Category Archives: How Trees Grow

Root structure and architecture

So we know what roots achieve for a tree, but how are they structured? To start with tree roots are either woody or non-woody. Woody roots have undergone secondary thickening and are long-lived, like the trunk and branches, and provide the structural framework for the tree.^ref

The ‘root collar’ is the area on the tree’s trunk where the roots join the main stem, and where there is typically a root flare (the root collar is still part of the trunk though, which is why it shouldn’t be buried in soil).^ref At the base of the root collar, there are usually five or more primary structural roots that “descend obliquely into the soil before becoming horizontal within a short distance of the trunk” and these taper rapidly within 1-2m of the trunk.^ref These are known as lateral roots since they grow in a lateral (horizontal) direction.

In his book ‘Trees, Their natural history’, Thomas says that trees develop a root plate, which is wide and shallow (vs the commonly held view of a root ball, which is only applicable to certain trees). Having a wide root plate helps trees achieve two of their main goals – to support and strengthen the tree against wind & weather, and to access waster and nutrients which are concentrated in the top layer of soil.

According to Thomas, root systems are more variable than shoot systems because the underground environment is more variable than aboveground. When roots encounter an obstacle underground, they fork, and as they fork and expand underground the main lateral roots can fuse into each other. This creates a criss-crossing of roots, which provides greater structural strength than if the roots were not connected. Roots can also connect to other trees’ roots (and even detect if they are ‘kin’ or not).

Structural lateral roots can develop into buttress roots, which have been found to provide tension strength in high-wind situations^ref – as a little girl growing up in Australia the best fun could be had climbing over the huge roots of the Moreton Bay Figs (Ficus macrophylla).

*Ficus macrophylla* in Kings Park, Perth Western Australia
http://skyfarming.com.au/public_html/great/firstrow/KPFig.html

In addition to lateral roots, most bonsai enthusiasts will have encountered the dreaded tap root. A tap root is the root generated by a new seedling (Thomas), which grows downwards and becomes a thick structural root. The tap root can become dominant in the root system and be a total pain for bonsai – it often generates its own lateral roots, creating a second root plate and makes it hard to get the tree into a bonsai pot. But luckily according to Thomas and others (and personal experience) the tap root isn’t necessary and can be removed. This is always best done sooner rather than later so that energy is not diverted to its growth vs the roots you do want to keep.

As well as tap roots, other structural roots trees create include sinker roots which go deeper into the soil (often to find water), can set up a secondary root plate, and also grow back upwards to create a ‘root cage’ (Thomas).

Susan Day et al^ref say “although structural roots comprise most of the root biomass, they account for a small percentage of total root length and root surface area.” The remainder of the root surface area is comprised of fine roots, which are the main mechanism for the tree to extract water and nutrients from the soil. Connecting the main structural roots to the fine roots are a network of tapering roots which branch off the structural roots.

A study of nine North American tree species found that in eight species roots <0.5 mm in diameter accounted for >75% of the total number and length of roots assessed.^ref Thomas quotes a study on Douglas fir estimating that 95% of the total root length comes from roots <1mm and about half less than 0.5mm.

As noted above the fine roots are non-woody and don’t undergo secondary thickening – this means they die and are replaced by new roots. It’s quite hard to measure this and there is differing information about fine root lifespan, but the above study found the average fine root lifespan to range from an average of 153 to 359 days. This is also expressed as a ‘fine root turnover rate’ and based on this data table fine roots of gymnosperms turn over more slowly than angiosperms (some Pinus species 20% per year vs beech 100% per year).

The fine roots are concentrated in the top part of the root plate, where most of the nutrients and water are located (20-30cm of soil, and the leaf litter & humus if present). Like the stems aboveground, the roots are constantly developing and growing, with new root tips being created by the root apical meristem (RAM) (this is described below). How the root goes about absorbing water and nutrients from the soil is covered in this post: How roots absorb water & nutrients.

These fine roots are what we are trying to encourage in bonsai as they enable the tree to extract the most water and nutrients from their environment, while still fitting into a small pot. What we want in the fine roots is lots of branching and ramification – just like aboveground – read more about encouraging this in ramification of Roots (lateral root development).

The below diagram shows the ratios of leaf, stem and root biomass to total tree mass for a data set including 3700 ‘woody’ plants (ie. trees!)

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/j.1469-8137.2011.03952.x

As you’ll notice, the larger the tree gets, the more the stem (trunk) represents of the total biomass. However the ratio of roots to total biomass stays within a range from 16% to 40%. By comparison the ratio of leaf mass has a much wider range all the way from 60% down to 2%. So there is a certain baseline amount of root biomass needed to maintain a tree.

This mass is mainly made up of the structural roots, as although the fine roots comprise the vast majority of the root surface area, they are very light in comparison to the woody roots.

So bonsai nerds, what to make of all this? Key info is the fact that fine roots die and regrow on a regular basis – and – kill that tap root! Help your tree be more stable by encouraging a root plate of connected structural roots, and you won’t need a deep root ball or a tap root. Nebari and root mass should be around 20% of the mass of the tree for an old tree look.

Root Exudates

I had never heard of root exudates before creating this website, but in fact their production is so important to plants that they “invest up to 20–40% of their photosynthetically fixed C”^ref in this process.

Root exudates are basically substances created by root cells and sent out into the nearby environment – known as the rhizosphere. These can be waste products which diffuse across the cell wall, or manufactured compounds which serve a specific purpose in response to the environment.^ref

There are many different exudates produced by plants, including carbohydrates (sugars), organic acids (such as acetic, citric or malic acid), amino acids, flavonols (molecules which can have protective effects on cells), enzymes (such as amylase, which helps to digest carbohydrates), plant growth regulators (substances which stimulate cell growth, such as auxins), phenolic acids (which have anti-oxidant properties), flavonoids, terpenoids, tannins, steroids and an assortment of other substances^ref1,^ref2.

The roles they play are just as diverse, including:

producing food in the form of carbon metabolites to support beneficial bacteria (such as nitrogen fixing bacteria), fungi, nemotodes and protozoa^ref1,^ref2, which in turn assist with nutrient uptake and the production of their own compounds such as phytohormones
producing phytotoxins (plant poisons) such as terpenes (also found in conifer sap) to repel pathogenic microbes, invertebrate herbivores and parasitic plants^ref1,^ref2
changing the pH of the surrounding soil^ref
detecting ‘kin’ (related plants) and avoiding competing plants which are not related^ref
changing the soil chemistry to allow for better nutrient uptake – for example exuding chelating substances which allow for better uptake of metallic micronutrients, or organic acids which enable better phosphorus uptake^ref

So it seems that the roots of a tree can act like a sort of pharmacy, creating compounds that protect and nurture the tree and its beneficial partners via the rhizosphere. In my opinion what this means for bonsai is that firstly you don’t want to damage the tree’s ability to produce exudates, and secondly you don’t want to remove too much of the soil from a healthy root ball.

You can damage the tree’s ability to produce exudates by underwatering/drought – and this may not be recoverable^ref, but also by failing to provide all of the nutrients and micronutrients needed for healthy growth (by not fertilising enough).

What’s in the bonsai pot is clearly more than just roots and soil – it’s an entire ecosystem delicately managed by the tree itself. So perhaps being less heavy-handed during repotting would be a good idea – replacing a good amount of the soil back into the pot along with its microbes, exudates and adjusted chemical makeup.

The Rhizosphere

Roots exist in a their own ecosystem along with soil, chemical compounds, microorganisms and variations in pH, humidity and temperature. This environment is known as the ‘rhizosphere’, a term created by Lorenz Hiltner in 1904, using the greek word for root ‘rhiza’.

The term refers to the area around the roots, and is broken into three parts. “The endorhizosphere includes portions of the cortex and endodermis in which microbes and cations can occupy the “free space” between cells (apoplastic space). The rhizoplane is the medial zone directly adjacent to the root including the root epidermis and mucilage. The outermost zone is the ectorhizosphere which extends from the rhizoplane out into the bulk soil.”^ref

The rhizosphere is FULL of microbes – this article^ref estimates there are 1000-2000 times the number which are found in non-rhizosphere soil. These include endomycorrhiza and ectomycorrhiza as well as beneficial (and pathogenic) bacteria. Below is an estimate of the number of genes represented in a sample rhizosphere across each type of organism (a list of the species included are in the research paper^ref)

https://academic.oup.com/view-large/figure/90643206/fmr12028-fig-0001-m.jpeg

Rather than passively respond to the rhizosphere, roots produce ‘exudates‘ – substances released from their cells – which are used both to sense the environment (such as, where competing roots are located and the presence of beneficial microbes and nutrients) and to alter it to the plant’s benefit. So the rhizosphere is a very dynamic place, teeming with life and being constantly manipulated by the tree for its own benefit. Below is a great image illustrating everything that’s going on – different mycorrhiza, bacteria and the roots interacting in the rhizosphere.

Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions
Paola Bonfante and Iulia-Andra Anca
Annual Review of Microbiology 2009 63:1, 363-383

‘Mycorrhiza’ are fungi which have a symbiotic relationship with roots – they each provide something of value to the other party. The word comes from the Greek words for ‘fungus’ and ‘roots’ so one should strictly call them mycorrhiza and not mycorrhizal fungi since the latter is an example of ‘RAS syndrome’ (redundant acronym syndrome, which itself is also an example of RAS syndrome).

According to one study, “for efficient nutrient uptake, most land plants need to be associated with mycorrhizal fungi that supply minerals, increasing their productivity and conferring resistance to stress.”^ref So these fungi are actually a critical part of life on earth, and necessary for healthy plant function.

Mycorrhiza are usually divided into two groups – endomycorrhiza and ectomycorrhiza.

‘Endo’ comes from the Greek ‘endon’ meaning ‘within’ – and endomycorrhiza (known as Arbuscular Mycorrhiza or ‘AM’) have hyphae (fungal threads) which actually penetrate the plant’s root cells and establish an intracellular symbiosis with the plant^ref. AMs scavenge for nutrients such as Phosphorus and Nitrogen released by saprotrophic microbes (ie. bacteria which feed off dead material) and make these available to the plant.^ref

‘Ecto’ comes from the Greek ‘ektos’ meaning ‘outside’ – and ectomycorrhiza (‘ECM’) form a thick mantle around root tips from which clusters of hyphae extend beyond the root zone.^ref They ‘mine’ Nitrogen and Phosphorus from the soil by producing enzymes which digest soil organic matter – they can then make these available to the trees in return for carbon sources such as sugars.

Whether a particular species of tree is associated with endo- or ectomycorrhiza is detailed in this site. The trees we’re interested in from a bonsai perspective fall in each camp: Associated with ECM are oak, beech, hornbeam, birch, hazel, alder (actually with both), tilia (lime/linden), chestnut and all of the Pinaceae family (including fir, cedar, larch, spruce, pine & hemlock). Associated with endomycorrhiza (AM) are grapevine, Prunus (cherry, peach, plum etc), pyrancantha, magnolia, Ilex (holly), Araucariaceae, wisteria, ficus, mulberry, ash, olive, all maples, horse chestnut, poplar/aspen, willow, buddleja, yew, camellia, elm, podocarps, flowering quince, hawthorn, apple, cotoneaster and all of the Cupressaceae family (including Cryptomeria japonica, cypress, junipers, redwoods and thujas),

Aside from this, azaleas are associated with a different mycorrhiza called ericoid.

Fungi aren’t the only microbes in the rhizosphere – it’s also teeming with bacteria – ‘rhizobacteria’. Symbiotic bacteria in the rhizosphere – known as Plant Growth Promoting Rhizobacteria (‘PGPRs’) deliver a raft of benefits to their host plants – some of which they literally could not survive without. They improve a plant’s resistance to pathogenic fungi, bacteria, viruses and nematodes as well as abiotic (environmental) stress like drought or heavy metal pollution, they also fix nitrogen into root nodules, convert organic nitrogen into inorganic forms (NH₄⁺ and NO₃^–) which are available for plants, improve the availability of phosphorus and iron, control other nutrients including sulphur, iron and manganese, and synthesise plant growth regulators which improve plant growth.^ref1, ^ref2 This study has a table showing some of the positive plant responses to specific bacteria in research studies.

They achieve these outcomes for their host plant partly by going about their task of decomposing organic matter, but crucially also by producing substances including siderophores which make iron available, enzymes which degrade the cell walls of pathogens, volatile compunds such as hydrogen cyanide, biosurfactants which lower the surface tension of liquids, antibiotics which target pathogenic bacteria and phytohormones which promote plant growth processes; all of these go into the soil and into roots.^ref Bacteria are also able to remove toxic metals from the soil through several different mechanisms and pathways.^ref

This is such a fascinating area – bacteria turn out to be tiny bespoke pharmacies available to plants to help them thrive. And plants are not just passive recipients of bacteria – they create root exudates which attract bacteria they specifically need at a point in time, they are able to manipulate the rhizosphere to meet their needs.^ref Plant genotype (ie. it’s genetic makeup) and the soil type are two main drivers that shape the rhizosphere microbiome.^ref pH is particularly important, with studies showing that bacterial diversity was highest in neutral soils and lower in acidic soils.^ref

The different bacterial species which are associated with different benefits for plants include the following^ref:

Plant Growth Promotion (supporting plant health & growth): Pseudomonas, Bacillus, Rhizobia, Achromobacter, Azotobacter, Arthrobacter
Biocontrol (fighting pathogens): Pseudomonas, Bacillus, Serratia, Pantoea, Acenetobacter, Xanthomonas, Alcaligens
Bioremediation (removing pollutants): Pseudomonas, Bacillus, Alcaligens, Arthobacter, Achromobacter, Azospirillum, Pantoea

On a final note, bacteria can produce ‘bad’ substances as well, particularly in anaeroic (no oxygen) conditions, when they produce phytotoxic nitrates and hydrogen sulphide. So avoid your bonsai substrate becoming too enclosed without aeration.

How roots absorb water and nutrients

Unlike animals, plants do not have a digestive system, although the sustainable food trust makes a good argument that ‘soil is the collective stomach of all plants’^ref Trees synthesise all of the substances they need to live and grow from 17 nutrients. It’s important to understand that plants don’t ‘eat food’ in the sense of consuming sugars, fats or proteins like animals do. Aside from oxygen, carbon and hydrogen (which come from air and water), trees absorb nutrients through their roots.

Water and nutrients are transported around trees via the xylem, a network of narrow dead cells which act like a kind of pipe. Nutrients are dissolved in the water (‘solutes’) and travel with it in the form of ions (charged molecules). To get into the xylem in the first place, water is absorbed into the root tips.

In many species this is done through the root hairs. Root hairs are “long tubular extensions of root epidermal cells that greatly increase the root surface area and thereby assist in water and nutrient absorption.”^ref According to Thomas most live only for a few hours, days or weeks, and are constantly replaced by new ones as the root growing tip elongates. Some conifers do not have root hairs and rely on mycorrhiza instead to assist nutrient and water absorption.

In order to absorb water, the root tips need to be in physical contact with it, so having root hairs that reach into the soil provides contact with more water (and nutrients). Nutrients in the form of ions are ‘pumped’ into root hairs (or cells, if the species has no root hairs) using a process called active transport, which uses some of the energy from photosynthesis. Because the root cells have dissolved nutrients in them, water is then attracted into the space by osmosis.

From the roots tips, water and solutes make their way to the ‘stele’ – this is the central part of the root which contains the vascular system (xylem & phloem, shown in blue and red respectively in the left hand diagram below). Surrounding the stele is the endodermis – seen below in orangey-brown cells with red lines through them.

https://onlinelibrary.wiley.com/doi/10.1111/jipb.12534

The red lines represent cells known as ‘Casparian strips’. They are full of lignin and other hydrophobic molecules, which basically plug any gaps between the endodermis cells. This forces any water or solute to pass through the endodermis cells. After this they travel through the root parenchyma cells into the xylem.^ref

The existence of Casparian strips leads to a pretty important insight, which suggests that most molecules entering the xylem from the outside world are actively invited in, and have to be able to traverse a cell membrane. So the tree can theoretically control or at least limit what can enter. Vogel says “the sap that rises up a tree trunk has to be nearly free of dissolved material. So much water gets transpired that the accumulation of dissolved solids, coming out of solution as water evaporated in the leaves, would make big trouble as the growing season advanced.” So this implies there aren’t a lot of non-nutrients dissolved in xylem sap. But in fact, xylem has a microbiome (it’s part of the endosphere) and literally thousands of dissolved molecules in it (described more in xylem), so obviously the Casparian strips are not a 100% barrier.

It’s not all down to the root hairs or root tips though, symbiotic fungus known as mycorrhiza play an important role in enabling root function, read more about this in The Microbiome and Symbiotic Microbes.

Foliar Feeding

Some products advise spraying them on the leaves of your trees – a process known as foliar feeding. At first glance this makes no sense, as plants synthesise everything they need from nutrients obtained from the soil and air and these nutrients come up with water through the roots and xylem. And leaves haven’t evolved for nutrient uptake, they have evolved for photosynthesis.

But could this actually work? Well, in order for the nutrients in foliar feed to be useful to plant cells, they would need to both penetrate the leaf and enter the cell.

Can substances on a leaf surface enter the leaf itself? For the most part they can’t as leaves are covered by a protective waxy layer known as the cuticle (described in the post Leaf Structure). One of the main roles of the cuticle is to stop pathogens and other environmental stressors entering the leaf.

But as so often happens with systems of mind-bending complexity like plants – it’s not that simple. For one thing, we know leaves have stomata which allow gas to enter the leaf. But it also turns out that the rest of the cuticle isn’t completely impregnable. The cuticle has tiny pores in it at the base of trichomes (hairy projections) and glands – these range from 0.45 to 1.18nm in diameter^ref. One study did indeed find that dissolved nutrients can enter the cell through these pores in the cuticle: “penetration of ionic compounds can be fairly rapid, and ions with molecular weights of up to 800 g mol(-1) can penetrate cuticles that possess aqueous pores.” The key term here is ‘aqueous’ – the pores need to be wet in order for nutrients to enter through them. For example carnivorous plants use this process to bring nutrients in from their traps via the pores in glands^ref.

A great article summarising the physics of nutrients entering a leaf is here – they conclude that it’s easier for positively charged ions (calcium, magnesium, potassium, ammonium-form nitrogen) to enter via the cuticle pores whilst it’s not as easy for negatively charged ions (phosphorous, sulfur, nitrate-form nitrogen). Similarly smaller molecules or those with a smaller positive charge are easier to translocate around the plant – including ammonium, potassium, and urea. Larger molecules will stay close to their point of entry, including calcium, iron, manganese , zinc and copper. Another study states that younger leaves are less able to transport nutrients out and so applying foliar feed to developing leaves may result in the nutrients staying within the leaf (which perhaps is an effect one might want to achieve?)^ref

So it seems that some amount of foliar feed may be able to enter via the cuticle’s aqueous pores, and a subset of this may be able to move around the plant.

But what about the stomata? Previous studies have said that “the combination of cuticular hydrophobicity, water surface tension and stomatal geometry should prevent water droplets from infiltrating the stomata”.^ref (ie. water can’t get through stomata) but apparently dissolved ions can in some circumstances, because the ions change the surface tension properties of the liquid. This study ‘confirmed the stomatal uptake of aqueous solutions’^ref; but also said this depended on whether the aqueous solution was chaotropic (reducing water tension) or kosmotropic (increasing water tension). So it’s easier for the ions on the left to enter via the stomata, and harder for those on the right.

from: https://water.lsbu.ac.uk/water/kosmotropes_chaotropes.html

But once in the leaf, can nutrients be used by plant cells? It seems so, in some cases, but the evidence is extremely varied and there are many different variables to untangle.

A research study was conducted by ‘Christmas Tree Specialist’ Chad Landgren for the Oregon Department of Agriculture in 2009 comparing foliar feeding to other forms of nutrient application^ref. They tested a range of approaches on blue spruce, Atlas cedar and four varieties of fir (abies), in pots and in the ground, using application methods including “helicopters, mist blowers and various backpack sprayers”. Their conclusions were: “Each conifer species and site are potentially different with regard to nutrient needs and response. Blue spruce appears rather “immune” to foliar application… Nordmann fir appeared to pick-up some of the foliar fertilizer… on other sites, no treatment (soil or foliar) appeared to move the foliar nutrient content levels.”

In another paper^ref the author concludes that “foliar application of particular nutrients can be useful in crop production situations where soil conditions limit nutrient availability.” and that fruit can benefit from direct sprays, but also that “applying fertilizers to leaves (or the soil) without regard to actual mineral needs wastes time and money, can injure plant roots and soil organisms, and contributes to the increasing problem of environmental pollution.”

And then of course it’s not just the leaves themselves. We now know that there is a phyllosphere – a symbiotic community of microbes in and on the leaves which perform a whole range of functions for their hosts, one of which includes producing cytokinins
that can be bioactive within the plant. If foliar feeding increases these bacteria, there may be effects throughout the plant not just on the leaf.^ref

The message from all of these seems to be that foliar feeding may work for leaves or fruit with specific mineral deficiencies which need to be corrected in-situ, if the nutrient in question can get through the cuticle or stomata. Or for plants which have environmental reasons for not being able to access nutrients through their roots (like pH?). But there needs to be a specific requirement in a specific location on the tree for it to make a difference – and it will be dependent on the species, environment, nutrient etc. In most cases I would say it would be better to provide the roots with the requisite nutrients instead.

Roots

The roots of your tree are *just* as important as the above-ground parts, with a lot of responsibilities which aren’t immediately obvious. I’ve summarised the main ones here but there is a lot more detail in separate posts with links provided below. So why are roots so important?

they absorb water from the soil to meet all the tree’s needs (both for photosynthesis and transpiration)
they absorb all the nutrients that the tree needs from the soil (using a different process to water, hence a separate point)
they transport nutrients & water up to the above-ground parts of the plant, and photosynthates (the products of photosynthesis) down to the root tips
they produce exudates (secretions) which sense and control the rhizosphere (the environment in which the roots are growing)
they produce plant growth regulators for signalling and enabling growth within the plant
they store food for later use
they provide structural strength and stability for the tree by attaching it into the soil

Points 1 and 2 are fundamental to the health and growth of the tree – the roots are the mechanism for the tree to obtain all of the water and nutrients it requires (despite the mythic popularity of foliar feeding, this is only a way of augmenting nutrient absorption and not a primary mechanism). The mechanics of how they do this is described in more detail in how roots absorb water and nutrients – in summary it’s the fine roots and their root hairs which do the majority of the absorption since they have the closest and most expansive contact with the soil. There needs to be enough root surface area to supply the stems, shoots and leaves with the water and nutrients they require.

Point 3 reflects the fact that roots are part of a tree’s vascular system, that is to say, they transport the fluids necessary for growth around the tree. Above the ground the vascular system is present in stems, shoots and leaves, and below the ground it is present in the roots. Water and nutrients are transported up from the roots through the xylem and photosynthates (the products of photosynthesis) are transported down from the leaves and other storage organs in the tree via the phloem, to provide the energy and nutrients for the roots to grow and function. Do roots grow all year round? Find out here: when do roots grow?.

Points 4 & 5 show that roots are very much an active participant in tree growth and not simply a set of supply pipes. They produce both cytokinin and auxin (read more in the post about plant growth regulators), they also produce a huge variety of substances known as exudates which both sense and control the rhizosphere (the environment in which the roots exist). Researchers believe that roots use exudates to “regulate the soil microbial community in their immediate vicinity, withstand herbivory, encourage beneficial symbioses, change the chemical and physical properties of the soil, and inhibit the growth of competing plant species”^ref. Read more about exudates and how they are produced in root exudates.

Point 6 reflects the fact that roots are used to store food, in the same way that the trunk and branches do this aboveground (throughout the ‘woody skeleton’ (Ennos)). I was going to tell you that a lignotuber is an example of this and show you a lovely picture of my eucalyptus, but then I read “contrary to common assumptions…the lignotuber in young eucalypt trees did not appear to be a specialized starch storage organ. Rather, the lignotuber resembled an extension of the stem because its starch concentrations and temporal fluctuations mirrored that of the stem.”^ref How roots store food and how much of a contribution to the plant’s overall storage capacity they make is debated. More on that in Root Food Storage (or, can I root prune before bud break?)

Finally as per point 7, the roots are responsible for physically holding the tree steady and stable against wind and gravity. They do this in many ingenious ways by adopting different root architectures – combining vertical taproots, lateral roots & sinker roots, creating ‘buttress’ roots, sending roots far from the trunk when needed and managing new root development in ways which stabilise the tree. More about this in root structure and architecture.

What all of this means from a bonsai perspective is that you need to pay just as much attention to the health and care of the roots of your tree as you do to the above-ground parts. Never mind developing a strong nebari for aesthetic purposes, you need to ensure that even though the roots of your bonsai trees are squashed into teeny-tiny pots, they are still able to perform the vital functions outlined above. Neglecting the roots will negatively affect the overall health of your tree.

Practically speaking, this is why you should aim to develop a well-ramified fine root ball, to provide the tree with lots of root surface area for nutrient & water uptake – taking into consideration the amount of biomass above-ground as this will determine how much root mass is needed.

The growing medium plays a huge role as well – this is your tree’s rhizosphere. It should provide the water, nutrients and micro-organisms the tree needs as well as (some) oxygen for root cell respiration, and ideally should not be disrupted so much so that exudates and microbes (fungi or bacteria) are lost. The risk associated with bare-rooting a tree (or excessive repotting) is that it destroys the rhizosphere all at once, leaving the tree vulnerable to pathogens and forcing it to regenerate exudates it has already created (which can use up to 40% of its stored carbon).

Your tree’s roots need to have a regular supply of nutrients, so they require fertiliser of some kind. Even if good compost is added during potting, the small size of bonsai pots will mean the nutrients won’t stay in there for very long. Trees will need added fertiliser – either home-made (for example, regular doses of diluted compost leachate), or purchased. And obviously – watering is critical. Given the role of symbiotic partners (such as fungi & bacteria), you can also add these to the soil – if your tree senses their presence and wants them to stick around – it will probably produce exudates to achieve this.

Vascular Cambium

The cambium – or more precisely the vascular cambium – is a layer of cells underneath the outer and inner bark and outside the wood of a tree. It’s officially defined as a ‘meristem’ – that is, a region of cells capable of division and growth^ref. You may recall the ‘shoot apical meristem’ in the post about How Trees Grow – this is the part of the shoot which is actively dividing and creating new cells at the tip of the shoot (known as primary growth). The vascular cambium does something similar – it divides to create the vascular system – a layer of xylem cells on one side and a layer of phloem cells on the other. The vascular cambium is where part of the secondary thickening of a tree takes place, as the xylem layers become the wood of the tree, and the phloem layers become the inner bark (the outer bark has another meristerm – more here). Always in between there is a single-cell thick^ref layer of vascular cambium. See below for an image of the cambial zone, phloem and xylem cells.

From The Plant Stem: A Microscopic Aspect 1st ed. 2018 Edition, Kindle Edition
by Fritz H. Schweingruber & Annett Börner

Two types of cells exist in the cambium – vertically elongated ‘fusiform initials’ and horizontally oriented ‘ray cell initials’. The fusiform initials produce xylem and phloem cells and the ray cell initials produce rays (which cut across the tree connecting xylem and phloem).^ref The ray cells can create gum and resin channels, which can also be activated when the cambium is wounded. You can see a resin duct cavity in the image above, as well as a ray.

Like a lot of growth in a plant, the activity of the cambium meristem involves plant growth regulators^ref. Auxin levels peak in the middle of the cambial zone, where cells are dividing, cytokinin peaks in the developing phloem cells and gibberellin peaks in the developing xylem cells. A study in Populus found that increased local biosynthesis of cytokinin led to increased trunk biomass and radial size (width).^ref ‘Local’ biosynthesis in this case meant a tree which had been transgenically modified to produce more cytokinin.

The vascular cambium slows down or stops completely during winter in temperate zones, this depends on the tree’s phenology. More detailed information about the vascular cambium can be found in this book.

From a bonsai point of view the main takeaway is that the vascular cambium tissue underneath the bark is critical for your tree’s growth so avoid damaging it.

Phloem

The word ‘phloem’ comes from the word for bark in ancient Greek. It is a parallel system to the xylem which transports water and nutrients up from the roots, but instead transports the products of photosynthesis (‘photosynthates’) from the leaves to the rest of the tree. A big callout to The International Association of Wood Anatomists for the images in this post, contained in this open-access publication.

One of the main photosynthates produced by trees’ leaves is sucrose (maple syrup anyone?), but others found in phloem include fructose and glucose, sugar alcohols and the raffinose family of oligosaccharides (RFOs). A sugar alcohol known as ‘D-pinitol’ has been found in substantial amounts in gymnosperms^ref and is believed to be the main carbon transport molecule for Scots pine. In addition to sugars, the phloem system is used for signalling and defence throughout the tree (as is the xylem), so plant growth regulators (including auxin, cytokinin and salicylic acid), proteins, minerals and RNA travel in the phloem sap as well. If a foliar insecticide/herbicide/fungicide has been applied and is able to penetrate the pores or stomata (see foliar feeding), and is able to get into the phloem vs staying inside adjacent cells, it will translocate throughout the plant.^ref As a result I would not be eating non-organic maple syrup (previously paraformaldehyde was used to reduce microbial attacks on maple trees for syrup product, but this was banned by 1989).^ref

There still seems to be quite a bit that’s unknown about how phloem actually works – an article published in 2014 said “Because of the difficulties in measuring phloem function, particularly in trees, we lack a basic natural history and phenomenology of tree phloem”^ref and another published as recently as 2021 said “phloem loading strategies in gymnosperm trees have been only tested in three species: P. sylvestris , Pinus mugo and Ginkgo biloba.”^ref

But the basic principle is that sugars are created by the process of photosynthesis, ‘loaded’ into the phloem cells (with assistance from adjacent cells) and transported to places in the plant where they are needed, then ‘unloaded’ (but even the mechanism for transportation of sugars in phloem is debated – a famous theory involving ‘osmotically generated pressure gradients’ has dominated but many recent articles point out the lack of data to support it.^ref) According to one account, sugars are loaded from leaves into phloem companion cells by active transport (a process which consumes energy) and then diffuse into the sieve tube elements through the plasmodesmata (cytoplasm which is shared between cells via small pores between them). Water then moves by osmosis into these cells (creating the phloem sap), and sugars translocate (move) when sinks (areas of the plant consuming energy) remove sugar and reduce its concentration in the phloem sap.^ref

Phloem is also believed to translocate (move from one place in the plant to another) sugars even when photosynthesis is not taking place – eg. in winter in deciduous species.^ref In this case the sugars are coming from storage tissues in the rays and roots.

The cells which make up the phloem system in gymnosperms are different to those in angiosperms (similarly to the difference in xylem), but the basic structure for both is that tubular cells, known as sieve cells (gymnosperms) or sieve tube elements (angiosperms), are connected together via pores in their end walls, and the phloem sap ‘flows’ through these sieve cells/tubes.^ref

Below is an image of pine sieve cells. The side and end walls are structurally similar, unlike the sieve tubes of angiosperms. The phloem sap flows from cell to cell downwards, through the pores. Many studies reference the fact that sieve cells & tubes contain material which would appear to create a barrier to flow, which calls into question the abovementioned ‘osmotically generated pressure gradients6’ theory.^ref

https://search.library.wisc.edu/digital/AVCQSJHVTUYFUP9D

If you’ve read the post about the cambium, you’ll know that there is a constant process of creating new xylem and phloem cells, and in the case of phloem, the most recent does the conducting.^refThe conducting phloem usually lasts for one season, but can remain ‘functional’ for one-two years (ie. the cell is still alive, even if it’s not conducting phloem any more). Like xylem, phloem rings are created – see the image to the right of pinus strobus – all of the dark cells are the annual phloem sieve cells which are now non-conducting. The conducting cells are in the lower purple region.

https://scholarlypublications.universiteitleiden.nl/access/item%3A2951200/view

A key difference between xylem and phloem is that phloem cells are living cells. This means that phloem sap must pass through living cells and their membranes in order to flow and this article^ref suggests that this mechanism provides a high degree of control for the plant in managing what gets into and out of the phloem system. The phloem passes through holes in the sieve cells known as sieve plates (see pics below both of ficus species, the left hand side shows a transverse section and the right hand side a lateral section).)

In order to create the space for the phloem sap, sieve cells and tubes are missing quite a bit of the normal cell machinery, including a nucleus, vacuole and ribosomes – so they can’t control their metabolism or make proteins. Although they still have some specific proteins (P-proteins – apparently previously known as ‘slime’!^ref), mitochondria, endoplasmic reticulum, and sieve element plastids.^ref Both types of sieve cells have helper cells alongside which metabolise on their behalf – companion cells in angiosperms and Strasburger cells in gymnosperms.

Since phloem is full of delicious sugar-rich fluid, it can be a magnet for insects, which in turn introduce microbial pathogens including bacteria and viruses.^ref Plants produce metabolites to defend themselves against these pathogens, and also induce sieve plate occlusion – basically blocking up the sieve cell or tube where the pathogen is located to avoid it spreading.^ref

Both the active phloem and the old phloem which no longer transports photosynthates are together known as the inner bark. Outside these phloem layers is the ritidome or outer bark. You can read more about bark here.

For bonsai there’s really not a lot you need to worry about with respect to phloem, unless you are wiring super tight and cutting off the phloem (but by then your wire will be well embedded in the outer bark).

Stomata

Stomata are “microscopic pores which mediate the uptake of CO₂ and loss of water from terrestrial plant leaves”^ref The pores exist in the cuticle of the leaf (refer back to Leaf Structure to learn about the cuticle). You can see a scanning electron microscope image of stomata below:

The stomata are the dark holes in the pictures, and each one is controlled by two guard cells. The guard cells bend or straighten to enlarge or close the hole, this controls the amount of air which can enter, and the amount of water vapour which can get out. The world of stomata is illustrated in beautiful detail on the Plant Stomata blog, and what you notice is just how symmetrical and perfect looking stomata are, even though they are only 20-70μm in size. In fact the creation of guard cells is choreographed by a gene known as MUTE – it triggers one round of cell division, then acts to stop any further division, resulting in one stomata with two guard cells^ref.

Stomata are the interface between the inside of the leaf and the outside world. They are “typically fully open under conditions favouring photosynthesis, but close when water supply is limited.”^ref They operate a control system which responds to several factors including CO₂ and water levels – lower CO₂ levels within the leaf space will open the stomata as will higher water levels and/or humidity. In most plants stomata close at night, since CO₂ is not being used by photosynthesis, but some also operate on a circadian rhythm – opening before dawn or closing for a period at midday (Vogel).

Stomata control the most fundamental life-giving processes of plants, and as such are an ancient structure, found on plant fossils from 400 million years ago^ref, basically from when plants first grew on land. As a result, stomata patterns can be used for paleontology, and for genus (and sometimes species) identification.

Stomata are distributed on bottom of leaves, and sometimes on the top as well. The guard cells have different shapes, including crescent, rectangular, dome and triangular^ref, and in conifers they are often sunk into the leaf, surrounded by structures and/or contain wax plugs. They are arranged in different patterns as part of the overall epidermal structure, so appear in rows in certain species, and in between the pavement cells in different patterns in others.

This photographer (http://www.foto-vision.at/) produces amazing microscope images of leaf and stem cross-sections. Below is a pinus mugo needle – look closely at the cuticle and you can see dark spaces where the stomata are, surrounded by the guard cells stained in bright orange.

Guard cells work by inflating with water – since they are pinned at each end, and stiff (in conifers the guard cells often have lignin in them) – when water enters the cells they bend outwards. To inflate, they transport positively charged potassium ions inward – this attracts negatively charged ions (like chloride) and water then is attracted as well to dissipate the concentration of ions back to baseline levels. Pressures generated by guard cells are surprisingly high – from 2-40 atmospheres,or 16-320x the normal blood pressure generated by humans (Vogel).

So aside from providing enlightenment, how does knowing about stomata aid your bonsai practice? Well to start with, more stomata provide more photosynthesising capability and hence more growth potential (assuming water availability). The number of stomata created on a leaf is not just genetic, but is impacted by the environment -“in a number of species both light intensity and CO₂ concentrations have been shown to influence the frequency at which stomata develop on leaves.”^ref So putting your trees out in the sunlight will increase the number of stomata – this is determined by the mature leaves being in the sunlight – they use ‘long-distance signalling’ to developing leaves to produce more stomata^ref. Researchers hypothesise this signalling is probably mediated through plant hormones, but it’s not currently known exactly how.

One bonsai practice which relates to stomata is the use of anti-transpirants. This is sometimes used after collecting a yamadori. It’s promoted to ‘protect leaves’ from various environmental challenges (heat, dryness, wind) and to ‘reduce excessive transpiration’. The product is “a film-forming complex of polyethylenes and polyterpenes that when applied to foliage will reduce the moisture vapor transmission rate”^ref – so basically you are spraying plastic onto the leaves and blocking the stomata.

My guess on this product is that most people are not spraying the bottoms of the leaves which is where the majority of stomata are located. This will indeed reduce transpiration (from the top of the leaf) but not prevent photosynthesis or gas exchange, because really most of the stomata are unaffected. I don’t really like the idea of spraying plastic on my trees though, and don’t think it should be necessary – if a plant is transpiring ‘excessively’ it needs more water, or it needs to be removed from the environment causing the transpiration (out of the wind or direct sun). Creating more humidity should have a similar effect (for example by covering with a plastic bag).

One situation where it may be justified might be when collecting yamadori, when more root has been removed than foliage, and the roots simply can’t keep up with the transpiration rate. Reducing the transpiration for a period of time would allow the roots to grow whilst keeping the foliage (otherwise in bonsai you would have to remove the foliage to match the root capability). But again, a plastic bag might work just as well, without the need for spray.

Leaf Structure

It’s useful for bonsai enthusiasts to understand how a leaf is structured, as this answers some questions about how water/air/nutrients/sugars get in and out of the leaf and therefore also the rest of the tree. Of course there are many different leaf types belonging to different trees in different environments, so there will be many differences between them. What’s important to know is the main structures which are common to most leaves. Below is a diagram of a leaf cross-section:

http://Scaling Functional Traits from Leaves to Canopies – Scientific Figure on ResearchGate. Available from: https://www.researchgate.net/figure/The-internal-structure-and-biochemistry-of-leaves-within-a-canopy-control-the-optical_fig2_342371888

The outside of the leaf is covered by the ‘cuticle’, which is the first line of cells between the leaf and the outside environment. This is not a passive line of cells, but instead “waxes, fatty acids, and aromatic components build chemically and structurally diverse layers with different functionality.”^ref Not only that, the cuticle changes as the leaf develops – building up its layers and constituents over time until the leaf has fully extended.^ref The above diagram only shows a cuticle on one side of the leaf – but apparently a cuticle “covers the outer epidermal surface of most above-ground tissues, such as leaves, fruit, and floral organs.”^ref

The main function of the cuticle is as a barrier. It protects the tissue beneath from mechanical damage by the elements, or from insects, and acts as the primary defence against pathogens.^ref It is composed of “the polyester cutin, containing oxygenated and unsubstituted fatty acids, glycerol, and phenolic acids, that is impregnated by waxes of very-long chain fatty acids (VLCFAs) and their derivatives.”^ref In another study the top layer of the cuticle was found to contain Kaempferol. This is a flavonol which is known to be an antifungal, antibacterial and antioxodant (see this article about HB-101).

Since the waxy cuticle is impermeable to water and CO₂, leaves have specially controlled holes distributed across it^ref – these are known as stomata (described below).

Underneath the cuticle is the epidermis – the upper epidermis at the top of the leaf and the lower epidermis at the bottom. Humans have an epidermis too – it’s the top layer of skin. Everything you could want to know about the plant epidermis is covered in an excellent article in ‘The Plant Cell’ journal from January 2022. The authors say “the epidermis plays many important roles including regulating the exchange of gases, water, and nutrients with the surroundings, responding to external threats such as pathogens, herbivores and abiotic stresses, resisting mechanical strain, detoxifying xenobiotics, and contributing to mechanical strength while allowing the flat and flexible shape necessary for maximum light capture.”

There are three main types of cells in the epidermis, and these develop into their final form starting from the leaf tip and gradually moving back towards the petiole until all of the cells are formed.

The first cell types are ‘pavement’ cells – so named because they interlock with one another and look like paving (sometimes it’s crazy paving – other times it’s very neat). Among the paving are stomatal guard cells – these “form microscopic valves in the leaf surface” so that gas can get in and out for photosynthesis. You may have heard of stomata – this is the name for the hole that is created and controlled by the stomatal guard cells. Basically plants breathe through their stomata – air comes in, oxygen from photosynthesis and CO₂ from respiration come out, and water vapour comes in and out as well. It’s actually reasonably easy to ‘see’ the stomata even with the naked eye – depending on the species of tree and the shape of the leaf. If you put adhesive tape on a leaf, and pull it off, you pull off some of the cuticle which shows the outlines of the stomata. There is quite a lot to say about these guys – see this post: Stomata.

Aside from the stomatal guard cells and the pavement cells, the epidermis can also have ‘trichomes’ which are hair-like protrusions from the surface. These can appear in lots of different forms, and can be ‘glandular’ (or not). If a trichome is glandular, it can “biosynthesize, store and secrete a large diversity of specialized metabolites including terpenoids, alkaloids, polysaccharides, and polyphenols” – such as the terpenoids that conifers exude to defend against insects^ref. This image from the journal nature shows the trichomes on white spruce:

https://www.nature.com/articles/s41598-020-69373-5

Anyway moving on past the cuticle and the epidermis, you come to the mesophyll. The mesophyll is “the parenchyma between the epidermal layers of a foliage leaf”^ref – OK great Merriam-Webster dictionary, now what is ‘parenchyma’? Parenchyma is “the essential and distinctive tissue of an organ”^ref which in the case of leaves means the cells which photosynthesise and store the products of photosynthesis. So the mesophyll is the engine room of the leaf.

Referring to the image at the top of this post, you will see there are two types of cell in the mesophyll – palisade cells and spongy mesophyll cells. The palisade cells face the light, and are located on the top of the leaf^ref. They are columnar cells (with the end of the column facing the light) and they are supposed to contain the majority of chloroplasts, which are the organelles responsible for photosynthesis. The spongy mesophyll cells are arranged in a lattice, with air gaps (like a sponge) to allow for the absorption of CO₂ – they also contain chloroplasts, but apparently not as many. Good luck trying to find a research paper which actually counts them! The best I could find was this data^ref looking at five species living in different light conditions, and the number of spongy mesophyll cells ranged from 40-50% of the total chloroplast count. Which isn’t exactly a minority.

The shape of these cells has evolved to improve photosynthesis. The palisade cells which are long and columnar, “act as light conduits”^ref distributing collimated (parallel) light to chloroplasts within the leaf. Internal light scattering also takes place, allowing photons of light to reach the chloroplasts in the spongy mesophyll cells. When a leaf has a different (usually lighter) colour on one side, this can keep light inside the leaf by reflection.

The final part of the leaf structure is the vascular bundle – this contains the water-transporting xylem and the sugar transporting phloem. See xylem & phloem.

Not to forget, leaves have their own microbiome, just like the roots. This is called the phyllosphere and contains many bacterial and fungal species in symbiotic relationships with the host plant.

You can dive even deeper into the structure of leaves by going into the plant cells themselves, looking at mitochondria, chloroplasts, vacuoles and the thousands of chemical reactions going on, but that’s a post for another day.