Showing papers in "Plant and Soil in 2009"

Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms

Abstract: The rhizosphere is a complex environment where roots interact with physical, chemical and biological properties of soil. Structural and functional characteristics of roots contribute to rhizosphere processes and both have significant influence on the capacity of roots to acquire nutrients. Roots also interact extensively with soil microorganisms which further impact on plant nutrition either directly, by influencing nutrient availability and uptake, or indirectly through plant (root) growth promotion. In this paper, features of the rhizosphere that are important for nutrient acquisition from soil are reviewed, with specific emphasis on the characteristics of roots that influence the availability and uptake of phosphorus and nitrogen. The interaction of roots with soil microorganisms, in particular with mycorrhizal fungi and non-symbiotic plant growth promoting rhizobacteria, is also considered in relation to nutrient availability and through the mechanisms that are associated with plant growth promotion.

The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms

Abstract: The rhizosphere is a hot spot of microbial interactions as exudates released by plant roots are a main food source for microorganisms and a driving force of their population density and activities. The rhizosphere harbors many organisms that have a neutral effect on the plant, but also attracts organisms that exert deleterious or beneficial effects on the plant. Microorganisms that adversely affect plant growth and health are the pathogenic fungi, oomycetes, bacteria and nematodes. Most of the soilborne pathogens are adapted to grow and survive in the bulk soil, but the rhizosphere is the playground and infection court where the pathogen establishes a parasitic relationship with the plant. The rhizosphere is also a battlefield where the complex rhizosphere community, both microflora and microfauna, interact with pathogens and influence the outcome of pathogen infection. A wide range of microorganisms are beneficial to the plant and include nitrogen-fixing bacteria, endo- and ectomycorrhizal fungi, and plant growth-promoting bacteria and fungi. This review focuses on the population dynamics and activity of soilborne pathogens and beneficial microorganisms. Specific attention is given to mechanisms involved in the tripartite interactions between beneficial microorganisms, pathogens and the plant. We also discuss how agricultural practices affect pathogen and antagonist populations and how these practices can be adopted to promote plant growth and health.

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

Abstract: 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.

Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis

Abstract: A comprehensive appraisal of the mycorrhizal literature provides data for 336 plant families representing 99% of flowering plants, with regard to mycorrhizas and other nutritional adaptations. In total, arbuscular (AM), orchid, ectomycorrhizas (EM) and ericoid mycorrhizas and nonmycorrhizal (NM) roots occur in 74%, 9%, 2%, 1% and 6% of Angiosperm species respectively. Many families of NM plants have alternative nutritional strategies such as parasitism, carnivory, or cluster roots. The remaining angiosperms (8%) belong to families reported to have both AM and NM species. These are designated as NM-AM families here and tend to occur in habitats considered non-conducive to mycorrhizal fungi, such as epiphytic, aquatic, extremely cold, dry, disturbed, or saline habitats. Estimated numbers of species in each category of mycorrhizas is presented with lists of NM and EM families. Evolutionary trends are also summarised by providing data on all clades and orders of flowering and non-flowering vascular plants on a global scale. A case study of Western Australian plants revealed that plants with specialised nutritional modes such as carnivory, cluster roots, or EM were much more diverse in this ancient landscape with infertile soils than elsewhere. Detailed information on the mycorrhizal diversity of plants presented here is linked to a website (mycorrhizas.info) to allow data to remain current. Over a century of research effort has resulted in data on mycorrhizal associations of >10,000 plant species that are of great value, but also somewhat of a liability due to conflicting information about some families and genera. It is likely that these conflicts result in part from misdiagnosis of mycorrhizal associations resulting from a lack of standardisation in criteria used to define them. Families that contain both NM and AM species provide a second major source of inconsistency, but even when these are excluded there is a ∼10% apparent error rate in published lists of mycorrhizal plants. Arbuscules are linked to AM misdiagnosis since they are used less often than vesicles to recognise AM associations in roots and apparently occur sporadically in NM plants. Key issues with the diagnosis of mycorrhizal plants are discussed using the Cyperaceae as a case study. Detailed protocols designed to consistently distinguish AM from endophytic Glomeromycotan Fungus Colonisation (GFC) are provided. This review aims to stimulate debate and provide advice to researchers delving into root biology.

Rhizosphere: biophysics, biogeochemistry and ecological relevance

Abstract: Life on Earth is sustained by a small volume of soil surrounding roots, called the rhizosphere. The soil is where most of the biodiversity on Earth exists, and the rhizosphere probably represents the most dynamic habitat on Earth; and certainly is the most important zone in terms of defining the quality and quantity of the Human terrestrial food resource. Despite its central importance to all life, we know very little about rhizosphere functioning, and have an extraordinary ignorance about how best we can manipulate it to our advantage. A major issue in research on rhizosphere processes is the intimate connection between the biology, physics and chemistry of the system which exhibits astonishing spatial and temporal heterogeneities. This review considers the unique biophysical and biogeochemical properties of the rhizosphere and draws some connections between them. Particular emphasis is put on how underlying processes affect rhizosphere ecology, to generate highly heterogeneous microenvironments. Rhizosphere ecology is driven by a combination of the physical architecture of the soil matrix, coupled with the spatial and temporal distribution of rhizodeposits, protons, gases, and the role of roots as sinks for water and nutrients. Consequences for plant growth and whole-system ecology are considered. The first sections address the physical architecture and soil strength of the rhizosphere, drawing their relationship with key functions such as the movement and storage of elements and water as well as the ability of roots to explore the soil and the definition of diverse habitats for soil microorganisms. The distribution of water and its accessibility in the rhizosphere is considered in detail, with a special emphasis on spatial and temporal dynamics and heterogeneities. The physical architecture and water content play a key role in determining the biogeochemical ambience of the rhizosphere, via their effect on partial pressures of O2 and CO2, and thereby on redox potential and pH of the rhizosphere, respectively. We address the various mechanisms by which roots and associated microorganisms alter these major drivers of soil biogeochemistry. Finally, we consider the distribution of nutrients, their accessibility in the rhizosphere, and their functional relevance for plant and microbial ecology. Gradients of nutrients in the rhizosphere, and their spatial patterns or temporal dynamics are discussed in the light of current knowledge of rhizosphere biophysics and biogeochemistry. Priorities for future research are identified as well as new methodological developments which might help to advance a comprehensive understanding of the co-occurring processes in the rhizosphere.

Plant-driven selection of microbes

Abstract: The rhizodeposition of plants dramatically influence the surrounding soil and its microflora. Root exudates have pronounced selective and promoting effects on specific microbial populations which are able to respond with chemotaxis and fast growth responses, such that only a rather small subset of the whole soil microbial diversity is finally colonizing roots successfully. The exudates carbon compounds provide readily available nutrient and energy sources for heterotrophic organisms but also contribute e.g. complexing agents, such as carboxylates, phenols or siderophores for the mobilization and acquisition of rather insoluble minerals. Root exudation can also quite dramatically alter the pH- and redox-milieu in the rhizosphere. In addition, not only specific stimulatory compounds, but also antimicrobials have considerable discriminatory effect on the rhizosphere microflora. In the “biased rhizosphere” concept, specific root associated microbial populations are favored based on modification of the root exudation profile. Rhizosphere microbes may exert specific plant growth promoting or biocontrol effects, which could be of great advantage for the plant host. Since most of the plant roots have symbiotic fungi, either arbuscular or ectomycorrhizal fungi, the impact of plants towards the rhizosphere extends also to the mycorrhizosphere. The selective effect of the roots towards the selection of microbes also extends towards the root associated and symbiotic fungi. While microbes are known to colonize plant roots endophytically, also mycorrhiza are now known to harbor closely associated bacterial populations even within their hyphae. The general part of the manuscript is followed by the more detailed presentation of specific examples for the selection and interaction of roots and microbes, such as in the rhizosphere of strawberry, potato and oilseed rape, where the soil-borne plant pathogen Verticillium dahliae can cause high yield losses; the potential of biocontrol by specific constituents of the rhizosphere microbial community is demonstrated. Furthermore, plant cultivar specificity of microbial communities is described in different potato lines including the case of transgenic lines. Finally, also the specific selective effect of different Medicago species on the selection of several arbuscular mycorrhizal taxa is presented.

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

Abstract: 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.

Plant root growth, architecture and function

Abstract: Without roots there would be no rhizosphere and no rhizodeposition to fuel microbial activity. Although micro-organisms may view roots merely as a source of carbon supply this belies the fascinating complexity and diversity of root systems that occurs despite their common function. Here, we examine the physiological and genetic determinants of root growth and the complex, yet varied and flexible, root architecture that results. The main functions of root systems are also explored including how roots cope with nutrient acquisition from the heterogeneous soil environment and their ability to form mutualistic associations with key soil micro-organisms (such as nitrogen fixing bacteria and mycorrhizal fungi) to aid them in their quest for nutrients. Finally, some key biotic and abiotic constraints on root development and function in the soil environment are examined and some of the adaptations roots have evolved to counter such stresses discussed.

Rhizosphere processes and management in plant-assisted bioremediation (phytoremediation) of soils.

Abstract: Plant-assisted bioremediation or phytoremediation holds promise for in situ treatment of polluted soils. Enhancement of phytoremediation processes requires a sound understanding of the complex interactions in the rhizosphere. Evaluation of the current literature suggests that pollutant bioavailability in the rhizosphere of phytoremediation crops is decisive for designing phytoremediation technologies with improved, predictable remedial success. For phytoextraction, emphasis should be put on improved characterisation of the bioavailable metal pools and the kinetics of resupply from less available fractions to support decision making on the applicability of this technology to a given site. Limited pollutant bioavailability may be overcome by the design of plant–microbial consortia that are capable of mobilising metals/metalloids by modification of rhizosphere pH (e.g. by using Alnus sp. as co-cropping component) and ligand exudation, or enhancing bioavailability of organic pollutants by the release of biosurfactants. Apart from limited pollutant bioavailability, the lack of competitiveness of inoculated microbial strains (in particular degraders) in field conditions appears to be another major obstacle. Selecting/engineering of plant–microbial pairs where the competitiveness of the microbial partner is enhanced through a “nutritional bias” caused by exudates exclusively or primarily available to this partner (as known from the “opine concept”) may open new horizons for rhizodegradation of organically polluted soils. The complexity and heterogeneity of multiply polluted “real world” soils will require the design of integrated approaches of rhizosphere management, e.g. by combining co-cropping of phytoextraction and rhizodegradation crops, inoculation of microorganisms and soil management. An improved understanding of the rhizosphere will help to translate the results of simplified bench scale and pot experiments to the full complexity and heterogeneity of field applications.

Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective

Abstract: Soils are the product of the activities of plants, which supply organic matter and play a pivotal role in weathering rocks and minerals. Many plant species have a distinct ecological amplitude that shows restriction to specific soil types. In the numerous interactions between plants and soil, microorganisms also play a key role. Here we review the existing literature on interactions between plants, microorganisms and soils, and include considerations of evolutionary time scales, where possible. Some of these interactions involve intricate systems of communication, which in the case of symbioses such as the arbuscular mycorrhizal symbiosis are several hundreds of millions years old; others involve the release of exudates from roots, and other products of rhizodeposition that are used as substrates for soil microorganisms. The possible reasons for the survival value of this loss of carbon over tens or hundreds of millions of years of evolution of higher plants are discussed, taking a cost-benefit approach. Co-evolution of plants and rhizosphere microorganisms is discussed, in the light of known ecological interactions between various partners in terrestrial ecosystems. Finally, the role of higher plants, especially deep-rooted plants and associated microorganisms in the weathering of rocks and minerals, ultimately contributing to pedogenesis, is addressed. We show that rhizosphere processes in the long run are central to biogeochemical cycles, soil formation and Earth history. Major anticipated discoveries will enhance our basic understanding and allow applications of new knowledge to deal with nutrient deficiencies, pests and diseases, and the challenges of increasing global food production and agroecosystem productivity in an environmentally responsible manner.

OCBIL theory: towards an integrated understanding of the evolution, ecology and conservation of biodiversity on old, climatically buffered, infertile landscapes

Abstract: OCBIL theory aims to develop an integrated series of hypotheses explaining the evolution and ecology of, and best conservation practices for, biota on very old, climatically buffered, infertile landscapes (OCBILs). Conventional theory for ecology and evolutionary and conservation biology has developed primarily from data on species and communities from young, often disturbed, fertile landscapes (YODFELs), mainly in the Northern Hemisphere. OCBILs are rare, but are prominent in the Southwest Australian Floristic Region, South Africa’s Greater Cape, and Venezuela’s Pantepui Highlands. They may have been more common globally before Pleistocene glaciations. Based on the premise that natural selection has favoured limited dispersability of sedentary organisms, OCBILs should have elevated persistence of lineages (Gondwanan Heritage Hypothesis) and long-lived individuals (Ultimate Self Hypothesis), high numbers of localised rare endemics and strongly differentiated population systems. To counter such natural fragmentation and inbreeding due to small population size, ecological, cytogenetic and genetic mechanisms selecting for the retention of heterozygosity should feature (the James Effect). The climatic stability of OCBILs should be paralleled by persistence of adjacent semi-arid areas, conducive to speciation (Semiarid Cradle Hypothesis). Special nutritional and other biological traits associated with coping with infertile lands should be evident, accentuated in plants, for example, through water-foraging strategies, symbioses, carnivory, pollination and parasitism. The uniquely flat landscapes of southwestern Australia have had prolonged presence of saline lakes along palaeoriver systems favouring evolution of accentuated tolerance to salinity. Lastly, unusual resiliences and vulnerabilities might be evident among OCBIL organisms, such as enhanced abilities to persist in small fragmented populations but great susceptibility to major soil disturbances. In those places where it is most pertinent, OCBIL theory hopefully lays a foundation for future research and for better informed conservation management.

Desirable plant root traits for protecting natural and engineered slopes against landslides

Abstract: Slope stability models traditionally use simple indicators of root system structure and strength when vegetation is included as a factor. However, additional root system traits should be considered when managing vegetated slopes to avoid shallow substrate mass movement. Traits including root distribution, length, orientation and diameter are recognized as influencing soil fixation, but do not consider the spatial and temporal dimensions of roots within a system. Thick roots act like soil nails on slopes and the spatial position of these thick roots determines the arrangement of the associated thin roots. Thin roots act in tension during failure on slopes and if they traverse the potential shear zone, provide a major contribution in protecting against landslides. We discuss how root traits change depending on ontogeny and climate, how traits are affected by the local soil environment and the types of plastic responses expressed by the plant. How a landslide engineer can use this information when considering slope stability and management strategies is discussed, along with perspectives for future research. This review encompasses many ideas, data and concepts presented at the Second International Conference ‘Ground Bio- and Eco-engineering: The Use of Vegetation to Improve Slope Stability—ICGBE2’ held at Beijing, China, 14–18 July 2008. Several papers from this conference are published in this edition of Plant and Soil.

The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

Abstract: Rhizosphere microorganisms have two faces, like Janus the Roman god of gates and doors who symbolizes changes and transitions, from one condition to another. One face looks at the plant root, the other sees the soil. The ears and the nose sense the other gods around and the mouths are wide open, swallowing as much as they can, and as described in Chapter 11, they also are busy talking. These faces may as well represent Hygieia (the Greek god of Health and Hygiene, the prevention of sickness and the continuation of good health) and Morta (the Roman god of death) for rhizosphere microbes can be beneficial, and promote plant growth and well being (Chapter 12) or detrimental, causing plant sickness and death (Chapter 13). It can be argued that many rhizosphere microbes are “neutral”, faceless saprophytes that decompose organic materials, perform mineralization and turnover processes. While most may not directly interact with the plant, their effects on soil biotic and abiotic parameters certainly have an impact on plant growth. Maybe they are Janus’ feet, the unsung heroes of the rhizosphere. This chapter addresses some aspects of the taxonomical and functional microbial diversity of the rhizosphere. Bacteria, Archea, viruses and Fungi will be at the heart of our discussion, while other rootassociated eukaryotes are the subjects of other chapters

Effect of fencing and grazing on a Kobresia-dominated meadow in the Qinghai-Tibetan Plateau

Abstract: Grazing is one of the most important factors influencing community structure and productivity in natural grasslands. Fencing to exclude grazers is one of the main management practices used to protect grasslands. Can fencing improve grassland community status by restraining grazing? We conducted a field community study and indoor soil analyses to determine the long-term effects of fencing and grazing on the above-ground community and soil in a Kobresia-dominated meadow in the Qinghai-Tibetan Plateau, NW China. Our results showed that fencing significantly improved above-ground vegetation productivity but reduced plant density and species diversity. Long-term fencing favored the improvement of forage grass functional groups and restrained the development noxious weed functional groups. There were significant positive effects of fencing on below-ground organic matter, total nitrogen, available nitrogen, total phosphorus and available phosphorus. The productivity of grazed meadow showed a weak decrease over time. There were long-term decreasing trends for plant density both in fenced and grazed meadows. Our study suggests that grazing can be considered as a useful management practice to improve species diversity and plant density in long-term fenced grasslands and that periodic grazing and fencing is beneficial in grassland management.

Arsenic toxicity to rice (Oryza sativa L.) in Bangladesh

Abstract: Natural contamination of groundwater with arsenic (As) occurs around the world but is most widespread in the river basin deltas of South and Southeast Asia. Shallow groundwater is extensively used in the Bengal basin for irrigation of rice in the dry winter season, leading to the possibility of As accumulation in soils, toxicity to rice and increased levels of As in rice grain and straw. The impact of As contaminated irrigation water on soil-As content and rice productivity was studied over two winter-season rice crops in the command area of a single tubewell in Faridpur district, Bangladesh. After 16–17 years of use of the tubewell, a spatially variable build up of As and other chemical constituents of the water (Fe, Mn and P) was observed over the command area, with soil-As levels ranging from about 10 to 70 mg kg−1. A simple mass balance calculation using the current water As level of 0.13 mg As L−1 suggested that 96% of the added arsenic was retained in the soil. When BRRI dhan 29 rice was grown in two successive years across this soil-As gradient, yield declined progressively from 7–9 to 2–3 t ha−1 with increasing soil-As concentration. The average yield loss over the 8 ha command area was estimated to be 16%. Rice-straw As content increased with increasing soil-As concentration; however, the toxicity of As to rice resulted in reduced grain-As concentrations in one of the 2 years. The likelihood of As-induced yield reductions and As accumulation in straw and grain has implications to agricultural sustainability, food quality and food security in As-affected regions throughout South and Southeast Asia.

Influence of potassium solubilizing microorganism (Bacillus mucilaginosus) and waste mica on potassium uptake dynamics by sudan grass (Sorghum vulgare Pers.) grown under two Alfisols

Abstract: The main aim of this research was to study the dynamics of K release from waste mica inoculated with potassium solubilizing microorganism (Bacillus mucilaginosus) and to investigate its effectiveness as potassic-fertilizer using sudan grass (Sorghum vulgare Pers.) var Sudanensis as test crop grown under two Alfisols. Results revealed that application of mica significantly enhanced biomass yield, uptake and per cent K recoveries by sudan grass than control (no-K). Biomass yield, uptake and per cent K recoveries increased further when mica was inoculated with bacterial strain in both the soils than uninoculated mica. Alfisol from Hazaribag recorded higher yield, uptake and K recoveries than Alfisol from Bhubaneswar. The dynamics of K in soils indicated that K was released from mica to water-soluble and exchangeable pools of K due to inoculation of mica with Bacillus mucilaginosus in both the soils. Significantly greater amounts of water-soluble, exchangeable and non-exchangeable K were maintained in Alfisol from Hazaribag than Bhubaneswar. Release kinetics of K showed significant release of K from mica treated with bacterial strain. Significant correlation between biomass yield, K uptake by sudan grass and different pools of K in soils were observed. X-ray diffraction analysis indicates greater dissolution of mica due to inoculation of Bacillus mucilaginosus strain in both the soils. Thus, bio-intervention of waste mica could be an alternative and viable technology to solubilize insoluble K into plant available pool and used efficiently as a source of K-fertilizer for sustaining crop production and maintaining soil potassium.

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

Abstract: 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.

Rhizosphere engineering and management for sustainable agriculture

Abstract: This paper reviews strategies for manipulating plants and their root-associated microorganisms to improve plant health and productivity. Some strategies directly target plant processes that impact on growth, while others are based on our knowledge of interactions among the components of the rhizosphere (roots, microorganisms and soil). For instance, plants can be engineered to modify the rhizosphere pH or to release compounds that improve nutrient availability, protect against biotic and abiotic stresses, or encourage the proliferation of beneficial microorganisms. Rhizobacteria that promote plant growth have been engineered to interfere with the synthesis of stress-induced hormones such as ethylene, which retards root growth, and to produce antibiotics and lytic enzymes active against soilborne root pathogens. Rhizosphere engineering also can involve the selection by plants of beneficial microbial populations. For example, some crop species or cultivars select for and support populations of antibiotic-producing strains that play a major role in soils naturally suppressive to soil-borne fungal pathogens. The fitness of root-associated bacterial communities also can be enhanced by soil amendment, a process that has allowed the selection of bacterial consortia that can interfere with bacterial pathogens. Plants also can be engineered specifically to influence their associated bacteria, as exemplified by quorum quenching strategies that suppress the virulence of pathogens of the genus Pectobacterium. New molecular tools and powerful biotechnological advances will continue to provide a more complete knowledge of the complex chemical and biological interactions that occur in the rhizosphere, ensuring that strategies to engineer the rhizosphere are safe, beneficial to productivity, and substantially improve the sustainability of agricultural systems.

Synchrotron-based techniques for plant and soil science: opportunities, challenges and future perspectives

Abstract: Spectroscopic approaches to plant and soil sciences have provided important information for several decades. However, many of these approaches suffered from a number of limitations and drawbacks especially in terms of spatial resolution and requirements for sample preparation. The advent of dedicated synchrotron facilities, that allow the exploitation of the particular qualities of synchrotron radiation as a research tool, has revolutionised the way we approach the investigation of nutrients and contaminants in environmental samples. Various synchrotron-based techniques are currently available that permit such investigations in situ and at the molecular level. The continuous development of these techniques is delivering substantial gains in terms of sensitivity and spatial resolution which allows analyses of diluted samples at the sub-micron scale. This paper aims at providing an introduction to synchrotron radiation and to the fundamentals of some widely used synchrotron-based techniques, in particular X-ray absorption, fluorescence and tomography. Furthermore, examples are provided regarding the applications of synchrotron-based techniques in the field of plant, soil and rhizosphere research. Finally, current limitations and future perspectives of synchrotron techniques are discussed.

Rooting depth and water use efficiency of tropical maize inbred lines, differing in drought tolerance

Abstract: Deep rooting has been identified as strategy for desiccation avoidance in natural vegetation as well as in crops like rice and sorghum. The objectives of this study were to determine root morphology and water uptake of four inbred lines of tropical maize (Zea mays L.) differing in their adaptation to drought. The specific questions were i) if drought tolerance was related to the vertical distribution of the roots, ii) whether root distribution was adaptive or constitutive, and iii) whether it affected water extraction, water status, and water use efficiency (WUE) of the plant. In the main experiment, seedlings were grown to the V5 stage in growth columns (0.80 m high) under well-watered (WW) and water-stressed (WS) conditions. The depth above which 95 % of all roots were located (D95) was used to estimate rooting depth. It was generally greater for CML444 and Ac7729/TZSRW (P2) compared to SC-Malawi and Ac7643 (P1). The latter had more lateral roots, mainly in the upper part of the soil column. The increase in D95 was accompanied by increases in transpiration, shoot dry weight, stomatal conductance and relative water content without adverse effects on the WUE. Differences in the morphology were confirmed in the V8 stage in large boxes: CML444 with thicker (0.14 mm) and longer (0.32 m) crown roots compared to SC-Malawi. Deep rooting, drought sensitive P2 showed markedly reduced WUE, likely due to an inefficient photosynthesis. The data suggest that a combination of high WUE and sufficient water acquisition by a deep root system can increase drought tolerance.

Isolation and characterization of phosphate solubilizing rhizobacteria to improve plant health of tomato.

Abstract: In the present study, 43 isolates of Phosphate solubilizing rhizobacteria (PSRB) were isolated from 37 rhizospheric soil samples of tomato collected from tomato growing regions of Karnataka. Among the 43 isolates, 33 were found to be positive for solubilizing both inorganic and organic forms of phosphorous. The isolates were analyzed for their ability to colonize roots of tomato and to increase the seed quality parameters under laboratory conditions. On the basis of above criteria, 16 isolates were selected for further studies. Organic acids from PSRB isolates were analyzed and phytase zymogram for two isolates viz., PSRB21 and 31 was prepared. Under greenhouse conditions, all selected isolates showed increased shoot length, root length, fresh weight, dry weight and phosphorous content of tomato seedlings to various extent with respect to control. Analysis of pH and available phosphorous in rhizosphere soil samples of 30 day-old-seedlings revealed that the available phosphorous content was high in rhizospheric soil samples of plants raised from seeds bacterized with PSRB isolates over control. Even though all selected PSRB’s were able to increase the plant growth, only few of them showed protection against fusarium wilt and none of them against early blight.

Novel approaches in plant breeding for rhizosphere-related traits

Abstract: Selection of modern varieties has typically been performed in standardized, high fertility systems with a primary focus on yield. This could have contributed to the loss of plant genes associated with efficient nutrient acquisition strategies and adaptation to soil-related biotic and abiotic stresses if such adaptive strategies incurred a cost to the plant that compromised yield. Furthermore, beneficial interactions between plants and associated soil organisms may have been made obsolete by the provision of nutrients in high quantity and in readily plant available forms. A review of evidence from studies comparing older traditional varieties to modern high yielding varieties indeed showed that this has been the case. Given the necessity to use scarce and increasingly costly fertilizer inputs more efficiently while also raising productivity on poorer soils, it will be crucial to reintroduce desirable rhizosphere-related traits into elite cultivars. Traits that offer possibilities for improving nutrient acquisition capacity, plant–microbe interactions and tolerance to abiotic and biotic soil stresses in modern varieties were reviewed. Despite the considerable effort devoted to the identification of suitable donors and of genetic factors associated with these beneficial traits, progress in developing improved varieties has been slow and has so far largely been confined to modifications of traditional breeding procedures. Modern molecular tools have only very recently started to play a rather small role. The few successful cases reviewed in this paper have shown that novel breeding approaches using molecular tools do work in principle. When successful, they involved close collaboration between breeders and scientists conducting basic research, and confirmation of phenotypes in field tests as a ‘reality check’. We concluded that for novel molecular approaches to make a significant contribution to breeding for rhizosphere related traits it will be essential to narrow the gap between basic sciences and applied breeding through more interdisciplinary research that addresses rather than avoids the complexity of plant–soil interactions.

Biochemical cycling in the rhizosphere having an impact on global change

Abstract: Changes in chemical properties in soil around plant roots influence many microbial processes, including those having an impact on greenhouse gas emissions. To potentially mitigate these emissions according to the Kyoto protocol, knowledge about how and where these gases are produced and consumed in soils is required. In this review, we focus on the greenhouse gases nitrous oxide and methane, which are produced by nitrifying and denitrifying prokaryotes and methanogenic archaea, respectively. After describing the microbial processes involved in production and consumption of nitrous oxide and methane and how they can be affected in the rhizosphere, we give an overview of nitrous oxide and methane emissions from the rhizosphere and soils and sediments with plants. We also discuss strategies to mitigate emissions from the rhizosphere and consider possibilities for carbon sequestration.

Long-term manuring and fertilization effects on soil organic carbon pools under a wheat-maize cropping system in North China Plain.

Abstract: The effects of organic manure and chemical fertilizer on total soil organic carbon (C T), water-soluble organic C (C WS), microbial biomass C (C MB), labile C (C L), C mineralization, C storage and sequestration, and the role of carbon management index (CMI) in soil quality evaluation were studied under a wheat–maize cropping system in a long-term experiment, which was established in 1989 in the North China Plain. The experiment included seven treatments: (1) OM: application of organic manure; (2) 1/2OMN: application of half organic manure plus chemical fertilizer NPK; (3) NPK: balanced application of chemical fertilizer NPK; (4) NP: application of chemical fertilizer NP; (5) PK: application of chemical fertilizer PK; (6) NK: application of chemical fertilizer NK; and (7) CK: unfertilized control. Application of organic manure (OM and 1/2OMN) was more effective for increasing C T, C WS, C MB, C L, C mineralization, and CMI, as compared with application of chemical fertilizer alone. For the chemical fertilizer treatments, balanced application of NPK (treatment 3) showed higher C T, C WS, C MB, C L, C mineralization, and CMI than the unbalanced use of fertilizers (treatments 4, 5, and 6). The C storage in the OM and 1/2OMN treatments were increased by 58.0% and 26.6%, respectively, over the NPK treatment, which had 5.9–25.4% more C storage than unbalanced use of fertilizers. The contents of C WS, C MB, and C L in organic manure treatments (treatments 1 and 2) were increased by 139.7–260.5%, 136.7–225.7%, and 150.0–240.5%, respectively, as compared to the CK treatment. The CMI was found to be a useful index to assess the changes of soil quality induced by soil management practices due to its significant correlation with soil bulk density and C fractions. The OM and 1/2OMN treatments were not a feasible option for farmers, but a feasible option for sequestering soil carbon, especially for the OM treatment. The NPK treatment was important for increasing crop yields, organic material inputs, and soil C fractions, so it could increase the sustainability of cropping system in the North China Plain.

Nitrogen fate and environmental consequence in paddy soil under rice-wheat rotation in the Taihu lake region, China

Abstract: Field undisturbed tension-free monolith lysimeters and 15N-labeled urea were used to investigate the fate of fertilizer nitrogen in paddy soil in the Taihu Lake region under a summer rice-winter wheat rotation system. We determined nitrogen recovered by rice and wheat, N remained in soil, and the losses of reactive N (i.e., NH3, N2O, NO3−, organic N and NH4+) to the environment. Quantitative allocation of nitrogen fate varied for the rice and wheat growing seasons. At the conventional application rate of 550 kg N ha−1 y−1 (250 kg N ha−1 for wheat and 300 kg N ha−1 for rice), nitrogen recovery of wheat and rice were 49% and 41%, respectively. The retention of fertilizer N in soil at harvest accounted for 29% in the wheat season and for 22% in the rice season. N losses through NH3 volatilization from flooded rice paddy was 12%, far greater than that in the wheat season (less than 1%), while N leaching and runoff comprised only 0.3% in the rice season and 5% in the wheat season. Direct N2O emission was 0.12% for the rice season and 0.14% for the wheat season. The results also showed that some dissolved organic N (DON) were leached in both crop seasons. For the wheat season, DON contributed 40–72% to the N- leaching, in the rice season leached DON was 64–77% of the total N leaching. With increasing fertilizer application rate, NH3 volatilization in the rice season increased proportionally more than the fertilizer increase, N leaching in the wheat season was proportional to the increase of fertilizer rate, while N2O emission increased less in proportion than fertilizer increase both in the rice season and wheat season.

Winter wheat roots grow twice as deep as spring wheat roots, is this important for N uptake and N leaching losses?

Abstract: Cropping systems comprising winter catch crops followed by spring wheat could reduce N leaching risks compared to traditional winter wheat systems in humid climates. We studied the soil mineral N (Ninorg) and root growth of winter- and spring wheat to 2.5 m depth during 3 years. The roots of the winter and spring wheat penetrated the soil at a similar rate (1.3 mm o C day �1 ) and by virtue of its longer growing period, winter wheat reached depths of 2.2 m, twice that of spring wheat (1.1 m). The deeper rooting of winter wheat was related to much lower amounts of Ninorg left in the 1 to 2.5 m layer after winter wheat (81 kg Ninorg ha �1 less). When growing winter catch crops before spring wheat, N content in the 1 to 2.5 m layer after spring wheat was not different from that after winter wheat. The results suggest that due to its deep rooting, winter wheat may not lead to as high levels of leaching as it is often assumed in humid climates. Deep soil and root measurements (below 1 m) in this experiment were essential to answer the questions we posed.

Higher plant diversity enhances soil stability in disturbed alpine ecosystems

Abstract: Plant diversity is hypothesised to increase soil stability by increasing the diversity of root types. To test this hypothesis, we took soil cores from machine-graded ski slopes and from the adjacent undisturbed vegetation as a control. We quantified aggregate stability as an indicator for soil stability in relation to (1) abiotic soil properties, (2) above-ground vegetation characteristics and (3) root parameters. From the three groups of variables, the number of plant species, root density (RD) and sand content showed the highest correlation with soil aggregate stability and explained 54% of its variance. In variance partitioning, the number of plant species was the most relevant factor explaining 19% of the variance in aggregate stability. Further, it explained another 11% through shared effects with RD and sand content. An additional 8% was explained through the shared influence with sand content. Plant species showing the highest correlation with overall diversity were from different functional groups (grasses, forbs and shrubs), meaning that beneficial effects can not only be assigned to one specific functional group, but to the combination of several groups. Our data demonstrate the positive effect of plant diversity on aggregate stability. We suggest that high plant diversity is one of the most relevant factors for enhancing soil stability at disturbed sites at high elevation.

Root cohesion of forest species in the Italian Alps

Abstract: Forests can prevent and/or mitigate hydrogeomorphic hazards in mountainous landscapes. Their effect is particularly relevant in the case of shallow landslides phenomena, where plants decrease the water content of the soil and increase its mechanical strength. Although such an effect is well known, its quantification is a relatively new challenge. The present work estimates the effect of some forest species on hillslope stability in terms of additional root cohesion by means of a model based on the classical Wu and Waldron approach (Wu in Alaska Geotech Rpt No 5 Dpt Civ Eng Ohio State Univ Columbus, USA, 1976; Waldron in Soil Sci Soc Am J 41:843–849, 1977). The model is able to account for root distribution with depth and non-simultaneous root breaking. Samples of European beech (Fagus sylvatica L.), Norway spruce (Picea abies (L.) Karst.), European larch (Larix decidua Mill.), sweet chestnut (Castanea sativa Mill.) and European hop-hornbeam (Ostrya carpinifolia Scop.), were taken from different locations of Lombardy (Northern Italy) to estimate root tensile strength, the Root Area Ratio and the root cohesion distribution in the soil. The results show that, in spite of its dramatic variability within the same species at the same location and among different locations, root cohesion can be coherently interpreted using the proposed method. The values herein obtained are significant for slope stabilisation, are consistent with the results of direct shear tests and back-analysis data, and can be used for the estimation of the stability of forested hillslopes in the Alps.

Selenium increases seed production in Brassica

Abstract: Selenium (Se) is essential for humans and animals but is not considered to be essential for higher plants. Although researchers have found increases in vegetative growth due to fertiliser Se, there has been no definitive evidence to date of increased reproductive capacity, in terms of seed production and seed viability. The aim of this study was to evaluate seed production and growth responses to a low dose of Se (as sodium selenite, added to solution culture) compared to very low-Se controls in fast-cycling Brassica rapa L. Although there was no change in total biomass, Se treatment was associated with a 43% increase in seed production. The Se-treated Brassica plants had higher total respiratory activity in leaves and flowers, which may have contributed to higher seed production. This study provides additional evidence for a beneficial role for Se in higher plants.

Strategies and methods for studying the rhizosphere—the plant science toolbox

Abstract: This review summarizes and discusses methodological approaches for studies on the impact of plant roots on the surrounding rhizosphere and for elucidation of the related mechanisms, covering a range from simple model experiments up to the field scale. A section on rhizosphere sampling describes tools and culture systems employed for analysis of root growth, root morphology, vitality testing and for monitoring of root activity with respect to nutrient uptake, water, ion and carbon flows in the rhizosphere. The second section on rhizosphere probing covers techniques to detect physicochemical changes in the rhizosphere as a consequence of root activity. This comprises compartment systems to obtain rhizosphere samples, visualisation techniques, reporter gene approaches and remote sensing technologies for monitoring the conditions in the rhizosphere. Approaches for the experimental manipulation of the rhizosphere by use of molecular and genetic methods as tools to study rhizosphere processes are discussed in a third section. Finally it is concluded that in spite of a wide array of methodological approaches developed in the recent past for studying processes and interactions in the rhizosphere mainly under simplified conditions in model experiments, there is still an obvious lack of methods to test the relevance of these findings under real field conditions or even on the scale of ecosystems. This also limits reliable data input and validation in current rhizosphere modelling approaches. Possible interactions between different environmental factors or plant-microbial interactions (e.g. mycorrhizae) are frequently not considered in model experiments. Moreover, most of the available knowledge arises from investigations with a very limited number of plant species, mainly crops and studies considering also intraspecific genotypic differences or the variability within wild plant species are just emerging.