Root-specific metabolism: The biology and biochemistry of underground organs

Summary The roots of higher plants comprise a metabolically active and largely unexplored biological frontier. Some of their prime features include the ability to synthesize a remarkably diverse group of secondary metabolites, and to adjust their metabolic activities in response to different abiotic and biotic stresses. This adjustment includes the ability to exude a wide array of micro- and macromolecules into the rhizosphere and to phytoremediate toxic metals, with the potential to affect and alter the relationships between plants and both beneficial and deleterious soil-borne pathogens. In the past, research on root biology has been hampered by the underground nature of roots and the lack of suitable experimental systems to study root-root and root-microbe communications. However, recent progress in growing roots in isolation with other elements of the rhizosphere has greatly facilitated the study of root-specific metabolism and contributed to our understanding of this organ.     

植物根系分泌物对土壤污染修复的作用及影响机理

生物修复是一种经济环保的土壤修复技术。根系分泌物是利用生物修复污染土壤过程中的关键物质,也是植物与土壤微生物进行物质交换和信息传递的重要载体,在植物响应污染物胁迫中扮演重要角色。研究植物根系分泌物对土壤污染修复的作用和影响机理,是深入理解植物和微生物环境适应机制的重要途径,对促进生物修复污染土壤有重要指导意义。从污染物胁迫对根系分泌物的影响、根系分泌物对土壤污染物环境行为的影响、根系分泌物在调控污染土壤中根际微生物群落结构和多样性中发挥的作用等几个方面综述了根系分泌物对土壤污染修复的影响及内在机制。研究结果表明,根系分泌物在降低重金属对植物的毒性、加速有机污染物降解等方面有非常重要的作用。根系分泌物对土壤微生物的丰度和多样性均有显著影响,其与根际微生物互作在土壤污染物的消减中发挥了重要的调控作用。在此基础上,提出了以往研究中的不足,并对污染物胁迫下根系分泌物未来研究的方向和趋势进行了展望。     

Rates of root and organism growth, soil conditions, and temporal and spatial development of the rhizosphere

BACKGROUND: Roots growing in soil encounter physical, chemical and biological environments that influence their rhizospheres and affect plant growth. Exudates from roots can stimulate or inhibit soil organisms that may release nutrients, infect the root, or modify plant growth via signals. These rhizosphere processes are poorly understood in field conditions. SCOPE AND AIMS: We characterize roots and their rhizospheres and rates of growth in units of distance and time so that interactions with soil organisms can be better understood in field conditions. We review: (1) distances between components of the soil, including dead roots remnant from previous plants, and the distances between new roots, their rhizospheres and soil components; (2) characteristic times (distance(2)/diffusivity) for solutes to travel distances between roots and responsive soil organisms; (3) rates of movement and growth of soil organisms; (4) rates of extension of roots, and how these relate to the rates of anatomical and biochemical ageing of root tissues and the development of the rhizosphere within the soil profile; and (5) numbers of micro-organisms in the rhizosphere and the dependence on the site of attachment to the growing tip. We consider temporal and spatial variation within the rhizosphere to understand the distribution of bacteria and fungi on roots in hard, unploughed soil, and the activities of organisms in the overlapping rhizospheres of living and dead roots clustered in gaps in most field soils. CONCLUSIONS: Rhizosphere distances, characteristic times for solute diffusion, and rates of root and organism growth must be considered to understand rhizosphere development. Many values used in our analysis were estimates. The paucity of reliable data underlines the rudimentary state of our knowledge of root-organism interactions in the field.     

Rhizosphere fauna: the functional and structural diversity of intimate interactions of soil fauna with plant roots

For decades, the term “rhizosphere fauna” has been used as a synonym to denote agricultural pests among root herbivores, mainly nematodes and insect larvae. We want to break with this constrictive view, since the connection between plants and rhizosphere fauna is far more complex than simply that of resource and consumer. For example, plant roots have been shown to be neither defenceless victims of root feeders, nor passive recipients of nutrients, but instead play a much more active role in defending themselves and in attracting beneficial soil microorganisms and soil fauna. Most importantly, significant indirect feed-backs exist between consumers of rhizosphere microorganisms and plant roots. In fact, the majority of soil invertebrates have been shown to rely profoundly on the carbon inputs from roots, breaking with the dogma of soil food webs being mainly fueled by plant litter input from aboveground. In this review we will highlight areas of recent exciting progress and point out the black boxes that still need to be illuminated by rhizosphere zoologists and ecologists.     

Studies on the rhizosphere microflora of yellow birch seedlings

Summary The rhizosphere microflora of yellow birch seedlings grown in a forest soil in tanks in the greenhouse has been investigated. In general it was found that the rhizosphere effect of yellow birch roots in the A horizon was lower than that observed with cropped plants; nevertheless a stimulation of microbial development was obtained. Of the micro-organisms studied, bacteria, and ammonifying and methylene-blue-reducing organisms appeared to be predominant types in the root zone. Counts were, on the whole, lowest when plants broke dormancy and began to increase in the later periods of growth. There was no appreciable difference between control and rhizosphere soils in regard to incidence of specific nutritional types of bacteria. Analysis of the rhizosphere population of roots growing in the B horizon showed a distinctly greater rhizosphere effect than that obtained in the A horizon. The data suggest that the rhizosphere effect in the latter was obscured because of its high organic-matter content and its abundant and active microflora.Contribution No. 481     

Variations in ergosterol content and ornithine decarboxylase activity of ectomycorrhizal root-soil systems

Influences of soil P fertilization on temporal changes in ergosterol content and ornithine decarboxylase (E.C. 4.1.1.17, ODC) activity were monitored in rhizosphere soil, non-rhizosphere soil and Pinus contorta roots ectomycorrhizal with Hebeloma crustuliniforme grown in a loamy sand. With addition of mycorrhizal inoculum to loamy sand, ODC activity mg^-1 root increased between 10% and 2 fold within 21 weeks of pianting. Inoculation also decreased root mass per seedling. Inoculation increased mycelia mass per root mass by up to 2 fold but no differences were observed for total seedling mass until 35 weeks. Intramatrical mycelia were detrimental to early plant growth, but inoculated seedlings had 1.7 times more root mass and 1.3 times more shoot mass at 35 weeks. Rhizosphere soil contained up to 5 times more mycelia and up to 6 times greater ODC activity than non-rhizosphere soil. Inoculation increased rhizophere metabolic activity and intramatrical mycelia mass. Their sensitivity to fungal inoculation, P fertilization and temporal trends may make the methods useful in studies of rhizosphere ecology and root-microbe relationships.     

Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p<0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed.     

Herbivore-induced changes in plant carbon allocation: assessment of below-ground C fluxes using carbon-14

Effects of above-ground herbivory on short-term plant carbon allocation were studied using maize (Zea mays) and a generalist lubber grasshopper (Romalea guttata). We hypothesized that above-ground herbivory stimulates current net carbon assimilate allocation to below-ground components, such as roots, root exudation and root and soil respiration. Maize plants 24 days old were grazed (c. 25–50% leaf area removed) by caging grasshoppers around individual plants and 18 h later pulse-labelled with¹⁴CO₂. During the next 8 h,¹⁴C assimilates were traced to shoots, roots, root plus soil respiration, root exudates, rhizosphere soil, and bulk soil using carbon-14 techniques. Significant positive relationships were observed between herbivory and carbon allocated to roots, root exudates, and root and soil respiration, and a significant negative relationship between herbivory and carbon allocated to shoots. No relationship was observed between herbivory and¹⁴C recovered from soil. While herbivory increased root and soil respiration, the peak time for¹⁴CO₂ evolved as respiration was not altered, thereby suggesting that herbivory only increases the magnitude of respiration, not patterns of translocation through time. Although there was a trend for lower photosynthetic rates of grazed plants than photosynthetic rates of ungrazed plants, no significant differences were observed among grazed and ungrazed plants. We conclude that above-ground herbivory can increase plant carbon fluxes below ground (roots, root exudates, and rhizosphere respiration), thus increasing resources (e.g., root exudates) available to soil organisms, especially microbial populations.     

Fluorescent pseudomonads in the rhizosphere of plants and their relation to root exudates

Fluorescent pseudomonads were present in chernozem soil not influenced by plant roots (10(3)-10(4) per g dry soil) in the rhizosphere soil of various plants (10(4)-10(5) per g soil) and on roots (10(3) to 10(7) per g fresh roots), depending on the species and age of the plant. Relative species representation of fluorescent pseudomonads changed on the roots and in the plant rhizosphere as compared with free soil. Pseudomonas fluorescens, representing 60-93% of the population of fluorescent pseudomonads predominated on the roots of all plants investigated. Somewhat different results were obtained in rhizosphere soil. Relatively higher numbers of P. fluorescens were detected in the rhizosphere soil of cucumber and maize, numbers in the rhizosphere soil of wheat were practically the same as in free soil and higher numbers of P. putida were found in the rhizosphere soil of barley. Almost all components contained in the root exudates of the plants studied, including beta-pyrazolylalanine from the root exudates of cucumbers were utilized as carbon and energy sources. Root exudates of wheat and maize were utilized by the strain P. putida K2 with an efficiency of 73-91%, depending on species and age of the plant.     

Adaptation of H+-pumping and plasma membrane H+ ATPase activity in proteoid roots of white lupin under phosphate deficiency

White lupin (Lupinus albus) is able to adapt to phosphorus deficiency by producing proteoid roots that release a huge amount of organic acids, resulting in mobilization of sparingly soluble soil phosphate in rhizosphere. The mechanisms responsible for the release of organic acids by proteoid root cells, especially the trans-membrane transport processes, have not been elucidated. Because of high cytosolic pH, the release of undissociated organic acids is not probable. In the present study, we focused on H+ export by plasma membrane H+ ATPase in active proteoid roots. In vivo, rhizosphere acidification of active proteoid roots was vanadate sensitive. Plasma membranes were isolated from proteoid roots and lateral roots from P-deficient and -sufficient plants. In vitro, in comparison with two types of lateral roots and proteoid roots of P-sufficient plants, the following increase of the various parameters was induced in active proteoid roots of P-deficient plants: (a) hydrolytic ATPase activity, (b) Vmax and Km, (c) H+ ATPase enzyme concentration of plasma membrane, (d) H+-pumping activity, (e) pH gradient across the membrane of plasmalemma vesicles, and (f) passive H+ permeability of plasma membrane. In addition, lower vanadate sensitivity and more acidic pH optimum were determined for plasma membrane ATPase of active proteoid roots. Our data support the hypothesis that in active proteoid root cells, H+ and organic anions are exported separately, and that modification of plasma membrane H+ ATPase is essential for enhanced rhizosphere acidification by active proteoid roots.     

Spatial variation of active microbiota in the rice rhizosphere revealed by in situ stable isotope probing of phospholipid fatty acids

This report is part of a serial study applying stable isotope labelling to rice microcosms to track the utilization of recently photosynthesized carbon by active microbiota in the rhizosphere. The objective of the present study was to apply phospholipid fatty acid-based stable isotope probing (PLFA-SIP) to detect the spatial variation of active microorganisms associated with rhizosphere carbon flow. In total, 49 pulses of 13CO2 were applied to rice plants in a microcosm over a period of 7 days. Rhizosphere soil was separated from bulk soil by a root bag. Soil samples were taken from rhizosphere and bulk soil, and the bulk soil samples were further partitioned both vertically (up layer and down layer) and horizontally with increasing distance to the root bag. Incorporation of 13C into PLFAs sharply decreased with distance to the roots. The labelling of 16:1omega9, 18:1omega7, 18:1omega9, 18:2omega6,9 and i14:0 PLFAs was relatively stronger in the rhizosphere while that of i15:0 and i17:0 increased in the bulk soil. The microorganisms associated with 16:1omega9 were active in both up- and down-layer soils. The microorganisms represented by i14:0, 18:1omega7 and 18:2omega6,9 exhibited a relatively higher activity in up-layer soil, whereas those represented by i15:0 and i17:0 were more active in down-layer soil. These results suggest that in the rhizosphere Gram-negative and eukaryotic microorganisms were most actively assimilating root-derived C, whereas Gram-positive microorganisms became relatively more important in the bulk soil. The active populations apparently differed between up- and down-layer soil and in particular changed with distance to the roots, demonstrating systematic changes in the activity of the soil microbiota surrounding roots.     

Impact of fertilizer type and rate on carbon and nitrogen pools in a sandy Cambisol

Diversity, structure and productivity of above-ground compartment of terrestrial ecosystems have been generally considered as the main drivers of the relationships between diversity and ecosystem functioning. More recently it has been suggested that plant population dynamics may be linked with the development of the below-ground community. The biologically active soil zone where root-root and root-microbe communications occur is named “Rhizosphere” where root exudates play active roles in regulating rhizosphere interactions. Root exudation can regulate the soil microbial community, withstand herbivory, facilitate beneficial symbioses, modify the chemical and physical soil properties and inhibit the growth of competing plant species. In this review, we explore the current knowledge assessing the importance of root exudates in plant interactions, in communications between parasitic plants and their hosts and how some soil microbial components could regulate plant species coexistence and change relationships between plants. This review will be focussed on several well documented biological processes regulating plant-plant communications such as exotic plant species invasions, negative root-root communication (allelopathy) and parasitic plant / host plant interactions and how some soil microbial components can interfere with signal traffic between roots. The reported data show that the overall effect of one plant to another results from multiple interacting mechanisms where soil microbiota can be considered as a key component.     

Microorganisms and nematodes increase levels of secondary metabolites in roots and root exudates of Plantago lanceolata

Plant secondary metabolites play an important role in constitutive and inducible direct defense of plants against their natural enemies. While induction of defense by aboveground pathogens and herbivores is well-studied, induction by belowground organisms is less explored. Here, we examine whether soil microorganisms and nematodes can induce changes in levels of the secondary metabolites aucubin and catalpol (iridoid glycosides, IG) in roots and root exudates of two full-sib families of Plantago lanceolata originating from lines selected for low and high constitutive levels of IG in leaves. Addition of soil microorganisms enhanced the shoot and root biomass, and the concentration of aucubin in roots of both Plantago lines without affecting IG levels in the rhizosphere. By contrast, nematode addition tended to reduce the root biomass and enhanced the stalk biomass, and increased the levels of aucubin and catalpol in root exudates of both Plantago lines, without affecting root IG concentrations. The Plantago lines did not differ in constitutive levels of aucubin and total IG in roots, while the concentration of catalpol was slightly higher in roots of plants originally selected for low constitutive levels of IG in leaves. Root exudates of “high IG line” plants contained significantly higher levels of aucubin, which might be explained by their higher root biomass. We conclude that soil microorganisms can induce an increase of aucubin concentrations in the roots, whereas nematodes (probably plant feeders) lead to an enhancement of aucubin and catalpol levels in root exudates of P. lanceolata. A potential involvement of secondary metabolites in belowground interactions between plants and soil organisms is discussed.     

Plant neighbor effects mediated by rhizosphere factors along a simulated aridity gradient

Aims

We investigated how rhizosphere factors (total rhizosphere, roots, arbuscular mycorrhizal fungal hyphae [AMF], and soil solution) and water availability affect interactions between neighboring Medicago sativa plants.

Methods

A three-compartment mesocosm was used to test the effects of rhizosphere factors on plant–plant interactions. A relative interaction index (RII) was calculated to indicate whether effects of neighbor plant on target plant were positive or negative (facilitative or competitive). Isotope tracers were used to test whether AMF hyphae mediated competition for nitrogen (N) between target and neighbor plants.

Results

The effects of rhizosphere factors on the interactions between neighboring M. sativa plants depended on water availability. The effects of total rhizosphere shifted RII from negative to positive as water availability increased. Interaction with the roots and rhizosphere soil solution of neighbor plants shifted RII from negative to positive as water availability increased but the opposite was true for AMF hyphae. AMF hyphae helped neighbor plants compete for ¹⁵N when water was available but not when water was limiting.

Conclusions

The effect of total rhizosphere on plant–plant interaction of M. sativa shifted from competitive to facilitative as water availability increased. Competition was reduced by neighboring soil solution and roots but was increased by AMF hyphae.     

Root colonization of different plants by plant-growth-promoting Rhizobium leguminosarum bv. trifolii R39 studied with monospecific polyclonal antisera.

Monospecific polyclonal antisera raised against Rhizobium leguminosarum bv. trifolii R39, a bacterium which was isolated originally from red clover nodules, were used to study the colonization of roots of leguminous and nonleguminous plants (Pisum sativum, Lupinus albus, Triticúm aestivum, and Zea mays) after inoculation. Eight weeks after inoculation of soil-grown plants, between 0.1 and 1% of the total bacterial population in the rhizospheres of all inoculated plants were identified as R. leguminosarum bv. trifolii R39. To characterize the associative colonization of the nonleguminous plants by R.leguminosarum bv. trifolii R39 in more detail, a time course study was performed with inoculated roots of Z. mays. R. leguminosarum bv. trifolii R39 was found almost exclusively in the rhizosphere soil and on the rhizoplane 4 weeks after inoculation. Colonization of inner root tissues was detected only occasionally at this time. During the process of attachment of R. leguminosarum bv. trifolii R39 to the rhizoplane, bacterial lipopolysaccharides were overexpressed, and this may be important for plant-microbe interaction. Fourteen weeks after inoculation, microcolonies of R. leguminosarum bv. trifolii R39 were detected in lysed cells of the root cortex as well as in intracellular space of central root cylinder cells. At the beginning of flowering (18 weeks after inoculation), the number of R. leguminosarum bv. trifolii R39 organisms decreased in the rhizosphere soil, rhizoplane, and inner root tissue.     

Cyanogenic pseudomonads influence multitrophic interactions in the rhizosphere

In the rhizosphere, plant roots cope with both pathogenic and beneficial bacterial interactions. The exometabolite production in certain bacterial species may regulate root growth and other root-microbe interactions in the rhizosphere. Here, we elucidated the role of cyanide production in pseudomonad virulence affecting plant root growth and other rhizospheric processes. Exposure of Arabidopsis thaliana Col-0 seedlings to both direct (with KCN) and indirect forms of cyanide from different pseudomonad strains caused significant inhibition of primary root growth. Further, we report that this growth inhibition was caused by the suppression of an auxin responsive gene, specifically at the root tip region by pseudomonad cyanogenesis. Additionally, pseudomonad cyanogenesis also affected other beneficial rhizospheric processes such as Bacillus subtilis colonization by biofilm formation on A. thaliana Col-0 roots. The effect of cyanogenesis on B. subtilis biofilm formation was further established by the down regulation of important B. subtilis biofilm operons epsA and yqxM. Our results show, the functional significance of pseudomonad cyanogenesis in regulating multitrophic rhizospheric interactions.     

Dynamics of soil water content in the rhizosphere

Water flow from soil to plants depends on the properties of the soil next to roots, the rhizosphere. Although several studies showed that the rhizosphere has different properties than the bulk soil, effects of the rhizosphere on root water uptake are commonly neglected. To investigate the rhizosphere’s properties we used neutron radiography to image water content distributions in soil samples planted with lupins during drying and subsequent rewetting. During drying, the water content in the rhizosphere was 0.05 larger than in the bulk soil. Immediately after rewetting, the picture reversed and the rhizosphere remained markedly dry. During the following days the water content of the rhizosphere increased and after 60 h it exceeded that of the bulk soil. The rhizosphere’s thickness was approximately 1.5 mm. Based on the observed dynamics, we derived the distinct, hysteretic and time-dependent water retention curve of the rhizosphere. Our hypothesis is that the rhizosphere’s water retention curve was determined by mucilage exuded by roots. The rhizosphere properties reduce water depletion around roots and weaken the drop of water potential towards roots, therefore favoring water uptake under dry conditions, as demonstrated by means of analytical calculation of water flow to a single root.     

Distribution of cutin and suberin biomarkers under forest trees with different root systems

Background and aims

The rhizosphere, the soil immediately surrounding roots, provides a critical bridge for water and nutrient uptake. The rhizosphere is influenced by various forms of root–soil interactions of which mechanical deformation due to root growth and its effects on the hydraulics of the rhizosphere are the least studied. In this work, we focus on developing new experimental and numerical tools to assess these changes.

Methods

This study combines X-ray micro-tomography (XMT) with coupled numerical simulation of fluid and soil deformation in the rhizosphere. The study provides a new set of tools to mechanistically investigate root-induced rhizosphere compaction and its effect on root water uptake. The numerical simulator was tested on highly deformable soil to document its ability to handle a large degree of strain.

Results

Our experimental results indicate that measured rhizosphere compaction by roots via localized soil compaction increased the simulated water flow to the roots by 27 % as compared to an uncompacted fine-textured soil of low bulk density characteristic of seed beds or forest topsoils. This increased water flow primarily occurred due to local deformation of the soil aggregates as seen in the XMT images, which increased hydraulic conductivity of the soil. Further simulated root growth and deformation beyond that observed in the XMT images led to water uptake enhancement of ~50 % beyond that due to root diameter increase alone and demonstrated the positive benefits of root compaction in low density soils.

Conclusions

The development of numerical models to quantify the coupling of root driven compaction and fluid flow provides new tools to improve the understanding of plant water uptake, nutrient availability and agricultural efficiency. This study demonstrated that plants, particularly during early growth in highly deformable low density soils, are involved in active mechanical management of their surroundings. These modeling approaches may now be used to quantify compaction and root growth impacts in a wide range of soils.     

The role of root exudates and allelochemicals in the rhizosphere

Plant roots serve a multitude of functions in the plant including anchorage, provision of nutrients and water, and production of exudates with growth regulatory properties. The root–soil interface, or rhizosphere, is the site of greatest activity within the soil matrix. Within this matrix, roots affect soil structure, aeration and biological activity as they are the major source of organic inputs into the rhizosphere, and are also responsible for depletion of large supplies of inorganic compounds. Roots are very complicated morphologically and physiologically, and their metabolites are often released in large quantities into the soil rhizosphere from living root hairs or fibrous root systems. Root exudates containing root-specific metabolites have critical ecological impacts on soil macro and microbiota as well as on the whole plant itself. Through the exudation of a wide variety of compounds, roots impact the soil microbial community in their immediate vicinity, influence resistance to pests, support beneficial symbioses, alter the chemical and physical properties of the soil, and inhibit the growth of competing plant species. In this review, we outline recent research on root exudation and the role of allelochemicals in the rhizosphere by studying the case of three plants that have been shown to produce allelopathic root exudates: black walnut, wheat and sorghum