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)

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.

‘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.