Respiration: powering living cells

Here is an instructional example. A ficus arrives as a gift in a glossy glazed pot with no drainage hole. Its owner waters whenever the surface looks dry, which is every day or two. A few weeks later the leaves droop, yellow, and begin to drop. Yet the pot is heavy, and the soil a finger's depth down is soaked. The tree is surrounded by water and behaving as if it had none.

To see why, follow the other half of the story. Lesson 6 showed how leaves make sugar. This lesson is about how every living cell spends it, and about the one ingredient that spending depends on: oxygen.

How living cells spend sugar

The sugar made by goes three ways. Some is spent as fuel, some is built into new cell walls and wood, and some is stored, mostly as starch, in living cells of the roots, trunk, and branches.

is how a living cell spends sugar for energy. The cell breaks sugar down step by step, uses oxygen to finish the job, and gives off carbon dioxide and water:

sugar + oxygen → carbon dioxide + water + usable energy

Most of this work happens inside , tiny structures found in nearly every living cell. The energy they release is captured in , a small molecule that carries energy in convenient amounts to wherever the cell needs it. On paper, respiration looks like photosynthesis run backward, but it is a separate process with its own machinery, and it needs no light.

That energy pays for growth at shoot tips, root tips, and the ; for upkeep, replacing worn proteins and membranes even when nothing seems to be happening; for uptake and transport, pulling mineral nutrients into roots (Lesson 10) and keeping sugar moving through the inner bark (Lesson 9); and for defense, such as making resin.

Every living cell, day and night

Respiration runs wherever cells are alive: in leaves and buds, in the cambium and inner bark, in living cells threaded through the sapwood, and in every root, down to the finest root tip. Most wood cells, nearly all of the corky outer bark, and heartwood, where a tree has it, are dead and do not respire (Lesson 3).

Cells hold only a small stock of ATP, so they keep making more around the clock, in sun and in darkness, in summer and in winter. Respiration slows in the cold, but in a living tree it never stops.

Two plant cells drawn side by side at the same scale. The leaf cell on the left is tall and column-shaped, lined with green chloroplasts and an even larger number of much smaller mitochondria. The root cell on the right is rounder, has no green chloroplasts, and holds many small mitochondria and clusters of pale starch grains. — Two living cells from the same tree: a leaf cell (left) with green chloroplasts and many smaller mitochondria, and a root cell (right) with mitochondria and stored starch but no chloroplasts. Both respire; only the leaf cell can photosynthesize. Simplified: real cells hold many more of each structure.Illustration

Go deeper · optional, not assessedInside the mitochondrion

As a chemical equation: C₆H₁₂O₆ (glucose) + 6 O₂ → 6 CO₂ + 6 H₂O, with the energy released captured as ATP and some lost as heat.

The first stage, glycolysis, splits glucose outside the mitochondria and yields a little ATP without oxygen. Inside the mitochondria, later stages break the pieces down to carbon dioxide and pass electrons along a chain of proteins, with oxygen accepting them at the end to form water. Without oxygen the chain stops, and the cell is left with glycolysis, kept running by fermentation, which produces ethanol or lactic acid. Respiration with oxygen yields about 30 ATP per glucose molecule; fermentation yields 2.

Making and spending, side by side

Photosynthesis and respiration run in the same tree on the same day, but not in the same places or at the same times:

	Photosynthesis	Respiration
Where	Green tissue with chloroplasts, mostly leaves and needles	Every living cell: leaves, buds, the living layers of trunk and branches, and roots
When	Only in light	All the time, in light and in darkness
Uses	Carbon dioxide and water, with energy from light	Sugar and oxygen
Produces	Sugar and oxygen	Carbon dioxide, water, and usable energy (ATP)
Sugar supply	Adds to it	Draws on it

In a sunlit leaf, both happen at once. The chloroplasts use far more carbon dioxide than the leaf's mitochondria give off, so overall the leaf takes in carbon dioxide and releases oxygen, and its respiration is hidden. At night only respiration remains, and in most trees the same leaf then takes in oxygen and gives off carbon dioxide.

Roots in the dark never photosynthesize, and the woody trunk, branches, and buds make little or none of their own sugar. They run on sugar sent from the leaves and on reserves stored earlier. So a tree's carbohydrate supply is a running balance: photosynthesis adds to it in daylight, respiration draws on it every hour, and only what is left over can go into growth and storage.

The simulation opens at midday on a sunny day. Compare the two meters in the sugar ledger, then press Replay to run the day from midnight to midnight, watching the What each part is doing list after sunset: does any part stop respiring? Then turn on Cloudy week, Warm night, and Leaves removed one at a time, switching the previous one off, and press Replay each time to run the whole day.

Simulation

Making and using sugar, day and night

Move the time of day, or press Play to run a whole day. Watch where photosynthesis and respiration happen and how the tree's carbohydrate supply changes. Then change the conditions.

Midday12:00 p.m.

Full sunWarm air

Carbon dioxideOxygenSugarRespiration

Time of dayMidday, 12:00 p.m.

Show on the tree

Conditions for the day

The leaves make far more sugar than the whole tree uses, so the supply is building.

The sugar ledger, right now

Made by photosynthesisVery high

Used by respirationModerate

Carbohydrate supplyBuilding

Higher than at midnight. The supply is building.

What each part is doing

LeavesPhotosynthesizing and respiring
PhotosynthesisRespiration
Photosynthesis takes in far more carbon dioxide than respiration gives off, so overall the leaves take in carbon dioxide and give off oxygen.
BudsRespiring
No photosynthesisRespiration
Living bud tissue uses sugar from the leaves and from stored reserves.
Trunk and branchesRespiring
Little or noneRespiration
The living cells (cambium, inner bark, and living sapwood) respire day and night. The inner bark also carries sugar to where it is used.
RootsRespiring
No photosynthesisRespiration
Roots in the dark substrate never photosynthesize. They depend on sugar sent from the leaves and on stored reserves, and they take oxygen from air in the pore spaces.

Text description

A trident maple bonsai stands on a bench outdoors, its pot cut away to show the roots in the substrate. A clock runs through one day, from midnight to midnight, with sunrise at 6 a.m. and sunset at 6 p.m. Beside the tree, a ledger compares the sugar being made by photosynthesis with the sugar being used by respiration, in words from none to very high, and charts the tree's carbohydrate supply through the day.

Photosynthesis happens almost entirely in the leaves, and only in light. In daylight, carbon dioxide moves from the air into the leaves and oxygen moves out. From sunset to sunrise there is no photosynthesis; twilight is too dim for the leaves to make more sugar than they use.

Sugar moves through the inner bark day and night. By day, newly made sugar travels from the leaves to the buds, trunk, and roots. At night the leaves keep sending out sugar, more slowly, from starch they stored during the day. With the leaves removed, stored reserves move up the trunk toward the buds.

Respiration never stops. Living cells in the leaves, buds, trunk and branches (the cambium, inner bark, and living sapwood), and roots take in oxygen, break down sugar for energy, and give off carbon dioxide, every hour of the day and night. It runs faster in warm air. Roots in the dark substrate never photosynthesize; they depend on sugar from the leaves and on stored reserves, and they take oxygen from air in the spaces between particles.

In bright daylight, photosynthesis in the leaves far outpaces their respiration, so overall they take in carbon dioxide and give off oxygen. The tree makes far more sugar than it uses, and its carbohydrate supply builds. Near dawn and dusk, production and use roughly balance and the supply holds steady. At night the tree only uses sugar, so the supply draws down. On a sunny day with a cool night, the day ends with a surplus that can go into growth and storage.

Cloudy week: less light reaches the leaves, so they make less sugar. The day ends about even, with little to spare.
Warm night: respiration runs faster through the night, so the supply draws down faster and the day's surplus is smaller.
Leaves removed: no sugar is made even in full sun. Buds, trunk, and roots keep respiring on stored reserves, so the supply draws down all day and night and the day ends in deficit.
Cloudy week and warm night together: the day ends in deficit.

Qualitative model: arrows show direction, not amounts. Simplified to 12 hours of daylight (sunrise 6 a.m., sunset 6 p.m.), and each day starts from the same supply at midnight so you can compare conditions. Sugar production is drawn in proportion to light; real leaves level off in bright sun, so the model overstates what clouds cost. Respiration is marked at a few sample points, but it happens in every living cell.

At midday the leaves made sugar far faster than the whole tree spent it. Through the night nothing was made while every part kept respiring, so the supply drew down. The sunny day still ended with a surplus for growth or storage.

A warm night spent more of that surplus. Like most chemistry in living cells, respiration speeds up with warmth: over ordinary growing temperatures, many plant tissues respire roughly twice as fast with each rise of about 10 °C (18 °F), and near freezing it slows to a crawl. A cloudy week left the day about even. With the leaves removed, nothing was made even in full sun, yet buds, trunk, and roots kept spending, so the day ended in deficit, paid for from stored reserves. Losing much of the foliage to pests or hail has a similar effect, and it does not end the moment new leaves appear: growing them draws on reserves too, until they are large enough to export sugar (Lesson 9).

Practice check · not scored

Instructional example: on a cold midwinter night, a trident maple bonsai has dropped all its leaves for its winter rest. Which statement about respiration in the tree is accurate?

Nothing in it respires until new leaves open in spring.

Its buds, living bark tissues, and roots respire slowly, on stored reserves.

Only its roots respire, because the soil around them stays warmer.

It respires only on mild afternoons, when sunlight warms the bark.

Where roots get their oxygen

Growing root tips, root hairs, and root cells taking up mineral nutrients all run on respiration, so roots need oxygen as steadily as they need water. In most trees, oxygen made in the foliage does not travel down to the roots in useful amounts. Roots depend on the air around them.

As Lesson 2 showed, that air sits in the of the substrate, the growing medium (plural, media). After watering, the larger pores of a well-drained pot empty and refill with air, linked in passages to the surface, so oxygen keeps diffusing in as roots use it. This supply is called .

Water-filled pores cannot do that job. Water holds far less oxygen than the same volume of air, and oxygen moves through it roughly ten thousand times more slowly.

Go deeper · optional, not assessedTrees that tolerate wet roots

A few trees of swamps and floodplains, such as bald cypress, can form spongy tissue with open air channels that carry some oxygen down toward their roots, and their roots cope with low oxygen better than most. Most trees grown as bonsai lack these adaptations, so how much wetness your own tree tolerates is worth finding out before you trust it to a wet pot.

When the pores stay full of water

A medium is when water fills all of its pores. A thorough watering fills most of a pot's pores for a short time. In a pot that drains, that brief saturation is normal: as the excess runs out, it draws fresh air into the larger pores behind it.

Predict first

A pot with no drainage hole is watered thoroughly, and its lower half stays saturated. Which do you expect to show trouble first: the root tips in that wet lower half, or the leaves? Why?

Your prediction (optional, not saved)

When saturation lasts, a chain of events follows:

Roots and soil microbes use up the oxygen dissolved in the water within hours to a day or so, sooner in warm weather, when they use it faster and the water holds less of it. The root zone falls into , too little oxygen for cells to respire normally, and in places becomes , with no oxygen at all.
Root cells fall back on , a way of getting energy from sugar without oxygen. It yields only a small fraction of the energy, and its byproducts can harm cells as they build up.
Short of energy, root tips stop growing and begin to die back, followed by the fine roots behind them.
With fewer working roots, the tree takes up less water and fewer mineral nutrients. The foliage can wilt, yellow, or drop, even though the pot is wet.
Some root-rot organisms, including water molds, thrive in waterlogged media and readily attack weakened roots.

Watch that chain in the simulation. It opens with the free-draining pot: press Water thoroughly and let the week play, then set Time since watering back to 1 hour and look at the magnified root tip. Next, choose No drainage hole, press Start over, and step through the week with Next, watching the Oxygen meter, the Root tip scale, and the Foliage row. Then try Pot in a saucer of water and Compacted, fine soil the same way, and finally turn on Warm weather.

Simulation

Air and water in the root zone

Choose a pot, then press Water thoroughly and follow the root zone through the next week. Compare how long water fills the pores, how much oxygen reaches the circled root tip, and what warm weather changes.

Container

Free-draining potPot in a saucer of waterNo drainage holeCompacted, fine soil

Saturated: every pore full of waterWater film on particlesAir in poresOxygenHealthy root tipDying root

Time since wateringBefore watering

Free-draining pot · Mild weather

Before watering

Around the circled root tip

WaterMoist

OxygenHigh

Root tip

Healthy
Stressed
Dying back

FoliageLooks normal

What is happening

Before wateringThe coarse medium is moist: films of water cling to every particle, and the larger pores hold air. Roots take in oxygen from that air.

Text description

A bonsai pot is shown in cross-section, with its tree above and its roots spread through the substrate. A circle marks one fine root tip near the bottom of the pot, and a magnified view shows that tip among the substrate particles: water films around the particles, air in the larger gaps (pores), and oxygen moving through the air to the root. Saturated medium, where water fills every pore, is shaded blue; in the magnified view, water films around particles are outlined in pale blue. Each pot starts moist and airy, is watered thoroughly once, and is then followed for a week: just watered, after 1 hour, 1 day, 3 days, and 1 week.

Free-draining pot: the excess water runs out of the drainage hole within the first hour. Air is drawn back into the larger pores while films of water stay around the particles, so oxygen around the root tip returns to high and the tip stays healthy all week. The pot slowly dries.
Pot in a saucer of water: the pot stands in a deep saucer, and water drained into it rises above the bottom of the pot. Inside the pot, the pores fill up to that level and a little above it, so the lowest part stays saturated for as long as the water stands. Around the root tip there, oxygen falls from low to very low within about a day. The tip is stressed after a day and dying back after about three days. The foliage may later look dull or limp.
No drainage hole: the water sinks through the medium and collects in the lower half of the pot, where it cannot leave, so that half stays saturated all week while the surface dries and can look as if it needs water. Oxygen around the tip runs very low within a day; the tip is stressed after a day and dying back by three days. Roots short of oxygen take up water poorly even before they die, so the foliage looks dull by three days, and with many fine roots lost, the tree wilts or yellows by the end of the week, even though the pot is wet.
Compacted, fine soil: water soaks in and drains slowly, and the small pores keep holding water, so the lower part stays nearly saturated for about a day and the soil holds less air than a coarse medium even when drained. In mild weather the root tip is stressed after a day, then recovers once air has returned, without dying back.

Warm weather makes roots and soil microbes use oxygen faster, and warm water holds less of it. In the pots that stay saturated, oxygen runs out within hours and root tips die back sooner: by about one day with a saucer or no drainage hole, and by about three days in compacted soil. In the free-draining pot the roots stay healthy either way.

Simplified: the pot is watered once and left for a week, and the times are illustrative. Real outcomes depend on the tree, the medium, the pot, the temperature, and time. Colors show water (blue) and oxygen (teal dots); amounts are not to scale.

Watering filled most of the pores in every pot; what differed was how long they stayed full. The free-draining pot shed its excess within the hour, air returned to the larger pores, and the root tip stayed healthy all week. In the saucer and no-hole pots, the bottom stayed saturated, oxygen at the tip fell to very low within a day, and the tip was stressed while the foliage still looked normal. It was dying back by three days, and only then did the leaves dull, droop, or yellow.

The no-hole pot is the gift ficus's trap: its surface dried and looked thirsty while its lower half stayed saturated, so each new watering added to the problem. Compacted soil drained slowly, held less air even once drained, and left its root tip stressed for a time. Warm weather sped up every harmful change.

Pots that stay waterlogged

The simulation's three problem pots are common. Many decorative glazed pots and outer covers have no drainage hole. A saucer, tray, or outer pot that collects drained water keeps the bottom of the pot wet from below. And garden soil packed into a pot, or old substrate whose particles have broken down, is mostly tiny pores that hold water and leave little room for air (Course 04, Soil, Substrates, and the Root Environment).

Two empty pots on a wooden potting bench. On the left, a glossy glazed decorative pot lies on its side with its solid base, which has no hole, turned toward the camera. On the right, a shallow brown bonsai pot turned upside down shows two large drainage holes with plastic mesh showing through them, small wire holes, and four short feet. — Check the underside of any pot your tree lives in. The decorative pot (left) has a solid base, so water poured into it has nowhere to go; the bonsai pot (right) has large mesh-covered drainage holes.

What growers call overwatering is rarely about how much water is poured at once. It is about a root zone that stays wet so constantly, or drains so poorly, that air never gets back in.

Practice check · not scored

Instructional example: a trident maple stands on a sunny patio in a deep saucer that has filled with rain. On a warm afternoon its leaves droop. The pot feels heavy, and a check deep in the pot finds the substrate soaked. Which is the best next step?

Water thoroughly now, since drooping leaves on a warm day show thirst.

Empty the saucer, hold off watering, and check that the pot drains freely.

Add fertilizer so the tree can grow new roots to replace damaged ones.

Mist the leaves through the afternoon so they can take in water directly.

Wilting has other causes too, from a dry root zone to hot, windy weather. Lesson 8 explains them, and why the root zone, not the leaves, tells you whether to water.

The bonsai decision

Water is only half of what roots need

Starting point

Make sure water can leave the pot and air can come back in: an open drainage hole, nothing holding water around the base, and a medium that drains freely instead of pooling. Then water when a check below the surface (Lesson 2 describes how) shows the root zone needs it, rather than on a fixed schedule. Course 03, Watering and Daily Observation, will go further.

This assumes

The tree is established and healthy, and not recently repotted. - It grows in an open, coarse bonsai mix in a pot with at least one drainage hole.

Change course if

The pot has no drainage hole: no watering routine can fix this. Check moisture deep in the pot before adding any water, and plan a move to a pot that drains (Course 11, Repotting and Root Development). - Water stands in a saucer, tray, or outer pot: empty it after watering, or raise the pot above the water on gravel or a grid. - Water pools on the surface, or the pot stays wet for days in warm weather while the tree is in leaf: the medium may be too fine, compacted, or broken down (Course 04). Even a sound medium dries slowly in cool weather, in shade, while a deciduous tree is bare, or when roots are already damaged. - The tree wilts or yellows while the medium is wet: do not water. Check drainage and the lower root zone, and investigate possible root damage (Course 07, Tree Health and Diagnosis). - The weather turns hot: waterlogging harms roots faster, and draining pots dry faster, so check more often.

Back to the question

Why can roots struggle in persistently saturated media?

Roots are living cells that respire constantly, so they need oxygen as surely as they need water, and they get it from air in the pore spaces of the substrate. When a medium stays saturated, water fills those spaces, oxygen moves through it about ten thousand times more slowly than through air, and roots and microbes use up what little is dissolved. Root tips fall back on fermentation, run short of energy, and die back, so the tree takes up less water and can wilt in a pot that is still wet.

Key takeaways

Respiration breaks down sugar with oxygen to release usable energy (ATP) in every living cell, from leaves to root tips, day and night. - Photosynthesis happens only in green tissue and only in light; growth and storage come from what is left after respiration. - Warmth speeds respiration, so warm nights spend more sugar and warm roots use oxygen faster. - Roots take oxygen from air in the pore spaces. Lasting saturation, from a pot with no hole, standing water, or a compacted medium, starves them of it. - Brief saturation after watering is normal in a pot that drains. Wilting in a wet pot calls for investigation, not more water.

Optional · not required for completion

Where does the water linger?

Poke several holes in the bottom of one clear plastic cup and leave a second cup intact. Fill both with the same substrate or garden soil, set the holed cup on two pencils laid across an empty bowl so it can drain, and pour the same amount of water into each, enough that some runs out of the holes.

Look through the sides after an hour, a day, and three days: saturated medium looks darker and glistens, with no air gaps. Where does water linger in each cup? A third holed cup of fine garden soil lets you compare it with a coarse bonsai mix.

No tree is needed, and none should be used.