Microbial Environmental Genomics (MEG)

ISBN-13: 9781071628706 / Angielski / Twarda / 2022 / 365 str.

Francis Martin; Stephane Uroz

Opis

This volume guides researchers on how to characterize, image rare, and  hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment.Chapters cover different organism types (i.e., archaea, bacteria, fungi, protest, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize of new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.

Spis treści

1. Metabarcoding Approaches For Soil Eukaryotes, Protists and Microfauna

Guillaume Lentendu, Enrique Lara,  and Stefan Geisen

 

2. Metabarcoding of the three domains of life in aquatic saline ecosystems

Delphine Melayah, Zélia Bontemps, Maxime Bruto, Agnès Nguyen, Philippe Oger, and Mylène Hugoni

 

3. Sample preparation for fungal community analysis by high-throughput sequencing of barcode amplicons

Karina E Clemmensen, Katarina Ihrmark, Mikael Brandström Durling, and Björn D Lindahl

 

4. Characterization of seed mycobiota using culture-dependent and -independent approaches

Gillian E. Bergmann, Sabrina J. Heitmann, Posy E. Busby, and Johan H.J. Leveau

 

5. Tissue Cultivation, Preparation, and Extraction of High Molecular Weight DNA for Single-Molecule Genome Sequencing of Plant-Associated Fungi

Laure Fauchery, Maxim Koriabine, Lillian P. Moore, Yuko Yoshinaga, Kerrie Barry, Annegret Kohler, and Jana M. U'Ren

 

6. Analysis of ancient microbial DNA

Olivier Gorgé, E. Andrew Bennett, Diyendo Massilani, Julien Daligault, Eva-Maria Geigl, and Thierry Grange

 

7. Whole Genome Sequencing of bacterial endophytes from fresh and preserved plant specimens.

Bram Danneels and Aurélien Carlier

 

8. Investigating the bacterial and fungal communities involved in dead biomass degradation in forest soils

Martina Štursová, Ruben López-Mondéjar, and Petr Baldrian

 

9. Stable isotope probing-RNA strategy to study plant/fungus interactions

Amandine Lê Van, Marie Duhamel, Achim Quaiser, and Philippe Vandenkoornhuyse

 

10. Targeted 16S rRNA Gene Capture by Hybridization and Bioinformatic Analysis

 Sophie Comtet-Marre, Oshma Chakoory, and Pierre Peyret

 

11. Construction of a transposon mutant library in the pathogen Agrobacterium tumefaciens C58 and identification of genes involved in gall niche exploitation and colonization

Marta Torres, Almudena Gonzalez-Mula, Delphine Naquin, and Denis Faure

 

12. High-throughput screening of fosmid libraries for increased identification of novel N-acyl homoserine lactone degrading enzymes

Stephane Uroz and Philippe Oger

 

13. Analyzing prokaryotic transcriptomics in the light of genome data with the MicroScope platform.

David Roche, Alexandra Calteau, and David Vallenet

 

14. MycoCosm, the JGI’s Fungal Genome Portal for Comparative Genomic and Multiomics Data Analyses

Steven R. Ahrendt, Stephen J. Mondo, Sajeet Haridas, and Igor V. Grigoriev

 

15. Investigating endobacteria that thrive within Mucoromycota

Alessandro Desirò, Yusuke Takashima, Gregory Bonito, Tomoyasu Nishizawa, Kazuhiko Narisawa, and Paola Bonfante

 

16. Confocal laser scanning microscopy approach to investigate plant-fungal interactions

F. Fracchia, V. Basso, F. Guinet, C. Veneault-Fourrey, and A. Deveau

 

17. Visualisation of fungi during wood colonisation and decomposition by microscopy: from light to electron microscopy

Arnaud Besserer, Christophe Rose, and Aurélie Deveau

Blurb

This volume guides researchers on how to characterize, image rare, and  hitherto unknown taxa and their interactions, to identify new functions and biomolecules and to understand how environmental changes condition the activity and the response of the organisms living with us and in our environment.

Chapters cover different organism types (i.e., archaea, bacteria, fungi, protist, microfauna and microeukaryotes) and propose detailed protocols to produce high quality DNA, to analyse active microbial communities directly involved in complex interactions or processes through stable isotope probing, to identify and characterize new functional genes, to image in situ interactions and to apply bioinformatics analysis tools to complex metagenomic or RNAseq sequence data. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Microbial Environmental Genomics (MEG): Methods and Protocols, Second Edition aims to serve as a primary research reference for researchers in microbiology working to in the expanding field of molecular ecology and environmental genomics.