Manipulating exudate composition from root apices shapes the microbiome throughout the root system

Kawasaki, Akitomo; Dennis, Paul G.; Forstner, Christian; Raghavendra, Anil; Mathesius, Ulrike; Richardson, Alan; Delhaize, Emmanuel; Gilliham, Matthew; Watt, Michelle; Ryan, Peter R.

doi:10.1093/plphys/kiab337

Cited by 59 publications

(39 citation statements)

References 81 publications

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“…The rhizo-deposits, including sugars, organic acids, amino acids, fatty acids, phenolics, nucleotides, sterols and vitamins, provide critical carbon sources for rhizobacteria and plant pathogens ( Sasse et al, 2018 ). In a stride to evaluate the impact of root exudates on proliferation of the microorganisms in the rhizosphere, Kawasaki et al (2021) altered the expression of transporters in rice ( Oryza sativa L.) and wheat ( Triticum aestivum L.), which affected the release of substrates (simple organic anions, including malate, citrate, and γ-amino butyric acid) from root apices. These altered level of root exudates, either separately or in combination, encouraged the proliferation of specific beneficial root microbiomes from the soil.…”

Section: Rhizosphere Biology and Microbial Diversitymentioning

confidence: 99%

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Kumar

Diksha

Sindhu

et al. 2022

Current Research in Microbial Sciences

212

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Highlights Agriculture plays an important role in a country's economy. In modern intensive agricultural practices, chemical fertilizers and pesticides are applied on large scale to increase crop production in order to meet the nutritional requirements of the ever-increasing world population. However, rapid urbanization with shrinking agricultural lands, dramatic change in climatic conditions and extensive use of agrochemicals in agricultural practices has been found to cause environmental disturbances and public health hazards affecting food security and sustainability in agriculture. Besides this, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health due to indiscriminate use of agrochemicals. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield under greenhouse and field conditions. The beneficial mechanisms of plant growth improvement include enhanced availability of nutrients (i.e., N, P, K, Zn and S), phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. This plant-microbe interplay is indispensable for sustainable agriculture and these microbes may perform essential role as an ecological engineer to reduce the use of chemical fertilizers. Various steps involved for production of solid-based or liquid biofertilizer formulation include inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. In addition, recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. Thus, inoculation with beneficial microbes has emerged as an innovative eco-friendly technology to feed global population with available resources. This review critically examines the current state-of-art on use of microbial strains as biofertilizers in different crop systems for sustainable agriculture and in maintaining soil fertility and enhancing crop productivity. It is believed that acquisition of advanced knowledge of plant-PGPR interactions, bioengineering of microbial communities to improve the performance of biofertilizers under field conditions, will help in devising strategies for sustainable, environment-friendly and climate smart agricultural technologies to deliver short and long terms solutions for improving crop productivity to feed the world in a more sustainable manner.

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Section: Rhizosphere Biology and Microbial Diversitymentioning

confidence: 99%

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Kumar

Diksha

Sindhu

et al. 2022

Current Research in Microbial Sciences

212

View full text Add to dashboard Cite

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“…For example, malate transport and cell wall biogenesis were among the most frequent enriched terms. Malate is a prominent root exudate involved in shaping rhizospheric microbiome composition 26 and cell walls form physical barriers as well as energy sources for microbes 27 . Together this analysis revealed that while observations of loci associated with the abundance of various microbes is environmentally dependent, some loci can be implicated across multiple environments and the processes by which the host plant modulates core microbiota are diverse.…”

Section: Resultsmentioning

confidence: 99%

Heritability and host genomic determinants of switchgrass root-associated microbiota in field sites spanning its natural range

Edwards

Saran

Bonnette

et al. 2022

Preprint

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A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here we characterized the root microbiota of a large population of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of >2000 samples, suggest field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, we find that relatively few highly prevalent bacterial taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit / filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e. microbes in >80% of samples) regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

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“…With new research developments in the field of root exudates, the present approach of inoculating the PGPRs with seed is going to be replaced with using root exudates to recruit beneficial microbes directly from soil. In this stride, Kawasaki et al (2021) altered the expression of transporters from the aluminum‐activated malate transporter and the multidrug and toxic compound extrusion families in rice ( Oryza sativa L.) and wheat ( Triticum aestivum L.), and found that these exudates significantly altered the microbiome composition throughout the root system. However, other factors such as root type, position along with root and soil type had a greater influence on microbiome structure.…”

Section: Plant Bioengineering and Endophytesmentioning

confidence: 99%

Wheat endophytes and their potential role in managing abiotic stress under changing climate

Ahlawat

Yadav

Kashyap

et al. 2022

Journal of Applied Microbiology

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Wheat (Triticum aestivum L.) cultivation differs considerably in respect of soil type, temperature, pH, organic matter, moisture regime, etc. Among these, rising atmospheric temperature due to global warming is most important as it affects grain yield drastically. Studies have shown that for every 1°C rise in temperature above wheat's optimal growing temperature range of 20-25°C, there is a decrease in 2.8 days and 1.5 mg in the grain filling period and kernel weight, respectively, resulting in wheat yield reduction by 4-6 quintal per hectare. Growing demand for food and multidimensional issues of global warming may further push wheat crop to heat stress environments that can substantially affect heading duration, percent grain setting, maturity duration, grain growth rate and ultimately total grain yield. Considerable genetic variation exists in wheat gene pool with respect to various attributes associated with high temperature and stress tolerance; however, only about 15% of the genetic variability could be incorporated into cultivated wheat so far. Thus, alternative strategies have to be explored and implemented for sustainable, more productive and environment friendly agriculture. One of the feasible and environment friendly option is to look at micro-organisms that reside inside the plant without adversely affecting its growth, known as 'endophytes', and these colonize virtually all plant organs such as roots, stems, leaves, flowers and grains. The relationship between plant and endophytes is vital to the plant health, productivity and overall survival under abiotic stress conditions. Thus, it becomes imperative to enlist the endophytes (bacterial and fungal) isolated till date from wheat cultivars, their mechanism of ingression and establishment inside plant organs, genes involved in ingression, the survival advantages they confer to the plant under abiotic stress conditions and the potential benefits of their use in sustainable wheat cultivation.

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Manipulating exudate composition from root apices shapes the microbiome throughout the root system

Cited by 59 publications

References 81 publications

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Heritability and host genomic determinants of switchgrass root-associated microbiota in field sites spanning its natural range

Wheat endophytes and their potential role in managing abiotic stress under changing climate

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