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Soil–Microbes–Plants: Interactions and Ecological Diversity

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Abstract

In interactions between plants and soil, microorganisms have significant roles. Ecological stability is contributed by the biogeochemical cycling of elements. An emerging body of research is distinguishing the impacts that root-associated microbial communities can have on plant fitness and growth. Rocks and minerals are weathered by the activities of plants, which exude various types of hormones, with a crucial role in the supply of organic matter and formation of soils. Various types of plant species have distinctive biological characteristics that show constraint to precise soil types. Plant–microbe interactions in soil are contributing to a new, microbially based perspective on plant community and ecology. These microorganisms are soil dwellers, diverse, and their interactions with plants vary with respect to specificity, environmental heterogeneity, and fitness impact. The key influences on plant community structure and dynamics are effected by two microbial procedures: microbial intervention of niche diversity in resource use and response dynamics among the soil community and plants. The hypothesis of niche diversity is based on various interpretations that the nutrients of soil are found in different chemical forms: the plant requires accessing these enzymes and nutrients, and the microorganisms of the soil are a major source of these enzymes. Plant–microbe interactions are a significant establishing force for extensive spatial gradients in species abundance. The positive response (a homogenizing force) and negative response (a diversifying force) of virtual balance may contribute to detected latitudinal (and altitudinal) diversity patterns. The microbially based perception for the ecology of plants promises to contribute to our understanding of long-standing issues in ecology and to disclose new areas of future investigation.

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... For example, rhizosphere interactions between plant roots and soil food webs are made up of self-reinforcing and self-regulating cycles. For example, positive feedback driven by root exudation, microbe population growth, microbially-induced nutrient release, and plant root nutrient uptake facilitates subsequent root exudation (a self-reinforcing process), while negative feedback driven by predator-prey consumption and initial nutrient availability govern nutrient turnover rates useful for plant growth (self-regulating cycles) (Figure 2 [33][34][35][36]). ...
... • Fertilization overcomes soil nutrient deficiencies by providing nutrients in plantavailable form, but artificially high resource conditions shift microbial community structure and activity away from guilds specializing in decomposition of organic compounds or potential synergistic plant root-microorganism symbioses; under reduced nutrient cycling, plant production increasingly relies on fertilization to meet nutrient needs at the field scale [36,[80][81][82] and can contribute nutrient-driven externalities at larger scales. • Irrigation overcomes soil moisture deficiencies that limit plant transpiration but often introduces salts and other chemicals into the rooting zone that accumulate over time with subsequent irrigation events (especially in situations with poor drainage and water quality, an effect known as secondary salinization). ...
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... Stress cell signaling pathways activate metabolic activities in plants for subsisting and molecular responses, like antioxidants induction, production, and accumulation of compatible solutes and stress proteins (Chinni 2016;Thangaraj et al. 2019). This chapter elaborates the theory of rhizospheric bacteria and their plant growth promotion mechanisms and remediation of abiotic stress with latest updates (Fahad et al. 2015;Ojuederie and Babalola 2017;Chandra and Enespa 2019c). Rhizobacteria which mitigate the abiotic stress in various agro-biotas have been offered to harvest the wide range of perspectives about their applicability is the modernized examples (Chandra and Enespa 2016;Enespa and Chandra 2019). ...
... The plant-microbe interactions may be useful and detrimental depends on characteristic of the bacterial community and its interaction pathway Hardoim et al. 2015). These rhizospheric microflora promote plant growth and provide high yields in crops and also work as a biocontrol against phytopathogens (Beneduzi et al. 2012;Ahemad and Kibret 2014;Chandra and Enespa 2019c). Furthermore, the observations indicate that the PGPR have capability to boost abiotic stresses (Grover et al. 2011;Kang et al. 2014). ...
Chapter
Rhizomicrobiome improves abiotic stress tolerance in plants and promote their improvement. These plant growth-promoting microbiomes stimulate the growth of the plants by diverse mechanisms. These microorganisms help the plants in acquisition of unavailable nutrients such as phosphorus, zinc, and potassium and produce siderophores and different phytohormones such as auxins, gibberellins, and cytokinins. They secrete subordinate metabolites and antibiotics that further stimulate the growth of the plants during stress condition. Therefore, use of PGPB is a novel approach, and use of such approaches in research is needed to appreciate the ecological, genetic, and biological associations in the territory.
... In terrestrial ecosystems, plants interact with a myriad of soil microbial communities that lead to the establishment of interdependent relationships [1], which drive plant community productivity [2], belowground biodiversity, and ecosystem multifunctionality [3][4][5]. These interactions are crucial for many aspects [6,7], including the nutrient acquisition of plants from heterogeneously distributed microsites. The responses of plants to spatially, heterogeneously distribute soil nutrients require a specialized physiological strategy commonly referred to as the root foraging mechanism, i.e., the proliferation of roots in nutrient-rich microhabitats [8,9] and microbially mediated mechanisms via a plantmicrobe symbiotic relationship to ensure the effective acquisition of soil nutrients [10]. ...
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The spatially heterogeneous distribution of soil nutrients is ubiquitous in terrestrial ecosystems and has been shown to promote the performance of plant communities, influence species coexistence, and alter ecosystem nutrient dynamics. Plants interact with diverse soil microbial communities that lead to an interdependent relationship (e.g., symbioses), driving plant community productivity, belowground biodiversity, and soil functioning. However, the potential role of the soil microbial communities in regulating the effect of soil nutrient heterogeneity on plant growth has been little studied. Here, we highlight the ecological importance of soil nutrient heterogeneity and microorganisms and discuss plant nutrient acquisition mechanisms in heterogeneous soil. We also examine the evolutionary advantages of nutrient acquisition via the soil microorganisms in a heterogeneous environment. Lastly, we highlight a three-way interaction among the plants, soil nutrient heterogeneity, and soil microorganisms and propose areas for future research priorities. By clarifying the role of soil microorganisms in shaping the effect of soil nutrient heterogeneity on plant performance, the present study enhances the current understanding of ecosystem nutrient dynamics in the context of patchily distributed soil nutrients.
... Fungi, protozoa, archaea, nematodes, oomycetes, bacteria, algae, and viruses are all frequent creatures found in the rhizosphere, and these organisms are referred to as rhizo-microbiomes [37,47]. These creatures dwell in the rhizosphere and feed on the plant's nutrients (organic acids, sugars, amino acids, fatty acids, vitamins, and growth hormones) [48]. ...
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Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
... This may be also true for organisms dwelling in soil environment heavily contaminated with plastic particles. The interactions between plants and soil organisms suggest their close occurrence in the environment (Bais et al. 2006;Adam et al. 2014;Wurst et al. 2018;Chandra and Enespa 2019;Topalovic et al. 2020). So, it may be suggested that the soilborne organisms cause quantitative enrichment of plastic particles and bound toxicants like HMs in the rhizosphere region of plants. ...
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Interactions of plastic particles with different organic/inorganic pollutants including heavy metals impact their ecotoxicological potential, and proper understanding in this regard is important for their ecological risk assessment. However, many studies have reported the interactions between micro-/nanoplastics (MNPs) and heavy metals (HMs), but the most prevalent interactive forces and factors monitoring their interactions are still not clear. So, the present review represents the mechanisms of interactions with special emphasis on major interactive forces and biophysicochemical and environmental factors influencing trace element’s adsorption onto the surface of MNPs. Electrostatic interaction and pore-filling mechanism can best explain the HMs adsorption to MNPs. A number of biophysicochemical factors (such as biofilm, size, crystallinity, and surface charge) and environmental factors (such as pH, salt, and temperature) act together for mediating interactions and ecotoxicities of MNPs and HMs in the real environment. From a toxicological point of view, the synergistic mode of action may be more active in animals, whereas the antagonistic activity may be prevalent in plants. Besides polymer density, biofilm formation and agglomeration property of MNPs can control the vertical distribution of MNPs along the water column. Finally, the ecotoxicological potential of MNPs in the natural environment can be considered as a function of spatiotemporal variation in abiotic (including MNPs and heavy metals) and biotic components. This review will be helpful in the detail understanding of ecotoxicological risk assessment of MNPs in relation to their interaction with heavy metals.
... For our field demonstration, the site chosen has nearly 100-300 parts per million (ppm) of weathered PCBs and was found to have insignificant regular microbial inhabitants which lacked PCB-degrading movement (Leigh et al. 2006;Sayler et al. 1978). PCBs can transform using soil microflora by either growth on specific chlorinated biphenyls, or congeners, as carbon source (Field and Sierra-Alvarez 2008) or by cometabolism (Borja et al. 2005;Chandra and Enespa 2019c). The natural growing inhabitants could not to degrade the PCBs by adding of ingredients alone or nutrients adding, so it is confirmed that these sites are not likely to go through natural re-establishment (Singer et al. 2000;Passatore et al. 2014;Enespa and Chandra 2017). ...
Chapter
In real polluted soils a wide variety of recalcitrant pollutants with several chemical white-rot fungi such as Pleurotus ostreatus, Irpex lacteus, Trametes versicolor, Phanerochaete chrysosporium, Lentinus edodes, Coriolus versicolor, Cyathus stercoreus, Heterobasidion annosum, and Ceriporiopsis subvermispora degrade the cell wall components simultaneously and have PCB-degrading capabilities. Hydroxylated and methoxylated PCBs, chlorobenzoates, and chlorobenzyl alcohols were observed as transformation products that specify that the fungal species have capabilities to oxidize and decay the aromatic moiety of PCBs in lands. Some white-rot fungi such as Phlebia brevispora, Bjerkandera adusta, Pycnoporus cinnabarinus, Phanerochaete magnolia, and Dichomitus squalens have already demonstrated their prospective for the elimination of PCBs. Lignin peroxidase (LiP, EC 1.11.1.14), manganese peroxidase (MnP, EC 1.11.1.13), and laccase (Lac, EC 1.10.3.2) enzymes possessed by WRF are involved in the oxidation of a wide range of organopollutants.
... The positive effects also show large variation across landscapes shows a positive effect, e.g., lower effects in more diverse landscapes. Though, the benefits of organic production for biodiversity have been shown to be greatest at field level in some cases, while increases at farm or landscape level may be lesser (Chandra & Enespa, 2019). ...
... Salt resistance plants have been associated to more effective antioxidant schemes, and a salt-tolerant bacterium P. simiae strain AU enriched antioxidants (peroxidase and catalase) and gene expression in soybean plants when treated with 100 mM NaCl stress disorder (Vaishnav et al. 2016;Chandra and Enespa 2019c). Drought stress effects in maize plants are alleviated by Pseudomonas spp. ...
Chapter
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Chapter
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Drought stress induces a range of metabolic responses in plants. Some of these responses are mediated by arbuscular mycorrhizae (AM), which occur almost ubiquitously in symbiotic associations. These changes are highly variable and depend on various factors related mainly to the diversity of plant and fungal species but are generally beneficial to the host plants. This chapter addresses the role of AM fungi in the amelioration and alleviation of drought stress in host plants and their positive effects on growth. We discuss the various biochemical, physiological, and molecular processes used by plants to alleviate drought stress. We provide an update of the recent progress in functional approaches for unraveling the mechanisms that promote resistance to drought stress and discuss their significance to the host plants. The positive aspects of AM are also discussed in the context of the ecosystem services provided by the symbiosis under environmental drought conditions. © Springer Science+Business Media New York 2014. All rights are reserved.
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The successful colonization of plant growth promoting rhizobacteria (PGPR) in the rhizosphere is an initial and compulsory step in the protection of plants from soil-borne pathogens. Therefore, it is necessary to evaluate the role of root exudates in the colonization of PGPR. Banana root exudates were analyzed by high pressure liquid chromatography (HPLC) which revealed exudates contained several organic acids (OAs) including oxalic, malic and fumaric acid. The chemotactic response and biofilm formation of Bacillus amyloliquefaciens NJN-6 were investigated in response to OA's found in banana root exudates. Furthermore, the transcriptional levels of genes involved in biofilm formation, yqxM and epsD, were evaluated in response to OAs via quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). Results suggested that root exudates containing the OAs both induced the chemotaxis and biofilm formation in NJN-6. In fact, the strongest chemotactic and biofilm response was found when 50 μM of OAs were applied. More specifically, malic acid showed the greatest chemotactic response whereas fumaric acid significantly induced biofilm formation by a 20.7–27.3% increase and therefore biofilm formation genes expression. The results showed banana root exudates, in particular the OAs released, play a crucial role in attracting and initiating PGPR colonization on the host roots. PGPR is a collective term used to describe a group of beneficial bacteria capable of colonizing the rhiz-osphere leading to the stimulation of plant growth and/or the protection of plants from soil-borne phy-topathogens 1. Plant growth promoting mechanisms include the production of antimicrobial compounds such as lipopeptides and polyketides which are bioactive against phytopathogens 2,3
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All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.
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Microbial transformations of cyclic hydrocarbons have received much attention during the past three decades. Interest in the degradation of environmental pollutants as well as in applications of microorganisms in the catalysis of chemical reactions has stimulated research in this area. The metabolic pathways of various aromatics, cycloalkanes, and terpenes in different microorganisms have been elucidated, and the genetics of several of these routes have been clarified. The toxicity of these compounds to microorganisms is very important in the microbial degradation of hydrocarbons, but not many researchers have studied the mechanism of this toxic action. In this review, we present general ideas derived from the various reports mentioning toxic effects. Most importantly, lipophilic hydrocarbons accumulate in the membrane lipid bilayer, affecting the structural and functional properties of these membranes. As a result of accumulated hydrocarbon molecules, the membrane loses its integrity, and an increase in permeability to protons and ions has been observed in several instances. Consequently, dissipation of the proton motive force and impairment of intracellular pH homeostasis occur. In addition to the effects of lipophilic compounds on the lipid part of the membrane, proteins embedded in the membrane are affected. The effects on the membrane-embedded proteins probably result to a large extent from changes in the lipid environment; however, direct effects of lipophilic compounds on membrane proteins have also been observed. Finally, the effectiveness of changes in membrane lipid composition, modification of outer membrane lipopolysaccharide, altered cell wall constituents, and active excretion systems in reducing the membrane concentrations of lipophilic compounds is discussed. Also, the adaptations (e.g., increase in lipid ordering, change in lipid/protein ratio) that compensate for the changes in membrane structure are treated.
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A wetland ecosystem is an important reservoir of microbial diversity and contributes significantly in mitigation of the Greenhouse gas emissions. Increased nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity loss and ecosystem functioning of wetlands, such as control of greenhouse gas emissions. The intensive biogeochemical activities in the wetlands are performed by microbs, which have an important role in improving water quality and nutrient recycling. It is well known that the structure and function of the microbial community enhance the restoration of nutrient cycling in wetlands. Investigating the interactions of structure and functions of microbes with wetland plants is important because the microbial taxa can be interconnected to specific transformations, biodegradation, biogeochemical cycles, survival, and restoration of the wetlands. The processes of nitrification, denitrification, mineralization, humification, and absorption are performed by physical, chemical, and microbial processes for the sustainability of the wetland. This chapter suggests that microbially mediated processes are directly and indirectly crucial in the restoration of wetland function and ecological aspects. The phenomenon and the working principle of microbes in wetlands are discussed in detail with emphasis on nutrient cycling. This chapter also describes how microbes are an indispensible part of wetland functioning and restoration.
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Natural products are important not only in the environment but also as useful compounds in various applications as in medicine or as phytopathogens. An enormous number of such compounds have been derived from fungal communities colonizing various habitats. Traditionally, the isolates of a fungal community have been explored as “biofactories” of novel bioactive substances, and they have not disappointed. Among the extracts and pure substances obtained from culture broths or fungal biomass, some have exerted antifungal and antibacterial activities ranging from moderate to powerful when tested on the pathogenic bacterial and fungal strains resistant to the antibiotics currently in use. Fungal communities that colonize the internal tissues of plants have been proven to produce a large number of structurally diverse novel secondary metabolites. Such as, the compound 3-O-methylfunicone isolated from Talaromyces sp., from mangrove environment, has shown antifungal, antitumor, and lipid-lowering properties. Petriella sp., an endophyte of the sponge Suberites domuncula produced a cyclic tetra peptide compound exhibited cytotoxicity against murine L5178Y lymphoma cells at an ED50 value of < 0.1 μg/ml. In this chapter, we reexamine the accumulated data on fungal communities isolated from plants and microbes that produce novel secondary metabolites with antimicrobial activity against plant and human pathogenic fungal and bacterial strains.
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Intraspecific variation can promote or inhibit species coexistence, both by increasing species’ competitive abilities, and by altering the relative strengths of intraspecific and interspecific competition. Effects of intraspecific variation on coexistence can occur via complementarity of different variants, and via a selection effect: initially‐variable populations are more likely to contain highly competitive variants that might determine the ability of the population as a whole to both invade and resist invasion. We tested the effects of intraspecific variation and composition on coexistence by assaying the mutual invasibility of populations of two competing bean weevil species (Callosobruchus maculatus and C. chinensis) when each was initiated with one, three, or five genetically‐ and phenotypically‐distinct lineages. Our results reveal that intraspecific variation is a double‐edged sword for species coexistence. Increasing intraspecific variation increased species’ abilities to invade, and to resist invasion, via selection effects and intraspecific niche complementarity among conspecific lineages, thereby creating the potential for exclusion among mismatched competitors. But intraspecific variation also increased the scope for resource partitioning, creating the potential for stable coexistence. Stable coexistence occurred only when intraspecific variation caused species to exhibit both relatively evenly‐matched competitive abilities and sufficiently‐strong resource partitioning. Our work explains the conflicting results of previous studies. This article is protected by copyright. All rights reserved.
Chapter
The soil is one of the main habitations of fungi and bacteria. Their interactions are part of a communication web that keeps microhabitats in balance in this amphitheater. Protuberant negotiator molecules of these inter- and intra-organismic relationships are inorganic and organic microbial volatile compounds (MVOCs). Various mixtures of gas-phase and carbon-based compounds are called volatile VOCs produced by microbes and have the capability to diffuse through the atmosphere and soils due to their small size. The volatile organic compounds benzothiazole, cyclohexanol, n-decanal, dimethyl trisulfide, 2-ethyl-1-hexanol, and nonanal are emitted by microorganisms. VOCs have possible potential as an alternative to harmful pesticides, fungicides, and bactericides as well as genetic modification. They play an important role in the inhibition of sclerotial activity, limiting ascospore production, and reducing disease levels in plant pathogenic fungi. Their role as below- and aboveground signals has been established decadely. Recently it is suggested evidently that they might have an important role in below- and aboveground level and involved in microbial-root interactions. Similarly, microbial VOCs appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. Various researchers specify that the MVOCs might provide an alternative to the use of chemicals to protect plants from pathogens and provide a setting for better crop welfare. It is well known that MVOCs can modify the plant physiology and microorganisms. In this assessment, we suggest that MVOCs can be exploited as an eco-friendly, cost-effective, disease-resistant, and sustainable strategy for agricultural practices. Our effort is making a comprehensive chapter of below- and aboveground interactions of microbial volatile diversity and their role against pathogenic fungi.
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Mass spectrometry imaging is a powerful analytical technique for detecting and determining spatial distributions of molecules within a sample. Typically mass spectrometry imaging is limited to the analysis of thin tissue sections taken from the middle of a sample. In this work, we present a mass spectrometry imaging method for the detection of compounds produced by bacteria on the outside surface of ant exoskeletons in response to pathogen exposure. Fungus-growing ants have a specialized mutualism with Pseudonocardia, a bacterium that lives on the ants' exoskeleton and helps protect their fungal garden food source from harmful pathogens. The developed method allows for visualization of bacterial-derived compounds on the ant exoskeleton. This method demonstrates the capability to detect compounds that are specifically localized to the bacterial patch on ant exoskeletons, shows good reproducibility across individual ants, and achieves accurate mass measurements within 5 ppm error when using a high-resolution, accurate-mass mass spectrometer.
Book
The roots of most plants are colonized by symbiotic fungi to form mycorrhiza, which play a critical role in the capture of nutrients from the soil and therefore in plant nutrition. Mycorrhizal Symbiosis is recognized as the definitive work in this area. Since the last edition was published there have been major advances in the field, particularly in the area of molecular biology, and the new edition has been fully revised and updated to incorporate these exciting new developments. . Over 50% new material . Includes expanded color plate section . Covers all aspects of mycorrhiza . Presents new taxonomy . Discusses the impact of proteomics and genomics on research in this area.
Book
An understanding of the mineral nutrition of plants is of fundamental importance in both basic and applied plant sciences. The Second Edition of this book retains the aim of the first in presenting the principles of mineral nutrition in the light of current advances. This volume retains the structure of the first edition, being divided into two parts: Nutritional Physiology and Soil-Plant Relationships. In Part I, more emphasis has been placed on root-shoot interactions, stress physiology, water relations, and functions of micronutrients. In view of the worldwide increasing interest in plant-soil interactions, Part II has been considerably altered and extended, particularly on the effects of external and interal factors on root growth and chapter 15 on the root-soil interface. The second edition will be invaluable to both advanced students and researchers.
Chapter
Plant growth-stimulating rhizobacteria (PGPR) are the symbiotic soil-dwelling bacteria existed at the outer part of the plant root and participate for growth and improvement of the crops. Various regulatory substances are secreted by these bacteria in the circumstances of rhizospheric regions. Normally, PGPR mechanisms simplify the growth of a plant by fixing the nitrogen from atmospheric regions, dissolved the phosphorus and other raw materials, siderophores assembly which liquefy the appropriated iron, or controlling the phytohormones levels at numerous phases of growth. When unplanned development of plant growth takes place, the activities of PGPR diminish or avoid the disastrous effect of one or more plant pathogens microbes in the form of biocontrol agents. Various researchers have been recognized to improve the fitness and proficiency of aquanaut’s species of plants by using the growth-supporting rhizospheric bacteria under systematic and harassed circumstances. The advantageous rhizobacteria of the plant may reduce the comprehensive dependency on hazardous agronomic compounds which disrupt the agro-biota. This chapter emphasizes on the insight of the rhizospheric microbe which supports the growth of plant under the existing viewpoints. Conclusively, these favorable rhizospheric bacteria in various agro-biotas have been offered scientifically under normal and stress circumstances to focus on current developments with the objectives to improve forthcoming visions.
Article
Priming is an adaptive strategy that improves the defensive capacity of plants. This phenomenon is marked by an enhanced activation of induced defense mechanisms. Stimuli from pathogens, beneficial microbes, or arthropods, as well as chemicals and abiotic cues, can trigger the establishment of priming by acting as warning signals. Upon stimulus perception, changes may occur in the plant at the physiological, transcriptional, metabolic, and epigenetic levels. This phase is called the priming phase. Upon subsequent challenge, the plant effectively mounts a faster and/or stronger defense response that defines the postchallenge primed state and results in increased resistance and/or stress tolerance. Priming can be durable and maintained throughout the plant's life cycle and can even be transmitted to subsequent generations, therefore representing a type of plant immunological memory. Expected final online publication date for the Annual Review of Plant Biology Volume 68 is April 29, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Chapter
The biology of migratory plant parasitic nematodes has been less studied than that of the sedentary endoparasites. The damage they cause is less obvious, their presence and number are more difficult to quantify and they are difficult organisms to study. Nevertheless, they are economically serious pests of many crops, from wheat and barley grown in low rainfall areas to horticultural crops (e.g. Lilium longiflorum) and tropical crops such as coffee, banana and sugarcane. The most studied migratory nematodes are the root lesion nematodes, Pratylenchus spp., the burrowing nematode Radopholus similis and the rice root nematode Hirschmanniella oryzae. In the life cycle of migratory nematodes apart from the egg, all stages of juveniles and adults are motile and can enter and leave host roots. They do not induce the formation of a permanent feeding site, but feed from individual host cells. They create pathways for entry of other root pathogens, often resulting in lesions, stunted roots, yellowing of leaves and plants showing symptoms of water stress, leading to yield loss and decreased quality of produce. In terms of genetic plant defences, no major genes for resistance to migratory nematodes have been found, and resistance breeding is usually based on QTL analysis and marker-assisted selection to combine the best minor resistance genes. Feeding damage reduces root function, and root damage and necrotic lesions the nematodes cause can then make them leave the root and seek others to parasitise. Infestation induces classical plant defence responses and changes in host metabolism which reflects the damage they cause, although detailed studies are lacking. New genomic resources are becoming available to study migratory endoparasites, and the knowledge gained can contribute to improved understanding of their interactions with hosts. Notably transcriptomes of Pratylenchus coffeae, Pratylenchus thornei, Pratylenchus zeae, R. similis and H. oryzae and the first genomic sequence, for P. coffeae, are now available. From these data, some candidate effector genes required for parasitism have been identified: many effectors similar to those found in sedentary endoparasites are present, with the exception of those thought to be involved in formation of feeding sites induced by the sedentary parasites. Belowground defence, in the form of enhanced resistance to migratory parasites, may also be achieved by transgenic expression of modified cysteine protease inhibitors (cystatins), anti-root invasion peptides and host-induced gene silencing (RNAi) strategies, demonstrating that migratory nematodes are amenable to control by these technologies. New more environmentally friendly nematicides, combined with better biological control agents, can be applied or used in seed coatings in integrated pest management approaches to defend roots from attack by migratory nematodes.
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Morphogenesis in Candida albicans requires hyphal initiation and maintenance, and both processes are regulated by the fungal quorum sensing molecule (QSM) farnesol. We show that deletion of C. albicans EED1, which is crucial for hyphal extension and maintenance, led to a dramatically increased sensitivity to farnesol, and thus identified the first mutant hypersensitive to farnesol. Furthermore, farnesol decreased the transient filamentation of an eed1Δ strain without inducing cell death, indicating that two separate mechanisms mediate quorum sensing and cell lysis by farnesol. To analyze the cause of farnesol hypersensitivity we constructed either hyperactive or deletion mutants of factors involved in farnesol signaling, by introducing the hyperactive RAS1(G13V) or pADH1-CYR1(CAT) allele, or deleting CZF1 or NRG1, respectively. Neither of the constructs nor the exogenous addition of dB-cAMP were able to rescue the farnesol hypersensitivity, highlighting that farnesol mediates its effects not only via the cAMP pathway. Interestingly, the eed1Δ strain also displayed increased farnesol production. When eed1Δ was grown under continuous medium flow conditions, to remove accumulating QSMs from the supernatant, maintenance of eed1Δ filamentation, although not restored, was significantly prolonged, indicating a link between farnesol sensitivity, production, and the hyphal maintenance-defect in the eed1Δ mutant strain. This article is protected by copyright. All rights reserved.
Article
From a screen of 36 plant-associated strains of Burkholderia spp., we identified 24 strains that suppressed leaf and pseudobulb necrosis of orchid caused by B. gladioli. To gain insights into the mechanisms of disease suppression, we generated a draft genome sequence from one suppressive strain, TC3.4.2R3. The genome is an estimated 7.67 megabases in size with three replicons, two chromosomes and the plasmid pC3. Using a combination of multilocus sequence analysis and phylogenomics, we identified TC3.4.2R3 as B. seminalis, a species within the Burkholderia cepacia complex that includes opportunistic human pathogens and environmental strains. We generated and screened a library of 3,840 transposon mutants of strain TC3.4.2R3 on orchid leaves to identify genes contributing to plant disease suppression. Twelve mutants deficient in suppression of leaf necrosis were selected and the transposon insertions were mapped to eight loci. One gene is in a wcb cluster that is related to synthesis of extracellular polysaccharide, a key determinant in bacterial-host interactions in other systems, and the other seven are highly conserved among Burkholderia spp. The fundamental information developed in this study will serve as a resource for future research aiming to identify mechanisms contributing to biological control.
Article
Signaling studies in the rhizosphere have focused on close interactions between plants and symbiotic microorganisms. However, this focus is likely to expand to other microorganisms because the rhizomicrobiome is important for plant health and is able to influence the structure of the microbial community. We discuss here the shaping of the rhizomicrobiome and define which aspects can be considered signaling. We divide signaling in the rhizosphere into three categories: (i) between microbes, (ii) from plants to microorganisms, and (iii) from microorganisms to plants. Signals act on diverse organisms including the plant. Mycorrhizal and rhizobial interkingdom signaling has revealed its pivotal role in establishing associations, and the recent discovery of signaling with non-symbiotic microorganisms indicates the important role of communication in shaping the rhizomicrobiome.
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Various types of biodiversities can be found within the cultivated plot and in its surrounding environment: plant, animal and microbial biodiversities; aboveground and belowground biodiversities; productive, resource, destructive biodiversities, etc.
Article
Metaproteomics - the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time - has provided new features to study complex microbial communities in order to unravel these "black boxes". New technical challenges arose which were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics. This article is protected by copyright. All rights reserved.
Article
Animal and plant microbiomes encompass diverse microbial communities that colonize every accessible host tissue. These microbiomes enhance host functions, contributing to host health and fitness. A novel approach to improve animal and plant fitness is to artificially select upon microbiomes, thus engineering evolved microbiomes with specific effects on host fitness. We call this engineering approach host-mediated microbiome selection, because this method selects upon microbial communities indirectly through the host and leverages host traits that evolved to influence microbiomes. In essence, host phenotypes are used as probes to gauge and manipulate those microbiome functions that impact host fitness. To facilitate research on host-mediated microbiome engineering, we explain and compare the principal methods to impose artificial selection on microbiomes; discuss advantages and potential challenges of each method; offer a skeptical appraisal of each method in light of these potential challenges; and outline experimental strategies to optimize microbiome engineering. Finally, we develop a predictive framework for microbiome engineering that organizes research around principles of artificial selection, quantitative genetics, and microbial community-ecology.
Article
Respected and known worldwide in the field for his research in plant nutrition, Dr. Horst Marschner authored two editions of Mineral Nutrition of Higher Plants. His research greatly advanced the understanding of rhizosphere processes and trace element uptake by plants and he published extensively in a variety of plant nutrition areas. While doing agricultural research in West Africa in 1996, Dr. Marschner contracted malaria and passed away, and until now this legacy title went unrevised. Despite the passage of time, it remains the definitive reference on plant mineral nutrition. Great progress has been made in the understanding of various aspects of plant nutrition and in recent years the view on the mode of action of mineral nutrients in plant metabolism and yield formation has shifted. Nutrients are not only viewed as constituents of plant compounds (constructing material), enzymes and electron transport chains but also as signals regulating plant metabolism via complex signal transduction networks. In these networks, phytohormones also play an important role. Principles of the mode of action of phytohormones and examples of the interaction of hormones and mineral nutrients on source and sink strength and yield formation are discussed in this edition. Phytohormones have a role as chemical messengers (internal signals) to coordinate development and responses to environmental stimuli at the whole plant level. These and many other molecular developments are covered in the long-awaited new edition. Esteemed plant nutrition expert and Horst Marschner's daughter, Dr. Petra Marschner, together with a team of key co-authors who worked with Horst Marschner on his research, now present a thoroughly updated and revised third edition of Marschner's Mineral Nutrition of Higher Plants, maintaining its value for plant nutritionists worldwide. A long-awaited revision of the standard reference on plant mineral nutrition Features full coverage and new discussions of the latest molecular advances Contains additional focus on agro-ecosystems as well as nutrition and quality.