Category Archives: Keeping Bonsai Healthy

Bonsai growing medium

Now here’s a topic to generate some internet debate! This is really a subject that every bonsai enthusiast has an opinion about – whether akadama is worth the money, whether cat litter is a legitimate medium, whether to add organic material, there is a ton of disagreement on this subject. So how might we take a scientific approach?

Well the starting point is that the growing medium needs to enable the supply of everything that the tree via its roots requires – specifically water, oxygen (for respiration) and nutrients^ref. Now, you may add nutrients via fertiliser, but the medium needs to catch those nutrients so that the roots (or symbiotic bacteria) can absorb them, similarly with water – so one important characteristic is that the medium must hold water in a form which is accessible to roots.

Another super-important attribute of the medium should be that it helps establish and nourish a thriving rhizospere. This means providing a home for beneficial bacteria and fungi, enabling the roots to come into contact and to interact with them and for the roots to generate their exudates. The medium needs to hold and release the substances which are important to these microorganisms, and it needs to allow them to breathe.

We also want to have a medium in which roots grow freely, and ramify, to better support the tree in the pot and provide more surface area for nutrient and water absorption.

Wouldn’t it be amazing if there was such a medium out there? Oh, well actually there is – soil! The world over, the nutrient, rhizosphere and root growth requirements of trees are supplied by soil. According to the Royal Society, “‘well-structured soil’ will have a continuous network of pore spaces to allow drainage of water, free movement of air and unrestricted growth of roots…typically, a ‘good’ agricultural soil is thought to consist of around 50% solids, 25% air and 25% water,”^ref

https://royalsociety.org/-/media/policy/projects/soil-structures/soil-structure-evidence-synthesis-report.pdf

They also say that “bacterial diversity is affected by soil particle size, with a higher percentage of larger sand particles (ie coarser soil) causing a significant increase in bacterial species richness” and “the ability of soil structure to hold moisture is linked to a high microbial diversity and more robust populations of soil mesofauna and macrofauna”^ref

This study found that bacterial and fungal abundance was positively associated with high phosphate, high pH, a lower Carbon:Nitrogen ratio, sandiness of soil texture and soil moisture. It was negatively associated with the presence of Chromium, Zinc, silt, a high Carbon:Nitrogen ratio or clay soils.^ref

So what can we conclude from all of this? In terms of structure we want the right ratios of soil/water/air (50% soil particles, 25% water, 25% air) and the soil to have a higher percentage of larger, sandy particles (not clay or silt). The question for bonsai comes down to water retention since a pot with a hole is much more draining than soil. Options for water retaining elements in bonsai medium include bark, compost, biochar, perlite or vermiculite. Clay also has high water retention but perhaps too much, as it can cause anaerobic conditions which results in nasty gases being produced by bacteria. Different components such as akadama, lava rock, pumice and so on can provide the structural part of the mix which create air spaces.

Some media have so-called pores – tiny holes which hold water which is accessible by roots. “The higher the large pore (macropore) density, the more the soil can be exploitable by plant roots… the presence of continuous macropores significantly benefits root growth.”^ref An example would be biochar which has a huge surface area thanks to many tiny tubes and pores throughout its structure.

What you want to avoid in your bonsai medium is anything which is too acidic (except if you have an acid-preferring tree) as this would reduce the microbes, or anything with anti-fungal or anti-bacterial properties (such as – ahem – cat litter or diatomaceous earth). You also want to avoid (per the above) anything which reduces the roots’ access to air & water by getting overly compacted or wet, or having overly draining components which don’t hold water.

Bonsai wisdom says that adding ‘organic’ components such as compost or leaf litter is bad for various reasons – they break down and reduce drainage, they run out of nutrients too quickly, they aren’t controllable. But personally I think adding organic matter of some kind is a good thing, as it mimics the natural world, has all sorts of beneficial compounds (such as those included in some non-nutrient additives) and provides some small particle sizes as part of an overall mix.

As it happens, I finally found a bonsai-specific research study! These are extremely rare. In the Journal of American Bonsai Society this article showed the results of an experiment measuring the water retention of different bonsai soil components. See below:

Based on this, if you were using the 25% air 25% water rule of thumb, most of these would be fine as bonsai soil with just a bit of added water retention. Interesting that pine bark is actually quite similar to akadama – I have recently been wondering whether you could grow trees entirely in bark if it was the right size. Maybe it’s time to try!

Another study looked at particle size, finding that “media components that differ significantly in particle size have lower total porosity, water-holding capacity and air-filled porosity than media composed of similar particle sizes.”^ref

One final word on different mediums for different trees. Obviously, different trees come from different habitats and happily grow on soils native to that habitat. I have a tiny olive in a tiny pot with extremely coarse medium that dries out easily and it’s thriving (albeit, I live in London). Angiosperms transpire more than gymnosperms so in theory need more a more moisture-retaining medium. A tree with a very high foliage ratio relative to the size of the tree will also need a lot of moisture. So think about the ‘natural’ habitat of your tree and what the soil conditions likely are, and try to adjust accordingly.

The nice thing about the scientific method is that it’s not all theory – observation and experiment is an integral part. If you start with a general medium, you can adjust it to be more water-retaining by adding compost or bark, or less by adding more akadama/pumice or increasing the particle size. See how things go and adjust when you repot.

Watering bonsai trees

They say that a lack of watering is the number one reason that newbies kill their bonsai trees. It is quite a surprise when you first learn about the hobby to find out that you need to water your trees *every day* and sometimes multiple times a day! It suddenly feels like more of a serious commitment than you might have been expecting. Taking a more zenlike attitude and instead learning to enjoy the time with your trees when they are being watered is just one of the delightful things you discover as you become more obsessed with bonsai.

As you’ve read elsewhere on this site, water is essential for bonsai trees. Water is essential for plants in general, including trees. It’s a key ingredient in the process of photosynthesis, along with CO₂ and sunlight, it’s a component of plant cells’ protoplasm, it’s essential for the structural support of leaves and stems (water creates ‘turgor’ ie. the water pressure which helps plant cells keep their shape), and it transports nutrients and photosynthates in the xylem and phloem sap. Water is estimated to comprise over 50% of the weight of woody plants.^ref

Surprisingly, the majority of water taken up by a tree (90% or more) is actually lost through transpiration (which means evaporation from the leaves)^ref. This is partly a by-product of having open stomata on leaves to enable the entry of CO₂, but also performs a useful function for the tree, pulling water and nutrients up from the roots by hydrostatic pressure – as the evaporating water causes a pressure differential in the xylem which pulls more water up.

What this all means is that trees need a LOT of water. They also store water for times when water is low – in this study^ref they found that Cryptomeria japonica can store 91.4 ml of water per kg of mass, distributed among leaves, sapwood and elastic tissue. For the first 2 hours of transpiration when photosynthesis started in the morning, they found that the water transpired was supplied exclusively from the tree’s leaves – it wasn’t until later in the day when stored water was low that the tree started to take up water from its roots.

OK so bonsai trees are small, they will need less than a full-sized tree of the same species, but sufficient water is necessary not just for photosynthesis but to maintain turgor in the cells, to allow the stomata to open and close, to resupply the water lost through transpiration, to bring nutrients up to its cells and sugars away from leaves, to build new cells and to avoid embolisms.

Trees in nature will spread their roots out to access water sources deep in the ground, but your bonsai doesn’t have that option. Trees in pots – such as bonsai – depend on their humans for water.

Furthermore, the water requirement of your tree (and thus how much watering is needed) will depend on several factors. In general, a tree will need more water if:

It has a lot of foliage, since the level of foliage determines the level of photosynthesis *and* the level of transpiration, both of which require more water (but the latter being the largest driver)
It gets a lot of sun, since sun exposure drives increased photosynthesis and transpiration (assuming foliage is present)
The weather is hot, dry or windy – all of these increase transpiration
Its growing medium is very open, free-draining or lacking moisture retaining components (such as bark). A more open, draining medium will lose water more quickly.
Its pot is very shallow, as this means the water quickly drains out.
It’s going through a growth spurt – making fruit, flowers or seed, or pushing sap up to push out embolisms
It’s in a low-CO₂ environment – conversely if you have your bonsai tree indoors where there are lots of people, it may benefit from the increased CO₂ by reducing its water requirements^ref

When and how should bonsai trees be watered? The unscientific answer is – whenever their owner is most likely to be available and remember to do it! Convenience is important, since missing a watering could damage the trees.

But from a scientific point of view…the latest time when watering is needed is when the tree is approaching the point of running out of water. Obviously you don’t want it to actually run out for the reasons explained above. Bonsai lore is actually well-founded in this case – look at the growing medium and check how dry it is, this gives you a good indication of whether the tree needs watering.

Trees don’t need a lot of water at night, because many/most of them close their stomata which reduces transpiration – except when they are getting ready for sunrise – this article says they open their stomata up during the night in order to get water up into the leaves to be able to photosynthesis immediately that the sun comes up: they “can calculate the time of sunrise in advance”^ref This is a one-time occurrence prior to sunrise though, and a lot less than the continuous transpiration that happens during the day. According to another article trees actually do the majority of their growing overnight (that is, creating new cells), due to the increased water availability and humidity during this time (due to the lack of transpiration)^ref These points have two implications for bonsai enthusiasts – 1. if you want your tree to grow, make sure it has enough water at night but 2. it’s not going to be at its highest water usage rate overnight, so this is likely not the time when it requires watering.

At night, there is also a water gain from dew, depending on location. This article shows how much net water loss happens overnight in different geographies^ref – “in parts of the tropics and at high latitudes” dew is actually greater than nocturnal evaporation. But on average there is 8% net water loss on land overnight.

The point at which a bonsai tree is going to start running out of water will depend on all the criteria above – foliage mass, pot size, growing medium, dryness, heat and its stage of growth. In most cases this will happen at some point during the day, after the tree has been transpiring. Depending on these factors, it may require a top-up again during the day. So maybe mid-morning to noon is a good time, with a possible follow-up water later in the day if it’s excessively hot or dry.

Most bonsai enthusiasts dream of the perfect automatic watering system. Unfortunately this is quite hard to find, for a number of reasons.

Firstly, the amount of water needed for each tree varies based on pot size/growing medium/transpiration rate. The only way to achieve this is to have individually controlled watering devices for each tree. Secondly, you ideally want to avoid wasting water by watering outside the pot or when it’s not needed – this again requires individual control for each tree, plus a spray pattern which covers just the pot area and nothing else.

The final issue is that there is risk associated with relying on an automated system. This summer when I went on holidays I set up timed sprinklers and grouped my trees together for a twice daily watering. This worked great – until one of the hose connectors popped off the tap. I had quite a few losses but on reflection probably could have avoided these by setting up two independent systems. An enthusiast from Twickenham Bonsai Club which I attend has used mini soaker hose and a garden irrigation system for his holidays which he says has worked well – but it doesn’t look good enough for continual use due to soaker hose being coiled on top of every pot.

The compromise most bonsai nuts end up with is hand-watering the majority of the time and a sprinkler or similar system while they are away.

Can you use water sources other than the tap? Find out in this post.

The water system of a tree

One of the first topics you come across when starting to study trees is the question of how they manage to lift water all the way to the leaves at the top of the canopy.

Different organs play their part in this system, starting with the roots where water is absorbed into the xylem. Xylem is a network of interconnected cells, which die quickly after birth, so that the cell contents is eliminated leaving a large space for water to enter. New xylem is constantly being created in the roots, trunk, branches and leaves, and this is all connected so that water can pass from one to the other.

But what causes it to rise up towards the leaves? The phenomenon is well described in pretty much any tree biology book you care to pick up (see references page). The answer (as is beautifully described in Ennos’s book ‘Trees’) is that it is pulled from above.

The force which pulls up the water actually starts at the leaves. Cells in leaves need gases to photosynthesise and respire (carbon dioxide and oxygen), and the waxy epidermis (outer layer) is impermeable to gas. So, leaves have small holes called stomata which are pores in the epidermis allowing gas to enter the leaf interior. These holes also allow water vapour to escape from the leaf, and as this water vapour evaporates from the leaf it pulls up the water underneath it by hydrostatic force. Water is strongly attracted to its own molecules (a force known as cohesion), and when they move upwards by evaporation it creates tension pulling more water up. This is known as the ‘cohesion-tension’ theory (Smith et al) and the process is known as transpiration. This is why trees need far more water than their size would suggest – the majority is evaporated from the leaves during transpiration.

As most bonsai enthusiasts know, when you cut a branch, water does not spurt out. So it’s obviously not being pumped from the roots. But you can make water spurt out, if you put a cut branch in a pressure vessel and apply pressure which is equal to the tension that the water was under. Experimentally this has shows stretching forces of over 20 atmospheres (294 p.s.i) (Ennos), evidence which has supported the cohesion-tension theory. There are those who disagree with this as the exclusive mechanism for water movement against gravity – one paper argues that there is an “interplay of several forces including cohesion, tension, capillarity, cell osmotic pressure gradients, xylem-phloem re-circulation, and hydrogel-bound gradients of the chemical activity of water”.^ref

Whatever the nuances of the forces involved, the transpiration flow is essential for other processes within the tree – it helps maintain cell turgor (stiffness), maintains solute levels in cells which are needed for metabolism, draws nutrients, plant growth regulators and metabolites up through the tree from the roots via the xylem sap, cools leaves via evaporative cooling, and supplies water to the top of the phloem for the transportation of photosynthates (Smith et al).

Artificial light for bonsai

It is possible to keep a bonsai alive with artificial light such as a lamp as long as the lamp emits the spectrums of light needed by plants to grow. This starts with their need to perform photosynthesis. Chloroplasts are the organelles within plant cells which are responsible for photosynthesis, and they do this using photosynthetic pigments – substances which absorb photons of light.

You may be surprised to learn that there are actually multiple photosynthetic pigments in chloroplasts and that land plants always have two forms of chlorophyll – chlorophyll a (C₅₅H₇₂MgN₄O₅) and chlorophyll b (C₅₅H₇₀MgN₄O₆)^ref, and six carotenoids – neoxanthin, lutein, β-carotene, violaxanthin, antheraxanthin and zea. The role of chlorophylls are to be “light collectors, whereas carotenoids, apart from participating in light harvesting, are also involved in photoprotection”.^ref Different levels of these pigments are contained in angiosperms vs gymnosperms – to see the differences you can review the data in this article (figure 4) but in summary gymnosperms have more chlorophyll (a + b) and deciduous angiosperms have the least chlorophyll b. The different chlorophylls and carotenoids absorb different spectrums of light as shown in the chart at the bottom of this post.

But it’s not just the process of photosynthesis which uses light in plants. Actually many of their growth responses depend on light – including seed germination, flowering, leaf senescence, stomatal and chloroplast development, cell differentiation and root growth. Plants also have a circadian clock which controls when processes happen – such as stomatal closing & opening, flower closing & opening, leaf position changes and so on. The circadian clock uses light sensors to keep the clock in time with the world.

Plants use phototropins, phytochromes, cryptochromes and UV detectors to perform different light sensing tasks and to trigger signals throughout the plant.

Phytochromes are red and far-red light photoreceptors, whose role in plants is to detect favourable conditions for growth and to signal within the plant accordingly – five have been identified, known as phytochromes A to E.^ref They function not just as light detectors but as temperature sensors since they are able to detect infrared light which is associated with heat.^ref I was interested to read that phytochromes A, B and E stimulate lateral root production while phytochrome D inhibits it.

Phototropins are responsible for the phenomenon of phototropism whereby a plant grows towards the light – they contain blue light photoreceptors.^ref Cryptochromes are another form of blue light photoreceptor only recently discovered, they’ve been shown to inhibit elongation of the germinating stem and to form an input to the circadian clock.^ref

Several plant growth processes have been found to be initiated by UV-B light, summarised in this table but including stomatal closing and the production of compounds such as anthocyanins which protect the plant from damaging UV levels. UV-B light has been found to be detected in plants by a receptor known as UVR8^ref.

So below there is a nice diagram put together by a producer of LED grow lamps (they’ve left the UV receptor off but everything else is there). As is clear to see, there is a wide range of spectra required by the different photoreceptor apparatus in a plant. So back to the whole point of this post – can you use artificial light? Well yes but for full functioning of your tree it should provide the spectra needed – which is basically most of the range of light from UV to infrared excluding green and yellow. The LED grow lamp seller has an article on finding lights which meet the requirements below (I do not know them, I just think their website makes sense).

https://www.ledgrowlightshq.co.uk/chlorophyll-plant-pigments/

The other factor to consider is that leaves are adapted to respond to the parallel rays of light from the sun. Their internal cell structure, for example, is organised to encourage the scattering of light to the spongy mesophyll cells which are underneath the palisade cells.^ref In general a light bulb or LED light is not going to produce parallel rays of light so the photosynthetic efficiency of the light will be reduced (since less light will make it into the spongy mesophyll cells) and more power will be needed from the light.^ref

Personally I’ve never used artificial light for a bonsai – the one indoor bonsai I have (a Ficus retusa) lives quite happily on a table near a window in my kitchen where it gets natural light throughout the day and copes with the large variations in photoperiod experienced in the UK. But theoretically it should be possible to use a light instead, assuming you have one which meets the requirements outlined in this post in terms of spectrum and intensity.

If you end up with a light which doesn’t reflect the spectra needed, this may impact your tree’s growth. For example “low blue light from warm white LEDs increased stem elongation and leaf expansion, whereas the high blue light from cool white LEDs resulted in more compact plants”^ref – you can end up with ‘leggy’ plants if you don’t have enough light.

What each nutrient does (x17)

Understanding the exact role of individual plant nutrients is actually quite complicated. This is because many nutrients have multiple roles, and research hasn’t always clearly identified each role. It’s also because nutrients don’t act on their own – they usually form part of a larger molecule, such as an enzyme, and they usually interact with other nutrients, molecules and environmental factors such as pH. Then it requires diving deep to the molecular level to work out how chemical reactions take place and even how individual electrons move in the presence of the enzyme. I’ve read a bunch of papers and articles about the nutrients below but there is sure to be more out there – consider this a taster.

Macronutrients

Macronutrients are those inputs which plants require in substantial volumes in order to grow and metabolise. There are six macronutrients, of which three are metals.

1. Nitrogen: nitrogen is needed by plants for various reasons but one of the most important is for photosynthesis. Nitrogen is a component of chlorophyll, the green pigment in leaves which absorbs the energy from sunlight to break apart water in the photosynthesis reaction. The chemical formula of chlorophyll is C₅₅H₇₂O₅N₄Mg – as you can see both nitrogen and magnesium are needed in addition to carbon, hydrogen and oxygen which is obtained from air and water.

Secondly, nitrogen is a key component of amino acids, which are used in all living things to make proteins. There are 21 amino acids in plants which are connected together in a myriad of different sequences and shapes to make the different proteins. Examples of plant proteins include the storage material in seeds and tubers, plant cell membranes and the enzyme known as RuBisCO. RuBisCO is present in leaf cells alongside chlorophyll, and enables carbon fixation during photosynthesis – it is said to be the most abundant protein on Earth and represents 20-30% of total leaf nitrogen^ref. So photosynthesis requires chlorophyll and RuBisCO, both of which rely on nitrogen as a component element.

Finally nitrogen is present in the four bases used to create DNA (adenine, thymine, guanine & cytosine) and RNA (adenine, urasil, guanine & cytosine) which enables cell replication^ref.

Nitrogen needs to be in soluble form to be used by plants, either as nitrate or ammonium, which requires the presence of specific bacteria either in the soil or in the plant’s roots. As I mentioned in my first post about nutrients, Hallé states that obtaining nitrogen is a constant challenge for plants. This is why the fertiliser industry is so prosperous – but unfortunately also so damaging for the environment. The Haber-Bosch process used to make Ammonia (NH₃) is “one of the largest global energy consumers and greenhouse gas emitters, responsible for 1.2% of the global anthropogenic CO₂ emissions”^ref and nitrate runoff from highly fertilised fields damages rivers and ecosystems.^ref The natural world has some clever ways to make nitrogen accessible – some plants incorporate bacteria into their roots which can do this, and in old growth Douglas fir forests, lichen in the canopy which contain cyanobacteria capture nitrogen from the atmosphere and when they fall to the forest floor they rot into components which trees can access (Preston, ‘The Wild Trees’). Similarly a relatively sustainable source of nitrogen for plants is rotting organic matter (along with the necessary microbes) – compost and manure are good options.

2. Phosphorus is needed in plants – and in fact in most living things – because it’s a key component of the molecule used to store, transport and release energy in cells. That molecule is called adenosine triphosphate (“ATP”) and it’s created during photosynthesis by adding a phosphorus atom to adenosine diphosphate. The ATP can then be transported throughout the organism to be used where energy is required, at which point it’s converted to ADP (adenosine diphosphate) which releases energy back to the cell. Phosphorus also provides the structural support for DNA and RNA molecules, needed for cell replication.

For plants phosphorus is fundamental to photosynthesis, as a phosphorus-containing substance called RuBP (C₅H₁₂O₁₁P₂) is used to regulate the action of RuBisCO in fixing carbon from carbon dioxide.

Phosphorus is a key part of most fertilizers and manure is a good source^ref.

3. Sulphur is a constituent of two amino acids – methionine and cysteine. Cysteine is used to create methionine as well as glutathione, an anti-oxidant which helps plants defend themselves against environmental stress^ref. Methionine is involved in cell metabolism and the majority of its use in the cell is to synthesise ‘AdoMet’ which is used in methylation reactions (such as DNA methylation which regulates gene expression) and to create the plant growth regulator ethylene^ref.

Manure is a source of sulphur for plants.

Metals

In addition to the top three outlined above, it turns out that plants need some atoms of various metals as well. In order to understand why, we need to know that plant cells are full of chemical reactions which perform all the different functions required for metabolism. Helping these chemical reactions along are a type of protein known as enzymes. Enzymes act as a catalyst to chemical reactions in cells, speeding them up without consuming the enzyme material itself. Some enzymes have metal ions at their heart which assist the reaction (called ‘co-factors’) and these play a critical role in the enzyme’s function (for example magnesium is used in RuBisCO).

Three of the six macronutrients needed by plants are metals – potassium, calcium and magnesium.

4. Potassium is one of the three major macronutrients usually found in NPK garden fertilisers (K is the chemical symbol for potassium), reflecting its important role across several different dimensions of plant growth. One important role is in the production of proteins. As outlined above, proteins make up a large part of plant biomass, and the key protein RuBisCO is necessary for photosynthesis. Proteins are manufactured on structures called ribosomes within the cell – and ribosomes need potassium in order to do their job^ref.

The other important role for potassium is in providing the pressure within plant cells which keep them stiff and ‘turgid’ – without it they would become flaccid and the plant would fall over. The manipulation of turgidity within leaves is one way a plant controls the level of air coming into the leaf – to close off the air holes (stomata) the guard cells around the stomata are made more turgid which closes the gap between them. Potassium is involved in this process.

In nature the main source of potassium is the weathering of rocks, but it’s also contained in organic matter, particularly in seaweed.

5. Magnesium is a component of the chlorophyll molecule and is key to the operation of RuBisCO, both of which enable photosynthesis. It is found in soil from the weathering of magnesium-containing minerals – the University of Minnesota recommends dolomitic limestone or tap water^ref.

6. Calcium isn’t just used for human skeletons, it’s also used for plant structure as it strengthens the cell walls in plants. Its presence (or absence) is also used for signalling of stresses to the plant, allowing it to activate defences against pathogens. Sources of calcium for gardening include lime or shells.^ref

Micronutrients

Micronutrients are required in much smaller amounts than macronutrients, although they are still required.

7. Boron appears to have been identified as a plant micronutrient mainly due to the effects of not having enough of it, with researchers having observed that boron deficiency leads to root, leaf, flower, and meristem defects. The precise role that boron plays is not easy to find in the literature, other than it being generally agreed to be important as a structural component of the plant cell wall, helping to provide rigidity^ref. Boron also appears to be required for reproduction, and a lack of it can affect pollen germination, flowering and fruiting. Because boron has poor mobility in a plant and cannot be moved from one part of the plant to another, continued exposure to it is needed in order to avoid a deficiency – but the exact levels vary widely by plant.

Sources of boron include borax (sodium borate) but since boron toxicity is apparently possible at high levels be very careful with this approach. Obtaining boron from organic matter or liquid seaweed instead may be less risky.

8. Chlorine was added to the plant micronutrient list in 1946 since it was found that chlorine molecules are required as part of the machinery of photosynthesis – particularly relating to the water-splitting system. In addition to this essential function, chlorine has also been found to be beneficial at macronutrient levels, enabling “increased fresh and dry biomass, greater leaf expansion, increased elongation of leaf and root cells”^ref.

Since most people will be using tap water for watering their bonsai, getting adequate chlorine to your trees should not be a problem, but if you are using rainwater perhaps consider tap water every now and then.

9. Copper is essential for plants because along with iron it makes up part of an enzyme called cytochrome oxidase which performs the last of a sequence of steps in respiration^ref. Cytochrome oxidase is present in the mitochondria of plant cells – these are separate organelles with their own unique DNA which are dedicated to energy production. Copper is also found in plastocyanin, a protein which is responsible for electron transfer in the thykaloid – the light-dependent part of the chloroplast^ref. This protein is key to the conversion of light energy to chemical energy in the cell during photosynthesis. Copper is found in the soil but apparently is deficient in soils with high amounts of organic matter^ref.

10. Iron is present in a large number of different enzymes within plant cells, appearing in chloroplasts (where photosynthesis takes place), mitochondria (where energy is created) and the cell compartment. Iron is therefore a key nutrient for growth and survival in plants – in just the same way it is with humans and other forms of life. Iron is a component of so many enzymes that there is a specific name for them – ‘FeRE’ or iron requiring enzymes (Fe is the chemical symbol for iron).

Iron can be toxic if too much is present, so plants have evolved mechanisms to remove it when it gets too high. ^ref1 ^ref2 ^ref3

11. Manganese is also a co-factor to enzymes involved in photosynthesis, as part of the ‘oxygen-evolving complex’ in photosystem II, which contains 4 manganese ions. Photosystem II “is the part of the photosynthetic apparatus that uses light energy to split water releasing oxygen, protons and electrons”^ref.

12. Molybdenum is used by certain enzymes to carry out redox reactions (reactions where electrons are gained or lost from a molecule); these include nitrate reductase, xanthine dehydrogenase, aldehyde oxidase and sulfite oxidase^ref. Its role facilitating the nitrogen pathway in a plant is important since nitrogen is the nutrient plants require the most of, and the presence (or absence) of molybdenum can make a big difference to the efficiency of nitrogen uptake which in turn affects growth rates and plant health.

13. Nickel is a co-factor to the enzyme urease which breaks down potentially toxic urea (a product of metabolism) into ammonia which can then be used as a source of nitrogen for the plant^ref.

14. Zinc is the final micronutrient alphabetically but not in terms of importance. It is associated with 10% of all proteins in eukaryotic cells including those of plants, assisting as a co-factor to many enzymes and so enabling many different biological processes including transcription, translation, photosynthesis, and the metabolism of reactive oxygen species. Zinc also plays a role in ensuring the correct folding pattern for proteins as they are created.^ref

Interestingly, zinc deficiency is associated with smaller leaves and internodes, which you might consider a benefit for bonsai, but perhaps not at the expense of your trees’ core biological processes!

Wait – I only got to 14 and there are supposed to be 17 – what the heck? Oh yeah – here they are (15) carbon and (16) oxygen from carbon dioxide, and (17) hydrogen from water (H2O). Did you know that the oxygen emitted from plant photosynthesis actually comes from the water and not from the carbon dioxide? More in Photosynthesis.

Embolisms

You may have heard of embolisms in the context of humans – this is when an artery is blocked by something like a blood clot or a bubble of air^ref. A similar process can happen with trees and their xylem (water carrying) vessels.

As outlined in trees’ water system, water enters the tree’s root cells and is pulled in a continuous stream up through the xylem by the negative pressure created by leaf transpiration in the canopy. The xylem is actually a “continuous water column that extends from the leaf to the roots”.^ref

If a bubble of air gets into the xylem, this breaks the water transport process and stops water from below the bubble being lifted any further. This stops water from reaching any parts of the tree dependent on the xylem cells which have been affected. Embolisms in trees are also known as ‘cavitation’. This process is even audible and apparently explains half of the sound heard from drying wood.^ref

Thomas explains this really well in chapter 3 of his book in the section ‘Air in the system’. He says embolisms can occur from water in the xylem being under too much tension (ie. the tree becoming too tall or too high a rate of water being transpired), from xylem damage, or from freezing.

Embolisms are relevant to bonsai enthusiasts for two main reasons. Firstly they explain why a tree may die if it isn’t watered. When in leaf (for deciduous trees) and all the time for evergreens, transpiration will occur as water evaporates from the leaves through their stomata. If transpiration happens faster than the tree can replace water through its roots, embolisms can occur. If too many embolisms occur, the tree might not have enough routes for water to reach the cells, or enough volume of water to meet their needs.

The second reason why embolisms are interesting from a bonsai perspective is that they also explain the two very different xylem structures which can be observed between trees and which have implications for their growth behaviour.

All conifers and some angiosperms called ‘diffuse porous’ trees, add to their xylem network each year, and have many smaller, narrower, interconnected xylem vessels which don’t allow large air bubbles to form. These trees have active xylem in multiple rings (Thomas says that conifers can have 30-40 years worth of rings still actively transporting water up the tree). In cross-section they have small ‘pores’ and a denser consistency.

The alternative approach is taken by ring porous trees, which regrow their xylem vessels every year, and only ever have a single ring of much larger, longer super-pipes of active xylem transporting water. These trees can grow much quicker because their water transport is more efficient in the right conditions (ie. not freezing). But they can’t break bud until they’ve constructed the new year’s xylem. This explains why some species such as oak leaf out relatively late – they have to spend time at the beginning of the season regrowing their xylem ring. An evergreen tree cannot be completely ring-porous, because it would not be able to supply water to its leaves through the winter.

Like everything in nature there are trees which are combination of the two as well. There are some nice microscope images of the xylem vessels of different types of wood here. The difference in size between coniferous species (whose xylem cells are called tracheids) and angiosperm species (whose xylem cells are called vessels) is show in the table below^ref:

As can be seen, conifers have tracheids which individually don’t get much longer than 2-3mm or wider that 10-12 μm (note that the table uses a logarithmic scale). Ring porous species on the other hand have vessels in the 1-12cm range in terms of length, and 20-80 μm wide.

The implication for this from a bonsai point of view is that even though our trees are small, for those species which are ring porous trees (mostly deciduous angiosperms) embolisms are perhaps even more of a risk. The scale at which we are working means there are only a small number of vessels available for water transport – a 20cm high tree might have single vessels all the way from root to crown. To mitigate this risk we should ensure these trees are well watered especially when it is hot or windy, and that they have the energy and nutrients to regrow their xylem every season.

I’m still trying to find a definitive source with a list of which species are ring porous and which are diffuse porous, but here’s what I’ve found so far (Ennos, Thomas, and some reference articles ref):

All conifers are diffuse porous, as they have tracheids (short & narrow) providing their water transport. Embolisms in these tracheids dissolve naturally due to their small size.
Diffuse porous angiosperms have narrower vessels – they are still vulnerable to embolism but less than ring porous trees, and have adapted mechanisms to resolve them, such as pumping water (sap) up from the roots to refill the vessels in spring (Ennos): poplars, beech, birch, maple,
Ring porous angiosperms have wide, fast flowing vessels and routinely get embolisms every winter, requiring a new set of vessels to be grown every year: oak, ash, black locust, catalpa, chestnut, hickory, mulberry,

Nutrients for Trees

Before we dive into this subject, it’s important to know there are two aspects of ‘feeding’ trees and the one we are going to cover in this article relates to the nutrients that plants need in order to generate new cells and growth.

The other aspect relates to the nutrients which can contribute to a better growing environment for the plant – for example, increasing mycorrhizal fungi, reducing pathogens, and improving the community of bacteria interacting with the roots of the plant. You can read about those in Non-nutrient Additives.

In general true nutrients – as they are referred to in the literature – are elements – ie. they are not able to be decomposed into smaller components, and you will find them all listed on the periodic table of elements. There are 17 elements which are recognised as plant nutrients, and from these trees synthesise their own biomass as well as everything that’s needed to make it (like secondary metabolites, enzymes, carbohydrates, plants produce literally thousands of compounds).

Three of the required elements are derived from air and water (oxygen, carbon and hydrogen). Of the remaining 14, there are six macronutrients (present in higher volumes) and eight micronutrients (required in smaller amounts).

This is important for bonsai because trees usually obtain all of their nutrients from air, water or soil. Since bonsai are not planted in soil, they are vulnerable to nutrient deficiencies. To learn more about how trees absorb nutrients, check out how roots absorb water & nutrients. For a description of each nutrient, why it’s needed and how it’s obtained by plants when not in a pot, please read the post on what each nutrient does. If you don’t want the detail, below is the (relatively) short version…

There are two ways in which nutrients are used by a plant and these relate to what the tree is, and what it does.

What are trees made of?

The main structural components of trees are lignin and carbohydrates. Lignin is a polymer which combines three types of alcohol (p-coumaryl, coniferyl & sinapyl) in different ways, which in turn combines with cellulose (a carbohydrate) to form wood. Lignin makes up 25–35% in gymnosperms^ref and 20–25% in angiosperms, cellulose makes up most of the rest, with 4-10% of other components. Whole text books have been written just on the topic of lignin and it isn’t fully understood as a substance – it could be considered the ‘secret sauce’ to tree success. Feel free to spend $183^ref to learn more…or buy another nice tree instead!

Both lignin and cellulose are made up of carbon, hydrogen and oxygen, all of which is obtained from air & water through photosynthesis.

What do trees need to function?

A tree can’t become a tree with just carbon, oxygen and hydrogen, even though those elements make up most of its structure. It needs chemical reactions to take place throughout its life to create the cellulose and lignin, and to manage all of the processes needed to maintain life. This is why it needs other elements in addition to C, O & H.

Key reactions within a tree include photosynthesis, nitrogen capture, cell division and defence against pathogens – but there are millions of chemical reactions going on inside a tree at any given time. Many of these depend on enzymes, a type of protein which acts as a catalyst – that is, it enables something to happen without being consumed by the reaction itself.

As a protein, enzymes are made up of amino acids, which all contain carbon, hydrogen, oxygen, nitrogen and (sometimes) sulphur. This is where the first two nutrients come in – nitrogen is needed in every enzyme, and sulphur is needed in some.

Enzymes are really interesting because they don’t just make reactions happen, they also speed them up in really clever ways (to learn more see Jim Al-Khalili’s book Life on the Edge: The Coming of Age of Quantum Biology^ref). To do this, they use other elements, including metals like potassium, iron, copper, manganese, magnesium, nickel & zinc. Boron, chlorine and molybdenum are non-metal enzyme co-factors (elements which enable enzymes to function).

The remaining two nutrients are calcium and phosphorus. Calcium is used by plants in a similar way to humans, as calcium pectate it acts as a skeleton, strengthening cell walls. It also acts as a chemical messenger as part of processes related to root and bud growth and responding to stress. Phosphorus has multiple roles, as a component of the molecule ATP (adenosine triphosphate) which is used by all living things to store and transfer energy, as the structural framework for DNA & RNA and as part of the carbon fixation process.

How to obtain nutrients for trees?

So we know that plants need significant levels of nitrogen, phosphorus, sulphur, potassium, calcium and magnesium and they also need smaller amounts of boron, chlorine, copper, iron, manganese, molybdenum, nickel and zinc. According to Hallé in his absolutely brilliant book ‘In Praise of Plants’, Nitrogen is a key limiting nutrient for plants. He says “Although they easily assimilate carbon, nitrogen remains a constant problem for plants. It is the reason that they are poor in proteins and rich in carbohydrates. The situation is the opposite in animals…”

Standard non-organic fertiliser does not contain all of these nutrients, so you need to make sure they are added somehow – either via an organic fertiliser or a combination of additives like liquid seaweed, compost or fermented/decomposed manure. Take care you understand what the definition of an organic fertiliser actually is. Unfortunately most fertilisers do not reveal their composition on their packaging, so look for one which does. My personal investment in fertiliser is my purchase of a Hotbin hot composting bin – this creates organic compost in 3 months and produces leachate which can be used as a liquid fertiliser. Also consider your carbon footprint. As mentioned in the what each nutrient does post, Ammonia production for chemical fertilizers is a major contributor to global warming as it uses fossil fuels as the main ingredient, as well as massive amounts of energy to produce, and contributes to ecosystem damage through nutrient runoff. Using compost with some manure is a more environmentally friendly way to provide nitrogen to your trees.

Consider your watering as well. Trees need *some* chlorine and grow better if they have a bit more than merely what they need – tap water can provide this nutrient if you use it for watering. You should check your local water company report as you may be able to obtain other nutrients from your water as well, including magnesium.

Whilst there are many research studies identifying the effects of nutrient deficiencies, there aren’t many with evidence for nutrient toxicity so it’s hard to work out if this is a myth or reality. Living things tend to have a system of homeostasis to manage levels of chemicals to avoid them getting too high (or low depending on the substance) so it may be that toxicity is rare due to homeostatic mechanisms removing excess nutrients.

Some bonsai practitioners are fans of foliar feeding. This can be useful in certain circumstances, but the better approach is to add nutrients to the soil.

How much is enough?

This is where the evidence starts to get very thin on the ground. Nutrient requirements vary between plant types and their ability to obtain nutrients is dynamic – it depends on the presence of other nutrients, temperature, pH, energy availability, the size of the plant – there are a lot of variables. Probably the best approach is to follow the guidance on the fertiliser you are using.

Reabsorption of Nutrients

A word of warning to those who like to remove those ‘messy’ dying leaves on deciduous trees at the end of the season. Towards the end of the growing season, once the tree has made enough wood and grown enough leaves, and, from the tree’s perspective, done everything it can to reproduce, it stops focusing on growth and goes into an orchestrated shutdown phase.

During this phase substances from the leaves are reabsorbed into the tree, to be stored in the rays and roots for use again next year – enzymes are again deployed to effect this absorption. This is why leaves change colour as different substances are reabsorbed. What is left in the leaf when it finally drops is actually quite low in nutrients. So let the tree drop its leaves as it wants, to optimise its health for next year.

Defoliation

There are quite a few research papers about tree defoliation because this can be caused by insects, creating a problem for the forestry industry. Defoliation is used on deciduous trees in bonsai to completely regrow a deciduous tree’s leaves, resulting in ramification and smaller leaves. This isn’t a practice for conifers, or at least, not for most of them, as many conifers simply can’t regenerate very easily and the effect will be weakening of the tree and not ramification. Although I must note here that my 2022 summer watering disaster caused a small larch forest of mine to defoliate and it looked fantastic after the foliage regrew!

Complete defoliation is a pretty drastic practice from the tree’s perspective and a double whammy – as not only does the tree have to use its stored energy reserves to regrow its leaves, it doesn’t have any energy coming in until those leaves are regrown. Defoliation significantly reduces the total stored carbon in a tree, and there is a point at which mortality occurs – one study found that once stored carbohydrates were less than 1.5% of the usual level, this will kill the tree.^ref

As described in this article about the effect of grazing animals, “Plants adjust to conditions of chronic defoliation and the associated reduction in whole-plant photosynthetic rates by altering resource allocation patterns and reducing relative growth rates.”^ref Although the article is focused on grasses, which are a different branch of the Plantae family to trees, it says that “root elongation essentially ceases within 24 hours after removal of approximately 50% or more of the shoot system…[and there is]…a rapid reduction in nutrient absorption”. So basically by defoliating 50% or more the roots will stop growing and nutrient absorption will reduce. Interestingly, several studies reported that photosynthetic capability of the remaining leaves on defoliated plants actually increases – perhaps a result of the resource allocation pattern change mentioned above.

The effect of defoliation is to force a deciduous tree to use the stored energy it has built up in the growing season straight away, instead of leaving it for the next season. Because of this, the tree doesn’t have the energy reserves to grow a full set of leaves at the same size it would normally, so it compensates by growing smaller leaves. Since this technique uses up stored energy, there isn’t much left for other types of growth, so it’s not a technique you would use if you were trying to thicken a trunk or grow branches.

This study^ref found that a 50% defoliation of prunus saplings reduced their growth rates for the following 5 years and brought forward bud burst for a similar period, while this one^ref found that larch recovered well from defoliation, but pinus did not. This one^ref said that partial and complete spring defoliation reduced first-year diameter, height, and volume growth of 4-year-old loblolly and slash pines.

This article says that “scientists found that growth was reduced in both half and entirely defoliated trees in the short and long-term…both half and entirely defoliated trees had less leaf area than control plants. Defoliated trees also allocated more carbon for storage than control trees with no defoliation.”^ref This suggests that defoliation in some way teaches your tree to divert resources to storage instead of foliage, not just once but into the future. Which means you really don’t want to do this while you are still establishing the branch structure and ramification because these will slow.

Interesting, Harry Harrington reports that some species don’t respond to complete defoliation by growing smaller leaves, instead they grow a small number of large leaves^ref. So overall a complete defoliation may be an unnecessarily unpredictable and heavy-handed way to achieve leaf reduction. One could hypothesise that defoliation of a tree which follows a fixed growth pattern (read more in Extending Shoots) might result in a greater leaf reduction effect, because buds and nascent leaves are not sitting there waiting to burst, they need to be completely regrown. But one could also hypothesise that this type of tree might struggle to regrow any leaves at all, depending on the weather conditions.

There are less drastic options than removing the entire foliage of a tree all at once – you can remove half of it for example, or do it in stages, so that new leaves can grow before the remove the next batch. It seems like you should be able to achieve a similar effect with constant low-level leaf pruning throughout the growing season, combined with bud pinching at the start of the season. A more gradual approach would allow photosynthesis and energy generation to continue, without stopping root extension and nutrient uptake, while still regrowing leaves and increasing ramification. It may be however that the shock of something more drastic is what’s needed to reduce leaf size significantly because the resources to regrow are shared more widely. An experiment for someone?

The timing of defoliation is really important. The tree needs to have had enough time with its new leaves to generate good energy stores for the next season and enough time to regrow and harden its leaves against frost. Somewhere in the middle of the growing season allows for both of these to happen^ref.

Should I remove flower buds or fruit?

That depends what tree you have and what you are trying to achieve. Obviously if you have satsuki azalea, you probably want to leave the flowers on the tree! If you have a crabapple, personally I don’t think there is much point if you don’t let a few fruit form. And I am really partial to rose-coloured larch cones. All trees form some kind of reproductive organs, whether they be conifers with their strobili (cones, either pollen or seed forming), ginkgo with their ovules, or angiosperms with their flowers and fruit. Some are almost unnoticeable and others are right in your face. Bonsai wisdom sometimes says these should be culled or removed entirely in order to avoid draining the tree of its energy.

When considering this question we need to understand the idea of resource ‘sources’ and ‘sinks’ in plants. A source is a material producer and exporter, and a sink is a material importer and consumer.^ref See the below table for sources and sinks in trees. As you’d imagine, leaves are a major source of carbon and a sink of inorganic nitrogen (nitrogen as a macronutrient). Roots are a source of inorganic nitrogen and leaves are a sink. So what about fruit, seeds, and flowers, which supposedly drain the tree? As you can see they are major sink organs – but not only sink organs…they are also source organs!

https://academic.oup.com/jxb/article/68/16/4417/3002648

Let’s have an interesting little diversion – did you know that it’s not only leaves which photosynthesise? This fascinating study^ref looked at the photosynthetic activity of (a) ears of wheat (b) sycamore seed pods (c) a green tomato (d) unripe and ripe strawberries (e) a greengage (f) unripe cherries; and (g) a green apple. The images below were taken using fluorescence imaging and anything with a colour indicates that there is photosynthesis taking place – with the red and orange areas the strongest. Check out the sycamore seed pods!

https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14633

How the heck can this happen – well there are various theories about the mechanism (including recycling CO₂ from respiration, and the presence of stomata on fruit) but the point is that maybe seeds and fruit, particularly if they have periods when they are green, don’t act as such as sink as we might think, and for a period are acting as a source and not a sink.

This study states that “reproduction in Beech does not deplete stored carbohydrates, but it does change the amount of nitrogen stored” and this study found that “fruiting is independent from old carbon reserves in masting trees”^ref which basically means that fruit uses current year photosynthates/energy and doesn’t actually deplete reserves.

On the other hand this study found that Douglas fir tree rings were narrower in years when they bore many seed-cones^ref and this one mentions that “experiments with apple trees have shown that roots can die from lack of carbohydrate supply when they are over cropped”^ref

All living things have processes for managing and balancing resource allocation^ref and this is likely an evolutionary differentiator. In trees, resource availability limits the amount of fruit which is allowed to develop – even pollinated flowers may not develop into fruit if the tree does not have enough resources available – these could include energy, or nutrients.^ref So to an extent the plant itself manages the resource allocation.

To complicate matters further many trees use a ‘masting’ strategy for reproduction, which means they have years where many more seeds are produced, often synchronised with other trees of the same species. One theory for how this happens is that the weather influences how pollen is distributed – in beech windy conditions lead to mast years whereas in oak short pollen seasons do.^ref Temperature and precipitation also affect pollen production and distribution (high temperature increases pollen production but high precipitation washes it away).^ref In this study on Japanese oak, “high seed production never occurred in two successive years, but successive years of low abundance were observed several times between 1980 and 2000.”^ref

Overall there are a lot of factors interacting when it comes to reproduction. Photosynthetic seeds or fruit can contribute to carbon production, and may use only current year photosynthates, so the tax may not be as high as thought, but there is some evidence that reproduction can divert energy from roots and foliage.

If you are really focused on trunk growth, branch structure or foliage development on your bonsai tree, you might want to divert the energy from reproduction to these areas by removing some or all reproductive organs, until you are happy with the trunk/foliage. At this point then you could then let the tree reproduce (noting that removing cones one year will cause more cones to develop the following year)^ref.