How Plants Tell Time - How Plants Work (2015)

How Plants Work (2015)

6 How Plants Tell Time

LIKE CLOCKWORK, the butter-and-cream daffodils in my garden are the first flowers to open, followed quickly by a painter’s palette of tulips, crocus, and irises. As spring expands into summer, lilacs and rhododendrons give way to gladiolas and asters. Flowers like clematis make a quick but stunning appearance, whereas others seem to flower all summer long, like my heavenly scented daphnes and gardenias. Taking the lead from the U.S. Postal Service, neither snow nor rain nor heat nor gloom of night stays these couriers from the swift completion of their appointed rounds. How do plants know when to grow and flower? How are they able to tell time?

Paul Simon begged mama not to take his Kodachrome away, and plants could make the same plaintive request about their phytochrome. Just like film, phytochrome changes when it’s exposed to light, and it’s these biochemical changes that allow plants to tell time. It’s because of phytochrome that plants know when to burst into bloom, when to fan out those new leaves, and when to pack it up for the year and go dormant.

Yes, we’re going to get into biochemistry again. But this time you don’t have to worry about complicated reactions and enzymes. We’re going to discover how different colors of light can transform phytochrome, and we’ll follow the amazing changes it causes in plant behavior.


Sunlight includes ultraviolet, visible, far-red, and infrared radiation.

Phytochrome: A Pigment for All Seasons

Phytochrome literally means plant pigment. Obviously it’s not the only one, but apparently people who name pigments ran out of clever ideas after naming chlorophyll (meaning green leaf), carotenoids (meaning carrot-like, referring to the orange color), and anthocyanins (meaning blue flower). This pigment is found in leaves but is not involved at all in photosynthesis. Instead, its value lies in being a shape-shifter and triggering some important changes inside the plant.

When phytochrome sits in the dark for a period of time it slowly reverts to a form that’s called phytochrome red or Pr for short. The name refers to this form of the pigment’s affinity for red light. After red light has been absorbed, the pigment quickly morphs into another form called phytochrome far-red or Pfr. As before, this is shorthand for what type of light this form of phytochrome absorbs. You can think of phytochrome as nature’s little mood ring, but it’s sunlight that triggers the response rather than emotions.

Okay, what the heck is far-red light? Let’s visit my spring garden to figure this one out. The sun’s shining, though scattered rainclouds threaten to drive us back inside. Suddenly a rainbow appears, the happy result of sunlight being segmented into distinct bands of color by prismatic raindrops. We’re able to see the range of color from red on top to violet below, but there are also wavelengths beyond what our eyes perceive. On the inner edge of the violet arc are the invisible ultraviolet wavelengths, while the outer red arc of the rainbow fades into the aptly named far-red wavelengths. We can’t see them, but plants can sense their presence.

Far-red light is not used for photosynthesis, although red light definitely is. And it’s exactly this fact that makes far-red light such a useful indicator for plants. Leaves contain lots of phytochrome molecules, and what’s important is the ratio of its two forms. If there is abundant red light—in other words, if full sun is striking the leaf—then most of the phytochrome will be in the Pfr form because red light converts the Pr form to Pfr. On the other hand, if there’s more far-red light than red light available—for instance, red light has been captured by a canopy of actively photosynthesizing leaves above the plant of interest—then phytochrome will be primarily in the Pr form. Put very simply, phytochrome tells plants whether there is enough of the right kind of light needed for photosynthesis, and plants respond accordingly. Let’s look at some of these responses in the garden, starting with every gardener’s bane: weeds.


Phytochrome changes form depending on what type of light it absorbs. When the plant sits in darkness for some time, Pfr reverts to Pr.


Though I put a thick layer of nice, chunky organic mulch down every year in my landscape, there’s always a patch or two where the wood chips get dislodged. I don’t notice until a crop of annoying weeds seems to explode from this bare patch of soil. I know the weed seeds were there all along, so why didn’t they grow through the mulch?

Many weeds, as well as desirable plants, have fairly small seeds. This is an important trait for immobile organisms like plants, which don’t have an easy way to farm the kids out. Small seeds are more easily blown by the wind or carried by water away from the parent plants. But small seeds also have small food reserves, and woe to the seedling that starts growing without enough sunlight to get the photosynthetic machine cranked up before reserves run out. These small seeds tend to be photodormant, meaning they will not grow unless they’re exposed to photosynthetically useful light.


When mulch layers become too thin, light will cause weed seeds to germinate.

Buried under a thick mulch layer, seeds receive very little red light, so their phytochrome ratio is skewed to the Pr form. This puts the brakes on any tendency the seeds might have to start germinating, even if water, oxygen, and nutrients are sufficient. So the seeds wait patiently, sometimes for months or even years, until the day when the mulch layer is disturbed enough to let sunlight filter through. Then boom! It’s off to the races, with the seedling growing frantically in an effort to get leaves out into the sunlight and start cranking out the carbohydrates before the pantry is bare.

Gardeners have personal experience with this phenomenon when they plant their vegetable gardens. Just look at the instructions on seed packets of lettuce, radishes, or carrots. These tiny seeds should barely be covered by soil, because they need sunlight to break their dormancy. On the other hand, the large seeds of plants like corn, beans, or peas can be buried quite deeply. They have sufficient levels of starchy food reserves to feed the developing seeding, so they’re not as influenced by light levels as their photodormant companions.

The photodormancy phenomenon is another good reason not to excessively work up your soil before planting. Not only does this destroy soil structure and hurt the roots of nearby trees and shrubs, it also brings huge numbers of weed seeds to the surface. Soils contain seed banks. Whenever you dig up the soil you are making a big withdrawal from these banks—right into your garden.

Seasonal Dormancy

Many small-seeded plants, both weeds and desirables alike, are also seasonal in their emergence. For instance, many of the weedy grasses and relatives like wild onions are spring annuals, meaning they germinate in the spring and grow into the summer. Others, like the wickedly sticky bedstraw, are winter annuals that germinate in the late summer or autumn and grow through the winter. (Fun fact: the tiny curved hooks found on bedstraw are similar to those on burrs, which were the inspiration for the invention of Velcro.) Seeds of seasonal annual weeds can sit there in full sun and not germinate if the season’s not appropriate, even if there’s sufficient water and warm temperatures. What keeps them in this holding pattern?

For seasonally dependent photodormant plants, the presence or absence of useful sunlight is not the only trigger controlling germination. They also need a clue to what time of year it is. As gardeners know, rainfall and temperature can vary wildly throughout the year and even from day to day. Plants need a more reliable system of figuring out when it’s time to start growing.

Watering and Dormancy


Decreasing irrigation in autumn to prevent late-season growth and encourage dormancy.


Lack of water will slow plant growth and force them into dormancy, similar to what occurs in many ornamental bulbs, corms, and tubers.


Trees and shrubs begin preparations for winter way back in the summer, when days stated getting shorter after the summer solstice. These changes are mostly internal, though you can see overwintering buds forming on many species. Curtailing water during this important physiological process injures the plants. In fact, insufficient summer and autumn irrigation is one of the reasons for poor bud bloom the following spring. Too little water in autumn can cause early leaf drop, meaning fewer resources for the plant to store over the winter. Fine roots die back and soils become less biologically active without water. Dry soil is also less insulative than moist soil.

Keep your plants and soils well watered into autumn. When you start to see the normal leaf color change, that’s your cue that winter dormancy is kicking in. Then you can probably put away the garden hose.


Plants need water all year around. Don’t cut back in autumn.

Once again, phytochrome’s ability to switch back and forth between forms is what plants depend on. In this case, however, the phytochrome shift is used to measure relative amounts of light and dark during a 24-hour period, what scientists call a photoperiod. Nearly all life forms on Earth have an internal clock or circadian rhythm (circa means about, and dian refers to day, so a circadian rhythm is about 24 hours). Let’s see how plants can use phytochrome shifts to figure out what time of year it is.

I’m not in my garden much on December 21, because it’s cold, wet, and, where I live in Seattle, dark for most of the day. This is the winter solstice, the shortest day of the year for those of us in the northern hemisphere. (In the southern hemisphere, June 21 is the shortest day, and for those living on the equator, there’s not much difference between the longest and shortest days.) Anyway, back in my Seattle garden, we get about 8 hours of daylight on the winter solstice. By the spring equinox on March 21 the whole world is getting exactly the same amount of light and dark (12 hours of each), and both my plants and I are starting to make appearances in the garden. On June 21, the summer solstice, we have about 16 hours of glorious daylight, and by the autumnal equinox on September 21 we’re back to equal day and night. And both my plants and I are thinking about cocooning through the upcoming winter months.

The important thing about this pattern is that it’s exactly the same, year after year, and this pattern of changing ratios of light and dark is what phytochrome measures. Remember, the Pfr form of phytochrome is changed to the Prform either by far-red light (a rapid process) or by darkness (a slow process). During the summer, plants have an abundance of Pfr phytochrome in their tissues, while in the winter they have more of the Pr form. This ever-changing ratio of Pfr to Pr can tell plants exactly what day it is, which allows annual seeds to tell if it’s the right season to start germination.

Observant gardeners will point out that not all spring annuals starting growing on exactly the same day, even those of the same species. That’s because phytochrome is only part of the alarm clock. The other part of the wake-up process includes warm temperatures, sufficient water, soil chemistry, and lots of other environmental factors that vary from place to place.

Sleeping Beauties

Internal clocks aren’t just for waking up, they’re also part of going to sleep. For plants, this means going dormant and existing in a state of suspended animation. We’ve just seen that seed photodormancy is controlled by the absence of red light. Your lawn will stop growing if you forget to water it, but as soon as you add water, off it goes again. Unlike these examples, however, true dormancy is controlled by the internal clock, rather than by some environmental factor like sunlight or water. Dormant plants will sleep, Rip Van Winkle style, until their internal alarm wakes them up.

My own garden is filled with plants that live more than one year. The trees, shrubs, herbaceous perennials, bulbs, and groundcovers all go dormant in autumn. In Seattle and other regions of the world where freezing temperatures are common, dormancy occurs in the winter. Plants in other areas such as deserts and grasslands may go dormant in the summer, when temperatures are high and water is scarce. But as we discussed earlier, rainfall and temperatures are unpredictable: it’s not unusual to have warm, sunny days in the winter or to have unexpected rainfall during the dry season. Dormancy allows plants to ignore these unseasonal temptations and remain prudently asleep. Species that weren’t dormant would joyfully burst forth, only to be gunned down by the next hard freeze or extended dry period.

Let’s look at what happens to my collection of rhododendrons through the seasons. In the spring, the flowers are the first to emerge from their buds—cautiously if it’s still cold and more vigorously if we’re having a warm spring. As the trusses fade, the leaf buds begin expanding and the year’s vertical growth is quickly added through June. By midsummer, expansion has virtually stopped and the shrubs settle into mass photosynthetic production. I can also watch next year’s flower and leaf buds emerge and swell during the long, warm days of summer. By autumn, the bud scales are starting to harden and soon everything is fully protected from harsh winter temperatures. Plant physiologists call this state cold hardiness.


In spring, rhododendron flowers emerge after a deep winter’s sleep. Leaves produce sugars all summer long as next year’s buds begin to form. In autumn, the rhododendron is ready for the first cold night to initiate dormancy. Though the plant is dormant, evergreen leaves continue to produce food on sunny winter days.

More important to my rhodies’ survival is what I can’t observe, what’s going on inside. Once June 21 has passed by (all too soon!), my shrubs start preparing for winter. The days are already getting shorter, and phytochrome rings the warning bell that winter is on the way. The biochemical processes that get plants ready for winter are complex and time consuming, so they must start long before autumn arrives. When night temperatures begin to dip low enough, the rhododendrons are ready to add the final touches to becoming fully cold hardy.

This same scenario is played out by every tree and shrub in my garden. The timing varies, of course. My rhododendrons have long stopped growing, while my coral bark maple tree continues to push out new leaves almost to the last possible minute. If I lived at a higher elevation, the process would start even earlier, because winter freezes come earlier here than they do in the lowlands. Given enough time, plants become acutely sensitive to their local conditions while always cocking an ear to the ticking of their internal clock. The total time a plant sleeps is usually enough to get it past dangerous freezing conditions. Once that specific period has ended, the plant is ready to begin growing again, and spring bloomers reward us with an ever-changing bouquet of botanical beauty.

Potassium to Increase Cold Hardiness


Wood ash or other sources of potassium are added to landscape plants to increase their cold hardiness.


Potassium strengthens cells walls and displaces cell water, making it more difficult for cells to burst during freezing temperatures.


We’ve already learned that plant cells don’t explode under freezing conditions, so we’ll discount that part of the explanation. But potassium is involved in water movement across membranes, so what do scientists say? It turns out that extra potassium has no clear role in improving cold hardiness. Although a few studies showed a positive effect, many more found either no effect or negative effects. Once again, adding a nutrient to soil without knowing its existing concentration is a great way to cause mineral imbalances. Get that soil test!

To Bloom or Not to Bloom

Just because plants begin growing in the spring doesn’t mean they immediately flower as well. Understanding why plants flower when they do was an interesting puzzle for gardeners and plant physiologists alike. Spring bloomers always flower in spring, though sometimes they might have an extra blooming period in autumn. Occasionally my spring-blooming rhododendrons might have a late bloom or two. Other common garden plants, like geraniums and lavender, flower all through the growing season, whereas still others, such as witch hazel and daphne, flower in the winter. For gardeners this is a blessing, because we can fill our gardens with plants that bloom throughout the seasons.

Early researchers had categorized plants as short day or long day plants based on their normal flowering periods. Autumn, winter, and spring bloomers were short day plants, whereas species that flowered in the summer months were long day plants. Plants that didn’t seem to give a fig about what season it was bloomed more-or-less continuously and were labeled day neutral plants. (Coincidentally, figs are day neutral plants!) The key factor is day length, and this was very useful information for nurserymen looking to force potted plants into bloom with artificial lighting conditions.

However, researchers continued to poke and prod at the flowering response and soon discovered an uncomfortable truth: it wasn’t day length at all that triggered the seasonal flowering response, but rather the dark period—an uninterrupted dark period. Once again, phytochrome was the sensing system plants used to measure the dark period and determine the exact time of year. Flowering progressed (or didn’t progress) from there.

What does that mean? Let’s look at chrysanthemums, common garden flowers prized for their habit of blooming in autumn and filling in those seasonal color gaps. Originally, mums were categorized as short day plants, and under normal circumstances you would find them blooming as the days get shorter. At the same time, the ratio of Pfr to Pr decreases (in other words, there’s less Pfr and more Pr) in the mum tissues. When the critical phytochrome ratio is reached, flower development begins.

Now suppose you were to go outside every night and shine a bright flashlight on your mums. You would be resetting their internal clock, which would perceive this night interruption as sunrise (even though it would be a very short one). If you were to measure phytochrome in the mums, you would find more Pfr and less Pr as a result of that flashlight interruption. Eventually, the Pfr would again revert to Pr in the dark, but then the ratio would shift again when the real sunrise occurs. If you continued to interrupt the dark period with light every night, the critical ratio to initiate flowering would never be reached under these endless summer conditions.

Chrysanthemums and other short day flowering plants are more accurately called long night plants. Exactly what constitutes a long night varies from species to species, but in general the uninterrupted dark period must be greater than 12 to 14 hours. In contrast, long day plants should be called short night plants, because they will only flower if the uninterrupted dark period is less than 10 to 12 hours. Bellflowers and carnations, two other common garden plants, are normally summer bloomers. If you did the flashlight experiment on these or other short night plants, you could extend their blooming season by starting it early or prolonging it later. Eventually, however, other environmental conditions such as cold temperatures will bring this runaway flowering to a screeching halt.

Day neutral plants are really night neutral and will flower whenever other environmental conditions are beneficial. Night neutral plants are good all-season performers and may grow well over a broad geographical range. Roses are an excellent example of a night neutral garden plant. Many weed species like dandelions are also night neutral, which partially explains their prolific (and annoying) flowering and seed dispersing abilities. In any case, shining a flashlight on roses or dandelions in the middle of the night won’t do much except cause your neighbors to worry about you a little bit.


Chrysanthemums bloom in autumn.


Interrupting the critical dark period of a plant may disrupt its normal flowering schedule.

Sabotaging the Clock

The evolution of shape-shifting phytochrome is an exquisite example of how plants can interpret and react to their environment without sensory organs such as eyes. For eons the phytochrome ratio has successfully informed plants about seasonal shifts so that dormancy and flowering can be carefully controlled. Unfortunately, the early evolutionary process did not take into account how one species—we humans—could alter the light environment through technology and throw a monkey wrench into the physiological machinery.

Let’s step away from civilization for a minute and consider natural plant ecosystems. Moonlight and starlight are the only nighttime light interruptions you can observe. Phytochrome machinery is not sensitive to this kind of low-level light, so any light from the night sky has no effect on it shifting forms. Now let’s consider what’s happened in urban and suburban areas over the last century. Advances in technology have led to the development of artificial light sources, from incandescent light bulbs to fluorescent tubes to high-intensity street lamps. These artificial light sources can cause phytochrome to shift forms, as we saw with the flashlight and chrysanthemum experiment. At your own home, high-powered security lights can affect flowering, dormancy, and cold hardiness of your garden plants. Diffuse, softer lighting, such as the glow from porch lights and solar-powered pathway lights, doesn’t seem to have an effect.

This realization can both explain some odd plant behaviors as well as help you avoid damage to your house and garden plants. Let’s consider the various holiday cacti that many gardeners nurture indoors or out. Their common names of Thanksgiving cactus, Christmas cactus, and Easter cactus should be big clues that they are all long night plants with slightly different critical ratios of phytochrome needed for flowering around those particular holidays. I have my late grandmother’s prize Thanksgiving cactus on a landing in a stairwell with indirect outdoor light. At night, of course, the stairway light is turned on and off several times. And as you might expect, we don’t get flower buds on the side of the plant facing the stairs. But the other side of the plant apparently doesn’t get enough light from the stairway to prevent it from setting buds. Once the buds are set, I turn the plant 180 degrees and let the other side of the plant get into flowering mode.

The Season for Tree Planting


Planting new trees in the spring.


If they are planted after the chance of a hard freeze is past, trees will establish more successfully.


Regardless of where you live, spring planting happens right before summer heat and/or drought. Newly planted trees will be establishing new roots for several months after transplant, and if the weather is too hot, the humidity too low, and the soil water too scarce, then the tree will suffer.

It’s really better to plant trees in autumn, when the aboveground parts are going dormant and aren’t using water. Roots, in contrast, never go dormant. Their growth slows with decreasing temperature, but a protective organic mulch layer will help keep the soil from freezing and roots will continue to grow, using all of the tree’s available resources rather than just a portion.


Trees planted in the spring often suffer drought stress during the summer.


Holiday cacti bloom in response to shorter days.

Some plants are a little pickier about their light exposure. Poinsettias are a good example, because absolute darkness is required 12-14 hours per day for several weeks to crank out the flowers. I’ve had questions from worried commercial growers who were concerned that new ball fields (with night lighting) would cause enough light pollution to affect their poinsettia production. Even worse, a local nursery lost an entire greenhouse of poinsettias when a student entered the greenhouse at night and turned on the lights shortly before the holiday season.


Poinsettias require extensive periods of uninterrupted dark to bloom.

It’s not just flowering that can be foiled by interrupted dark periods. Woody plants preparing for dormancy can be confused by high-intensity lights, such as those used along streets or in high security areas. The phytochrome perception that summer has been prolonged can delay dormancy to the extent that affected trees and shrubs may not be cold hardy enough to avoid damage of tender tissues by winter freezes.

Native Plants


Using only native plants for landscaping.


Native species are adapted to the area so they require less water and fertilizer and are more resistant to local diseases and pests.


If you and your plants live in a developed part of the world, you aren’t really in the original, native environment anymore. Land once dominated by forests or grasslands no longer has much of these original plant communities left. Soils have been stripped and compacted and amended. Urban areas aren’t natural, and some of the plants that once grew there won’t tolerate these drastically different conditions. Those that do hang on may be more susceptible to opportunistic pests and diseases, rather than more resistant. And stressed natives may well require additional water, fertilizers, and pesticides in their struggle to survive.

Limiting one’s garden to strictly native species can decrease your plant diversity, which in turn limits the diversity of birds, insects, and other nifty animals that can enrich your landscape. Instead, make room for some wisely chosen, noninvasive ornamentals that can improve species diversity, provide resources for wildlife, and be aesthetically appealing.

If plants were like animals, they’d probably pack up their petals and move south for the winter. But plants can’t move—at least not in a migratory sense. Plant parts, however, can reposition themselves in spite of having no skeleton or muscles. Let’s find out how and why sunflowers lift their leaves and clematis swirls their stems.