Phyte club: inside the plant microbiome

Gareth Raynes, Aberystwyth University

By Gareth Raynes, Aberystwyth University

The human microbiome is becoming more and more widely known and extensively studied, which is great! However, we’re not unique in having our own personal legions of friendly bacteria; far from it in fact. Not only do other animals have extensive microbiomes (especially ruminant animals, which are pretty much big fermentation tanks on legs), plants do too. But what do plants need bacteria for and where do they live?

Much like we host different populations of bacteria in our gut, on our skin and in our mouths, plants have different regions that are inhabited by different bacteria. These are divided into different ‘spheres’; the surface of the above-ground portion of the plant is the episphere, the roots and closely associated soil are the rhizosphere, and the internal tissues of the plant are the endosphere. For me, my research focuses on endophytes; the bacteria living within the endosphere of the plants, but there are also bacteria and fungi in the rhizosphere and episphere too. These microbes aren’t causing disease, and can even provide the host plant with a really wide range of benefits!

Just like our bacteria provide us with various nutrients, plant associated bacteria feed their host; nitrogen fixing bacteria, either in root nodules in legumes or living endophytically, fix atmospheric nitrogen into forms useable by the plant. Microbes in the roots use iron-binding siderophores to gather iron, while others can even dissolve rocks with organic acids to free up their minerals for use. Endophytes can make or inhibit plant hormones like auxin and ethylene to tweak how the plant responds to stimuli, enabling plants to tolerate stresses like high salt levels in the soil.


Transmission electron microscope image of a cross section though a soybean root nodule (endophyte). The bacteria, Bradyrhyzobium japonicum, infects the roots and establishes a nitrogen fixing symbiosis. This high magnification image shows part of a cell with single bacteriods (bacterium-like cell or modified bacterial cell) within their symbiosomes (Credit: Louisa Howard – Dartmouth Electron Microscope Facility).

They don’t just feed the plant; they protect it as well. The plant microbiome can reduce plant disease by directly eliminating pathogens with antimicrobial compounds, outcompeting them for resources (using things like the siderophores mentioned above) and even by activating the plant’s own immune response. This induced systemic resistance activates more rapidly than usual in response to pathogens, improving the effectiveness of the response and limiting the disease before it can take hold. Other microbes produce insecticidal compounds to protect the plants from herbivorous insects!

Boosting plant growth and protecting them from disease sounds great! But, how can we use these in the real world? The answer is, we already do! For example, Bacillus thuringiensis has been used for decades as a living insecticide, protecting crops from predation. Commercially available nitrogen fixing bacteria have been available for a while too. However, it’s still early days; research into this area is still young, but rapidly increasing, and will likely have a huge impact. Nitrogen fixing bacteria have the potential to greatly reduce our reliance on nitrogenous fertilisers for crops and growth-boosting bacteria could give high crop yields on lower quality soil opening up more land for food or energy crops.


Spores and crystals of Bacillus thuringiensis serovar morrisoni strain T08025 (Microscopy by Jim Buckman).

This is just a very broad overview. With the enormous variety of plants, and of microbes, we’ve only begun to scratch the surface on what the plant microbiome can do and I’ve not even started to cover everything we do know already. Plant microbiology is a really exciting field to be part of. There’s so much potential and so much more to learn, I love it!


About Me 

I’m Gareth Raynes, a PhD student in the Institute of Biological, Environmental and Rural Sciences (IBERS) at Aberystwyth University, researching endophytic bacteria.

My blog:

Twitter: @friendlybugblog

Some Resources and further reading:

Farrar, K., Bryant, D., & Cope-Selby, N. (2014). Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. Plant Biotechnology Journal, 12(9), 1193–206.

Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J., & Dowling, D. N. (2008). Bacterial endophytes: recent developments and applications. FEMS Microbiology Letters, 278(1), 1–9.

Glick, B. R. (2012). Plant Growth-Promoting Bacteria: Mechanisms and Applications. Scientifica, 2012, 1–15.

Today is Fascination of Plants Day 2017. If you enjoyed this post and like a challenge check out the Biochemical Society plant quiz!

This post is the second in our microbiome series. The first, Microbiome manipulation – full steam ahead? by Tilly Potter, was published in April. If you are interested in reading more on this topic, check out the April issue of The Biochemist, which focuses on the microbiome. 

2 thoughts on “Phyte club: inside the plant microbiome

  1. Nice post Gareth! I’ve at the beginning of a PhD on biocontrol rhizobacteria. This is a great intro to plant microbiomes that I can point people to if they’re interested in learning more. Cheers!

    Liked by 1 person

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