Tag Archives: Photosynthesis


Another epic topic which has occupied scientists for the best part of 400 years, the equation for photosynthesis itself was not understood until the 1930s.ref

Photosynthesis is the process of turning energy from sunlight into chemical energy, a process which famously is performed by plants, specifically by plant cells containing ‘chloroplasts’. Chloroplasts contain a substance called chlorophyll. Chlorophyll is often described as a ‘pigment’ – but this makes it sound like its only role is to colour things green! Which of course it isn’t – being green is just a result of its real function which is to absorb sunlight of a certain spectrum. Chlorophyll absorbs visible light in two regions, a blue band at around 430 nanometers and a red band around 680 – according to Vogel. Other sources state the bands are 680 nm and 700 nmref. Everything else is reflected, which looks green. Chloroplasts are believed to have originally been cyanobacteria which were incorporated into plant cells to provide photosynthetic capability (Lane, 2005). To see where chloroplasts and chlorophyll are present within a leaf, check out this post on leaf structure.

The sequence of reactions which happen during photosynthesis are known as the Calvin-Benson-Bassham cycle, after the scientists who discovered it. The simplified equation describing photosynthesis is as follows:
6CO2 + 6H2O –light energy–> C6H12O6 + 6O2.

This suggests that photosynthesis is the exact opposite of respiration, creating glucose instead of consuming it. But actually this equation is incorrect as photosynthesis does not create glucose. The Calvin et al cycle produces a molecule called G3P which is a 3 carbon sugar which can be used to create other molecules. Anyway, that’s probably not super-relevant for bonsai! The main insight from the equation above is that light energy is needed for plant survival and growth – this is why trees do not like being inside unless they have a suitable artificial light source.

Another point to note is that plant cells, like all living cells, respire. Plant cell respiration is like animal respiration, that is, cells consume oxygen and glucose to produce energy, while emitting carbon dioxide and water. Cells use respiration to generate the energy they need for metabolism (basically, keeping the cell alive and functioning). All cells in a tree respire, including the leaves, roots and stems, 24 hours a day. This means trees offset some of their photosynthesis by respiring – in particular at night when no photosynthesis occurs.

On balance, leaves produce a lot more sugars and oxygen through photosynthesis than they use during respiration – and this provides the energy they need to maintain themselves and grow. In fact the point at which they *don’t* produce more than they use through respiration is as low as 1% of full sunlight (Vogel). Note that this low level can be reached if a leaf is entirely shaded by 2 other leaves, since the typical light transmission through a leaf is only 5%.

Another interesting fact about photosynthesis is that leaves can only use about 20% of full sunlight before the photosynthetic system saturates (Vogel). This number actually varies depending on the species and leaf type. So leaves below the top layer (likely to be ‘shade leaves’ described in this post: Leaves) can still get enough light from partial exposure, if they are slightly shaded or lit for only part of the day, to saturate and max out their photosynthetic capability. The majority (99%) of the energy absorbed is used to maintain the leaf itself, so only 1% is released for growth.

But – back to the photosynthesis equation – which is an extremely simplified version of what is actually happening. Photosynthesis requires 150 discrete steps involving a similar number of genesref. A good reference is this Nature article.

Photosynthesis takes place in two stages. First the ‘light dependent’ reactions happen. Light energizes electrons within the chlorophyll, and these electrons are harnessed to produce ATP (adenosine triphosphate) and NADPH (nicotinamide adenine dinucleotide phosphate) which are molecules used by cells for energy and as an electron source. The chlorophyll replaces its lost electrons by taking some from water – effectively they ‘burn’ or oxidise water, leaving the oxygen behind as a waste product (Al-Khalili).

After this the ‘light independent’ reactions happen. These are facilitated (sped up) by an enzyme known as RuBisCO. Using the energy sources created in the first step (ATP and NADPH), RuBisCO ‘bolts’ together the hydrogen from the water, and the carbon and oxygens atom from the carbon dioxide, along with phosphorus, to make the 3 carbon sugar glyceraldehyde-3-phosphate (C3H7O7P) (Lane, 2005). This is known as carbon fixation.

In reality there is also a third stage where the ingredients for the cycle are regenerated so that it can continue running.

The full equation (the Calvin-Benson-Bassham cycle) – is:
3 CO2 + 6 NADPH + 6 H+ + 9 ATP + 5 H2O → C3H7O7P + 6 NADP+ + 9 ADP + 8 Pi   
(Pi = inorganic phosphate, C3H7O7P = glyceraldehyde-3-phosphate or G3P)

Sorry for geeking out for a minute there!

An important point is that photosynthesis doesn’t just go up with increasing sunlight, it has a set of limiting factors which were described by Blackman in 1905 in his articleref “Optima and Limiting Factors”. He said “When a process is conditioned as to its rapidity by a number of separate factors, the rate of the process is limited by the pace of the slowest”. The limiting factors he described for photosynthesis included light intensity, carbon dioxide and water availability, the amount of chlorophyll and the temperature in the chloroplast.

The amount of sun needed to max out photosynthesis from a light intensity point of view is not as high as you would imagine. Vogel says a leaf “absorbs about 1000W per square metre from an overhead sun shining through a clear sky” and photosynthesis only consumes 5% of this – 50W per square metre. Obviously this is going to vary depending on the species and whether a leaf is a sun leaf or a shade leaf.

But what does it mean for bonsai? Well – you might have spotted some other elements in the photosynthesis equation. NADPH (formula C21H29N7O17P3) contains nitrogen and phosphorus, as does ATP (formula C10H16N5O13P3). RuBisCO relies on a magnesium ion to perform its role as a catalyst. There are a bunch of other enzymes and co-factors which are required to support photosynthetic reactions as well – which explains why certain nutrients (including Nitrogen, Phosphorus, Magnesium, Potassium, Chlorine, Copper, Manganese and Zinc) are critical for trees in varying amounts – more here: Nutrients for Trees.

And if you’re concerned about whether your trees have enough light for photosynthesis, you can see exactly how much energy is arriving on your outside bonsai at this site. Find your location and download the PDF report and you’ll see the irradiation levels – which can be useful in understanding how your bonsai trees will fare. As an example, the max in my location is 328Wh/m2 in April which explains why the olive trees in London are so unhappy looking – if you look at irradiance in Greece, where they thrive, it barely ever goes under 328Wh/m2 even in winter! Trees in Greece receive nearly double the amount of irradiance than those in South West London.

One final point of interest with admittedly little relevance to bonsai – some plants (nineteen different plant families, independently of each other) evolved an improved photosynthetic process which is known as C4 photosynthesis. This concentrates CO2 nearer to the RuBisCO enzyme, reducing its error rate. Unfortunately most trees use C3 photosynthesis with its associated inefficiency – other than Euphorbia, which are apparently “exceptional in how they have circumvented every potential barrier to the rare C4 tree lifeform”ref.


Rather naively, when setting up this website, I made a note to create a post on the topic of ‘leaves’. Several days of research later it’s clear, there can’t just be one post about leaves! Why? Well, leaves are the reason that complex life on earth exists. Their ability to photosynthesise – to turn energy from the sun into energy that living things can use – is fundamental to our planet. So – there is a lot going on inside a leaf. My starting point for this post is the wonderful book ‘The Life of a Leaf’ by Steven Vogel, and I am going to cover the purpose of leaves, respiration, transpiration, and how leaves deal with environmental challenges like heat, wind and cold. There is a lot more to know about leaves, to read this check out all the other posts tagged with ‘leaves’, or start with leaf structure.

So, what is the purpose of leaves? Simply, they are the energy generating mechanism for plants. Through the process of photosynthesis they use energy from the sun to ‘burn’ water, removing its oxygen atom and bolting the remaining hydrogen onto carbon dioxide to create sugars. These sugars are used to power the life and growth of the plant. And as a side-product, oxygen is created, for animals and humans to breathe. Photosynthesis only happens when a leaf is illuminated by the right kind of light – in nature, this is sunlight during the day. If you want to geek out with more detailed information about how photosynthesis actually works, try this post: photosynthesis

A key concept when it comes to leaves is transpiration. It turns out that up to 97% of the water used by plants is actually evaporated back into the air – a process known as transpiration. The reason for this is because plants need to get CO2 into their leaves in order to supply it to the chloroplasts (organelles which perform photosynthesis) and to make this possible they need to open holes on the leaf surface to allow CO2 molecules to enter – these holes are known as stomata. When the stomata are opened, water naturally evaporates from within the leaf – it is the negative pressure in the xylem caused by this evaporation which pulls the water (and nutrients) up from the roots. What this means for bonsai is that your trees need a lot more water than you might think based on their size – remember up to 97% of it will be evaporated out. But if you water on a sunny day, will you burn the leaves? Find out here.

Did you realise that individual trees have leaves of different shapes and sizes, depending on their position on the tree? Shade leaves are larger, thinner, darker green (containing more chlorophyll) and less lobed, with fewer stomata than sun leaves; conversely sun leaves are smaller, thicker, lighter yellowish green, more lobed, and have more stomata – each leaf is more efficient in their niche of light exposure (Thomas). In her book The Arbonaut, Meg Lowman describes a coachwood tree with each leaf having its own unique formula for success – the lower leaves are long-lived and better structured to harvest low amounts of filtered light, the upper leaves are short-lived “extremely high-powered chlorophyll factories…[which]…produce sugars that keep the entire tree alive, healthy and growing”. And between these, variations to suit the different light conditions. All of this is called ‘photomorphogenesis’, or a “developmental process in plants in which the incident light determines the growth of the plant”ref. One research team even discovered a gene which could force the growth of sun leavesref and resulted in 30% greater photosynthesis.

What this means for bonsai is unclear as it’s not obvious from the research at what scale these differences can manifest. In theory there will be a layer of leaves around the canopy of the bonsai tree which could be sun leaves, and leaves below and within it which could be shade leaves. If it is literally only the sun exposure on a bud which determines what type of leaf is grown, then theoretically these two different leaf types could appear on a bonsai. If so, then removing the top layer of leaves – as is often recommended in bonsai, to ‘let light into the tree’ may not be the best course of action. If the leaves below have grown as shade leaves they may struggle to tolerate their new position in full sun. Anyone noticed sun & shade leaves on their bonsai? Let me know at info@bonsai-science.com.

‘Leaf morphology’ – or the shapes and sizes of leaves – is another rabbit hole you can joyfully enter via Google if you so desire, but to sum things up, leaves have differing physical attributes, each lending the leaves different properties – “leaf traits may reflect the adaptation mechanisms of plants to the environment.”ref

A key measure related to leaves is the ‘specific leaf area’ – the ratio of total leaf area (ie. the total amount of leaf surface) to total leaf dry mass (the total weight of the leaves without water). SLA is used as a measure of the overall health of a plant, as it reflects the efficiency of carbon gain relative to water lossref.

What is observed is that different trees have different strategies for optimising specific leaf area – in addition to photosynthesis mentioned above. Three interrelated attributes include leaf size & shape, leaf venation (how the xylem & phloem ‘veins’ are structured) and stomatal conductance (the number and distribution of stomata on the leaf).ref The model in this article suggests several predictions related to these attributes.

One of these is that a leaf with a larger width to length ratio can support higher carbon production factors, stomatal conductance, and leaf area than a leaf with smaller width to length ratio. So long, narrow leaves are less efficient and have higher ‘stomatal resistance’ – ie. they are less efficient at transporting gas and water vapour in and out of their leaves. This also applies for thick leaves, which have higher stomatal resistance than thin leaves.

That’s not all bad though, because higher stomatal resistance is correlated with smaller xylem, which are more resistant to embolism. These tradeoffs help different trees thrive in different conditions and drive evolutionary adaptation.

The implications of this model that on average narrow leaved species will do better in more arid conditions with less available water, since they transpire more slowly and are less at risk of embolism, and as water becomes more available the broadleaved trees will do better. So conifers may do better on a mountain top, and angiosperms such as beech will do better in the valleys. Translated to bonsai medium, this suggests that a narrow leaved tree (including most conifers) will prefer a more well-drained medium (hence the advice that conifers don’t tend to like getting ‘their feet wet’). Your tropical trees on the other hand – like a Ficus – may be perfectly happy with extremely wet conditions (as long as they don’t become anoxic – ie. so wet they prevent any oxygen from entering).

Leaves have more to contend with than ‘just’ photosynthesising and transpiring – they also have to deal with extremely large temperature variations – “on windless days, ordinary leaves on ordinary trees quite commonly run around 10°C, nearly 20°F, above the air that surrounds them. Under exceptional (exceptionally bad) circumstances they can reach twice that.” So explains Vogel, who then describes in detail the different strategies used by leaves to cool down – starting with evaporation but also including reradiation (radiating heat back into the air) and convection (transferring heat to the air from leaf surfaces and edges). He suggests that smaller, more lobed leaves are better at cooling than large wide leaves – and that large wide leaves avoid horizontal positioning in order to reduce overheating. What this means for bonsai is probably just that the natural leaf shape and positioning of a particular species helps it achieve a temperature balance (as well as photosynthesis) – and also perhaps that highly ramified trees with lots of smaller leaves may have improved temperature regulation (due to improved convection).

Another environmental challenge faced by leaves is freezing temperatures through the winter. One obvious strategy for avoiding these is to be deciduous, but there are plenty of evergreen trees out there and many of them thrive in extremely cold conditions (eg. the boreal forest where snow cover lasts for months and “gymnosperms such as Abies, Larix, Pinus, and Picea dominate”ref). Of the various strategies deployed to avoid damage from freezing (four at least are described in detail by Vogel, as well as in this paperref), the strategy most relevant to bonsai is that the tree generates substances within its cells and organs – such as dissolved sugars, resins and anti-freeze proteins – which reduce the freezing temperature in cells, reduce ice crystal formation and prevent ice crystals from growing within cells. The reason this is relevant is because one of these mechanisms – the creation of anti-freeze proteins – requires a gradual acclimation to the cold. This allows the tree to turn on the genes which produce the anti-freeze proteins, and gives it enough time to accumulate them. So it is a bad idea to move a conifer from a warm/protected area directly into the freezing cold. But if that tree has been in the same place as the seasons change, it will likely have time to build its defences against freezing temperatures.

The final environmental challenge described in fascinating detail by Vogel is the wind. Leaves are adapted to deal with wind so that they can continue to photosynthesise but also not tear, or build up enough resistance to pull the tree over. They do this by bending with the wind into aerodynamic shapes which minimise drag – Vogel’s research includes a great photo illustrating how four different groups of leaves move into cone shapes as the wind increases. One key point for the bonsai enthusiast though – leaves are more resistant to the wind once they have hardened off – if they are new spring leaves they are more prone to being wind damaged.

It’s not just the leaves which contend with all these environmental challenges though, it’s all the microbes on the leaves, in its phyllosphere.

I could write pages and pages more on this fascinating aspect of tree biology but for now I am going to leave it there.