Molecular microbial ecology of the rhizosphere / edited by Frans J. de Bruijn.

Formerly CIP. Uk

Contains paper authored by IT Carlow staff members.

Includes bibliographical references and index.

[Section 1 Focus Chapters] Introduction -- Using genomics to unveil bacterial determinants of rhizosphere life style -- Benefits of breeding crops for yield response to soil organisms -- Microbial interactions in the Rhizosphere -- Culture-independent molecular approaches to microbial ecology in soil and the rhizosphere -- Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere -- Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities interactions in the rhizosphere -- Microbially Mediated Plant Functional Traits.

[Section 2 Plant-mediated Structuring of Bacterial Communities in the Rhizosphere] Unraveling the shed of unexplored rhizosphere microbial diversity -- Analysis of bacterial communities in the rhizosphere- what do advanced molecular tools tell us about the ecology of interactions? -- Challenges in assessing links between root exudates and the structure and function of soil microbial communities -- Root secretions: interrelating genes and molecules to microbial associations. Is it all that simple? -- The use of stable isotope labelling and compound-specific analysis of microbial phospholipid fatty acids to quantify the influences of rhizodeposition on microbial community structure and function -- Metarhizobium robertsii, a rhizosphere-competent insect pathogen that expresses a specific subset of genes in plant root exudate -- Shaping of microbial community structure and function in the rhizosphere by four diverse plant species -- Exploration of hitherto-uncultured bacteria from the rhizosphere -- The use of molecular methods to assess chemotactic-competent bacterial populations in the rhizosphere -- Assessment of rice root-associated bacteria -- Phylogenetic analysis of Azospirillum species isolated from the rhizosphere of field grown wheat based on genetic and phenotypic features -- Influence of intercropping and intercropping plus rhizobial inoculation on microbial activity and community composition in rhizosphere of alfalfa (Medicago sativa L.) and siberian wild rye (Elymus sibericus L.) -- Root exudates, crucial for molecular understanding of interactions in the rhizosphere -- Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits?

[Section 3 Plant Genetics and Rhizobacterial Communities] Arabidopsis thaliana as model in the study of root-inhabiting bacteria -- Genetic and developmental control of rhizosphere bacterial communities -- Arabidopsis thaliana: a useful but limited mosel to investigate stress impacts on rhizosphere community composition and function -- Medicago truncatula root proteomics.

[Section 4 Hormones and other Signals and Rhizomicrobes] Control of the cooperation between plant growth-promoting rhizobacteria and crops by rhizosphere signals -- Small molecules involved in transkingdom communication between plants and rhizobacteria -- Bacterial biosynthesis of indole-acetic acid: Signal messenger service -- Fixing and non-fixing Rhizobia affect Arabidopsis root architecture by interfering with the auxin signalling pathway -- Terpene production by bacteria and its involvement in plant growth promotion, stress alleviation and yield increase -- Rapid identification of plant growth promoting rhizobacteria using an agar plate co-cultivation system with Arabidopsis -- Strigolactone biosynthesis and biology -- Chemistry of strigolactones: why and how do plants produce so many strigolactones? -- Strigolactones: crucial cues in the rhizosphere.

[Section 5 Endophytes] Bacterial endophytes: Who and where and what they are doing there -- Properties of bacterial endophytes leading to maximized host fitness -- DNA-Based stable isotope probing for identifying active bacterial endophytes in potato -- Visualization of niches of colonization of Firmicuyes with Bacillus spp in the rhizosphere, rhizoplane and endorhiza of grapevine plants at flowering stage of development by FISH microscopy -- The poplar endophyte Pseudomonas putida W619 as a key to a succesfull phytoremediation of volatile organic contaminants -- NifH gene expression and nitrogen fixation by diazotrophic endophytes in sugarcane and sweet potato -- Surveying diverse Zea seed for populations of bacterial endophytes.

[Section 6 Symbiotic Plant-Microbe Interactions] Molecular mechanisms governing arbuscular mycorrhiza development and function -- Diversity and evolution of nitrogen-fixing legume symbionts -- Lipochitooligosaccharide perception and the basis of partner recognition in root endosymbioses -- Rhizobial genetic repertoire to inhabit legume- and non-legume rhizospheres -- Who is controlling whom within the ectomycorrhizal symbiosis: Insights from genomic and functional analyses -- Role of carotenoid metabolism in the arbuscular mycorrhizal symbiosis -- Bacterial colonization of the arbuscular mycorrhizal.fungal hyposphere -- Role of Quorum Sensing in the Sinorhizobium meliloti-Alfalfa Symbiosis -- Roles for flavonoids in symbiotic root-rhizosphere interactions -- Exopolysaccharides and Nodule Invasion in the Sinorhizobium meliloti-Alfalfa Symbiosis.

[Section 7 PGPR, Biocontrol and Disease-Suppressive Bacteria] Plant growth promotion by microbes -- Microbial control of plant root diseases -- Biocontrol and Osmoprotection for Plants under Saline Conditions -- Genetics and evolution of 2,4 di acetylphloroglucinol synthesis in Pseudomonas fluorescence -- Suppression of crown gall disease by rhizosphere bacteria and Agrobacterium-specific bacteriophages -- Molecular-based strategies to exploit the inorganic phosphate solubilization ability of Pseudomonas in sustainable agriculture -- The biocontrol bacterium Pseudomonas fluoresens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots -- Marker-Assisted Selection of Novel Bacteria Contributing to Soilborne Plant Disease Suppression -- Combined effects of wheat roots and pathogenic fungus Gaeumannomyces graminis vartritici on Gene Expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp -- Biocontrol of Tree Root Diseases -- Plant growth modulation by bacterial volatiles: a focus on Burkholderia species -- Plant growth promoting microorganisms: The road from an academically promising result to a commercial product -- The effect of agricultural practices on resident soil microbial communities: Focus on biocontrol and biofertilization.

[Section 8 Biofilm Formation and Attachment to Roots] Biofilm Formation in the Rhizosphere: Multispecies Interactions and Implications for Plant Growth -- Probiotics for plants: Rhizospheric microbiome and plant fitness -- Motility, biofilm formation and rhizosphere colonization by Pseudomonas fluorescens F113 -- CMEIAS: An improved computing technology for quantitative image analysis of root colonization by rhizobacteria In Situ at single-cell resolution.

[Section 9 Quorum Sensing and Signalling] Understanding root-microbiome interactions -- An interkingdom signaling mechanism in rhizosphere Pseudomonas -- N-Acylhomoserine-lactone quorum-sensing signalling in phenazine and cyclic lipopeptide-producing Pseudomonas sp. CMR12 from the red cocoyam rhizosphere -- The response of plants towards N-acyl homoserine lactones of quorum sensing active bacteria in the rhizosphere -- In situ calling distances and high population independent N-acylhomoserine lactone- mediated communication on plant root surfaces -- Quorum-sensing quenching by volatile organic compounds emitted by rhizosphere bacteria -- The biological significance of the degradation of N-acylhomoserine lactones-Quorum sensing and quorum quenching in Burkholderia and Agrobacterium -- Altering Plant-Microbe Interactions Through Artificially Manipulating Bacterial Quorum Sensing -- Rhizosphere microbial communication in soil nutrient acquisition -- Agony to harmony - What decides? Calcium signalling in beneficial and pathogenic plant-microbe interactions: What we can learn from the Arabidopsis/Piriformospora indica symbiosis.

[Section 10 Genomic Sequencing and Screening of Genes/Promoters Activated in the Natural Environment] Genome transcriptome analysis and functional characterization of a nitrogen fixation island in root-associated Pseudomonas stutzeri -- Genome analysis, ecology and plant growth promotion of the endophyte Burkholderia phytofirmans strain PsJN -- Identification and mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in complex environments -- Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42 -- Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638.

[Section 11 Marker and Reporter Genes For Plant-Host Interaction Studies] Approaches for the design of genetically engineered bacteria for ecological studies and biotechnological applications -- Construction of signature-tagged mutant libraries and application to plant-symbiotic bacteria -- Use of DOPE-FISH tool to better visualize colonization of plants by beneficial bacteria? An example with Saccharothrix algeriensis NRRL B-24137 colonizing grapevine plants -- Combining rhizobox, reporter gene systems and molecular analysis to assess the effects of humic substances on plant-microbes interactions in soil rhizosphere -- Multi-parameter flow cytometry for characterization of physiological states in Pseudomonas fluorescens DR54 biocontrol inoculants under dry formulation and long-term storage in clay carrier -- Endophytic lifestyle of biocontrol strains of Pseudomonas spp. in olive roots.

[Section 12 Phytoremediation and heavy metal tolerance in the Rhizosphere] Improving phytoremediation through plant associated bacteria -- Ecology of alkane-degrading bacteria and their interaction with the plant -- Abiotic stress remediation by the arbuscular mycorrhizal symbiosis and rhizosphere bacteria / yeast interactions -- Potentially plant growth promoting and nitrogen fixing rhizobacteria associated with pioneer plants growing on mine tailings -- Stimulation of rhizosphere microbial communities during chemophytostabilization of a Pb-Zn mine soil -- Arbuscular mycorrhiza in glucosinolate-containing plants: The story of the metal hyperaccumulator Thlaspi praecox (Brassicaceae) -- Novel metal resistance genes from the rhizosphere of extreme environments: A functional metagenomics approach.

[Section 13 Climate Change Effects on Soil / Rhizosphere Microbial Communities] Soil warming effects on beneficial plant-microbe interactions -- Soil respiration, climate change and the role of microbial communities -- Rhizosphere responses to elevated atmospheric CO2 -- Applying stable isotope probing of phospholipid fatty acids and ribosomal RNA in rice fields to study the composition of the active methanotrophic bacterial communities in situ.

[Section 14 Metagenomics and the Soil / Rhizosphere] Impact of mangrove roots on bacterial composition -- Prediction of an ectomycorrhizal metabolome from transcriptomic data -- Metagenomic analysis on the rhizosphere soil microbial community -- Bacterial diversity in rhizosphere soil from antarctic vascular plants of Admiralty Bay, in maritime Antarctica -- Arbuscular mycorrhizal fungi throughout the year: Using massively parallel pyrosequencing to quantify spatio-temporal seasonal dynamics -- Transcriptomics and metatranscriptomic analysis of the response of rhizosphere bacteria to environmental change -- Unraveling the rhizosphere using the CPN60 genomic marker and pyrosequencing -- Rhizosphere metatranscriptomics: Challenges and opportunities.

[Section 15 Engineering the Rhizosphere : The "Biased Rhizosphere" Concept] The "Biased Rhizosphere" concept and advances in the Omics era to study bacterial competitiveness and persistence in the phytosphere -- Bacterial inositol and rhizopine catabolism - a sweet ride into the host -- Exogenous glucosinolate produced by transgenic Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots -- Reciprocal interactions between plants and fluorescent pseudomonads in relation to iron in the rhizosphere -- Enhancement of plant-microbe interactions using rhizosphere metabolomics driven approach and its application in the removal of polychlorinated biphenyls.

[Section 16 Concluding Chapters] Rhizophagy - a new dimension of plant-microbe interactions -- The Rhizosphere as a Reservoir for Opportunistic Human Pathogenic Bacteria -- Mechanisms of plant colonization by human pathogenic bacteria: an emphasis on the roots and rhizosphere -- Perspectives on the Molecular Microbial Ecology of the Rhizosphere.

229.72 (set of 2 vols.)