February 20th, 2017 / Claudia Canales, B4FA

Plants do not grow in isolation: even the smallest amount of soil is home to millions of very diverse microorganisms, mostly bacteria and fungi, which interact with plants and affect the way they grow and cope with environmental and biotic stresses.

These microbes have co-evolved with plants since they colonised the land – indeed some early root associations with fungi have been discovered in fossils. The relationship is mutual – plants sustain microbial communities, providing carbon sources for their growth and protection and influencing the composition and activity of root-associated microbial communities. Bacteria and fungi greatly increase the ability of roots to extract nutrients from the soil, especially nitrogen and phosphorus, and provide protection against other disease-causing bacteria, viruses, and fungi.

The complete genetic content of the microbial communities that live in a specific habitat is referred to as the microbiome. Microbial communities associated with plant roots live in both the soil, influenced by root secretions and accompanying microorganisms (called the rhizosphere), and the cells of the root without causing any disease. Some of these microorganisms have been used successfully for many years as biofertilisers, due to their positive effects on plant growth and tolerance to stress.

From the point of view of the plant’s physiology, the soil microbiome can be considered as a second, much larger, complex and dynamic plant genome (or complete set of genes). Just as a healthy microbiome in the intestines of humans is crucial for their good health, a healthy soil microbiome is essential for healthy, fertile soils.

Conversely, agricultural lands that have been degraded by continuous cultivation with single crops or by the excessive use of chemicals are poor in terms of the numbers and kinds of the microbes they host. Determining the part played by soil microbes in enabling plants to resist stresses has therefore become an important aim for research.

Microbial communities can benefit high soil salinity, which severely affects 15–50 per cent of all agricultural soils

There is increasing awareness of the potential of beneficial microbial communities to improve the way plants cope with stress, such as drought and high soil salinity (which severely affects between 15 and 50 per cent of all agricultural soils), while at the same time mitigating environmental impacts. Hence, the manipulation of soil microbes by influencing their activity and composition is an important addition to the toolkit which complements plant breeding to increase the productivity and resilience of crops. Quite literally, a “bottom up approach”!

Root microbial communities improve the tolerance of plants to drought and high salinity in many different ways. One is by influencing the production and activity of plant hormones, such as ethylene that plants produce in excess when subjected to a variety of stresses, inhibiting root growth. Several root-associated bacteria are however able to break down the chemical precursor of ethylene, overcoming the inhibition and allowing the plant to absorb more water from the soil. And as a bonus, this chemical reaction results in the production of ammonia, which can be used by the plant as a source of nitrogen.

Root-associated microorganisms can also enhance the uptake of important plant nutrients during droughts or in saline soils such as phosphorous, potassium and iron, fix atmospheric nitrogen and improve efficiency of the use of water (for example, as shown in this study on tomato). In conditions of high salinity, the soil microbes can help limit the entry of salt into the plant by secreting a protective film around its roots; limit the ability of the plant to absorb salt; increase the ability of roots to absorb water from soils; and by helping the plant to resist the higher production of damaging reactive oxygen produced during stress.

A mixture of traditional techniques, such as the isolation of pure microbial strains in the laboratory (which is not always possible), and modern high-throughput sequencing technologies are being used to develop full catalogues of the microbial species associated with plants in different soils, including arid and saline ones. These initiatives include the Earth Microbiome Project, which aims to systematically characterize global microbial taxonomic and functional diversity, and a large-scale survey of the microbiome in 10 Sub-Sahara African countries – Botswana, Côte d’Ivoire, Ethiopia, Kenya, Mozambique, Namibia, Nigeria, South Africa, Zambia, and Zimbabwe. It is expected that this project will be expanded to ultimately map the below-ground microbial diversity of the whole continent.

Root-associated microorganisms can also enhance the uptake of important plant nutrients during droughts or in saline soils

While most of the initial studies focused on the interaction between plants and one specific set of microorganisms (such as in this study), there is an increasing awareness of the need to look at the interaction between plants and the microbiome. One compelling, practical reason is that inoculation of soils with individual strains is generally ineffective due to competition with the microbial communities already in the soil. What is needed is a constructed microbial community approach, through which a mixture of beneficial, high viability microorganisms (the core microbes) is introduced to engineer rhizosphere microbes for optimizing crop plants. This is possible due to the functional redundancy in microbial communities across diverse environments, which means that only a proportion of the soil microorganisms is needed to maintain a functioning ecosystem. Identifying the key components of the core microbes is critical.

The potential to engineer plants that can alter the composition and activity of beneficial microbes is also being explored. Synthetic microbial communities, developed though biotechnology, are also being considered as possible solutions. These will be reviewed in a later entry.


Claudia Canales Holzeis is a plant molecular biologist with a near-decade of experience in plant genetics research.  She previously worked as Senior Project Officer for the International Service for the Acquisition of Agri-Biotech Applications (ISAAA), based in the Philippines.  A graduate of the University of Reading in Environmental Biology, Claudia Canales gained a DPhil. in Plant Genetics at Oxford.