Role of the Plant Root Microbiome in Abiotic Stress Tolerance

Caddell, Daniel; Deng, Shijie; Coleman‐Derr, Devin

doi:10.1007/978-3-030-10504-4_14

Cited by 37 publications

(19 citation statements)

References 231 publications

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“…To achieve such a goal, hybrid experimental approaches that combine existing and developing genomic technologies and classical microbiology techniques will be required [204]. For example, genome editing tools like the CRISPR-Cas9 system now permit the development of mutant lines of important crop species like rice and wheat [205] so that hypotheses about the roles certain genes play in regulating plant responses to abiotic stress can be experimentally tested.…”

Section: Discussionmentioning

confidence: 99%

Interactions between plants and soil shaping the root microbiome under abiotic stress

Hartman

Tringe

2019

Biochemical Journal

243

153

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Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

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Section: Discussionmentioning

confidence: 99%

Interactions between plants and soil shaping the root microbiome under abiotic stress

Hartman

Tringe

2019

Biochemical Journal

243

153

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“…Betaine represents one of the most robust and widely utilized biomarkers of plant responses to drought (31, 48). We hypothesized that other metabolites with roles in plant drought response would share a similar abundance pattern during drought.…”

Section: Resultsmentioning

confidence: 99%

“…Drought promotes changes in exudate composition, stimulating the exudation of primary and secondary metabolites, including osmoprotectants such as sugars and amino acids. These root and rhizosphere metabolites are predicted to play a role in regulating microbiome associations during drought (30, 31).…”

Section: Introductionmentioning

confidence: 99%

Drought shifts sorghum root metabolite and microbiome profiles and enriches the stress response factor pipecolic acid

Caddell

Louie

Bowen

et al. 2020

Preprint

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Interactions between plants and their root-associated microbiome are important for determining host fitness during periods of stress. During drought, monoderm bacteria are more abundant in sorghum roots than in those of watered controls. Additionally, a reversion from monoderm to diderm dominance occurs in drought-stressed roots one week after rewatering. However, the mechanisms driving this rapid microbiome composition shift is currently unknown. To understand if changes in host metabolism are correlated with this shift, we employed 16S amplicon sequencing and metabolomics of root, rhizosphere, and soil at the peak of a preflowering drought and 24 hours after rewatering. The microbiomes of droughted roots, rhizospheres, and soils differed from watered controls, and shifts in bacterial composition were observed in root and rhizosphere 24 hours after rewatering, highlighting the rapid response of microbes to the cessation of drought. Next, we performed metabolomic profiling to identify putative drivers of this process. During drought, we observed a high abundance of abiotic stress response factors, including antioxidants, osmolytes, amino acids, and plant hormones. After rewatering, large shifts in metabolite abundances were observed in rhizosphere, whereas shifts in root and soil were subtle. In addition, pipecolic acid, a well-characterized systemic acquired resistance signalling compound, was enriched in roots and rhizosphere during drought. We found that exogenous application of pipecolic acid suppresses root growth via a systemic acquired resistance-independent mechanism. Collectively, these data provide a comprehensive characterization of metabolite shifts across three compartments during drought, and elucidate a potential role of pipecolic acid in the sorghum drought response.IMPORTANCEPlant-associated microbial communities shift in composition and contribute to host fitness during drought. In particular, Actinobacteria are enriched in plant roots and rhizosphere during drought. However, the mechanisms plants use to drive this shift are poorly understood. Here we apply a combination of bacterial and metabolite profiling in root, rhizosphere, and soil during drought and drought-recovery to investigate potential contributions of host metabolism towards shifts in bacterial composition. Our results demonstrate that drought alters metabolic profiles and that the response to rewatering differs between compartments; we identify drought-responsive metabolites that are highly correlated with Actinobacteria abundance. Furthermore, our study reports for the first time that pipecolic acid is a drought-enriched metabolite in sorghum roots. We demonstrate that exogenous application of pipecolic acid is able to provoke one of the classic drought responses in roots, root growth suppression, and that this activity functions independently from the systemic acquired resistance pathway.

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“…3A) may provide stability and resilience to the plant microbiome and simultaneously improve the phenotype of host plants via the genes carried by community members. A subset of naturally occurring microbes are well known to promote growth of their plant hosts 51 , accelerate wastewater remediation and nutrient recycling 52 , and shield plant hosts from both abiotic and biotic stresses 53 , including opportunistic pathogens [54][55][56] . The application of SynComs to Mars-based agriculture motivates additional discussions in tradeoffs between customized hydroponics versus regolith-based farming, both of which will require distinct technology platforms and applied SynComs.…”

Section: Food and Pharmaceutical Synthesismentioning

confidence: 99%

Towards a Biomanufactory on Mars

Berliner¹,

Hilzinger²,

Abel³

et al. 2020

Preprint

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A crewed mission to and from Mars may include an exciting array of enabling biotechnologies that leverage inherent mass, power, and volume advantages over traditional abiotic approaches. In this perspective, we articulate the scientific and engineering goals and constraints, along with example systems, that guide the design of a surface biomanufactory. Extending past arguments for exploiting stand-alone elements of biology, we argue for an integrated biomanufacturing plant replete with modules for microbial \textit{in situ} resource utilization, production, and recycling of food, pharmaceuticals, and biomaterials required for sustaining future intrepid astronauts. We also discuss aspirational technology trends in each of these target areas in the context of human and robotic exploration missions in the coming century.

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Role of the Plant Root Microbiome in Abiotic Stress Tolerance

Cited by 37 publications

References 231 publications

Interactions between plants and soil shaping the root microbiome under abiotic stress

Interactions between plants and soil shaping the root microbiome under abiotic stress

Drought shifts sorghum root metabolite and microbiome profiles and enriches the stress response factor pipecolic acid

Towards a Biomanufactory on Mars

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