annual income in order‭ ‬to approach a middle-class lifestyle,‭ ‬that is a match.

These small matches are the everyday acts that reflect the larger‭ struggle between values, customs, lifestyle, and positive self-image on one side and the monetization of human interactions on the other. Farmers and farm workers often aspire to farming in an environmentally friendly manner and creating community. They value their connection to the outdoors. They have a need to see themselves as good people doing the right thing. However, Big Organic, largely from California, has driven down prices at the farm gate, all but wiping out the price premium that organic producers could count on to compensate for lower yields and higher expenditures on labor. Instead, the higher retail price of organic produce accrues to the intermediaries farther along in the food chain. The organic farmers profiled in the book have to depend on special circumstances to make a living, including inherited property with an easement that limits its use to agriculture and natural environment, farmer mentors, a zeitgeist where buying local is valued, personal connections to buyers and volunteers, and a non-farming source of income, not to mention one member of the farming couple having a knack for handling the organic certification paperwork.

‭One of key practices of the subject farm is their CSA, an acronym standing for Community Supported Agriculture. The practice entails selling season subscriptions to local consumers and then providing them with a weekly basket of whatever produce the farmers have to offer at that time. This arrangement provides up-front cash when it is needed at the beginning of the season, when farmers might otherwise have to take out loans. It benefits the environment by giving farmers extra incentive to plant a diversity of crops, and also giving them the ability to opt out of the use of chemicals if one of those crops should fail. It strengthens the community by bringing together neighbors who volunteer to help fill produce baskets on pickup day and giving subscribers at least some personal connection with the farmers. And it benefits the organic movement by occupying a niche that Whole Foods and Walmart have had difficulties moving into.

‭Fitzmaurice and Gareau detail the ways in which the profiled farmers take the extra effort to make their vision of organic agriculture work. They put in long hours planting, weeding, harvesting, packaging, record-keeping, negotiating. At one point they hand-pruned the flowers from a field of potatoes in order to keep bees from succumbing to the biopesticide to be used on the Colorado potato beetles. They pack extra turnips into a bunch to make a good impression on the CSA members. Perhaps most problematic, they forgo the comfort of the middle-class lifestyle that their education level might afford them and their children. Fitzmaurice and Gareau decry the disproportionate burden that small farmers must shoulder in bringing about a more sustainable agriculture.

‭From my agroecological standpoint, I paid more attention to the details of pest management than Fitzmaurice and Gareau with their sociological focus. Bt bacteria might have been the biopesticide used on the potato beetles. If so, there should have been no danger to bees visiting sprayed flowers, as the strain of Bt used on beetles would be beetle-specific. I cannot say for sure, as Fitzmaurice and Gareau do not name the biopesticide. Other pest problems on the farm included aphids on the chervil and hornworms on the tomatoes. The chervil was unsalvageable, and the more experienced member of the farming couple was considering interplanting flowers in the following year’s tomato crop to attract beneficials that might reduce the hornworm population. It is well known that more diverse vegetation reduces pest populations, and nectar sources in particular attract predators and parasitoids that kill pests. How unfortunate that young farmers with years of experience did not already know to intercrop flowers with their chervil and tomatoes. To me this was an indicator of lack of institutional support to provide education and training for farmers who strive to farm more sustainably.

‭In the end, Fitzmaurice and Gareau concede that Julie Guthman’s political economic analysis is correct. Under a neoliberal economic order, local organic produce is considered another niche market. Elite consumers make individual choices to consume status-symbol foods according to their preference, reinforcing wealth inequality, while the powerful economic players make allowances for such individualistic activity and continue to steamroll society with industry consolidation, downward pressure on wages, regulatory capture, defunding of public support for small farmers, increasing uniformity with the illusion of choice, and further exploitation of the environment. Fitzmaurice and Gareau’s philosophical answer is that any socioeconomic current that might eventually supplant neoliberalism will necessarily emerge as a component of the existing neoliberal order. As such, a movement of conscientious community-building farmers who create alternative socio-economic relationships (“matches”) might be the seed for an as-yet inchoate new economic paradigm.

‭As hopeful yet critical theorists, Fitzmaurice and Gareau make some recommendations, based on the Plentitude model‭. First is a transformation of the CSA model. The profiled farmers lamented that the CSA was not creating more community. The subscribers would show up on pick-up day, exchange a few words or hold a brief conversation, and then leave, never taking part in any of the actual farming activities. Fitzmaurice and Gareau envision a Community-Supported Community Agriculture, something perhaps akin to a community garden with professional farmers guiding it all. The consumer community would plant and care for the produce that they would harvest and eat, not in the atomized fashion that the carefully demarcated plots in existing community gardens necessitate, but as a rational agroecological whole.

‭Second is an extension of current farm-to-institution arrangements, such as farm-to-school programs. Students could go beyond enjoyment of fresh local produce by actually interning on local farms. They could earn credits for their efforts, and the institutional underwriting of such a program would provide support for the farmers and the community-building.

‭Third is an explicit inclusion of farm labor justice in organic certification, perhaps through separate third-party certifiers. Fourth is a stronger commitment by organic farms to environmental consciousness, from the number of trips CSA subscribers make to the farm, to tighter on-farm nutrient cycling and generation of energy, to cropping choices more suited to the local conditions than to consumer demand. Finally, movement organic agriculture must continually strive to remain alternative as Big Organic moves in to co-opt the innovations of sustainability, and the key to this is using community-centered development to counteract the power of money.

Anyone have other ideas?