Conditioned soils reveal plant-selected microbial communities that impact plant drought response

Monohon, Samantha J; Manter, Daniel K.; Vivanco, Jorge M.

doi:10.1038/s41598-021-00593-z

Cited by 20 publications

(13 citation statements)

References 46 publications

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“…In recent years, evidence has been mounting that upon perceiving environmental stress, plants actively shape their microbiome to recruit microbes that help alleviate such harmful conditions 18 , as has been reported for plants responding to nutrient deficiency 40,41 , drought [42][43][44] or salinity 45 , but also to stress caused by microbial pathogens 13,14,20,46,47 . The disease-induced recruitment and buildup of beneficial microbes is thought to result in the creation of disease-suppressive soils [18][19][20][21]48,49 .…”

Section: Discussionmentioning

confidence: 98%

Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes

Goossens

Spooren

Baremans

et al. 2023

Preprint

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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.

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Section: Discussionmentioning

confidence: 98%

Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes

Goossens

Spooren

Baremans

et al. 2023

Preprint

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“…By providing a diverse carbon‐rich environment, plant species harbor a distinctive microbial community in their rhizosphere which, in turn, confers several fitness advantages to the plant host, shaping their assemblage and modulating their beneficial traits (Badri & Vivanco, 2009; Mönchgesang et al, 2016; Trivedi et al, 2020). In addition, root exudate‐derived metabolites act as important mediators structuring a stress‐resistant microbiota to alleviate plant abiotic stresses including nutrient deprivation, disease and drought stress (Ab Rahman et al, 2018; Monohon et al, 2021; Olanrewaju et al, 2017; Pieterse et al, 2014; Venturi & Keel, 2016; Vessey, 2003). Identification of stress‐derived metabolome and microbiota constitutes a feasible strategy to deal with abiotic and biotic constraints, however, the beneficial effects of root‐enriched microbial taxa driven by specialized root exudate derived metabolites remain understudied (Hong et al, 2021; Pantigoso, Manter, & Vivanco, 2020; Pantigoso, Yuan, et al, 2020).…”

Section: Plant–microbial Interactions In the Rhizospherementioning

confidence: 99%

The rhizosphere microbiome: Plant–microbial interactions for resource acquisition

Pantigoso

Newberger

Vivanco

2022

Journal of Applied Microbiology

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While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant's own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant-microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.

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“…Previous studies have reported a clear contribution from plant-associated microbial members to plant growth and resilience during drought conditions [30][31][32].…”

Section: Introductionmentioning

confidence: 98%

Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience

et al. 2022

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Background Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities. Results In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest – MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii. Conclusions Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.

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Conditioned soils reveal plant-selected microbial communities that impact plant drought response

Cited by 20 publications

References 46 publications

Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes

Congruent downy mildew-associated microbiomes reduce plant disease and function as transferable resistobiomes

The rhizosphere microbiome: Plant–microbial interactions for resource acquisition

Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience

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