The soybean rhizosphere: Metabolites, microbes, and beyond—A review

Sugiyama, Akifumi

doi:10.1016/j.jare.2019.03.005

Cited by 132 publications

(88 citation statements)

References 91 publications

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“…Metabolites secreted into the rhizosphere are degraded by microbes and adsorbed onto soil organic matter and clay minerals, depending on the soil type and microbes present (Canarini, Kaiser, Merchant, Richter, & Wanek, 2019;Soma & Soma, 1989;Sugiyama, 2019). In order to gain insight into daidzein distribution in soybean fields, we used grey lowland soils obtained from a soybean farm where soybeans had been cultivated for more than 5 years.…”

Section: Simulation Of Daidzein Distributionmentioning

confidence: 99%

“…Previous studies provided evidence that plant metabolites secreted from roots provoke changes in rhizosphere microbial communities and mediate plant–microbe interactions, from symbiotic to commensal to pathogenic, suggesting the importance of plant metabolites in the rhizosphere for promoting the growth and health of plants (Berendsen, Pieterse, & Bakker, ; Massalha, Korenblum, Tholl, & Aharoni, ; Sasse, Martinoia, & Northen, ). Despite the importance of root‐secreted metabolites, little is known of the distribution and fate of these molecules in the rhizosphere (Sugiyama, ). Plant metabolites can be divided into primary and secondary, or plant specialized, metabolites (Pichersky & Lewinsohn, ).…”

Section: Introductionmentioning

confidence: 99%

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Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Okutani

Hamamoto

Aoki

et al. 2020

Plant Cell & Environment

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Plant roots nurture a wide variety of microbes via exudation of metabolites, shaping the rhizosphere's microbial community. Despite the importance of plant specialized metabolites in the assemblage and function of microbial communities in the rhizosphere, little is known of how far the effects of these metabolites extend through the soil. We employed a fluid model to simulate the spatiotemporal distribution of daidzein, an isoflavone secreted from soybean roots, and validated using soybeans grown in a rhizobox. We then analysed how daidzein affects bacterial communities using soils artificially treated with daidzein. Simulation of daidzein distribution showed that it was only present within a few millimetres of root surfaces. After 14 days in a rhizobox, daidzein was only present within 2 mm of root surfaces. Soils with different concentrations of daidzein showed different community composition, with reduced α‐diversity in daidzein‐treated soils. Bacterial communities of daidzein‐treated soils were closer to those of the soybean rhizosphere than those of bulk soils. This study highlighted the limited distribution of daidzein within a few millimetres of root surfaces and demonstrated a novel role of daidzein in assembling bacterial communities in the rhizosphere by acting as more of a repellant than an attractant.

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Section: Simulation Of Daidzein Distributionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Okutani

Hamamoto

Aoki

et al. 2020

Plant Cell & Environment

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“…Respiration by roots, for example, is associated with the consumption of oxygen and production of carbon dioxide, thereby causing local changes in gas composition. Meanwhile, the excretion of exudates by plant roots provides a food source for heterotrophic microbes and promotes the establishment of distinct microbial communities [1–3]. Furthermore, the selective uptake of nutrients by roots, release of protons or bicarbonate ions in exchange with absorbed nutrients, and the release of plant-derived organic acids or chelators to solubilize sparingly soluble salts cause changes in the chemical composition of the rhizosphere [4].…”

Section: Introductionmentioning

confidence: 99%

Properties of rhizosphere soil associated with herbaceous plant roots analyzed using small-scale protocols

Yamazaki

Ochiai

Motokawa

et al. 2019

Preprint

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22The rhizosphere, which is the region of soil adjacent to plant roots, is affected by 23 the activities of both plant roots and associated microorganisms which cause changes in 24 soil properties including nutrient mineral composition. Accordingly, the actual 25 availability of plant nutrients may not be the same as that estimated on the basis of bulk 26 soil analysis. However, the extent and manner in which the availability of plant nutrients 27 in bulk and rhizosphere soils differ remain unclear. Therefore, the present study defined 28 the rhizosphere as the soil adhered to plant roots, established a set of small-scale protocols 29 for analyzing the nutrient minerals of small soil samples, and then characterized the 30 rhizosphere soil of sorghum, Sorghum bicolor (L.) Moench. The mineral contents of the 31 bulk and rhizosphere soil differed significantly, with nutrient contents generally greater 32 in the rhizosphere, and particularly remarkable accumulation was observed in regards to 33 ammonium ion and exchangeable potassium concentrations. Such accumulation might be 34 due, in part, to the greater per weight surface areas of rhizosphere soil particles, but other 35 mechanisms, including the accumulation of organic matter, could also be involved.3 36 Introduction 37 The environment in the immediate vicinity of plant roots, the rhizosphere, is 38 generally considered to be distinct from that of the surrounding soil (i.e., bulk soil), and 39 the differences in these two regions can be attributed to multiple factors. Respiration by 40 roots, for example, is associated with the consumption of oxygen and production of 41 carbon dioxide, thereby causing local changes in gas composition. Meanwhile, the 42 excretion of exudates by plant roots provides a food source for heterotrophic microbes 43 and promotes the establishment of distinct microbial communities [1][2][3]. Furthermore, the 44 selective uptake of nutrients by roots, release of protons or bicarbonate ions in exchange 45 with absorbed nutrients, and the release of plant-derived organic acids or chelators to 46 solubilize sparingly soluble salts cause changes in the chemical composition of the 47 rhizosphere [4]. Together, the resulting differences between the nutrient availabilities of 48 bulk and rhizosphere soil can have significant effects on plant growth. However, the 49 extent and manner in which the availability of plant nutrients in bulk and rhizosphere 50 soils differ remain unclear. For example, the ammonium ion (NH 4 + ) levels of rhizosphere 51 soil have been reported to be both higher [5][6][7] or lower [8,9] than that of bulk soil, and 52 the same trend has been reported for potassium (K) [10][11][12]. 53To gain insights into the rhizosphere, soil needs to be fractionated according to 54 distance from plant roots. The so-called "rhizobox" technique, for example, allows roots 55 grow within a compartment of soil that is separated from the surrounding region with fine 56 mesh, which prevents the roots from mixing with the surrounding soil but...

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“…However, the addition of RE significantly screened the ENM biological effects. Despite the low final concentration of RE, the compounds that are known to be secreted by soybeans such as sugars, organic acids, isoflavones, and saponins (Table S5, Supporting Information) [29][30][31] Table S2, Supporting Information), Cd in RE-supplemented medium inhibited the specific growth rate of B. diazoefficiens by 50% of that observed in minimal medium alone. The RE-induced mitigation of Cd toxicity to bacteria might have derived from the complexation of toxic metal ions with organic ligands that reduced free Cd-ion concentrations and consequently the bioavailability of Cd to B. diazoefficiens.…”

Section: Soybean Root Exudates Ameliorated Effects Of Ceo 2 Nps Mwcnmentioning

confidence: 99%

Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N₂‐Fixing Bacterium Bradyrhizobium diazoefficiens

Mortimer

Liu

Wang

et al. 2020

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The pathogenicity and antimicrobial properties of engineered nanomaterials (ENMs) are relatively well studied. However, less is known regarding the interactions of ENMs and agriculturally beneficial microorganisms that affect food security. Nanoceria (CeO 2 nanoparticles (NPs)), multiwall carbon nanotubes (MWCNTs), graphene nanoplatelets (GNPs), and carbon black (CB) have been previously shown to inhibit symbiotic N 2 fixation in soybeans, but direct rhizobial susceptibility is uncertain. Here, Bradyrhizobium diazoefficiens associated with symbiotic N 2 fixation in soybeans is assessed, evaluating the role of soybean root exudates (RE) on ENM-bacterial interactions and the effects of CeO 2 NPs, MWCNTs, GNPs, and CB on bacterial growth and gene expression. Although bacterial growth is inhibited by 50 mg L −1 CeO 2 NPs, MWCNTs, and CB, all ENMs at 0.1 and 10 mg L −1 cause a global transcriptomic response that is mitigated by RE. ENMs may interfere with plant-bacterial signaling, as evidenced by suppressed upregulation of genes induced by RE, and downregulation of genes encoding transport RNA, which facilitates nodulation signaling. MWCNTs and CeO 2 NPs inhibit the expression of genes conferring B. diazoefficiens nodulation competitiveness. Surprisingly, the transcriptomic effects on B. diazoefficiens are similar for these two ENMs, indicating that physical, not chemical, ENM properties explain the observed effects.

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The soybean rhizosphere: Metabolites, microbes, and beyond—A review

Abstract: Graphical abstract

Cited by 132 publications

References 91 publications

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Properties of rhizosphere soil associated with herbaceous plant roots analyzed using small-scale protocols

Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N₂‐Fixing Bacterium Bradyrhizobium diazoefficiens

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The soybean rhizosphere: Metabolites, microbes, and beyond—A review

Abstract: Graphical abstract

Cited by 132 publications

References 91 publications

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Rhizosphere modelling reveals spatiotemporal distribution of daidzein shaping soybean rhizosphere bacterial community

Properties of rhizosphere soil associated with herbaceous plant roots analyzed using small-scale protocols

Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N2‐Fixing Bacterium Bradyrhizobium diazoefficiens

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Physical Properties of Carbon Nanomaterials and Nanoceria Affect Pathways Important to the Nodulation Competitiveness of the Symbiotic N₂‐Fixing Bacterium Bradyrhizobium diazoefficiens