Abstract
The construction of a complex genomic library is one of the comprehensive ways to study a complex bacterial community and to access the variety of metabolic pathways present in the rich soil environment. In this report, we developed a new protocol whereby we are able to retrieve nearly complete microbe genomic fragments from soil samples, which are employed to generate a metagenomic library for visualizing the basic scaffolding of the soil microbial community. The use of direct cell lysis within soil-embedded agarose plugs, along with a double-size selection, enabled us to successfully isolate pure and high-molecular weight DNA (0.1-1 Mb) without the need for any further purification. A metagenomic library containing 1.2 Gbp of DNA in total was constructed. Furthermore, analysis of the microbial community structure using 16S rDNA partial sequences found the dominant phylotypes to consist of alpha-Proteobacteria and Actinobacteria, which are similar to those seen in forest and agricultural soils, and numerous uncultured microbes from a wide variety of bacterial taxa as well. In conclusion, this study presents a novel protocol for generating a metagenomic library that carries much larger and diverse DNA fragments from soil bacter...Continue Reading
References
Jun 1, 1997·Genomics·R Zimmer, A M Verrinder Gibbins
Oct 10, 1997·Nucleic Acids Research·S J StrongC T Amemiya
Sep 19, 1998·Genomics·K OsoegawaP J de Jong
May 26, 1999·Proceedings of the National Academy of Sciences of the United States of America·M R RondonJ Handelsman
Jun 1, 2000·Applied and Environmental Microbiology·M R RondonR M Goodman
Oct 24, 2001·Journal of Bacteriology·A MajerníkR Daniel
Aug 22, 2002·Journal of the American Chemical Society·Sean F BradyJon Clardy
Oct 9, 2002·Environmental Microbiology·Achim QuaiserChrista Schleper
Jan 7, 2003·Applied and Environmental Microbiology·Sophie CourtoisJean-Luc Pernodet
Oct 9, 2003·Applied and Environmental Microbiology·S VogetW R Streit
Nov 18, 2003·Molecular Microbiology·Achim QuaiserChrista Schleper
Feb 13, 2004·Nature·Gene W TysonJillian F Banfield
Apr 7, 2004·Science·J Craig VenterHamilton O Smith
Apr 22, 2004·Nature Reviews. Microbiology·Ulrich DobrindtJörg Hacker
Aug 13, 2004·Environmental Microbiology·Hanno TeelingFrank Oliver Glöckner
Aug 13, 2004·Environmental Microbiology·Alexander H TreuschChrista Schleper
Aug 13, 2004·Environmental Microbiology·Christian S RiesenfeldJo Handelsman
Sep 9, 2004·Science·Steven J HallamEdward F DeLong
Apr 23, 2005·Science·Susannah Green TringeEdward M Rubin
Jun 3, 2005·Nature Reviews. Microbiology·Rolf Daniel
Aug 20, 2005·PLoS Computational Biology·Kevin Chen, Lior Pachter
Citations
Jun 1, 2008·Indian Journal of Microbiology·So-Youn Park, Geun-Joong Kim
May 19, 2009·Journal of Microbiological Methods·Miriam Martínez-CastroCarlos Barreiro
Sep 23, 2014·Chemistry & Biology·Aleksandr MilshteynSean F Brady