ecologists on intercropping

Why isn’t there more intercropping?  It is common in the global south, but in the north, whereas cover cropping and rotation are mainstays of organic agriculture, intercropping is an exception.  Some authors cast doubt upon reports of overyielding, the term for an increase in total yield by a mix of crops grown together compared to the component crops grown in monoculture.  Ford Denison for one maintains that, in the intercropping studies he is aware of, the component monocrops are generally not grown at the appropriate density, and that the trials are not continued for enough seasons.  Beyond that, in mechanized agriculture the machinery is traditionally designed for monocrops, and besides a handful of crop combinations known to work well under particular circumstances, there is a shortage of research into what makes a productive intercrop.

In response, an international consortium of researchers led by Rob W. Brooker, in a 2015 New Phytologist paper that was one of the journal’s top ten most-cited papers of 2016, presents food for thought and promising directions for future research in intercropping.   These are ecologists, agronomists, and plant physiologists who look to recent advances in their fields that can be applied to intercrop design.

The basic premise of intercropping is that different species grown together can either benefit each other or escape the kind of competition that individuals of the same species would experience, through the differential use of resources known as niche complementarity, through actually helping each other by facilitation, or through more complex effects on the environment or other organisms.  The question is how to harness these effects.  One important point of Brooker et al. is that facilitative interactions between plant species predominate more in environments with greater stress, meaning conditions where environmental factors such as water, temperature, nutrients, or disturbance are significantly limiting upon plant growth, an ecological principle known as the Stress Gradient Hypothesis.  They suggest that differences in environmental stress might be responsible for variability in intercrop results.  Indeed, an advantage gained by mixed cropping in a poorer environment would be consistent with the more extensive practice of intercropping found among more marginalized farmers.

Some insight into potential avenues for improving intercropping comes from grassland ecology studies.  For instance, phylogenetic distance, meaning the degree of relatedness between species (or more precisely, unrelatedness), is a significant determinant of grassland productivity, with greater productivity found when more phylogenetically diverse grassland species are growing together.  Also, the association between diversity and greater productivity becomes more pronounced over time, an effect that is due to increases in soil organic matter and soil nitrogen, which lead to more optimum carbon and nitrogen cycling, what organic growers might call soil improvement.

Other insights come from plant physiology and plant-soil interactions.  Intercrops can show increased resource use efficiency, which is an increased production of biomass without any increase in a given input, such as light or water.  Deep-rooted plants can make use of different soil water stores than shallow-rooted plants, and can even redistribute water to their companions.  Some crops have adaptations for correcting soil pH or otherwise solubilizing minerals by exuding compounds into the soil, to the benefit of all plants in that soil.  Of course, legumes are known to interact with companion crops in terms of compensating for nitrogen removed by companion crops, and can even release nitrogen for their neighbors to take up in some circumstances.  Also, legumes shaded by companion crops generally make more efficient use of the reduced light.

In a bit more of a stretch, the field of microbial evolution finds that bacteria evolved in mixed-species communities are more productive than those evolved in monoculture.  Indeed, Brooker et al. remind us that modern plant breeding, an abbreviated type of evolution, has generally been carried out using monocultures, whereas the traits that allow a crop species to function well in an intercrop may be different from those that show an advantage in monocrop.

The consortium concludes by calling first for simply testing new combinations of crops that possess qualities already known to function in intercrops.  In regard to the machinery issue, an allusion they make to precision agriculture leaves it obvious that, with sufficient commitment, modern machinery can be designed to do anything.  Beyond that, breeding crops explicitly for use in intercrops would likely improve resource use efficiency, including selecting for traits deemed complementary and even using computer modelling of ecology research findings involving resource capture.  Meanwhile, considerations of phylogenetic distance and long-term coevolution are in need of more investigation before they can be applied to intercrop design.

Agriculture researchers, agricultural machinery engineers, and crop breeders, take note!

R. Ford Denison’s Darwinian Agriculture

I am a fan of Ford Denison.  It was his lab that reconciled the fact of the legume-rhizobium symbiosis with the evolutionary theory predicting that such a mutualistic relationship should fall apart because of cheaters.  When I saw he had a book out on agriculture I snapped it up.

Only Denison could have written Darwinian Agriculture.  As both an evolutionary biologist and a past director of UC Davis’ LTRAS, the Long-Term Research on Agricultural Systems project, he is well versed in the two fields and can evaluate agriculture trends using an analysis that is rare among agricultural scientists.  For instance, the Green Revolution was initiated by grain crop varieties that were higher yielding not mainly because they were more responsive to higher inputs, but rather because they were bred for cooperation over competition.

A plant, say, rice, growing in a field of other rice plants with different genotypes, will compete for sunlight by attempting to grow taller than its neighbors.  If the plant can capture more sunlight, it will be rewarded by having a larger share of the next generation made up of its own offspring, offspring that will carry the parent’s genes that made it competitive.  This competition for sunlight comes with a cost, however.  By expending so much of its resources on all that stem tissue, it has less left over for seed production than it would if it had no neighbors with which to compete.  Meanwhile, the neighbors are also growing taller in an attempt to improve their own reproductive success.

What if all the plants in the field had identical genes?  Competition would then be a zero-sum game, whereby the amount of extra seeds that a plant could produce by out-competing its neighbors would not increase the representation of its genes in the next generation at all, considering that the seeds they would supplant would have had those same genes.  This shared genetic fate allows for the possibility of cooperation.  If a breeder comes up with a variety that does not grow tall, and if it is grown in monoculture, it can give a higher yield than a related variety that expends valuable resources on extra stem production.

Of course growing a single variety in monoculture is problematic for other reasons.  A pest or pathogen that is able to overcome the genetic resistance contained in that variety will be able to overcome the entire field in short order.  Without a diversity of genotypes for natural selection to operate on, there can be no survival of the fittest among equals.  Also, a plant variety without a competitive drive will do poorly against weeds.  Thus, Green Revolution seeds are sold with a package of manufactured inputs to compensate.  There are other undesirable outcomes of Green Revolution technology as well, but the evolutionarily sound principle of selection for cooperation remains useful.

Perhaps the best example of selection for cooperation that Denison presents involves chicken breeding.  Chickens are evolved to be individually competitive as much as plants are, and they will peck at each other to the point of reduced overall egg output.  One investigator, however, had the idea of selecting not the best individual chickens for breeding, but rather the best groups.  Chickens were kept in pens of four individuals, and the ones allowed to breed were those with the greatest number of eggs per pen.  In six generations fighting was way down and egg production was up.  Through group selection chickens were bred to be cooperative.  The key was to measure the output of groups rather than individuals, a principle that could be applied to small plots of crops as well.

Denison also returns to the example of cooperation in the legume-rhizobium symbiosis.  Legumes produce nodules on their roots to host bacteria that can convert atmospheric nitrogen into nitrogen fertilizer.  The plant rewards the nodule-dwelling bacteria, collectively known as rhizobia, with food that it produces from photosynthesis.  It would seem like a beneficial relationship to both partners, but any bacteria that could harness the plant’s feeding system without going through the trouble of producing fertilizer would do even better.  These “cheater” rhizobia are common, and evolutionary theory predicts that they should have long ago displaced beneficial rhizobia unless the plant could somehow pick and choose among rhizobia strains.  Denison and his students showed that legume plants can indeed punish a poor-performing strain enclosed in a single nodule, causing that strain’s reproduction to suffer.  However, because of various considerations, detailed in Professor Denison’s explanation of the Hamilton r coefficient, the legume’s sanction system is only just good enough to get the fertilizer it needs for the current season, leaving plenty of poor performers in the population that is released back into the soil.  With this in mind, Denison comes up with a scheme for breeding legumes for stronger sanctions, involving the use of a test crop to evaluate the legacy rhizobial benefit left by the previous season’s plant, and then going back to breed from the seeds that had been collected from the plants that were subsequently shown to have left the most beneficial rhizobia behind.

Denison has an opinion on genetic engineering of crop plants that is different from most.  He is not opposed to genetic engineering in principle, but maintains that most such research will have little to show for the vast sums of money spent on it.  The reason is that the kinds of intervention that are possible by tweaking genes have already been tried over millions of years of evolution and thousands of years of coevolution, and any unequivocally beneficial simple modifications have already been adopted.  Additional modifications involve tradeoffs and are not likely to make a significant difference.  He does leave open the possibility of modifications that are too complex for evolution to have stumbled upon, such as re-engineering the chloroplast to recycle the byproducts of photorespiration, but most modifications of that level of complexity are beyond the scope of genetic engineering.

My biggest complaint about the book is the straw man that Denison sets up to provide a false balance for his critique of genetic engineering.  He selects some of the philosophers of alternative agriculture such as Wes Jackson and uses them to stand in for the science of agroecology.  He then provides a very reasoned scientific critique of some philosophical exhortations to farm using nature as a model to mimic, using his arguments to attack a certain conception labeled “agroecology” while ignoring the science of agroecology as actually practiced.  Agroecological scientists do indeed look to natural systems − as well as to traditional agriculture − for principles that can be used for improving modern agriculture, but then they test any ideas that come from such an examination.  That is what makes agroecology a science, and Denison even advocates for this kind of examination and testing.

Throughout the book I find many other points that I want to respond to, but on the whole the work is valuable, and a blog post cannot fully do it justice.  Denison is a very accessible writer, and part of the book is background on agriculture and on evolution for the uninitiated.  The text is peppered with interesting tidbits, such as the wasp that can smell when a butterfly is about to lay eggs and pursues her or hitches a ride on her to parasitize those eggs after she has left them.  Most importantly, though, agriculture cannot escape the principles of evolution, and Denison has provided plenty of food for thought.

biocontrol hits the dirt

Biocontrol agents targeting soilborne plant disease organisms have not lived up to expectations,‭ ‬according to a new review by Mark Mazzola and Shiri Freilich in the journal Phytopathology.‭  ‬Whereas classical biocontrol‭ ‬−‭ ‬the release of a pest‭’‬s natural enemy into an agricultural system to control that pest‭ ‬−‭ ‬has‭ a long string of ‬proven successes in the control of aboveground pests,‭ ‬there has been only limited success of species introductions into soil for controlling disease-causing organisms.  Typically a biocontrol agent introduced into soil will have a very low survival rate.

From an agroecological standpoint,‭ ‬the failure of introduced species to establish a presence in soil is not a surprise.‭  ‬Any two areas of soil can have multiple differences,‭ ‬including sand and clay content,‭ ‬mineral type,‭ ‬organic matter level and composition,‭ ‬vegetation history,‭ ‬water regime,‭ ‬microflora and‭ ‬-fauna,‭ ‬and even crop genotype,‭ ‬all of which can affect survival of a microbe.‭  ‬The existing microbial community is the one that makes the most sense for the particular set of conditions,‭ ‬and the conditions change over the seasons.‭  ‬As microbiologists like to say,‭ ‬everything is everywhere,‭ ‬and the environment selects.‭

This observation reminds me of the time when as a teenager I saw a play by Anton Chekhov.‭  ‬Everyone in the play was leading a troubled life,‭ ‬and no one seemed capable of breaking out of the‭ ‬established pattern and doing what would make them happy.‭  ‬I didn‭’‬t like the play,‭ ‬and I wished I could walk into the scene and tell everyone what they should do:‭  ‬“He loves you‭ ‬−‭ ‬stay with him.‭”‬  “He‭’‬s fragile‭ ‬−‭ ‬be more gentle with him.‭”‬  “Don‭’‬t try to be what you are not just to impress them.‭”‬  An alternate,‭ ‬more mature assessment‭ ‬is that if I‭ ‬somehow‭ ‬ended up in that setting with those characters,‭ ‬I would likely be caught up in the same malaise and change nothing.

So it is with those microbe additions.‭  ‬You introduce a promising strain of‭ ‬Pseudomonas into a soil system,‭ ‬one good at controlling disease in potting medium,‭ ‬and it gets lost in the crowd,‭ ‬unable to mount a takeover of the existing microbial community because it finds the physical conditions unaccommodating or gets overwhelmed by the other characters in the community.

Fortunately,‭ ‬Mazzola and Freilich present a proven alternative.‭  ‬If you change the environment using certain management options,‭ ‬you can select for a microbial community that is suppressive to disease.‭  ‬One example is anaerobic soil disinfestation,‭ ‬a radical alteration of the soil environment where‭ ‬the grower incorporates a carbon source like rice bran or alcohol into the soil,‭ ‬saturates it with water,‭ ‬and covers it with plastic.‭  ‬Anaerobic bacteria use up the oxygen and produce organic acids,‭ ‬killing pathogens.‭  ‬Another example is biofumigation,‭ ‬where mustard seed meal or other mustardy residues are incorporated into the soil,‭ ‬hitting the pathogens with‭ ‬a‭ ‬fatal‭ ‬wasabi-burn.‭  ‬Even after treatments are completed and the crops planted,‭ ‬there is‭ ‬a‭ ‬lasting effect of pathogen suppression, an outcome not found with chemical fumigation.

The reasons for the continuing benefit from these treatments are complex, as expected, and still being worked out.  There is evidence pointing to an advantage given to endemic microbes, and suggestions that some microbial groups that are associated with biological control make up an increased proportion of the surviving microflora.  There is evidence that the carbon source used for creating an anaerobic environment can make a difference in the microbial groups selected.

Beyond soil treatments, there can be other ecological interactions that contribute to soil disease suppression.  Root secretions from plants of certain genotypes can foster the proliferation of pathogen-suppressive bacteria populations.  Plant genotypes can interact in a complex fashion with soil management interventions.  Is it any wonder that a reductionist approach involving isolation of a microbial strain from a disease-suppressive soil, quantifying the antagonism that it possesses toward a select pathogen in the lab, and releasing it into a novel soil environment will fail in so many cases?  An agroecological approach, taking into account the multiplicity of factors that are operative in soil, is crucial for managing soil disease in a real world situation.

And the next time you see a‭ ‬Chekhov play,‭ ‬sit back and enjoy the way the characters struggle within the bounds of their milieu, and then reflect on what difference you can make in your own world.

cover crop rotation

Can you grow the same cover crop year after year?  Harvested crops get rotated to prevent soil buildup of pathogens toward any single crop species.  When it comes to cover crops, though, the standard for my area is a mix of bell beans and barley.  Variations on the theme exist, with oats, rye, or wheat being substitutable for the barley, and even peas or clover taking over the role of nitrogen fixation in place of the bell beans.  The trouble is, the grains are all members of the grass family, and the nitrogen fixers are all in the legume family.  If you grow a legume-grass cover crop every year, shouldn’t the soil build up diseases of legumes and grasses?  If cover crop rotation is necessary, what non-grass could function as a grass?  And does a nitrogen-fixing non-legume crop even exist?

Maria Finckh and her colleagues have a handle on the subject, in two chapters in the compendium Plant Diseases and Their Management in Organic Agriculture.  Yes, bell beans do get soilborne diseases.  Yes, they share diseases with other legumes.  One pathogen, Aphanomyces euteiches, the cause of pea root rot, has spores that can survive up to 14 years in soil and threatens pea production in France.  And yes, small grains share diseases − even weedy grasses can harbor some of these diseases.  Organic and sustainable farming are completely dependent on nitrogen fixation by legumes, even for manure production by livestock.  What is a grower to do?

Fortunately, Finckh and colleagues have suggestions for disease management in legumes and small grains.  For annual legumes, it is advisable to plant these in only three years out of a six-year rotation, counting both harvested and green manure species, and it is critical to never use the same species back-to-back as a green manure and a harvested crop.  Perennial legumes should be grown for a maximum of three years.  There are some pathogens that target dicots in general, so grass family crops are a good choice to follow a legume (or presumably non-grass monocots like garlic, asparagus, or others).

Regarding the sharing of pathogens, there are some with very broad host ranges, some that target only a single species, and just about every possibility in between.  Bell beans are subject to chocolate spot disease.  Their recommended rotation frequency is 4-6 years.  Clovers get clover scorch and clover rot, but white clover is generally resistant to these.  There are diseases that affect alfalfa but not its close relative black medic.  Soybean is susceptible to few diseases of the other legumes, and its recommended rotation time is the shortest, 0-3 years, while that of peas is the longest, 6-7 years.  The pea root rot pathogen can infect many legume species, as well as beets, but it is peas that sustain the greatest damage.

One legume has me intrigued − serradella, Ornithopus sativus.  I had never heard of this, but based on the legume-disease matrix presented in the chapter, this species gets none of the common legume diseases.  It is less cold-hardy than some legumes, but evidently it is well suited to a maritime Mediterranean climate, as there is a feral population reported in Santa Cruz County.  However, it seems that the seeds are commercially available only from Australia or South Africa.

Regarding small grains, the advice is less involved.  Rye and barley can harbor the pathogen that causes take-all of wheat, so wheat should never follow rye or barley.  Oats, however, are resistant, and they may be suppressive to diseases.  Non-grass, non-legume cover crops include mustard-family crops, Phacelia tanacetifolium , and flax.  I have been trying out Phacelia, a member of the water-leaf family, as a green manure, and it is giving me good stand coverage where it has established.

Planning out a cover crop rotation is an important component of disease management, but it is best complemented by disease monitoring and identification, which will give a clearer indication of what crops can follow.  Beyond rotation, there are cultural recommendations for disease management.  Because many pathogens are persistent in crop residues, one should insure effective residue breakdown.  A healthy soil microbiome fed by plentiful organic matter from a variety of sources and crop types can be antagonistic to soilborne pathogens.  Wet or waterlogged conditions will promote certain diseases.  Some pathogens are seedborne, and thus a sanitary source of seeds is important.  For some diseases, particularly mildews, mowing is helpful, and even in the case of clover rot a late fall mowing may save some of the crop.  Planting mixtures can reduce disease.  And the dreaded pea root rot?  If you have a history of this and are thinking of planting peas again, the soil should first be bio-tested.

Bart Thomma on Verticillium

Bart Thomma gave an interesting talk on‭ ‬Verticillium dahliae,‭ ‬the pathogen that causes verticillium wilt, able to attack most broadleaf plants.‭  ‬The strains that are pathogenic owe their virulence to the gene with the code name‭ ‬Ave1.‭  ‬This is the gene that turns the plant‭’‬s defense system off.‭  ‬The interesting part is where‭ ‬the pathogen got that gene.

Thanks to advances in DNA sequencing technology, there are genome sequences of hundreds of species searchable on the web.  Genes that are very closely related to Ave1 are also found in a few unrelated fungal pathogens and a bacteria, but they are found most widely in plants, where they regulate water relations by controlling the opening of leaf stomates.  This evidence suggests that Verticillium dahliae (V. dahliae for short) picked up a copy of the gene from a plant it was living in and incorporated it into its own DNA.

How unusual, Thomma thought, that the pathogen should overcome the plant’s defense response by stressing it through dessication.  The gene product definitely had the machinery for controlling stomates.  The trouble was, when the Thomma lab modified the fungus, substituting stomate-opening genes from other species for the Ave1 gene, the fungus could no longer cause disease in the plant.  Stomate control was not the mechanism by which the fungus defeats the plant.

This led Thomma to approach the issue the hard way, adding the Ave1 gene product to a solution of plant cell components to see what it interacted with.  With the use of specially tailored antibodies, the interacting plant proteins can be pulled out of solution and then characterized.  This approach is hit-or-miss, but in this case there was a promising hit — plant chitinase.

Fungi have cell walls made of a tough substance known as chitin.  This is the same chitin that makes up insect and crab exoskeletons, but it evolved independently in fungi.  Chitinase, as signified by the “-ase” ending, is an enzyme that dissolves chitin, giving plants an important defense against fungi.  With further investigation, the Thomma lab found that the Ave1 gene product indeed has a powerful capacity to inhibit chitinase.

My jaw dropped.  The fungus got hold of a plant’s stomate-regulation gene, and it evolved a chitinase-inhibiting function.  That would be like buying a used windowsill air conditioning unit, tinkering with it to make it function as a dashboard radar detector, and yet still keeping its cooling capacity!  The gene ended up in the rapid-evolution portion of the fungal genome, the 3-12% of the genome where the fungus allows mutations to happen without constraint, where once in a great while evolution’s workshop comes up with an innovative weapon that disables the plant’s arsenal.  The lucky fungal strain uses such a newfound advantage to proliferate in the environment, and a new plant disease is born.