Manipulating the Microbiome to Induce Plant Defense

Research Brief Publication Date: September 28, 2021
Last Updated: April 29, 2024

Dr. Cara H. Haney, Department of Microbiology and Immunology, The University of British Columbia,
Christina L. Wiesmann, Department of Microbiology and Immunology, The University of British Columbia,
Dr. Lori R. Shapiro, Department of Organismic and Evolutionary Biology, Harvard University
Dr. Ryan A. Melnyk, Department of Microbiology and Immunology, The University of British Columbia
Lucy R. O'Sullivan, Department of Molecular Biology, Massachusetts General Hospital
Sophie Khorasani, Department of Molecular Biology, Massachusetts General Hospital,
Li Xiao, Faculty of Land and Food Systems, The University of British Columbia
Jiatong Han, Department of Microbiology and Immunology, The University of British Columbia
Jenifer Bush, Department of Molecular Biology, Massachusetts General Hospital
Dr. Juli Carrillo, Faculty of Land and Food Systems, The University of British Columbia
Dr. Naomi E. Pierce, Department of Organismic and Evolutionary Biology, Harvard University
Dr. Frederick M. Ausubel, Department of Molecular Biology, Massachusetts General Hospital

About this Brief

This research brief was prepared by the BC Food Web team, based on an article published in Molecular Ecology. 


Plant roots, whether domesticated or wild, are associated with a community of bacteria. This community is referred to as the plant’s microbiome, just as we have a community of bacteria in our guts. This microbiome, which is found in the soil immediately surrounding plant roots  (known as the rhizosphere), is an important part of a plant’s defense mechanism against pathogens (disease-causing agents) and even some insect herbivores. There is a group of such bacteria called Pseudomonas whose different strains are able to offer different benefits to plants. When studied with Arabidopsis, a model plant that is a close relative of Brassica crops, some strains of Pseudomonas have resulted in resistance both against specific bacterial pathogens and against herbivores, namely a caterpillar called the cabbage looper. Other strains of Pseudomonas induce resistance against herbivores; however, they also increase susceptibility to bacterial pathogens. 

Researchers aimed to explore these two Pseudomonas strains, which we will refer to as the resistant strain and susceptible strain, and how they affect the plant immune system on a molecular level. If we can better understand these systems, we may be able to manipulate them for agricultural benefit by creating stronger plants that may not need chemical sprays. A compound called salicylic acid (SA) is a key hormone that is produced after damage from piercing and sucking herbivores and is involved in activating the defense responses of plants, including those effect against pathogens. Another plant defense related hormone called jasmonic acid (JA) is typically produced after damage from chewing insects, like the cabbage looper and other caterpillars, and after exposure to pathogens that kill plant tissue. The authors found that the resistant and susceptible strain had different effects on plant salicylic acid and jasmonic acid signaling, which explains the differing effects on plant immune function.

The goal of this study was to better understand how belowground beneficial bacteria (Pseudomonas) affect plant defenses against above-ground enemies. This study used the model plant Arabidopsis, coupled with Pseudomonas bacteria in its microbiome, to explore how bacteria can help plants fight off pathogens, herbivores, or both. It also aimed to explain the underlying mechanism of this resistance, examining how strains affect the plant defense hormones jasmonic and salicylic acid. This information could be of crucial agricultural importance, as farmers could manipulate their plants’ microbiomes in order to induce the defenses most needed, at the lowest cost to both the farmer and the plant. 

Research Process

Arabidopsis plants were grown in the greenhouse under 12 hours of light / 12 hours of darkness, with a 23/20° C day/night temperature, and cool fluorescent lighting. Their soil was amended with Pseudomonas bacteria, comprising around 10% of the total microbiome. Either the resistant or susceptible strain was added nine days after seed germination. 

After a little over a month of growth, leaves were infected with a bacterial pathogen. After 2 days of infection, plant leaves were sampled to determine the bacterial load, which allowed the researchers to know whether bacterial treatment in the roots resulted in increased or decreased pathogen load in the leaves. To determine the effects of herbivory on Arabidopsis plants, newly hatched cabbage looper caterpillars were randomly placed on each plant after they had been growing for 30 days. The caterpillars were allowed to feed for seven days, after which they were weighed. Their weight was used as a metric for herbivory success. 

Aphids were collected from lettuce plants at the University of British Columbia in order to test defense against piercing and sucking herbivores, in comparison to cabbage loopers which are chewing herbivores. Wingless female aphids of roughly similar sizes were placed on 30-day-old Arabidopsis plants and were allowed to feed and reproduce for 8 days, after which time they were counted. Lastly, for all experimental groups one infected or herbivore-damaged leaf was chosen and its DNA was extracted in order to examine the molecular pathways of defense. 


The susceptible strain induced plant resistance to the cabbage looper, measured by reduced caterpillar weight gain. The resistant strain also induced resistance to the cabbage looper, as expected. However, in the susceptible strain there was a trade-off for this resistance at the cost of plant defense against bacterial pathogens, which is due to the fact that the susceptible strain was found to induce jasmonic acid signaling. Jasmonic acid can help the plant defend against chewing herbivores, but inhibits plant defense against bacterial pathogens. The resistant strain, on the other hand, is able to promote both jasmonic and salicylic acid defenses, which explains why it is able to promote plant resistance to both bacterial pathogens and herbivores.

The study also found that the susceptible strain had no effect on plant defenses against aphids. This was surprising as JA based defenses can be effective against piercing and sucking insects. These results suggest that aphid resistance is dependent on multiple signalling pathways and interactions between them. Interestingly, the resistant strain proved to not be effective in inducing plant defense against aphids, and rather aphids increased on plants treated with the resistant strain. This was surprising as the salicylic pathways that resistant strains utilize are typically induced after herbivory attack by aphids.


This study illustrates that different strains of Pseudomonas can offer different defense mechanisms to plants due to their utilization of different defense hormones i.e. jasmonic and salicylic acid. Though susceptible strains are not effective at protecting plants from bacterial pathogens, they may still be beneficial in environments where herbivore resistance is the primary concern because these plants will not be wasting energy and resources on a defense they do not require. Meanwhile, resistant strains are able to defend against both chewing herbivores and pathogens making them a good choice where both herbivores and pathogens pose a threat. 

Ultimately, these results highlight that variation in the microbiome may contribute to varied defense abilities of plants. Plants may evolve to associate with specific bacteria that will be most beneficial to them in their environment. We can utilize this information to cultivate different strains of bacteria, which can then be added to the microbiomes of agricultural fields, depending on the specific defenses that are needed. This has the potential to be both an effective and more natural way to protect plants by eliminating the need for chemical sprays and the need for continuous monitoring. 

About this Research

This brief is based on the following journal article:

Haney, Cara H., et al. 2018. Rhizosphere‐associated Pseudomonas Induce Systemic Resistance to Herbivores at the Cost of Susceptibility to Bacterial Pathogens. Molecular Ecology, 27: 8. DOI:


Key Findings

  • Different strains of Pseudomonas can trigger different defense mechanisms to plants - including resistance to bacterial pathogens and a variety of herbivores.
  • Variation in the microbiome contributes to varied defense abilities of plants.
  • Manipulating the microbiome of agricultural fields can be an effective, natural way to protect plants while eliminating the need for chemical sprays and continual monitoring.