Category Archives: Keeping Bonsai Healthy

Pathogens – nasty tree microbes

A pathogen is a microorganism such as a virus, bacterium, oomycete (water mould) or fungus which causes disease and/or death.^ref Examples you might have heard of include Dutch Elm disease (caused by the fungus Ophiostoma ulmi), Horse Chestnut bleeding canker disease (caused by the bacterium Pseudomonas syringae v. aesculi), Ash dieback (caused by the fungus Hymenoscyphus fraxineus), Sudden Oak Death (caused by the oomycete Phytophthora ramorum) and mosaic viruses in vegetables.

The groups of pathogens causing forest tree diseases and their prevalence is shown in the chart below. 85% of these are fungi and the remainder are divided among bacteria, viruses, nemotodes (microscopic worms) and oomycetes. Oomycetes appear similar to fungi but are actually not genetically similar, and are classed in the Chromista kingdom.^ref

Link to source article here; original sources Butin, 1995; Capretti and Ragazzi, 2010; Manion, 1991; Tainter and Baker, 1996

Note that as they are not microorganisms, insects are not classified as pathogens, although they can also cause significant damage and death to trees. Insect damage is a subject for another post, but for this one, their main role is in introducing pathogens to trees by delivering microbes on them into wounds they create (this is called being a pathogen ‘vector’).

Every living thing is in a battle for survival so that its genes can be passed on to future generations. This means that both trees and pathogens are constantly evolving to outsmart each other. But fungi and bacteria can also be beneficial and even necessary for trees, so you can’t just try to kill off every fungus or bacteria as this will destroy the ones that trees actually want and need.

The other thing to keep in mind is that plants have a completely different ‘lifestyle’ to animals in the sense that they are plastic and can grow new tissues, synthesise new compounds and respond to pathogens in a very different way to humans. As noted elsewhere, in response to wounds, trees ‘don’t heal they seal’ and they don’t have an immune system in the same way as animals.

But, there are three ways to help your trees avoid damage from pathogens. The first is to prevent them from being exposed to pathogens in the first place. The second is to remove any pathogens which do take hold. The third is to bolster your trees’ defences so they can fight off the pathogen and its effects.

How can you prevent exposure to pathogens? A tree’s first line of defence is its bark, leaf cuticle, and the pectin and lignin in cell walls, which are physical barriers which prevent pathogens from entering its cells.^ref Since they can’t run away, this is the main way that trees avoid exposure. But in bonsai we do a heck of a lot of pruning, which unfortunately breaks the physical barrier, leaving the tree vulnerable.

To minimise the chance of nasty microbes attacking your tree as a result of pruning there are some steps you can take. Firstly, practice excellent hygiene and make sure your pruning tools are disinfected regularly, particularly when moving between trees. But be careful that the disinfecting method you use doesn’t damage your tools (carbon steel is particularly vulnerable). Soap and water can work (but dry off the water), or you could use an antimicrobial oil such as tea tree oil (from Melaleuca alternifolia) or oregano oil (from Origanum vulgare) – not only are these antimicrobial^ref1,^ref2 but they also protect steel from corrosion.^ref1,ref2

Another approach is to prune during the wintertime. The latter helps because in general most living things are more active in warmer weather – including pathogens. Pruning in winter reduces the likelihood that a pathogen will enter a wound before the tree can seal it off.^ref Also many fungi and oomycetes prefer a moist environment, so when pruning try to avoid leaving the wound wet. Angling pruning wounds towards the sun can also be beneficial, since sunlight has disinfecting as well as drying properties (although probably not so much during the wintertime in higher latitudes).^ref

Contrary to some advice, wound sealants have not been shown to reduce bacterial or fungal infection on tree wounds.^ref This is because a tree wound is not sterile so any sealant can seal pathogens in as well as out. One wonders whether applying an antimicrobial oil to a wound might work, but I cannot find any studies looking into this. Recently I tried applying raw linseed oil to the cut ends of various crabapple branches I was trying to propagate, but these ended up with large communities of mould on them regardless (possibly because I was using high humidity which is perfect for fungal growth).

One interesting pathogen avoidance method is to decouple the seasonal timing between the host plant and the pathogen vector (vector means the delivery method of the pathogen, often an insect). One study found that Dutch Elm disease was avoided by trees which flushed early, since they were not as susceptible to infection after this point.

The second way to help your trees avoid pathogens is to remove them once there. This is tricky since by definition a pathogen is microscopic and impossible to see with the naked eye. You can’t go and squash every bacterium on your tree! It is possible to kill pathogens using antibiotic and/or antifungal substances, but effectiveness varies depending on what you need to remove and usually involves unpleasant and toxic chemicals (such as glyphosate) which also kill good microbes.

Biological control is an alternative to chemicals, this means finding another organism which feeds on or somehow damages the pathogen in question. An example of biological control is the introduction of the Myxoma virus into Australia to control the rabbit population. In trees, the fungus Trichoderma is used as a biological control agent, and it is found in bacterial inoculants for plants such as this one. Species of Trichoderma have been found to be effective against Armillaria root rot (also known as the dreaded honey fungus) and pine pitch canker.^ref

The final way to help your trees is to bolster the natural processes they use to resist the negative effects of pathogens. Plants produce a huge range of substances which have defensive effects, and can detect pathogens with surprising speed and specificity. When a pathogen is detected by a plant, it first activates a specific ‘pattern-triggered immunity’ response which is believed to be sufficient to defend against a wide range of pathogens.^ref This is known as ‘basal resistance’. A second line of defence detects the so-called ‘effectors’ – substances that pathogens create to avoid the pattern-triggered response. This second ‘effector-primed immune response’ causes cell death at the site, limiting the spread of the pathogen^ref and is known as the ‘hypersensitive response’. Plants also synthesise a wide range of defensive compounds such as resins in conifers, terpenoids or essential oils, saponins and flavonoids (of which 9,000 are known).^ref1,ref2 These help them deter pathogens by making their cells poisonous or unpalatable.

So ensuring your plant is not stressed by lack of water, light or nutrients is one way to help it have the resources to defend itself. Another way is to provide it with beneficial microbes such as mycorrhizal fungi and beneficial bacteria. One study found that providing the bacteria Bacillus cereus to tomato plants enhanced their resistance to pathogens by activating the plant growth hormones salicylic and jasmonic acids. Cultivating a healthy rhizosphere (root microbiome) which supports your tree’s health can be achieved by using a well-aerated soil mix and by not constantly repotting. Repotting risks losing the microbiome which a tree has built up over time, for this reason I always try to add back in some of the previous soil when I repot.

So what should you be doing as a bonsai enthusiast to avoid any nasty pathogens ruining your great work? I’d suggest three things. The first is good pruning practices – minimising wounds, avoiding pruning wounds becoming wet or humid, and vigilance in disinfecting tools and pots. The second is to keep your trees vigorous and healthy – particularly before doing large-scale pruning or defoliation. Give your trees lots of water, nutrients and sunlight to help them bolster their defences. And finally help your trees out with the addition of beneficial fungi & bacteria; products containing these can be found online.

Water Sources for Bonsai

While many of us might simply use the hosepipe to water our bonsai, there are actually a range of options for recycling or collecting water for this purpose. I’ve looked into some of these below to understand how suitable water from different sources is for watering your trees.

Dehumidifier water – good unless you have a dessicant humidifier and toxic air

Dehumidifiers remove water from the air in a few different ways. One common type is a compressor dehumidifer. This type pulls air through a filter and over cooled metal coils which cause water in the air to condense onto the coils and drip into a reservoir.^ref Since this is effectively distilling the water, it should be relatively pure. Where contamination could come into play is if the coils or the water reservoir are not kept clean, but for bonsai tree watering, this shouldn’t be an issue.^ref You should be cleaning the reservoir anyway to avoid Legionnaire’s disease (see below). The water from a dehumidifier won’t have any minerals or nutrients in it (unlike rainwater), so fertiliser would be needed.

A dessicant-type dehumidifier pulls water through a dessicant material – such as zeolite^ref (if you’re wondering where you’ve heard that name before, it’s used as a bonsai soil additive^ref). Water is absorbed in the dessicant then this material is heated and the water drips out into the reservoir. It’s not exactly the same as distilling because the water is in contact with the dessicant as it is condensed and could hold dissolved compounds. Researching the properties of zeolite will take you down an entirely new internet rabbit hole (including 1.24M research paper results on Google scholar). But this substance is known for extracting heavy metals and other contaminants from liquids^{ref1 , ref2}. So in theory the zeolite could hold other molecules which could be released into the water as it condenses. This might be an issue if you are using dehumidifier water from a location with particularly toxic or polluted air. If not, the risk to your bonsai should be fairly low. As above cleaning the water reservoir and dessicant regularly is important.

Tumble dryer water – good if condensing, less good if venting

Tumble dryers also work in slightly different ways but the main mechanism for extracting water is that warm air evaporates water from the clothes, then this air either passes over a condenser or is vented outside, in both cases water condenses from the air as it cools.

With a condensing dryer, the process is another form of distillation so should be relatively pure water and fine for use on bonsai.

If you are using a vented machine however there may be microplastics, particulates and lint from the drying clothes coming through the venting pipe. In 2021 tumble dryers were found to be a leading source of microfibre air pollution.^ref You might not think this would affect your tree very much, but it has been found that nanoplastics and microplastics can enter plants through their roots, carrying a range of toxic substances including pesticides, polybrominated diphenyl ethers (PBDEs), endocrine-disrupting chemicals (EDCs), polycyclic aromatic hydrocarbons (PAHs), phthalates, and bisphenol-A. PLA microplastics have also been shown to negatively impact arbuscular mycorrhizal fungi diversity and community structure.^ref If you want to avoid microplastics in your pots and tree roots you probably don’t want to use vented tumble dryer water.

Air conditioner water – good

Air conditioners work similarly to dehumidifiers and dryers – they pull air through a mechanism which cools it, and in doing so water is condensed from the air. So it’s fine to use for watering (although as above will contain no nutrients).

Boiler condensates – not good

I’m not sure how many people would be trying to use boiler condensates for watering but just in case you think of it, boilers which use fossil fuels produce condensates containing carbonic acid, sulphuric acid and nitric acid, all of which reduce the pH of the water coming from the system.^ref Although slightly acidic water (in the range 5.5-6.5) has been show to optimise plant growth^ref, boiler condensates can be as low as 3 which is toxic to plants.^ref

Rainwater – good – maybe the best

Rainwater is a different proposition to the previous water sources. Whilst it is distilled from air just like the others, it has to fall through the atmosphere to reach the ground. As it does this, rain absorbs compounds present in the air in particulates and gases. It also runs off roof surfaces, down drains and pipes and into storage tanks. So rainwater collects contaminants along the way. As atmospheric carbon dioxide is one of the molecules rain collects, it has an average pH value of about 5.6 (just at the lower end of preferred plant water pH which is 5.5-6.5)^ref

The chemical composition of rain varies geographically even before it hits the ground. For example in Samoa the rainwater composition is highly influenced by marine sources, which makes sense since it’s an island.^ref Locales near the ocean have rainwater with a similar (diluted) composition to sea water^ref but those inland vary depending on natural and manmade influences such as industry, topography and weather. Raindrops have also been found to contain airborne bacteria and fungi.^ref

Rainwater in the UK is monitored for ions of sodium, calcium, magnesium, potassium, phosphate, nitrate, ammonium, sulphate, sulphur dioxide and chloride, and for acidity/pH and conductivity.^ref The latest measurement at my nearest monitoring station showed the following contents from a 3mm sample – nutrients are there but nowhere near the same levels as a seaweed fertiliser.

The other factor to consider is where you store your rainwater. Outdoor water reservoirs are usually colonised by bacteria, fungi and other organisms, and have rotting plant matter, bird faeces, dead insects and other detritus. This may also be a good source of fertiliser, depending on how concentrated your detritus gets, or a source of toxic microbes and algae, particularly if there isn’t much flow and replenishment of the water.

But overall rainwater is a good choice for watering bonsai. It has a favourable pH for plants, and is a mild fertiliser containing a range of macro and micro nutrients. As it doesn’t have carbonates like groundwater, using rainwater can help you avoid limescale marks on leaves & pots if you live in a hard water area. Just try to avoid leaving it standing or stagnant for long periods particularly if the temperature is above 20^oC (see Legionnaire’s disease below).

Aquarium water – maybe depending on your tank

The subject of aquarium water almost warrants its own post. Anyone wanting to better understand the chemical and biological parameters inside a planted aquarium should read the brilliant book “Ecology of the Planted Aquarium: A Practical Manual and Scientific Treatise” by Diana Walstad.

The water in your aquarium is likely to be completely fine for bonsai if it’s fine for fish. They have high standards – and can’t handle large pH ranges, excessive levels of nitrites, ammonia or excessive nutrients like heavy metals. In fact this water can be an excellent source of nitrogen since fish in aquariums excrete ammonia, which is the main source of nitrogen for most fertilizers. Usually when doing a water change on an aquarium the levels of rotting organic matter have accumulated and ammonia levels are at their highest – one of the main reasons for doing water changes is to reduce them. Planted aquariums which use soil as a substrate and have fish (and fish food as an input) also contain other macro and micronutrients, to the extent that fertiliser isn’t necessary. So aquarium water could be a good addition to your bonsai, as a fertiliser.

On the other hand, if you have certain plants in the aquarium, some are known to be ‘allelopathic’ – that is they produce compounds to inhibit other organisms. For example the water lily Nuphar lutea kills duckweed and lettuce seedlings (Walstad, 2012). Aquatic algae and bacteria can also behave allelopathically, to the extent that Diana Walstad keeps her prized plants in their own substrate and even in separate tanks to stop them being killed by competitive organisms. So there is a risk with water from planted aquariums or aquariums with algae that there may be allelopathic compounds which damage your tree. It’s hard to make a recommendation since it’s impossible to know without testing whether toxic compounds are in your aquarium water. If you have no algae or plants, then the water is probably fine.

Greywater – not unless you treat it

Grey water is waste water from your bath, shower, washing machine, dishwasher and sink.^ref It can contain detergents, oil, dirt, organic matter like food, skin particles, microplastics, bacteria, fungi or anything that you wash off yourself, your dishes or your clothes. As such greywater isn’t suitable for watering your bonsai. Some larger properties like hotels recycle their greywater, but it’s treated first using UV light, chemicals or serious filtration systems.^ref So unless you have access to a high quality greywater filtration system, do not use this to water your trees.

Blackwater – no

The things you learn about when researching bonsai websites. We won’t go there – just – no.

Seawater – not unless you have a desalination plant

Unless you are growing kelp forests, do not water your bonsai with sea water. Excess salt is extremely detrimental to plants, and can kill them.^ref

Lakes, streams, rivers, boreholes, wells or ponds – it depends

Natural water sources such as these are not treated and can contain all sorts of things aside from water, but this really depends on what runs into them, what happens and lives on and in them. Some lakes & streams are very clean, others have industrial runoff, pesticides, sewage overflow^ref, algal blooms from excess fertiliser runoff and worse. What you want to avoid with a water source is dissolved contaminants which might harm your tree – usually these will derive from human activity going on upstream. So before using such a water source, it would be wise to investigate what might be entering it and perhaps to invest in some testing.

It’s thought that water obtained from aquifers underground (eg. via wells or bore holes) is of higher quality if it comes from a deeper confined aquifer than from a shallow one.^ref Shallow aquifers are more open to contamination from pollutants.

pH is a consideration when using a natural water source. According to the Kentucky Geological Survey: “Streams and lakes in wet climates such as Kentucky typically have pH values between 6.5 and 8.0. Soil water in contact with decaying organic material can have pH values as low as 4.0, and the pH of water that has reacted with iron sulfide minerals in coal or shale can be even lower. In the absence of coal or iron sulfide minerals, the pH of groundwater typically ranges from about 6.0 to 8.5, depending on the type of soil and rock contacted. Reactions between groundwater and sandstones result in pH values between about 6.5 and 7.5, whereas groundwater flowing through limestone strata can have values as high as 8.5.”^ref Since you want to keep water pH between 5.5 and 6.5 for plant watering, it would be a good idea to test the pH of any natural water source you are using.

A note on Legionnaire’s disease

Legionnaire’s disease is a potentially fatal form of pneumonia caused by inhaling mist or droplets of water containing Legionella bacteria^ref. This bacteria can grow in any non-sterile water^ref, feeds on algae, rust, scale or sludge, and thrives in temperatures between 20^oC and 45^oC.^ref So it could be present in some of the above sources, particularly when water is left standing. It’s worth being more careful when temperatures are above 20^oC as you really don’t want to get this disease, which may already be a risk to bonsai practitioners since another source of Legionnaire’s is compost & potting soil.^ref In warmer weather it may be safer to use tap water for bonsai.

So to wrap all of this up from a bonsai perspective – feel free to use rainwater or water which comes from the distillation process of condensing humidifiers, tumble dryers or air conditioners. Be careful though if this water has been standing for a long time in temperatures above 20^oC. Feel relatively free to use aquarium water (but keep an eye on your trees to monitor for allelopathic effects) or dessicant-type dehumidifiers. Test the water if you’re using an untreated natural water source like a river, lake or well. Avoid using water from vented tumble dryers. And definitely do not use sea water, boiler condensate, untreated grey water or black water. Happy watering!

The Endosphere

Although it might sound like we’re veering into science fiction territory, the endosphere is actually part of a plant’s microbiome, like the rhizosphere and the phyllosphere. It is the community of microbes which live inside the plant itself – that is, between and in its cells. It’s only in the last few decades that research on the endosphere has accelerated – this has found that in fact a wide variety of microbes including bacteria and fungi live inside plants for at least a part of their lifecycle.^ref They are known as endophytes – and some of these are symbiotic whilst others can be pathogens.

Endophytes are found throughout the plant, in leaves, roots and stems, in spaces between cells as well as within cells themselves; the greatest number are found in roots, then leaves, then fruit/flowers. The types of microbes in residence depends on the microenvironment in each part of the plant, the specific physical and chemical characteristics in each environment attract different microbes.^ref

To enter the plant in the first place, microbes come from outside, through the root tips and hairs, through stomata and trichome pores in leaves, fruit & flowers, through holes in the stem made by insects, or by producing enzymes which break down plant cell walls to create an opening. Often these microbes are present in the rhizosphere or phyllosphere, and they migrate into the plant for all or part of their lifecycle.^ref Usually they live between cells, but some examples of bacteria and fungi entering plants cells have also been found. Endophytes can be transmitted vertically (from mother plant to seed), and horizontally (from the outside environment).^ref

Of all the spheres, the endosphere is the hardest to study, so there isn’t a huge amount of research which demonstrates what endophytes actually do when they are inside plants and how the host plant might benefit. Some findings are that endophytes are able to detect Reactive Oxygen Species (“ROS”) and may be able to help plants fight high ROS levels (eg. acting as an anti-oxidant).^ref Others have found endophytic fungi which produce the plant growth regulators gibberellic acid and indole acetic acid (auxin), and that this contributes to greater root & shoot mass.^{ref1 ref2} One study found an endophyte which conferred resistance to Dutch Elm Disease in vitro^ref. Finally a large number of endophytes associated with trees have been found to produce Taxol^ref, the best-selling cancer drug ever manufactured^ref and this promises to be a way for greater volumes of the drug to be created.^ref So like bacteria & fungi across the microbiome, these microbes appear to be pop-up pharmacies within the tree.

The endosphere probably doesn’t need to be your prime concern from a bonsai perspective. Like the other components of the tree’s microbiome, you want to foster a healthy one, which benefits the tree, and not an unhealthy one. Doing this mainly involves not killing them off!

The Phyllosphere

The phyllosphere is the community of microbes which live in and on a plant’s leaves. I had no idea that this even existed before writing the section for this website about the microbiome. Of course, if you think about it for a microsecond, it must! Our world has more microbes than anything else by several orders of magnitude, so, there must be microbes in a tree’s leaves. But the phyllosphere has been less publicised due to the intense interest in the rhizosphere (root microbiome) and in its beneficial microbes which can help plants grow by manipulating the soil and root environment.

The phyllosphere is different to the rhizosphere in that its main microbial members are bacteria and not fungi, although fungi are present, along with some archaea. It has been estimated that there are 1 million -10million bacterial cells per cm² of leaf surface.^ref And worldwide, the phyllosphere is an important microbiome, with a possible 10²⁶ cells! But it’s a relatively hostile environment, with fluctuating temperature & humidity and limited nutrients on the leaf surface. The shape and structure of the leaf at a microscopic level provides a range of microhabitats for bacteria, including the bases of trichomes, stomata, hydathodes (leaf pores), grooves along the veins, epidermal cell junctions, and cuticle depressions.^ref A study into tree phyllospheres found 129 bacterial species were significantly associated with the gymnosperms including Armatimonadetes, Actinobacteria, Bacteroidetes, Acidobacteria, TM7, TM6, Deltaproteobacteria, OD1, Fusobacteria, and FBP and 79 with the angiosperms including Chlamydiae, Proteobacteria, Gammaproteobacteria, Alphaproteobacteria, and Firmicutes.^ref

Bacteria on a leaf surface, from: https://www.ethlife.ethz.ch/archive_articles/090915_blattleben_kw/index_EN.html

What determines the microbial mass and mix on leaves is a combination of different factors, including the nitrogen content of leaves, the specific leaf area (related to carbon availability), wood density and seed mass^ref and the largest part of the variation seen between phyllospheres comes down to the host species. Conifers have a different phyllobiome than other species, for example they have less ice nuclei active bacteria (bacteria which can cause ice crystals to form) and they have Frankiaceae which is involved in nitrogen fixing in the soil.^ref Location also plays a role, with urban trees displaying a different phyllosphere makeup – correlated to ultrafine particulate matter and black carbon on the leaves.^ref

Bacteria usually require an available carbon source. You might be surprised to know that similar to roots, leaves also produce exudates (substances they exude into the environment). These include a wide range of carbon compounds, such as carbohydrates, amino acids, organic acids, and sugar alcohols, primarily products of photosynthesis, as well as proteins, oils, secondary metabolites and mucilage.^ref These carbon sources are not the only ones – the Methylobacterium species can use methanol exuded from the leaf from the breakdown of pectin as its only carbon source.^ref One of the bacterial families found on birch – Rhodospirillaceae – is able to photosynthesise, removing the dependence on leaf carbon sources. Another study discovered that certain phyllosphere bacteria can use diesel for their carbon source!^ref

Similarly, bacteria in the rhizosphere produce a range of substances just like they do in the rhizosphere – biosurfactants which reduce surface tension, degrade hydrocarbons and improve moisture levels and dissolved nutrients on the leaf surface, plant growth regulators which open up the leaf cells and cause them to leak nutrients, enzymes which help break down nutrients and protect the bacteria from solar radiation, and phytotoxins (if the bacteria is a pathogen).^ref

The benefits of phyllosphere microbes to their host are similar to those in the rhizosphere – for example Acetic Acid Bacteria have been found to perform nitrogen fixation within the needles of Pinus flexilis^ref, others confer resistance to Bursaphelenchus xylophilus-induced pine wilt disease^ref, some phyllosphere fungi produce zeatin, a cytokinin (plant growth regulator)^ref and others auxins, some also produce anti-freeze proteins which lower the freezing temperatureon the leaf.^ref Bacteria are implicated in the bioremediation of harmful chemicals or pollutants^ref, improved tolerance to stress, production of proteins which trigger the plant to mount defences against pathogens as well as those which attract populations of beneficial fungi.^ref

So, just like the rhizosphere, the phyllosphere is a very active place with many microorganisms playing different roles and constantly interacting in a dynamic ecosystem. What this means for bonsai is that there likely are organisms in the foliage which benefit your plant. Similar to the advice in general around the microbiome, applying fungicides, anti-bacterials and chemical pesticides can kill phyllosphere organisms so avoiding this is a good idea.

Choosing a pot

Of course your choice of pot has a lot to do with the aesthetic vision you have for your tree, and I’m certainly not going to get into a debate about ‘feminine’ and ‘masculine’ trees and pots (hint – I’m not a fan of gendered bonsai!) Or glazed/unglazed (etc).

The pot for your bonsai is more than just its physical receptacle, it is also a life support system, holding water, soil & microbes and providing physical support. There are some physical attributes of pots which promote or inhibit a tree’s health, including materials, volume, width/depth ratio, drainage and even colour.

To start with materials. I had quite an unsatisfactory experiment with concrete in the form of hypertufa, for a while I was trying to save money by making bonsai pots using this material. Hypertufa is a combination of cement, sand, an organic material like moss or coir, and perlite/vermiculite. It worked well for making pots, but I found that they dried out really quickly; further reading told me that cement and particularly hypertufa is very porous. It also can leach calcium & silicon, which may or may not harm/benefit your tree depending on how much comes out.

A study on tomatoes showed better results for plastic pots in winter, and clay pots in summer, which related to the temperature of the pot.^ref Clay/ceramic pots did not heat up to the same degree as plastic. As an illustration of this is below – a thuja occidentalis has suffered heat stress damage on one side of the pot.

https://www.researchgate.net/profile/Avner-Silber/publication/332235948_Chemical_Characteristics_of_Soilless_Media/links/625e92ad709c5c2adb86e7cb/Chemical-Characteristics-of-Soilless-Media.pdf#page=324

This comes down to the principle of temperature buffering – or, the ability to withstand temperature variations without transmitting these to the roots. Buffering is improved when the pot is larger, and when the surface area at the top of the pot is reduced. On the other hand, some species respond well to having warm (not hot) roots.

Be aware that a dark or black pot will get hot out in the summer sun. In one study, a black pot caused the growing medium to be up to 10 degrees C higher than the air temperature.^ref In a sunny or hot locale, this could prove deadly to roots if maintained for too long. Where the pot is positioned and the foliage of the tree in it will affect how much sun hits the pot. One study found that plants grown in white pots had 2.5 times the root density of those grown in black or green pots.^ref

The geometry of the pot affects evaporation rates, since more surface area provides more space for evaporation to take place. You can see the differences in the table below. Yellow highlights show two pots of similar volume. The 7cm radius pot with 5cm of depth has a similar volume to the 9cm radius with 3cm depth. But the second pot’s surface area is 1.7 times larger than the first. This will significantly increase evaporation. It’s probably no great surprise to anyone who has bonsai that a shallow wide pot requires more careful attention to watering.

Another aspect to consider in choosing a pot is the geometry relative to the tree being blown over. Whilst a heavy pot can compensate for geometry somewhat, a tree wired into a pot is effectively a giant lever with the fulcrum at the edge of the pot. Wind coming sideways onto the tree will push the lever and if the pot is too narrow relative to the height of the tree, the tree will fall.

You can calculate the force needed to turn a tree over based on the fulcrum position of the edge of the pot. The larger the difference between the pot radius and the centre point of wind force on the tree, the less force is needed to push it over. I’ve done some calculations on a 2.5kg tree with a 30cm-ish diameter foliage canopy, and you can see below that once it gets to 50cm tall with a 20cm wide pot, the wind needed to push it over becomes much lower.

If the centre point of wind force on the trunk moves upwards, the surface area of the foliage increases, or the pot width decreases, you can soon end up with instability. My suggestion is to test this when you’ve repotted, push the tree at the point where you think the wind will be centred, and see how much force is needed to push it over.

Biochar

(Thanks to Dr. Karen O’Hanlon of Probio Carbon for answering some of my questions about biochar).

Biochar is a product which has been advertised as a beneficial component of bonsai soil over recent years. So what exactly is it?

Biochar is basically charcoal which has been “produced from organic waste using pyrolysis technology under temperatures ranging from 400C to 700C where oxygen is either absent or depleted”.^ref Pyrolosis means decomposing carbon-based materials through the application of heat.^ref So a feedstock (source material) is acquired and heated in the absence of oxygen for a given period of time to create what you would probably recognise as charcoal. The structure of biochar is shown in the image – as you can see, it has many, many holes in it.

Scanning Electron Microscope image of biochar
https://www.rhs.org.uk/soil-composts-mulches/biochar

So why would you add biochar to your bonsai soil? There are a few good reasons. It has been proven to improve water availability^ref, act as a fertiliser reducing the need for chemical fertilisers^ref and increase microbial biomass^ref (ie. it attracts beneficial microbes).

An experiment conducted in Colchester, UK by the Bartlett Tree Research & Diagnostic Laboratory amazingly found that ash trees treated with biochar did *not* get infected by ash dieback disease over a period of 4 years even when the disease was present in adjacent trees on the same site. They believed the reason for this was that the biochar enhanced the trees’ immune system and improved root growth.^ref

The microbe aspect of biochar is really interesting – in one study it was found that microbes living in it were able to ‘mine’ the biochar pores for phosphorus. So it appears to have synergy between its composition (with nutrients for plants) and its attractiveness to microbes which can help get those nutrients into plants.

One of the key physical properties of biochar is that it has a massive surface area, relative to its size – in one study on malt spent rootlets (a residue from brewing) it was 340 m² per gram!!^ref That’s larger than the size of a tennis court for every gram of biochar.^ref This increased surface area along with the physical structure of biochar having lots of tiny pores, results in greater water retention in the soil.^ref

Biochar can be made from basically any organic material, from forestry to food production to agricultural by-products and this source material is the main determinant of its chemical properties.^ref So when choosing a biochar for your bonsai soil, you want to know what it has been made from, and what this means in terms of its properties. Some of the properties which vary significantly include pH, surface area and cation exchange capability/electrical conductivity. For bonsai I would say you want high surface area & pore volume (to assist with water availability) and high microbial mass. The fertiliser aspects are probably a nice-to-have. Looking at the table below this means probably biochar made from a wood-based source material is best.

There is quite a bit of research out there on different biochar properties, which I will summarise here for you to read through. Unfortunately I haven’t found any research which looks at volume of microbes for each feedstock, but I would expect this to be positively associated with surface area.

Biochar Feedstock	Properties
Wood	Highest surface area (leading to better water retention) and highest pore volume (a factor of 10 higher than manure) Lowest cation-exchange capability Largest amount of C Contain less plant-available nutrients More electrical conductivity Lowest ash content (associated with lower pH) Micro-nutrient content mixed (see table here) Total bioavailable nutrients mixed (see table here)
Crops & grasses	Highest average particle size Highest K content Lowest calcium carbonate equivalents Micro-nutrient content mixed (see table here) Total bioavailable nutrients mixed (see table here)
Manure	Lowest surface area and lowest pore volume Highest cation-exchange capability Highest calcium carbonate equivalents Lowest average particle size Highest ash content (associated with higher pH) Greatest N, S, P, Ca, and Mg concentrations Highest micro-nutrient content (Fe, Cu, Zn, B, Mn, Mo, Co, Cl) Total bioavailable nutrients mixed (see table here)

Source: https://link.springer.com/article/10.1007/s42773-020-00067-x/tables/1

The temperature at which the biochar is created makes a difference too. Increasing pyrolisis temperature leads to “increased biochar C, P, K, Ca, ash content, pH, specific surface area (SSA), and decreased N, H, and O content”^ref

Like many things in life though, you can have too much of a good thing. In some studies, too much or the wrong biochar in soil has led to phytotoxicity^ref You might also be wondering why it doesn’t just remove all the nutrients in the soil like activated carbon, which is used in aquariums and drink bottles to remove metals, chlorine and contaminants. When asked this question Dr. Karen O’Hanlon at Probio Carbon said it was because biochar is not ‘activated’ to the same degree as activated carbon. Reading more about this, the absorbent properties of biochar are “1/6th to 1/12th that of high quality activated carbons”.^ref Activation forces more pores and surface area into the charcoal, this is done by varying the temperature and pyrolysis process. So whilst there probably is some nutrient absorption, it’s not going to be at the same level as activated carbon and can be compensated for by the nutrients within the biochar themselves and the increased microbial activity.

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.

https://journals.ashs.org/downloadpdf/journals/hortsci/25/3/article-p274.pdf

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.

https://academic.oup.com/treephys/article/40/10/1355/5861906

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.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15462

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.

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.

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.