A plasmid of Rhizobium meliloti 41 encodes catabolism of two compounds from root exudate of Calystegium sepium.

Our objectives were to identify substances produced by plant roots that might act as nutritional mediators of specific plant-bacterium relationships and to delineate the bacterial genes responsible for catabolizing these substances. We discovered new compounds, which we call calystegins, that have the characteristics of nutritional mediators. They were detected in only 3 of 105 species of higher plants examined: Calystegia sepium, Convolvulus arvensis (both of the Convolvulaceae family), and Atropa belladonna. Calystegins are abundant in organs in contact with the rhizosphere and are not found, or are observed only in small quantities, in aerial plant parts. Just as the synthesis of calystegins is infrequent in the plant kingdom, their catabolism is rare among rhizosphere bacteria that associate with plants and influence their growth. Of 42 such bacteria tested, only one (Rhizobium meliloti 41) was able to catabolize calystegins and use them as a sole source of carbon and nitrogen. The calystegin catabolism gene(s) (cac) in this strain is located on a self-transmissible plasmid (pRme41a), which is not essential to nitrogen-fixing symbiosis with legumes. We suggest that under natural conditions calystegins provide an exclusive carbon and nitrogen source to rhizosphere bacteria which are able to catabolize these compounds. Calystegins (and the corresponding microbial catabolic genes) might be used to analyze and possibly modify rhizosphere ecology.     

The Multifunctional Role of Ectomycorrhizal Associations in Forest Ecosystem Processes

Belowground biological interactions that occur among plant roots, microorganisms and animals are dynamic and substantially influence ecosystem processes. Among these interactions, the ectomycorrhizal (ECM) symbiosis is remarkable but unfortunately these associations have mainly been considered within the rather narrow perspective of their effects on the uptake of dissolved mineral nutrients by individual plants. More recent research has placed emphasis on a wider, multifunctional perspective, including the effects of ectomycorrhizal symbiosis on plant and microbial communities, and on ecosystem processes. This includes mobilization of N and P from organic polymers, release of nutrients from mineral particles or rock surfaces via weathering, effects on carbon cycling, interactions with mycoheterotrophic plants, mediation of plant responses to stress factors such as drought, soil acidification, toxic metals, and plant pathogens, rehabilitation and regeneration of degraded forest ecosystems, as well as a range of possible interactions with groups of other soil microorganisms. Ectomycorrhizas are almost invariably characterized by a Hartig net composed of highly branched hyphae which entirely surround the outer root cortical cells. The Hartig net is the place of massive bidirectional exchanges of nutrients between the host and the fungus. Through these branched hyphae ectomycorrhizal fungi connect their plant hosts to the heterogeneously distributed nutrients required for their growth, enabling the flow of energy-rich compounds required for nutrient mobilization whilst simultaneously providing conduits for the translocation of mobilized products back to their hosts. In addition to increasing the nutrient absorptive surface area of their host plant root systems, the extraradical mycelium of ectomycorrhizal fungi provides a direct pathway for translocation of photosynthetically derived carbon from their hosts to microsites in the soil and a large surface area for interaction with other soil micro-organisms. The detailed functioning and regulation of these mycorrhizosphere processes is still poorly understood and needs detailed molecular approach to study these mycorrhizosphere processes but recent progress in ectomycorrhizal associations is reviewed and potential benefits of improved understanding of mycorrhizosphere interactions are discussed.     

An extended root phenotype: the rhizosphere,its formation and impacts on plant fitness

Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root?soil?microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.     

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     

Herbivorous insect decreases plant nutrient uptake: the role of soil nutrient availability and association of below‐ground symbionts

1. Plants take nutrients from the rhizosphere via two pathways: (i) by absorbing soil nutrients directly via their roots and (ii) indirectly via symbiotic associations with nutrient‐providing microbes. Herbivorous insects can alter these pathways by herbivory, adding their excrement to the soil, and affecting plant–microbe associations. 2. Little is known, however, about the effects of herbivorous insects on plant nutrient uptake. Greenhouse experiments with soybean, aphids, and rhizobia were carried out to examine the effects of aphids on plant nutrient uptake. 3. First, the inorganic soil nitrogen and the sugar in aphid honeydew between aphid‐infected and ‐free plants were compared. It was found that aphid honeydew added 41 g m^?2 of sugar to the soil, and that aphids decreased the inorganic soil nitrogen by 86%. This decrease may have been caused by microbial immobilisation of soil nitrogen followed by increased microbial abundance as a result of aphid honeydew. 4. Second, nitrogen forms in xylem sap between aphid‐infected and ‐free plants were compared to examine nitrogen uptake. Aphids decreased the nitrogen uptake via both pathways, and strength of the impact on direct uptake via plant roots was greater than indirect uptake via rhizobia. The reduced nitrogen uptake by the direct pathway was as a result of microbial immobilisation, and that by the indirect pathway was probably because of the interaction of microbial immobilisation and carbon stress, which was caused by aphid infection. 5. The present results demonstrate that herbivorous insects can negatively influence the two pathways of plant nutrient uptake and alter their relative importance.     

微生物肥料及其生产应用中的问题

微生物肥料和微生物制剂是新世纪实行绿色农业的重要技术保障,关键是因其中含有大量的有效微生物的生命活动产生特定的肥效或其他生理功能,导致增产,微生物肥料包括根瘤菌肥,解磷菌肥、解钾菌肥、5406菌肥,植物根际促生菌,VA菌根等等,有机肥料堆制剂中含有多种降解农业有机废料的菌种,可缩短堆肥周期,提高养份利用率,由于微生物本身的特殊性,相关市场监督机制不健全,微生物肥料的生产,应用领域存在很多问题,甚至出现明显的伪科学,科研、生产、行政各有关部门应加强基础研究,提高全民科普水平,健全市场监督机制,依靠专家设计严格试验,优选可靠技术,保证良好的经济效益和社会效益。     

Ecological aspects of mycorrhizal symbiosis: with special emphasis on the functional diversity of interactions involving the extraradical mycelium

Different symbiotic mycorrhizal associations between plantsand fungi occur, almost ubiquitously, in a wide range of terrestrialecosystems. Historically, these have mainly been consideredwithin the rather narrow perspective of their effects on theuptake of dissolved mineral nutrients by individual plants.More recent research has placed emphasis on a wider, multifunctionalperspective, including the effects of mycorrhizal symbiosison plant and microbial communities, and on ecosystem processes.This includes mobilization of N and P from organic polymers,release of nutrients from mineral particles or rock surfacesvia weathering, effects on carbon cycling, interactions withmyco-heterotrophic plants, mediation of plant responses to stressfactors such as drought, soil acidification, toxic metals, andplant pathogens, as well as a range of possible interactionswith groups of other soil micro-organisms. Mycorrhizal fungiconnect their plant hosts to the heterogeneously distributednutrients required for their growth, enabling the flow of energy-richcompounds required for nutrient mobilization whilst simultaneouslyproviding conduits for the translocation of mobilized productsback to their hosts. In addition to increasing the nutrientabsorptive surface area of their host plant root systems, theextraradical mycelium of mycorrhizal fungi provides a directpathway for translocation of photosynthetically derived carbonto microsites in the soil and a large surface area for interactionwith other micro-organisms. The detailed functioning and regulationof these mycorrhizosphere processes is still poorly understoodbut recent progress is reviewed and potential benefits of improvedunderstanding of mycorrhizosphere interactions are discussed. Key words: Arbuscular mycorrhiza, biotic interactions, carbon flow, ectomycorrhiza, ericoid mycorrhiza, mycelium, nutrient uptake, symbiosis, weathering Received 22 January 2008; Revised 7 February 2008 Accepted 7 February 2008     

Carbon flow in the rhizosphere: carbon trading at the soil–root interface

The loss of organic and inorganic carbon from roots into soil underpins nearly all the major changes that occur in the rhizosphere. In this review we explore the mechanistic basis of organic carbon and nitrogen flow in the rhizosphere. It is clear that C and N flow in the rhizosphere is extremely complex, being highly plant and environment dependent and varying both spatially and temporally along the root. Consequently, the amount and type of rhizodeposits (e.g. exudates, border cells, mucilage) remains highly context specific. This has severely limited our capacity to quantify and model the amount of rhizodeposition in ecosystem processes such as C sequestration and nutrient acquisition. It is now evident that C and N flow at the soil–root interface is bidirectional with C and N being lost from roots and taken up from the soil simultaneously. Here we present four alternative hypotheses to explain why high and low molecular weight organic compounds are actively cycled in the rhizosphere. These include: (1) indirect, fortuitous root exudate recapture as part of the root’s C and N distribution network, (2) direct re-uptake to enhance the plant’s C efficiency and to reduce rhizosphere microbial growth and pathogen attack, (3) direct uptake to recapture organic nutrients released from soil organic matter, and (4) for inter-root and root–microbial signal exchange. Due to severe flaws in the interpretation of commonly used isotopic labelling techniques, there is still great uncertainty surrounding the importance of these individual fluxes in the rhizosphere. Due to the importance of rhizodeposition in regulating ecosystem functioning, it is critical that future research focuses on resolving the quantitative importance of the different C and N fluxes operating in the rhizosphere and the ways in which these vary spatially and temporally.     

Cluster roots--an underground adaptation for survival in extreme environments

Cluster roots are a characteristic of members of the Proteaceae and of several other plant species that are adapted to habitats of extremely low soil fertility, usually without formation of mycorrhizal associations. Functionally linked with intense mobilization of nutrients (P, Fe, Zn, Mn) by root-induced chemical changes (pH, root exudates, redox potential) in the rhizosphere, cluster-rooted plant species can serve as model plants to study rhizosphere processes and regulatory aspects of plant adaptations for chemical mobilization of nutrients in the rhizosphere.     

Deploying microbes as drivers and indicators in ecological restoration

Ecosystem degradation is a major environmental threat. Beyond conservation, restoration of degraded ecosystems is a prerequisite to reinstate their ability to provide essential services and benefits. Most of the restoration efforts focus on aboveground restoration, that is, plants, under the assumption that establishment of plant species will reestablish the faunal and microbial species. While this may be true for some cases, it is not a general rule. Reestablishment of microbial communities by dedicated efforts is also necessary for successful restoration, as cycling of essential nutrients for plant growth and decomposition of organic matter is dependent on them. The role of microbial fertilizers and efficient organisms used in agriculture needs to be explored in restoration. Testing of symbiotic interactions between potential plant growth-promoting Rhizobacteria and plants native to a degraded ecosystem can be conducted and utilized for successful establishment of plant species. However, utmost care must be taken while introducing new microbial species or non-native plant species to an area, as they can adversely affect the resident microbial community. Techniques like phospholipid fatty-acid analysis can be used for taxonomic identification of large microbial groups in non-degraded reference ecosystems before introducing microbial species into a degraded ecosystem. For use of microbes in restoration, more studies on microbe-plant interactions need to be conducted. For use of Soil Microbial Community (SMC) as indicators of restoration, their role and function in the ecology of the area need to be elucidated by employing all the available techniques.     

Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants

Nitrogen is generally considered one of the major limiting nutrients in plant growth. The biological process responsible for reduction of molecular nitrogen into ammonia is referred to as nitrogen fixation. A wide diversity of nitrogen-fixing bacterial species belonging to most phyla of the Bacteria domain have the capacity to colonize the rhizosphere and to interact with plants. Leguminous and actinorhizal plants can obtain their nitrogen by association with rhizobia or Frankia via differentiation on their respective host plants of a specialized organ, the root nodule. Other symbiotic associations involve heterocystous cyanobacteria, while increasing numbers of nitrogen-fixing species have been identified as colonizing the root surface and, in some cases, the root interior of a variety of cereal crops and pasture grasses. Basic and advanced aspects of these associations are covered in this review.     

The rhizosphere microbiome: Plant–microbial interactions for resource acquisition

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.     

Contrasting Soil Ciliate Species Richness and Abundance between Two Tropical Plant Species: A Test of the Plant Effect

We still have a rudimentary understanding about the mechanism by which plant roots may stimulate soil microbial interactions. A biochemical model involving plant-derived biochemical fractions, such as exudates, has been used to explain this “rhizosphere effect” on bacteria. However, the variable response of other soil microbial groups, such as protozoa, to the rhizosphere suggests that other factors could be involved in shaping their communities. Thus, two experiments were designed to: (1) determine whether stimulatory and/or inhibiting factors associated with particular plant species regulate ciliate diversity and abundance and (2) obtain a better understanding about the mechanism by which these plant factors operate in the rhizosphere. Bacterial and chemical slurries were reciprocally exchanged between two plant species known to differ in terms of ciliate species richness and abundance (i.e., Canella winterana and plantation Tectona grandis). Analysis of variance showed that the bacteria plus nutrients and the nutrients only treatment had no significant effect on overall ciliate species richness and abundance when compared to the control treatment. However, the use of only colpodean species increased the taxonomic resolution of treatment effects revealing that bacterial slurries had a significant effect on colpodean ciliate species richness. Thus, for particular rhizosphere ciliates, biological properties, such as bacterial diversity or abundance, may have a strong influence on their diversity and possibly abundance. These results are consistent with a model of soil bacteria-mediated mutualisms between plants and protozoa.     

Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.     

Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus)

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.     

Toxicity of Cadmium and nickel in the context of applied activated carbon biochar for improvement in soil fertility

Toxicity induced by heavy metals deteriorates soil fertility status. It also adversely affects the growth and yield of crops. These heavy metals become part of the food chain when crops are cultivated in areas where heavy metals are beyond threshold limits. Cadmium (Cd) and nickel (Ni) are considered the most notorious ones among different heavy metals. The high water solubility of Cd made it a potential toxin for plants and their consumers. Accumulation of Ni in plants, leaves, and fruits also deteriorates their quality and causes cancer in humans when such a Ni-contaminated diet is used regularly. Both Cd and Ni also compete with essential nutrients of plants, making the fertility status of soil poor. To overcome this problem, the use of activated carbon biochar can play a milestone role. In the recent past application of activated carbon biochar is gaining more and more attention. Biochar sorb the Cd and Ni and releases essential micronutrients that are part of its structure. Many micropores and high cation exchange capacity make it the most acceptable organic amendment to improve soil fertility and immobilize Cd and Ni. In addition to improving water and nutrients, soil better microbial proliferation enhances the soil rhizosphere ecosystem and nutrient cycling. This review has covered Cd and Ni harmful effects on crop yield and their immobilization by activated carbon biochar. The focus was made to elaborate on the positive effects of biochar on crop yield and soil health.     

Root exudates as mediators of mineral acquisition in low-nutrient environments

Plant developmental processes are controlled by internal signals that depend on the adequate supply of mineral nutrients by soil to roots. Thus, the availability of nutrient elements can be a major constraint to plant growth in many environments of the world, especially the tropics where soils are extremely low in nutrients. Plants take up most mineral nutrients through the rhizosphere where micro-organisms interact with plant products in root exudates. Plant root exudates consist of a complex mixture of organic acid anions, phytosiderophores, sugars, vitamins, amino acids, purines, nucleosides, inorganic ions (e.g. HCO₃ ^–, OH^–, H⁺), gaseous molecules (CO₂, H₂), enzymes and root border cells which have major direct or indirect effects on the acquisition of mineral nutrients required for plant growth. Phenolics and aldonic acids exuded directly by roots of N₂-fixing legumes serve as major signals to Rhizobiaceae bacteria which form root nodules where N₂ is reduced to ammonia. Some of the same compounds affect development of mycorrhizal fungi that are crucial for phosphate uptake. Plants growing in low-nutrient environments also employ root exudates in ways other than as symbiotic signals to soil microbes involved in nutrient procurement. Extracellular enzymes release P from organic compounds, and several types of molecules increase iron availability through chelation. Organic acids from root exudates can solubilize unavailable soil Ca, Fe and Al phosphates. Plants growing on nitrate generally maintain electronic neutrality by releasing an excess of anions, including hydroxyl ions. Legumes, which can grow well without nitrate through the benefits of N₂ reduction in the root nodules, must release a net excess of protons. These protons can markedly lower rhizosphere pH and decrease the availability of some mineral nutrients as well as the effective functioning of some soil bacteria, such as the rhizobial bacteria themselves. Thus, environments which are naturally very acidic can pose a challenge to nutrient acquisition by plant roots, and threaten the survival of many beneficial microbes including the roots themselves. A few plants such as Rooibos tea (Aspalathus linearis L.) actively modify their rhizosphere pH by extruding OH^– and HCO₃ ^– to facilitate growth in low pH soils (pH 3 – 5). Our current understanding of how plants use root exudates to modify rhizosphere pH and the potential benefits associated with such processes are assessed in this review.     

Is —— the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement?

The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.     

Achieving similar root microbiota composition in neighbouring plants through airborne signalling

The ability to recognize and respond to environmental signals is essential for plants. In response to environmental changes, the status of a plant is transmitted to other plants in the form of signals such as volatiles. Root-associated bacteria trigger the release of plant volatile organic compounds (VOCs). However, the impact of VOCs on the rhizosphere microbial community of neighbouring plants is not well understood. Here, we investigated the effect of VOCs on the rhizosphere microbial community of tomato plants inoculated with a plant growth-promoting rhizobacterium Bacillus amyloliquefaciens strain GB03 and that of their neighbouring plants. Interestingly, high similarity (up to 69%) was detected in the rhizosphere microbial communities of the inoculated and neighbouring plants. Leaves of the tomato plant treated with strain GB03-released β-caryophyllene as a signature VOC, which elicited the release of a large amount of salicylic acid (SA) in the root exudates of a neighbouring tomato seedling. The exposure of tomato leaves to β-caryophyllene resulted in the secretion of SA from the root. Our results demonstrate for the first time that the composition of the rhizosphere microbiota in surrounding plants is synchronized through aerial signals from plants.Subject terms: Microbial ecology, Soil microbiology