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.