Preparation of high-molecular weight dna and metagenomic libraries from soils and hot springs

Methods in Enzymology

Volumn 496, Issue , 2011, Pages 319-344

  Reigstad, Laila J ^a   Bartossek, Rita ^a   Schleper, Christa ^a,b  

^a UNIVERSITY OF BERGEN   (Norway)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

Ammonia oxidizing archaea; Fosmid; Hot springs; Metagenomic library; Pulsed field gel electrophoresis; Soil

Indexed keywords

AGAROSE; BACTERIAL DNA; DNA; GENOMIC DNA;

ACIDITY; AGAR GEL ELECTROPHORESIS; ARTICLE; BACTERIOPHAGE LAMBDA; BIOFILM; CELL ISOLATION; DNA ISOLATION; DNA LIBRARY; DNA PURIFICATION; DNA VECTOR; ELUTION; ESCHERICHIA COLI; FOSMID; FOSMID LIBRARY; GENE LIBRARY; GENETIC SCREENING; HABITAT; HIGH THROUGHPUT SCREENING; HOST CELL; METAGENOMICS; MOLECULAR CLONING; MOLECULAR WEIGHT; NONHUMAN; PLASMID; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; QUALITY CONTROL; SOIL; THERMAL SPRING;

EID: 79955503452     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-386489-5.00013-0     Document Type: Chapter

References (35)

1. R. Bartossek, G.W. Nicol, A. Lanzen, H.P. Klenk, and C. Schleper Homologues of nitrite reductases in ammonia-oxidizing archaea: Diversity and genomic context Environ. Microbiol. 12 2010 1075 1088
2. O. Beja, L. Aravind, and E.V. Koonin Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea Science 289 2000 1902 1906
3. O. Beja, M.T. Suzuki, and E.V. Koonin Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage Environ. Microbiol. 2 2000 516 529 (Pubitemid 33136690)
4. J. Collins, and B. Hohn Cosmids: A type of plasmid gene-cloning vector that is packageable in vitro in bacteriophage lambda heads Proc. Natl. Acad. Sci. USA 75 9 1978 4242 4246 (Pubitemid 9025986)
5. E.F. DeLong Microbial community genomics in the ocean Nat. Rev. Microbiol. 3 6 2005 459 469
6. J. Gans, M. Wolinsky, and J. Dunbar Computational improvements reveal great bacterial diversity and high metal toxicity in soil Science 309 2005 1387 1390 (Pubitemid 41209368)
7. S.J. Hallam, K.T. Konstantinidis, and N. Putnam Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum Proc. Natl. Acad. Sci. USA 103 2006 18296 18301 (Pubitemid 44871652)
8. J. Handelsman Metagenomics: Application of genomics to uncultured microorganisms Microbiol. Mol. Biol. Rev. 68 2004 669 685 (Pubitemid 39628532)
9. J. Herschleb, G. Ananiev, and D.C. Schwartz Pulsed-field gel electrophoresis Nat. Protoc. 2 2007 677 684 (Pubitemid 47040029)
10. K.S. Kakirde, L.C. Parsley, and M.R. Liles Size does matter: Application-driven approaches for soil metagenomics Soil Biol. Biochem. 42 11 2010 1911 1923
11. U.J. Kim, H. Shizuya, P.J. de Jong, B. Birren, and M.I. Simon Stable propagation of cosmid sized human DNA inserts in an F factor based vector Nucleic Acids Res. 20 5 1992 1083 1085
12. S. Lee, and S.J. Hallam Extraction of high molecular weight genomic DNA from soils and sediments J. Vis. Exp. 10 33 2009 10.3791/1569, pii: 1569
13. P. Lorenz, and J. Eck Metagenomics and industrial applications Nat. Rev. Microbiol. 3 6 2005 510 516 (Pubitemid 40716178)
14. A.B. Martin-Cuadrado, F. Rodriguez-Valera, and D. Moreira Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions ISME J. 2 2008 865 886
15. A.P. Monaco, and Z. Larin Construction of yeast artificial chromosome libraries by pulsed-field gel electrophoresis Trends Biotechnol. 12 7 1994 280 286
16. A. Quaiser, T. Ochsenreiter, and H.P. Klenk First insight into the genome of an uncultivated crenarchaeote from soil Environ. Microbiol. 4 2002 603 611 (Pubitemid 35211944)
17. L.J. Reigstad, A. Richter, H. Daims, T. Urich, L. Schwark, and C. Schleper Nitrification in terrestrial hot springs of Iceland and Kamchatka FEMS Microbiol. Ecol. 64 2008 167 174 (Pubitemid 351533426)
18. L.J. Reigstad, S.L. Jorgensen, and C. Schleper Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka ISME J. 4 2010 346 356
19. M.R. Rondon, P.R. August, and A.D. Bettermann Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl. Environ. Microbiol. 66 2000 2541 2547 (Pubitemid 30353963)
20. C. Schleper, E.F. DeLong, C.M. Preston, R.A. Feldman, K.Y. Wu, and R.V. Swanson Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum J. Bacteriol. 180 1998 5003 5009 (Pubitemid 28470924)
21. C. Schleper, G. Jurgens, and M. Jonuscheit Genomic studies of uncultivated archaea Nat. Rev. Microbiol. 3 6 2005 479 488 (Pubitemid 40716174)
22. H. Shizuya, and H. Kouros-Mehr The development and applications of the bacterial artificial chromosome cloning system Keio J. Med. 50 2001 26 30 (Pubitemid 33605901)
23. H. Shizuya, B. Birren, U.J. Kim, V. Mancino, T. Slepak, Y. Tachiiri, and M. Simon Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector Proc. Natl. Acad. Sci. USA 89 1992 8794 8797
24. J.L. Stein, T.L. Marsh, K.Y. Wu, H. Shizuya, and E.F. DeLong Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon J. Bacteriol. 178 1996 591 599 (Pubitemid 26036628)
25. M. Strous, E. Pelletier, S. Mangenot, T. Rattei, A. Lehner, M.W. Taylor, M. Horn, H. Daims, D. Bartol-Mavel, P. Wincker, V. Barbe, and N. Fonknechten Deciphering the evolution and metabolism of an anammox bacterium from a community genome Nature 440 7085 2006 790 794
26. M. Taupp, S. Lee, A. Hawley, J. Yang, and S.J. Hallam Large insert environmental genomic library production J. Vis. Exp. 23 31 2009 10.3791/1387, pii: 1387
27. V. Torsvik, L. Ovreas, and T.F. Thingstad Prokaryotic diversityMagnitude, dynamics, and controlling factors Science 296 2002 1064 1066 (Pubitemid 34517113)
28. A. Treusch, and C. Schleper Environmental genomics: A novel tool to study uncultivated microorganisms C.W. Sensen, Handbook of Genome Research 2005 Wiley-VCH, Verlag GmbH, Weinheim Germany
29. A. Treusch, and C. Schleper The microbial soil flora: Novel approaches for accessing the phylogenetic and physiological diversity of prokaryotes H. Konig, A. Varma, Intestinal Microorganisms of Termites and Other Soil Invertebrates 2006 Springer Verlag, Berlin, Heidelberg, Germany
30. A.H. Treusch, A. Kletzin, and G. Raddatz Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea Environ. Microbiol. 6 2004 970 980 (Pubitemid 39123251)
31. A.H. Treusch, S. Leininger, A. Kletzin, S.C. Schuster, H.P. Klenk, and C. Schleper Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling Environ. Microbiol. 7 2005 1985 1995 (Pubitemid 41752386)
32. T. Urich, A. Lanzen, J. Qi, D.H. Huson, C. Schleper, and S.C. Schuster Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome PLoS One 3 2008 e2527
33. J.C. Venter, K. Remington, and J.F. Heidelberg Environmental genome shotgun sequencing of the Sargasso Sea Science 304 2004 66 74 (Pubitemid 38451457)
34. S. Yooseph, G. Sutton, and D.B. Rusch The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families PLoS Biol. 5 2007 e16
35. J. Zhou, M.A. Bruns, and J.M. Tiedje DNA recovery from soils of diverse composition Appl. Environ. Microbiol. 62 1996 316 322 (Pubitemid 26047397)