Omics in Soil Science.

Intro -- Contributors -- Contents -- Preface -- 1: Soil as a Biological System -- Introduction -- Main characteristics of soil as a biological system -- Soil biota and their functions in soil -- Microbial diversity, soil functions and the holistic approach -- The omics approaches in soil -- 2: Functional Genomics Analysis of Key Bacterial Traits Involved in Rhizosphere Competence -- Introduction -- Bacterial species specifically selected by the rhizosphere -- Bacterial functions enriched in the rhizosphere -- Motility and chemotaxis: early phase traits required for rhizocompetence -- Microbial growth in the rhizosphere: the contribution and relevance of central metabolism -- Denitrification: a promising model linking microbial metabolic flexibility and community structure -- Surviving in the rhizosphere: the relevance of stress and detoxification traits -- Secretion systems: important functional traits involved in rhizosphere competence -- Secondary metabolism: specialized functions involved in competitive rhizosphere fitness -- Conclusions and future directions -- 3: Soil Metagenomics - Potential Applications and Methodological Problems -- Introduction -- Metagenomics for fostering our understanding of soil habitats -- A case study - the metagenomics assessment of the chitinolytic process in soil -- Metagenomics for bioexploration -- The search for novel chitin-degrading enzymes - a case study -- Outlook -- 4: Screening Phylogenetic and Functional Marker Genes in Soil Microbial Ecology -- Introduction -- Marker genes as biomarkers -- Phylogenetic and functional marker genes -- Methodologies for marker gene screening in soil samples -- Primer and probe designing (non-protein-coding sequences and protein-coding sequences) strategies.

Experimental design for screening of the bacterial 16S rDNA marker gene with short read producing high-throughput sequencing technologies -- Concluding remarks and potentials -- 5: Soil Metatranscriptomics -- Introduction -- The experimental and bioinformatic workflow -- Recent achievements in metatranscriptomics -- Conclusions and outlook -- 6: Soil Proteomics -- Introduction -- Soil proteomics -- Specificity of soil proteomics -- Conclusions -- 7: Soil Volatile Organic Compounds as Tracers for Microbial Activities in Soils -- Introduction -- Soil smells? -- Volatiles produced by microorganisms -- Volatiles from plant roots -- Microbial volatiles affecting plant growth -- Degradation of VOCs -- Retention, emission and measurement -- Methods of VOC measurement -- Microbial mass products -- Conclusions -- 8: Proteogenomics: A New Integrative Approach for a Better Description of Protein Diversity -- Introduction -- The current proteomic tools and approaches -- Genome annotation of soil microflora gains in number but not in quality -- Proteogenomics, mapping proteome data onto genome sequence -- N-terminomics, new tools for an avalanche of results. -- Contribution of proteogenomics to a better assessment of soil microflora -- Concluding remarks -- 9: Analysis of Soil Metagenomes using the MEtaGenome ANalyser (MEGAN) -- Introduction -- Taxonomic analysis -- Functional analysis -- Sequence alignment -- Comparison of datasets -- Conclusion -- 10: Classical Techniques Versus Omics Approaches -- Introduction -- The promises of omics methods -- The pitfalls of omics methods -- Research that is best suited for omics approaches -- Index.

This volume presents the state-of-the-art of omic applications in soil science, a field that is advancing rapidly on many fronts. Distinguished authors describe the application of metagenomics, metatranscriptomics and proteomics to soil science. In particular the book covers the current and emerging omics techniques and the contribution of these approaches to a better assessment of soil functionality. The authors also explore the specific problems encountered in the application of various omics technologies to soil science and the future research requirements necessary to overcome the current limitations in this area. Topics covered include soil functional genomics, soil metagenomics, soil microbial ecology, soil metatranscriptomics, soil proteomics, soil volatilomics and soil proteogenomics. Omics techniques are also discussed in comparison with classical techniques. This book is both a practical guide and a recommended reference volume for all soil scientists.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.