what’s wrong with my plants?

A year and a half ago I moved into a place with a yard. The yard had been neglected, and I was determined to beautify it. I planted both seeds and potted plants, and I can’t help noticing that there’s something wrong.

For one thing, the majority of the potted perennials died. They were purchased locally and consisted of plants adapted to the xeric conditions here. The annual wildflower seed mix did better, and had the curious property that different species bloomed in the different areas of the yard, even though all the areas received the same mix. Most notably, the wildflower patches in the back became dominated by the decorative flax, with two lupine species also doing well, but the other plants were stunted. The grass seed I sowed in the bare spots in the back lawn came up like tiny threads that never filled in the spots, but the perennial clover seed has grown aggressively. I love a good mystery!

Here are some of the clues: The houses in the neighborhood were built when modernist architecture seemed appropriate for living in — the 50s and 60s. Before that it was farmland. The soil is a swelling clay that shifts the foundation and distorts the door frames when it’s dry. The back lawn had suffered from drought when I got here, with only clumps of the hardiest grass surviving, although the lawnmowing service continued biweekly. The other parts of the backyard were covered by bark on top of weed cloth, with three stonefruit trees and a rosemary bush growing in openings in the cloth; I pulled up patches of the bark and cloth for the new plants.

I admit guilt in the death of one shade-loving perennial. I planted it under the the big tree in front, only to watch the the tree drop its leaves and the winter sun slip its rays under the branches to cook the poor plant. Another perennial turned out to be frost sensitive. Four other ill-fated perennials, however, seemed to do well until the summer, when they showed some wilting in the heat. I watered them, and they further wilted and died.

When I saw how well the lupines – native legumes – grew in the back, I planted two legumes from the faraway prairie – an annual and a perennial. The annual was stunted, and the perennial did not survive past seedling stage. Also showing stunting was the existing peach tree in the middle. One of the lupine plants collapsed suddenly while flowering. And now in the second season I see that one of the patches in back has taller and greener flax on the edges, while in the middle the flax is shorter and yellower.

What could be the matter? My first thought was nitrogen deficiency. Years of farming may have left the soil degraded, and biweekly removal of the grass clippings would have robbed the lawn of the nutrients the grass had been able to scrounge up. Clover and lupine do well under nitrogen-limited conditions because they harbor nitrogen-fixing bacteria in their roots. If nitrogen were plentiful in the soil, the grass would be expected to out-compete the clover, but a pioneering study by Stern & Donald working in Australia in the early 1960s showed that clover will win the competition if nitrogen is low, thanks to that self-fertilizing capability. The back lawn seemed like a clear example of this second scenario.

What about the other stunted plants? Could they also be suffering from nitrogen deficiency? Shouldn’t the prairie legumes have done better with their own supply of nitrogen fertilizer? Maybe not. These two species host different strains of nitrogen-fixing bacteria from those of clover or lupine. The clover seeds came coated with their preferred strain. The lupines, growing in their native range, might have found suitable strains already present in the soil. Perhaps the prairie legumes, far out of their range, found no bacteria they could work with and ended up starved for nitrogen.

Nitrogen deficiency might also explain the shorter yellower flax plants in the center of the one patch. The plants on the edge presumably have access to soil outside the patch where no competing plants are growing. It is conceivable that a dose of extra nitrogen from the outside would give these edge plants a darker green color and an extra increment of height.

So is the nitrogen limitation hypothesis correct? What about some of the other observed phenomena, like the vigor of the flax, the collapsing lupine, or the lack of history of mowing in the formerly mulch-covered seedbeds? Considering the lupines again, these are unusual among legumes in that they do not form mycorrhizae, the mutually beneficial relationship in which specialized fungi grow within a root and extend out into the soil, helping the plant take up phosphate and other minerals in exchange for sugar from the plant. Non-mycorrhizal plants have roots that use other tricks to maximize phosphate uptake. Is there a way that this peculiarity could be involved in the differential growth?

As a first approximation, the mycorrhizal symbiosis is win-win arrangement, but deeper investigation has shown that different fungal strains vary in the amount of benefit that they provide the plant. Some cheater strains take the sugar and provide no benefits at all. Fungal strains that produce lots of spores are thought to be expending energy on these survival structures at the plant’s expense. Ecologist Jim Bever presented findings that a plant can tell if a root has been taken over by a cheater strain and can respond by shutting off the sugar spigot. This defense fails, though, when there is a mix of strains on a root and the plant can’t distinguish the cheater. The specialized fungi, for their part, have to be connected to a plant root to live.

The history of farming on this soil might have left a predominance of cheater strains. Farm fields often remain fallow at the end of harvest, leaving no crop roots and not even many weed roots to allow for the continuity of living mycorrhizal fungi. Instead, spores from more selfish strains are left to sprout when the next crop is planted. The mixing of the soil from tillage would have left the plants confused as to which were the cheater strains. Additional years of weed cloth cover might also have been particularly hostile to all but the spores from the selfish strains, with only the occasional stonefruit root supporting its isolated bloom of living mycorrhizal fungi. In such a situation the non-mycorrhizal lupine, carrying no burden of cheater strains, might be expected to have an advantage over mycorrhizal plants. Are there other non-mycorrhizal plants that might provide supporting evidence for the hypothesis of deleterious or absent mycorrhizal fungi? As a matter of fact, a closer look at the flax-dominated patches reveals a second layer made up of flowering sweet alyssum, a plant in the famously non-mycorrhizal mustard family. The other plant species in the mix are expected to be mycorrhizal, and these are stunted.

Except the flax. Does the flax disprove the hypothesis about absent or cheater mycorrhizal fungi? Not necessarily. Ecologist Nancy Collins Johnson showed that spores of mycorrhizal fungi found in soil after a soybean crop were parasitic on soybeans but beneficial on corn. And the grande dame of mycorrhizae research Sally Smith pointed out that some plants will form mycorrhizae without showing a growth difference. The flax might just have a different response to the mycorrhizal fungi in the soil from the other mycorrhizal plants.

While I’m exploring alternative hypotheses, I should consider the obvious. After years without plants, the covered patches would have lost organic matter. The soil foodweb would have unraveled, losing decomposing organisms ranging from microbes to earthworms. The soil would have compacted. Roots would have a harder time penetrating, and they would be short of the oxygen necessary to do their work. The plants might very well show stunting in compacted soil. Might the flax, the lupines, and the sweet alyssum just be better at dealing with compaction than the other plants?

Another possible cause of growth abnormalities is allelopathy, the inhibition of plant growth by plant-derived chemical compounds. The stunted peach tree happens to be right next to the rosemary bush. There are documented cases of aromatic plants inhibiting the growth of other plants around them through the chemicals they exude, such as the work of ecologist C.H. Muller on chaparral plants. My husband once got a splitting headache from breathing in the fumes of a rosemary plant he was chopping out – I wonder if anyone has tested the effect of rosemary fumes on the growth of peach trees. Another source of allelopathy could be the bark mulch. Decaying organic matter can release compounds that inhibit plant growth, and some of the better known of these compounds are breakdown products of lignin and hemicellulose, such as would be found in bark. Growing plants exposed to these cell wall components have their tissues prematurely hardened, often leading to a visibly pinched stem. Indeed, I saw a pinched stem on a second-season lupine growing from a seed that had fallen into the bark mulch. It was growing in the shade, and it collapsed as the changing sun angle in spring exposed it to more drying conditions. Might those compounds also have leached through the weed cloth and remained in the patches of soil, causing stunting of some of the other plants? Several of the species that failed to thrive in the formerly mulched areas bloomed beautifully in the other areas.

And then there are nematodes. The conventional wisdom for diagnosing a plant-parasitic nematode infestation, at least among non-nematologists, is that if a patch of plants fails to thrive, and if other factors such as nutrient deficiency or disease can be ruled out, suspect nematodes. These thread-like microscopic worms can damage roots and cause yellowing or stunting of plants. Whereas wildland soil also contains predatory nematodes that hunt down the plant-parasitic nematodes, agricultural chemicals will kill off the predatory nematodes, according to nematology professor Howard Ferris, leaving intact the populations of plant-parasitic nematodes. Interestingly, there was a study by Widmer and Abawi out of Cornell University that found green manure of two types of flax to be suppressive of nematodes due to the production of cyanide from chemical reactions in the chopped leaves. If the roots of the decorative flax could produce cyanide to deter nematode attack, then nematodes might be a neat explanation for the stunting of the other species.

None of these hypotheses are good explanations for the wilt-water-die pattern of the transplanted perennials, though. This pattern is a known phenomenon among some plants adapted to dry summers, such as members of the Protea family. Such plants may be champions of reaching and conserving water, but they are lacking in defenses against Phytophthora, part of the group of organisms known as water molds. As the common name suggests, pathogenic Phytophthora species take to water like a fish, producing spores that swim through saturated soil toward roots they sniff out. The pathogen that germinates from these spores rots the root it infects, interfering with water uptake. The amount of infection, coupled with warming temperatures, can reach a point where the plant wilts. The pathogen is favored by excess water, warmer temperatures, and neutral or alkaline pH. If you give a plant suffering from a Phytophthora infection lots of water when it wilts, the swimming spores will worsen the infection. Did I do that to those dry-adapted perennials?

There are other notable wilt pathogens. I once watched a pumpkin plant collapse over the course of an afternoon of gardening. A plant pathologist told me that it was probably Fusarium, a type of fungus that is the bane of organic farmers due to its ability to thrive in fertile soil high in organic matter. Some other wilt pathogens are Verticillium, Pythium, Armillaria, and Rhizoctonia, which are, respectively, a Fusarium relative, a water mold, a mushroom, and a mushroom relative.

The suspect lineup now includes wilt pathogens, plant-parasitic nematodes, allelopathy, compaction, cheater mycorrhizal fungi, and nitrogen deficiency. How would one single out the true culprit? An examination of roots would reveal whether pathogens were causing rot or nematodes were leaving lesions or cysts. In the case of the legumes it would also show the extent of nodules of nitrogen-fixing bacteria. Nitrogen deficiency in the soil could be revealed by a soil test. Compaction is measured using a penetrometer, but establishing the effect of the level of compaction on the growth of plants would take an actual experiment growing those particular plants in the compacted soil versus in a soil exactly like it minus the compaction. Allelopathy is tested by collecting the compounds using foam or resins that absorb them and then growing the plants in the presence or absence of the extracted compounds. Testing for cheater mycorrhizal fungi would involve isolating the strains of fungi out of the roots, a tricky endeavor given the inability of these fungi to live without a connection to a plant root, but doable. The plants would then be grown with or without the isolated strains to see if there is a growth difference.

And after all that work, it might turn out that several or all of the culprits had ganged up on the plants. Fortunately the solutions to all these problems are found in agroecology or ecology. Since the legumes are producing their own nitrogen fertilizer, they are increasing the amount of nitrogen in the yard. Recycling of lawn cuttings and other materials will counter the loss of nitrogen and nutrients, either through using them as mulch or in compost. Simply growing plants will eventually ease compaction, and if a diversity of living host plants is always available, any beneficial mycorrhizal fungi present will get a boost over spore-formers. Avoiding soil disturbance will also advantage the beneficial fungi. Growing resistant plants is one of the best strategies for dealing with nematodes and soilborne diseases. Planting a diversity of plants will help insure the presence of some resistant types, and the mechanism of environmental filtering will eliminate the susceptible ones. If any predators of nematodes are present, they will be conserved by avoiding the use of agrochemicals. There is even some research being done on organisms that eat soilborne pathogens, such as the recent paper by Pei Zhang and colleagues working out of North Carolina State, who found that a fungus-eating species of nematode and a fungus-eating species of springtail were able to reduce the loss of tomato seedlings to a common species of Pythium in a laboratory setting. Such fungus eaters can be encouraged to multiply in soil by organic matter addition (I know, Pythium is a water mold, not a fungus, but don’t tell the fungus eaters). As for allelopathy, I recall that there is a protective effect of greater plant biomass, such as larger seeds and higher plant densities, which seems to dilute the inhibitory compounds.

Did I miss anything? Would you do something different? Let me know your thoughts in the comment section. Now if you’ll excuse me, I have some yardwork to take care of.