BackgroundPlants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants.ResultsPlants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response.ConclusionCollectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0537-x) contains supplementary material, which is available to authorized users.

Looking forward includes looking back every now and then. In 2007, David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research has provided a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high-throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plantassociated microbiomes. Here, we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern and emerging microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.

Plants deposit photosynthetically-fixed carbon in the rhizosphere, the thin soil layer directly around the root, thereby creating a hospitable environment for microbes. To manage the inhabitants of this nutrient-rich environment, plant roots exude and dynamically adjust microbe-attracting and -repelling compounds to stimulate specific members of the microbiome. Previously, we demonstrated that foliar infection of Arabidopsis thaliana by the biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) leads to a disease-induced modification of the rhizosphere microbiome. Soil conditioned with Hpa-infected plants provided enhanced protection against foliar downy mildew infection in a subsequent population of plants, a phenomenon dubbed the soil-borne legacy (SBL). Here, we show that for the creation of the SBL, plant-produced coumarins play a prominent role as coumarin-deficient myb72 and f6’h1 mutants were defective in creating a Hpa-induced SBL. Root exudation profiles changed significantly in Col-0 upon foliar Hpa infection, and this was accompanied by a compositional shift in the root microbiome that was significantly different from microbial shifts occurring on roots of Hpa-infected coumarin-deficient mutants. Our data further show that the Hpa-induced SBL primes Col-0 plants growing in SBL-conditioned soil for salicylic acid (SA)-dependent defenses. The SA-signaling mutants sid2 and npr1 were unresponsive to the Hpa-induced SBL, suggesting that the protective effect of the Hpa-induced shift in the root microbiome results from an induced systemic resistance that requires SA-signaling in the plant.

In this thesis, I have investigated microbiomes of plants that are under attack by obligate biotrophic pathogens that cause downy mildew disease. In particular, I have studied the phyllosphere bacterial communities of laboratory cultures of the downy mildews Hyaloperonospora arabidopsidis (Hpa) and Peronospora effusa (Pe) on their respective hosts Arabidopsis thaliana and Spinacia oleracea (henceforth Arabidopsis and spinach). Within these two pathosystems, we observed consistent enrichment of specific bacteria in distinct cultures (Chapters 2 and 4), and for the Arabidopsis system we demonstrated that the genomes of the specific bacteria enriched in distinct laboratory cultures across Europe were isogenic (Chapter 2). These bacteria were further shown to reach higher abundances in the phyllosphere upon Hpa infection (Chapter 2). Also in the rhizosphere, we observed increased colonization by downy mildew-associated bacteria on plants that were grown on soil that was conditioned by downy mildew-infected plants. This suggests that the downy mildew-associated microbes are part of a soil-borne legacy of disease that can be inherited by future generations of plants grown on the same soil (Chapter 3). Moreover, the microbes that are enriched in downy mildew-associated communities appear to be geared towards plant protection (Chapter 3), suggesting that their assembly is indeed directed by the host plant. Lastly, similarities were observed between Pe-associated microbiomes in laboratory cultures and naturally Pe-infected field-grown plants (Chapter 4), highlighting that these microbiomes are not only a laboratory phenomenon. Together, these findings suggest that phyllosphere bacterial communities of plants that are under downy mildew attack are modulated to benefit the plant, meaning that a plant’s cry for help towards the microbiome upon pathogen attack may be a contributing factor to phyllosphere microbiome assembly. Finally, these findings are discussed in a broader perspective in chapter 5, focusing on the mechanisms that may underly the recruitment/enrichment of specific bacteria in downy mildew-infected leaves.

Root-associated microbiota can protect plants against severe disease outbreaks. In the model-plant Arabidopsis thaliana, leaf infection with the obligate downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) results in a shift in the root exudation profile, therewith promoting the growth of a selective root microbiome that induces a systemic resistance against Hpa in the above-ground plant parts. Here we show that, additionally, a conserved subcommunity of the recruited soil microbiota becomes part of a pathogen-associated microbiome in the phyllosphere that is vertically transmitted with the spores of the pathogen to consecutively infected host plants. This subcommunity of Hpa-associated microbiota (HAM) limits pathogen infection and is therefore coined a resistobiome. The HAM resistobiome consists of a small number of bacterial species and was first found in our routinely maintained laboratory cultures of independent Hpa strains. When co-inoculated with Hpa spores, the HAM rapidly dominates the phyllosphere of infected plants, negatively impacting Hpa spore formation. Remarkably, isogenic bacterial isolates of the abundantly-present HAM species were also found in strictly separated Hpa cultures across Europe, and even in early published genomes of this obligate biotroph. Our results highlight that pathogen-infected plants can recruit protective microbiota via their roots to the shoots where they become part of a pathogen-associated resistobiome that helps the plant to fight pathogen infection. Understanding the mechanisms by which pathogen-associated resistobiomes are formed will enable the development of microbiome-assisted crop varieties that rely less on chemical crop protection.