Tag Archives: Fungi


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 vitroref. Finally a large number of endophytes associated with trees have been found to produce Taxolref, the best-selling cancer drug ever manufacturedref 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 Microbiome and Symbiotic Microbes

It has been known for over a century that tree roots are colonised with microbes, particularly fungi, but it’s only in the last twenty-five years or so that this idea has captured the public imagination, with Suzanne Simard’s discovery that trees can actually communicate and share resources via their fungal networks.ref

Of course, our knowledge about microbes – a collective name which refers to any living thing so small that a microscope is needed to see it – has massively increased in recent years. Studies into the human microbiome have shown that our own cells are outnumbered ten to one by the cells of microorganisms which live in and on us (Collen). These are mostly bacteria but also include viruses, fungi and archaea, and some of them perform important roles in human health – for example comprising a key part of our immune system.

The same concept applies to trees. Microbes are everywhere on and even in trees, above-ground and below-ground, and some of these are beneficial to the tree, whilst others are detrimental. Microbes colonize the germinating seed right at the beginning of the tree’s life, then move on to colonize the radicle (root) as it emerges and then the cotyledons (first true leaves). Over the tree’s life the species and number of microbes will shift and change. It has been shown in a recent pre-publish study that 95% of the fungi and bacteria present in acorns were transmitted to seedlings, and it is expected that further research will show this is inherited from the parent tree.ref

So not only do seeds inherit their genes from their parents, they also inherit their microbiome.

The microbiome (community of microbes) of trees comprises the phyllosphere (microbes in the foliage), rhizosphere (microbes in the roots), and the endosphere (microbes within the plant itself). Within these live a wide variety of bacteria and fungi, co-habiting, interacting, supporting and competing, with a range of different impacts to their host. A newly emerging term in this field is the ‘holobiont’ – this is a host with its microbiota and recognises that they interact with each other as well as the host. A tree and its microbiome are a holobiont.


To understand more about the microbes in each sphere and what they do, read the three posts I linked to in the previous paragraph, each has guidance relevant to their different domains.

From a bonsai point of view, we want to help our trees cultivate a healthy community of beneficial microbes in their microbiome, since this helps them access nutrients, fight pathogens and stress and thrive. There are three things we can do to help with this. The first is to avoid killing the microbes! For example, adding pesticides, chemicals, anti-biotics, weed-killers, anti-fungals etc could damage your mycorrhizal and bacterial communities. There are hundreds of studies showing that glyphosate kills off AMs and ECMs, and it has been shown to negatively influence microbial survival directly as it inhibits an enzyme of the ‘shikimate’ pathway, which produces essential amino acids in both plants and the majority of microbes.

The second thing is that you can add mycorrhiza and beneficial bacteria to your bonsai soil, particularly if you are repotting and losing the existing communities, also if you are creating new bonsai through collection, seed growing, air layering etc. You can buy dried mycorrhiza and bacteria mixes which can be sprinkled into the pot and watered in – I have my mycorrhiza in a salt shaker and my bacterial inoculant in a pepper shaker. The research is a bit mixed about how effective this is since microbes don’t necessarily establish the required density to contribute to plant defences & health, but you can optimise their chances by ensuring your substrate has plenty of nooks & crannies for bacteria to live (eg. this is one of the main claims for the benefits of biochar). Check the product you are buying to ensure it matches the type of mycorrhiza your tree associates with (some products have both ECM and AM). Alternatively, if you can find some soil or humus from an unfertilized, chemical-free forest with similar species, grabbing a handful and stirring it into your bonsai soil will also add benefical microbes .

The third thing that can be done is to create an environment for your trees which microbes prefer. Good soil, a good level of moisture, drainage, a carbon source (in most cases – roots) and not too much disruption of the roots, good lighting and avoiding large temperature variations, and air flow around the foliage.

Microbes aren’t all sweetness & light though, some are pathogenic not just to plants but to humans as well. Improperly composted manure can introduce bacteria including Salmonella, E. coli and Enterococcus. More relevant to bonsai enthusiasts is the fact that the Legionella bacteria which causes Legionnaire’s disease (a potentially fatal pneumonia) is present in many composts including those made from wood, bark, green waste and peat.ref As a result, whilst we certainly should appreciate our friendly microbes for their role in our bonsai practice, we should also make sure to wash hands and tools thoroughly, and avoid breathing in any organic matter such as compost. When mixing bonsai substrate, doing this under a cover, outside or in a bag is preferable to doing it in a way which sends dust particles into the air.