Tag Archives: Pruning

Root-Shoot Connections (aka sectional growth) – when will pruning one kill the other?

Sometimes in a bonsai context it’s said that specific branches are connected to specific roots – often in discussions about pruning and carving. For example it may be suggested that pruning a specific branch will kill an associated root, or vice versa.

As I’ve learned over the last 6 months researching this site, when it comes to trees – ‘it depends’.

The effect of pruning branches or roots on the rest of the tree comes down to its ‘plumbing’ – that is, the way in which the xylem (water) sap and the phloem (sugar) sap flow around the tree. That plumbing is laid down as new shoots and other organs develop – each new organ has a connection to a vascular bundle with xylem and phloem ‘pipes’. These pipes (in reality different types of cells which connect to each other), then connect to the vascular system in a branch, then in the trunk, then to the roots.

Trees can have what is called ‘sectorial’ growth in one or both of these systems. Phloem appears to be more sectorial than xylem – there is less of it, it only runs around the outside of the trunk in a thin layer and it has fewer connections between cells than xylem. Since roots are dependent on phloem from leaves, this would suggest that roots might be more likely to die from a branch being cut than the other way around.

Xylem is a different system, and the way the xylem cells of a particular species are structured determines how sectorial that species is – trees with more connections between their xylem cells are less so (because water has more routes it can travel to reach an organ).ref

If you’ve read the post on xylem, you’ll know that all gymnosperms/conifers (and some angiosperms) accumulate water-conducting xylem rings over time and have many layers conducting at once. This type of wood is called diffuse porous. Some angiosperms have a different strategy – they regrow their conducting xylem every year and only use that one outer layer for water transport. These trees are called ring porous.

It may then be obvious to you that ring porous species are more sectored than diffuse porous species. This was confirmed in one study using dye injections into xylem vessels – diffuse porous Acer saccharum, Betula papyrifera, and Liriodendron tulipifera had dye show up in more leaves than ring porous species Castanea dentata, Fraxinus americana, and Quercus rubra.ref This is presumably because in diffuse porous trees there are more water conducting cells and more options for water to travel – it is less likely to get cut off.

Trees which have more isolated root – leaf paths include Quercus, Fraxinus, Prunus, Ulmus, Cotoneaster, Crataegus, Sorbus, Populus, Salix, some Acer and Olive.ref1 ref2 If you prune their roots, there is a higher risk of removing a xylem sap flow path to certain leaves and vice versa. Interestingly, if you look at anecdotal reports of ‘summer branch drop’ where trees drop their branches for no obvious reason, the species most susceptible to it appear to be these trees – Quercus, Fraxinus, Populus, Salix and Ulmus are all known for this phenomenon.ref This implies that a sector has died – perhaps due to embolism (air gaps in the xylem cells) – and the branch has dropped off as a result. The same could happen to your bonsai trees of this species, either by root pruning or by underwatering. Fellow bonsai enthusiasts have reported this in Salix (willow) and Morus (mulberry – also a ring porous species). The upside of this behaviour is the survival of the tree – since the death of one part of it doesn’t cause the death of the rest of it.

Trees which are more integrated include all gymnosperms/conifers and these have more uniform water distribution.ref Therefore they should be less susceptible to losing sectors due to root pruning or uneven watering. But once you’ve reached the point where they aren’t getting enough water overall (due to overly aggressive root pruning) or energy overall (due to overly aggressive leaf pruning), the tree is more likely to die since it is less able to keep one part alive separately to the others.

Note that trees may also drop branches for ‘economic’ reasons, when they don’t get enough return on investment from that branch, but that’s a post for another day.

Bonsai Tree Growth Stages

Most bonsai trees progress through stages of development, each with a different objective. In general the progression is thicken trunk -> achieve branch & root structure -> achieve branch, foliage & root ramification -> reduce leaf size -> evolve as branches grow/fall off. The faster we can move through the first few development stages, the faster we will have beautiful, well-proportioned bonsai – harnessing the tree’s natural growth is a way to speed this up. We also want to avoid doing things which slow down a tree’s growth during these phases, as this will mean it takes longer to get the tree we want. Read about how trees grow before starting at #1 below. Also consider what do old trees look like?

1. Trunk

Some bonsai enthusiasts collect mature trees for bonsai specifically so they can start with a thick trunk, following a collection process which minimises damage to the tree. The alternative is growing your tree’s trunk. Once a tree has its roots and foliage reduced in size in a bonsai pot, it won’t generate the energy needed to make significant sapwood additions and its girth will only increase by small increments every year. So you really need to be happy with the trunk size first before you stick it in a tiny pot. But – how big should a bonsai tree’s trunk be?

2A. Branch Structure & Overall Shape

Arranging the branches is what gives you the canopy and overall foliage shape that you’re after and the first step in this process is growing (or developing) the branches you want in the positions they are needed. Growing a branch starts with a new bud, which, unless it’s a flower bud, becomes an extending shoot and eventually a new branch. So firstly you need to work out where new buds will grow on your tree and then deal with the extending shoots as needed to get the required internode length.

You may need to remove some buds and shoots if they don’t help achieve the shape you are looking for – this should be done as soon as possible to avoid wasting the tree’s finite energy reserves. You have a trade-off to make here because leaving more foliage on the tree will provide more energy overall which contributes to its health and ability to recover from interference. However, growing areas of the tree which won’t be part of the future design is a waste of energy. You don’t want to remove so much of the tree’s foliage that it struggles to stay alive or develop the areas that you do want to grow out.

When you are creating your branch structure, often you will need to reposition branches – this is done with a wide range of different tools and techniques. A more advanced technique for adding new branch structure is grafting.

Sometimes the trunk itself or larger branches need a rework, to make them more interesting or to make them look more like old trees – for example adding deadwood or hollowing out the trunk. Usually this is achieved through carving.

2B. Creating a Strong Root System

The trunk thickening and branch structure phases both work best when the tree has lots of energy and so letting it grow in the ground or in a decent sized pot during these phases will get you there quickest. This also allows the roots to keep growing, but you want to understand about the role of roots, and root structure & architecture even if you still have your bonsai in a training pot. Particularly in this case, knowing about how to foster the the rhizosphere will help your tree stay vigorous. To maximise the roots’ exposure to nutrients and water you want to encourage Ramification of Roots (lateral root development).

Eventually it’s time to move the tree into a bonsai pot. This requires cutting back the roots, but as long as the roots are balanced with the foliage in terms of biomass, the tree should be OK. Root growth is usually prioritised outside of times of stem/foliage growth, and above 6-9 degrees C. So repotting might be best conducted at times that meet this criteria. Your growing substrate/medium is an important consideration.

3. Ramifying Branches & Foliage

Ramification is when branches subdivide and branch, giving the impression of age and a full canopy – and a well-ramified tree is a bonsai enthusiast’s goal. There are some techniques for increasing the ramification of branches and foliage. But not as many as there are for root ramification.

This stage also involves ongoing branch selection and reshaping (see 2A above). Another consideration is whether to keep or remove flower buds.

4. Reducing Leaf Size

An end stage in the journey to bonsai perfection is leaf size reduction. In nature, leaf sizes reduce relative to the biomass of the tree as it ages but since bonsai are small this effect doesn’t translate since the biomass never gets large enough. The tried and tested method for reducing deciduous tree leaf size is actually to practice one of the various methods of defoliation. A couple of others are covered here in reducing leaf size.

When to conduct these various activities depends on when the tree can best recover from them – which is a function of the Tree Phenology (or Seasonal Cycles).

5. Evolving Branches

Trees are not static organisms – they obviously continue to grow which is what we harness in the above steps. Part of this is that eventually branches may become too large for the design, or they may fall off (Peter Warren notes that Mulberry are known for this). As bonsai artists we want to have this in mind so that branches are being developed which can take their place in the future. This is an ongoing version of step 2A.

secateurs and bonsai scissors


Once your tree has grown in the general direction and shape you want, you can refine it through pruning. Cutting into a tree can affect its health & vigour, so it’s helpful to understand exactly what happens to a tree when you do this. A really excellent paper explaining the effect of pruning is available from Purdue Universityref but to summarise, pruning has the following effects on a tree:

  1. it removes photosynthetic material (leaves) thereby reducing the tree’s ability to generate energy
  2. it reduces transpiration (the evaporation of water from the canopy) and the rate of water transport up the tree
  3. it disrupts the pathways of plant growth regulators, causing regrowth but also consuming stored energy
  4. if the main xylem vessels in the trunk are cut, it causes embolisms which reduce the water carrying capacity of the tree
  5. it exposes the internal vascular system to the environment where bacteria and fungi can enter (by causing a wound)
  6. on some conifers, pruning the shoot or branch removes options for future bud growth because dormant buds and meristem tissue is often concentrated in the more recent growth

Minor Pruning

Minor or leaf pruning is used in bonsai to keep the shape of a tree according to a design, but also to create ramification and reduce leaf size (or, keep leaves small). As per point 3 above, pruning leaves drives the tree to refoliate and it does this by activating dormant or suppressed buds. In deciduous trees there is usually a bud in every leaf axil and this will go on to produce at least 2 shoots, so you also get increased ramification. With only stored reserves to use for refoliation, shared across twice as many buds, leaf size will be reduced. Read more in: ramification of branches and foliage.

Major Pruning

Major pruning which involves cutting off branches or significant parts of the foliage may have more impact on the tree. The first thing is that removing large amounts of foliage will reduce the tree’s ability to generate energy. It will also reduce the tree’s energy requirements but not by as much as is lost (since leaves are working for the whole tree and not just to sustain themselves). See this article: Defoliation.

Major pruning is often required to get the design you want for a bonsai. So is it better to grow out then cut back, or cut back then grow? Growing first generates lots of energy but also lots of wasted growth, which is eventually removed. Cutting first saves energy by directing it all to the places you want to develop on the tree, but it reduces the total amount of energy available for growth.

To test this look at the following calculation. If you start with two identical 50-leaved plants, and the goal of reaching a particular level of refined foliage in 5 years time, you have two options. Scenario 1 lets the plant grow unpruned all the way to the end of the period then has a major prune back down to the target level of foliage. Scenario 2 prunes every year, gradually building up to the target level. Although they start and end in the same place, the first plant has generated a whopping 195,250 ‘leaf units’ of energy for growth – 12x what the second plant has generated.

cut and grow model

As much as 80% of the energy created by leaves is exported to the other organs of the plantref. These energy units could have been used in places that don’t eventually get removed in the ‘Cut’ scenario, such as thickening the trunk, storing reserves for stronger budding or refoliation.

The most obvious risk with major pruning is the fact that you are effectively wounding your tree. Read more about how it responds in repairing (?) damage.

What kind of pruning tools should you use? Learn about the difference between carbon and stainless steel bonsai tools here.


Root Food Storage (or, can I root prune before bud break?)

One piece of advice often given to bonsai enthusiasts is that root pruning should be avoided until bud break – usually the advice says you should wait until the buds are just about to burst and then you can repot to your heart’s content. But is there any scientific basis to this? The rationale for the advice is the belief that trees store energy for bud burst in their roots, which translocates prior to bud burst and is used to power bud swelling and opening.

Below is a chart showing non-structural root carbohydrate levels through the year for Prunus avium – these include sucrose, glucose, fructose, sorbitol, raffinose & inositol. FB indicates when the tree was in full bloom, and H was the fruit harvest. As can be seen, the root carbohydrates don’t deplete until after bloom has happened (this species flowers before leafing out) and then builds up again after leafing, is depleted at fruiting and then builds up again. So in this case the tree has used the majority of root carbohydrates after blooming, and they were built back up again once the leaves were out.


Labelling studies use radioisotopes to track where carbon has moved over a period of time. These have shown evidence that carbohydrates from roots are translocated to the first formed leaves and flowers in apple, cherry, pecan & grape.ref This study also confirms that “In broadleaf deciduous trees, non-structural carbohydrates are depleted during winter dormancy and at the onset of spring growth, then replenished during the growing season”, however “in evergreen conifers non-structural carbohydrates accumulate in the crown in late winter and gradually decrease during the growing season”.ref In evergreen angiosperms (Eucalyptus in this case) it was found that root carbohydrates did vary somewhat between a peak in summer and a minimum in spring, with starch being the major storage molecule – not only that, the researchers also found a lot more starch in the roots than in the lignotuber which is commonly believed to be some kind of storage organ (but apparently isn’t).ref

So in general it is correct that trees are using their root-stored carbohydrates to flower and leaf out – although it would appear that they use these for actual leafing and not just to get to the bud stage. So theoretically it may be better if you are doing a major root prune to do this once the leaves are out (taking care not to remove so many roots that the leaves can no longer access the water they need).

Another study looked at the age of sugars in the woody and fine roots of different tree species. They found a big difference between those of ring-porous vs diffuse-porous trees – remember that ring-porous trees have a smaller and more defined ring of conducting xylem – and in some of these trees the xylem completely seizes up during the winter and a new conducting layer is grown every year. In the chart below ring-porous trees are on the left and diffuse-porous (which includes all conifers) on the right.


In both types of trees, the youngest sugars are in the smallest coarse roots, suggesting these are being used as a sugar supply within a season. The sugars in the larger roots are aging with the tree, suggesting that the tree has obtained enough carbohydrates by other means (from photosynthesis or other storage tissues such stemwood) and hasn’t needed to tap the coarse root food storage.

The obvious difference between the two is that ring porous trees have younger sugars in their fine roots as well. It looks like ring-porous trees, which probably have a higher energy requirement since they need to regrow conducting xylem as well as buds & leaves, are tapping the fine roots for energy as well as the small coarse roots. Diffuse porous trees on the other hand do not appear to be using fine roots for this purpose.

But how much are roots contributing relative to other storage tissues in the tree? One study looked at a range of different trees in Harvard Forest near Harvard University in Massachusetts in the USA.ref See below for the data showing the change in total non-structural carbohydrates throughout the year starting at January and going through to December for five species. What’s obvious is that root storage plays a different role depending on the species – and is least important in the white pine.


What’s also interesting is that the only gymnosperm in the study (white pine), has a different peak – in June (midsummer when the sun is highest in the northern hemisphere). The other species peak in October after a season of photosynthesising.

Why do we care about this as bonsai enthusiasts? Well, stored energy helps to power processes within the tree, so whenever we prune storage tissues such as branches, stem & roots, we are removing energy reserves. So ideally we’d prune these when stores are lowest. When this is depends on the species but the above chart would indicate that actually August is a good time to remove roots – which goes against the advice often provided. Using the same chart would suggest that April pruning is best for branches. Which maybe suggests that bud break is being driven more by branch stored carbohydrates than root stored carbohydrates.