Metagenomics of the Microbial Nitrogen Cycle : Theory, Methods and Applications.

Intro -- Contents -- Contributors -- Preface -- Foreword -- 1: Functional Assignment of Metagenomic Data: Insights for the Microbial Nitrogen Cycle -- Introduction -- Microbial nitrogen cycle -- Exploring the nitrogen cycle using genomic and metagenomic techniques -- Terrestrial nitrogen cycle -- Aquatic nitrogen cycle -- Future scope -- 2: Microbial Metagenomics of Oxygen Minimum Zones -- Introduction -- Metagenomic insights into OMZ metabolism -- Drivers of community structure -- Challenges -- 3: Interactions between Methane and Nitrogen Cycling: Current Metagenomic Studies and Future Trends -- Introduction -- Interactions between methane and nitrogen cycling -- Current metagenomic studies -- Future perspective -- 4: Quantification of Functional Microbial Nitrogen Cycle Genes in Environmental Samples -- Introduction -- N cycle -- Analysis of N cycle-related functional communities -- cPCR and qPCR -- Quantification of functional genes using qPCR -- 5: Stable Isotope Probing the Nitrogen Cycle: Current Applications and Future Directions -- Introduction -- Nitrogen uptake is limited in many environments -- The utility of molecular approaches -- DNA stable isotope probing -- 15N-DNA stable isotope probing -- Nitrogen fixation -- Biodegradation and bioremediation -- Inorganic N cycling -- Organic nitrogen -- The way forward -- Metagenomics -- Combining 15N-SIP, metagenomic sequencing and flow cytometry -- Protein stable isotope probing -- Chip stable isotope probing -- Conclusions -- 6: Application of Metaproteomics to the Exploration of Microbial N-cycling Communities -- Introduction -- Metaproteomics and the nitrogen cycle -- Protein-SIP and the nitrogen cycle -- Proteomics of microbial isolates relevant to the nitrogen cycle -- Conclusions -- Future trends.

7: Functional Molecular Analysis of Microbial Nitrogen Cycle by Microarray-based GeoChip: Insights for Climate Change, Agriculture and Other Ecological Studies -- Introduction -- Microarray technology and functional gene array -- GeoChip technology -- GeoChip application in investigating N functional genes -- Challenges for GeoChip technology and future directions -- 8: Functional and Taxonomic Diversity of the Nitrogen Cycling Guild in the Sargasso Sea Metagenomes -- Introduction -- Taxonomic diversity of the Sargasso Sea microbial communities -- Functional diversity of the N-cycling guild in the Sargasso Sea -- Discussion -- Exclusion by filtering -- A cautionary tale on ignoring the masses -- Future trends -- 9: Microbial Nitrogen Cycle: Determination of Microbial Functional Activities and Related N-compounds in Environmental Samples -- Introduction -- Microbial functional activities of the N-cycle -- Determination of some N-compounds relative to the N-cycle -- 10: Functional Metagenomics of the Nitrogen Cycle in Freshwater Lakes with Focus on Methylotrophic Bacteria -- Introduction -- Functional metagenomics uncover the dominant methylotrophs, Methylobacter and Methylotenera, and identify nitrogen metabolism strategies -- Nitrate supplement causes specific responses by the Methylophilaceae ecotypes -- Functional metagenomics focused on methane metabolism highlights effect of nitrate and suggest cooperative behaviour -- Discussion -- Future directions -- 11: The Fungal Contribution to the Nitrogen Cycle in Agricultural Soils -- Introduction -- Phylogenetic considerations on fungal assimilatory nitrate reductase -- Survey of gene pools and expression levels of fungal assimilatory nitrate reductase in agricultural soils -- Fungal euknr in public databases -- Concluding remarks -- Future directions.

12: Biofilms in Nitrogen Removal: Population Dynamics and Spatial Distribution of Nitrifying- and Anammox Bacteria -- Introduction -- Diversity and ecology of nitrifying and anammox bacteria -- Life and death in nitrifying and anammox biofilms -- Methods for studying microbial diversity -- Investigations of nitrifying biofilms - a case study -- Topic Index -- Taxonomic Index.

Written by renowned researchers specialised in the most relevant and emerging topics in the field, this book provides comprehensive information on the new theoretical, methodological and applied aspects of metagenomics and other 'omics' approaches used to study the microbial N cycle. Recommended for microbiologists, environmental scientists and anyone interested in microbial communities, metagenomics, metatranscriptomics and metaproteomics of the microbial N cycle. This volume provides a thorough account of the contributions of metagenomics to microbial N cycle background theory, reviews state-of-the-art investigative methods and explores new applications in water treatment, agricultural practices and climate change, among others.

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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.