Metagenomics for the study of soil microbial communities

Molecular Approaches to Soil, Rhizosphere and Plant Microorganism Analysis

Volumn , Issue , 2006, Pages 42-54

  Steele, Helen L ^a   Streit, Wolfgang R ^a  

^a UNIVERSITY OF DUISBURG ESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84885138960     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (89)

1. Acosta-Martínez, V. and Tabatabai, M.A. (2000) Arylamidase activity of soils. Soil Science Society of America Journal 64, 215-221.
2. Allen, E.E. and Banfield, J.F. (2005) Community genomics in microbial ecology and evolution. Nature Reviews Microbiology 3, 489-498.
3. Anderson, I.C. and Cairney, J.W.G. (2004) Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environmental Microbiology 6, 769-779.
4. Béjà, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., Jovanovich, S.B., Spudich, E.N. and DeLong, E.F. (2000) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289, 1902-1905.
5. Bertrand, H., Poly, F., Van, T.V., Lombard, N., Nalin, R., Vogel, T.M. and Simonet, P. (2005) High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction. Journal of Microbiological Methods 62, 1-11.
6. Brady, S.F. and Clardy, J. (2004) Palmitoylputrescine, an antibiotic isolated from the heterologous expression of DNA extracted from Bromeliad Tank water. Journal of Natural Products 67, 1283-1286.
7. Brady, S.F., Chao, C.J. and Clardy, J. (2004) Long-chain N-acyltyrosine synthases from environmental DNA. Applied and Environmental Microbiology 70, 6865-6870.
8. Brooksbank, C., Cameron, G. and Thornton, J. (2005) The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Research 33, D46-D53.
9. Courtois, S., Frostegård, Å., Göransson, P., Depret, G., Jeannin, P. and Simonet, P. (2001) Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environmental Microbiology 3, 431-439.
10. Courtois, S., Cappellano, C.M., Ball, M., Francou, F.-X., Normand, P., Helynck, G., Martinez, A., Kolvek, S.J., Hopke, J., Osburne, M.S., August, P.R., Nalin, R., Guérineau, M., Jeannin, P., Simonet, P. and Pernodet, J.-L. (2003) Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Applied and Environmental Microbiology 69, 49-55.
11. Curtis, T.P. and Sloan, W.T. (2004) Prokaryotic diversity and its limits: microbial community structure in nature and implications for microbial ecology. Current Opinion in Microbiology 7, 221-226.
12. Curtis, T.P. and Sloan, W.T. (2005) Exploring microbial diversity - a vast below. Science 309, 1331-1333.
13. Daniel, R. (2005) The metagenomics of soil. Nature Reviews Microbiology 3, 470-478.
14. DeSantis, G., Zhu, Z., Greenberg, W.A., Wong, K., Chaplin, J., Hanson, S.R., Farwell, B., Nicholson, L.W., Rand, C.L., Weiner, D.P., Robertson, D.E. and Burk, M.J. (2002) An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives. Journal of the American Chemical Society 124, 9024-9025.
15. Díaz, D. (2004) Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility. International Microbiology 7, 173-180.
16. Diaz-Torres, M.L., McNab, R., Spratt, D.A., Villedieu, A., Hunt, N., Wilson, M. and Mullany, P. (2003) Novel tetracycline resistance determinant from the oral metagenome. Antimicrobial Agents and Chemotherapy 47, 1430-1432.
17. Dumont, M.G. and Murrell, J.C. (2005) Stable isotope probing - linking microbial identity to function. Nature Reviews Microbiology 3, 499-504.
18. Edwards, R.A. and Rohwer, F. (2005) Viral metagenomics. Nature Reviews Microbiology 3, 504-509.
19. Elend, C., Schmeisser, C., Leggewie, C., Babiak., P., Carbealleira, J.D., Steele, H.L., Reymond, J.-L., Jaeger, K.-E. and Streit, W.R. (2006) Isolation and biochemical characterization of two novel metagenome derived esterases. Applied and Environmental Microbiology, 72, 3637-3645.
20. Entcheva, P., Liebl, W., Johann, A., Hartsch, T. and Streit, W.R. (2001) Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Applied and Environmental Microbiology 67, 89-99.
21. Erwin, D.P., Erickson, I.K., Delwiche, M.E., Colwell, F.S., Strap, J.L. and Crawford, R.L. (2005) Diversity of oxygenase genes from methane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain aquifer. Applied and Environmental Microbiology 71, 2016-2025.
22. Eschenfeldt, W.H., Stols, H., Rosenbaum, H., Khambatta, Z.S., Quaite-Randall, E., Wu, S., Kilgore, D.C., Trent, J.D. and Donnelly, M.I. (2001) DNA from uncultured organisms as a source of 2,5-diketo- D-gluconic acid reductases. Applied and Environmental Microbiology 67, 4206-4214.
23. Eyers, L., George, I., Schuler, L., Stenuit, B., Agathos, S.N. and Fantroussi, S.E. (2004) Environmental genomics: exploring the unmined richness of microbes to degrade xenobiotics. Applied Microbiology and Biotechnology 66, 123-130.
24. Fadiel, A., Lithwick, S. and Naftolin, F. (2005) The influence of environmental adaptation on bacterial genome structure. Letters in Applied Microbiology 40, 12-18.
25. Frostegård, Å., Courtois, S., Ramisse, V., Clerc, S., Bernillon, D., Le Gall, F., Jeannin, P., Nesme, X. and Simonet, P. (1999) Quantification of bias related to the extraction of DNA directly from soils. Applied and Environmental Microbiology 65, 5409-5420.
26. Gabor, E.M., Alkema, W.B.L. and Janssen, D.B. (2004a) Quantifying the accessibility of the metagenome by random expression cloning techniques. Environmental Microbiology 6, 879-886.
27. Gabor, E.M., de Vries, E.J. and Janssen, D.B. (2004b) Construction, characterisation, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environmental Microbiology 6, 948-958.
28. Gans, J., Wolinsky, M. and Dunbar, J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309, 1387-1390.
29. Gillespie, D.E., Brady, S.F., Bettermann, A.D., Cianciotto, N.P., Liles, M.R., Rondon, M.R., Clardy, J., Goodman, R.M. and Handelsman, J. (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Applied and Environmental Microbiology 68, 4301-4306.
30. Ginolhac, A., Jarrin, C., Gillet, B., Robe, P., Pujic, P., Tuphile, K., Bertrand, H., Vogel, T.M., Perrière, G., Simonet, P. and Nalin, R. (2004) Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Applied and Environmental Microbiology 70, 5522-5527.
31. Gupta, R., Berg, Q.K. and Lorenz, P. (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Applied Microbiology and Biotechnology 59, 15-32.
32. Hahn, M.W. and Pöckl, M. (2005) Ecotypes of planktonic actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical and tropical freshwater habitats. Applied and Environmental Microbiology 71, 766-773.
33. Handelsman, J. (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68, 669-685.
34. Handelsman, J., Rondon, M.R., Brady, S.F., Clardy, J. and Goodman, R.M. (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry and Biology 5, R245-R249.
35. Healy, F.G., Ry, R.M., Aldrich, H.C., Wilkie, A.C., Ingram, L.O. and Shanmugam, K.T. (1995) Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose. Applied Microbiology and Biotechnology 34, 667-674.
36. Henne, A., Daniel, R., Schmitz, R.A. and Gottschalk, G. (1999) Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Applied and Environmental Microbiology 56, 3901-3907.
37. Henne, A., Schmitz, R.A., Bömeke, M., Gottschalk, G. and Daniel, R. (2000) Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Applied and Environmental Microbiology 66, 3113-3116.
38. Hernandez, M.E., Kappler, A. and Newman, D.K. (2004) Phenazines and other redox-active antibiotics promote microbial mineral reduction. Applied and Environmental Microbiology 70, 921-928.
39. Inoue, K., Makino, Y. and Itoh, N. (2005) Purification and characterization of a novel alcohol dehydrogenase from Leifsonia sp. strain S749: a promising biocatalyst for an asymmetric hydrogen transfer bioreduction. Applied and Environmental Microbiology 71, 3633-3641.
40. Jaspers, E. and Overmann, J. (2004) Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Applied and Environmental Microbiology 70, 4831-4839.
41. Kauffmann, I.M., Schmitt, J. and Schmid, R.D. (2004) DNA isolation from soil samples for cloning in different hosts. Applied Microbiology and Biotechnology 64, 665-670.
42. Knietsch, A., Bowein, S., Whited, G., Gottschalk, G. and Daniel, R. (2003a) Identification and characterisation of coenzyme B12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic libraries derived from enrichment cultures. Applied and Environmental Microbiology 69, 3048-3060.
43. Knietsch, A., Waschkowitz, T., Bowein, S., Henne, A. and Daniel, R. (2003b) Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Applied and Environmental Microbiology 69, 1408-1416.
44. Krsek, M. and Wellington, E.M.H. (1999) Comparison of different methods for the isolation and purification of total community DNA from soil. Journal of Microbiological Methods 39, 1-16.
45. Lee, S.-W., Won, K., Lim, H.K., Kim, J.-C., Choi, G.J. and Cho, K.Y. (2004) Screening for novel lipolytic enzymes from uncultured soil microorganisms. Applied Microbiology and Biotechnology 65, 720-726.
46. Leveau, J.H.J., Gerards, S., de Boer, W. and van Veen, J.A. (2004) Phylogeny-function analysis of (meta)genomic libraries: screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridisation (LIL-FISH). Environmental Microbiology 6, 990-998.
47. Liebeton, K. and Eck, J. (2004) Identification and expression in E. coli of novel nitrile hydratases from the metagenome. Engineering and Life Sciences 4, 557-562.
48. Lorenz, P. and Schleper, C. (2002) Metagenome - a challenging source of enzyme discovery. Journal of Molecular Catalysis B: Enzymatic 19-20, 13-19.
49. MacNeil, I.A., Tiong, C.L., Minor, C., August, P.R., Grossman, T.H., Loiacono, K.A., Lynch, B.A., Phillips, T., Narula, S., Sundaramoorthi, R., Tyler, A., Aldredge, T., Long, H., Gilman, M., Holt, D. and Osburne, M.S. (2001) Expression and isolation of antimicrobial small molecules from soil DNA libraries. Journal of Molecular Microbiology and Biotechnology 3, 301-308.
50. Marchesi, J.R. and Weightman, A.J. (2003) Comparing the dehalogenase gene pool in cultivated alpha-halocarboxylic acid-degrading bacteria with the environmental metagene pool. Applied and Environmental Microbiology 69, 4375-4382.
51. Martinez, A., Kolvek, S.J., Yip, C.L.T., Hopke, J., Brown, K.A., MacNeil, I.A. and Osburne, M.S. (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Applied and Environmental Microbiology 70, 2452-2463.
52. Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R. and Pühler, A. (2003) GenDB - an open source genome annotation system for prokaryotic genomes. Nucleic Acids Research 31, 2187-2195.
53. Miller, D.N., Bryant, J.E., Madsen, E.L. and Ghiorse, W.C. (1999) Evaluation and optimisation of DNA extraction and purification procedures for soil and sediment samples. Applied and Environmental Microbiology 65, 4715-4724.
54. Moreira, D., Rodríguez-Valera, F. and López-García, P. (2004) Analysis of a genome fragment of a deep-sea uncultivated group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes. Environmental Microbiology 6, 959-969.
55. Nannipieri, P., Ascher, J., Ceccherini, M.T., Landi, L., Pietramellara, G. and Renella, G. (2003) Microbial diversity and soil functions. European Journal of Soil Science 54, 655-670.
56. Nercessian, O., Bienvenu, N., Moreira, D., Prieur, D. and Jeanthon, C. (2005) Diversity of functional genes of methanogens, methanotrophs and sulfate reducers in deep-sea hydrothermal environments. Environmental Microbiology 7, 118-132.
57. Niemeyer, J. and Gessler, F. (2002) Determination of free DNA in soils. Journal of Plant Nutrition and Soil Science 165, 121-124.
58. Pettit, R.K. (2004) Soil DNA libraries for anticancer drug discovery. Cancer Chemotherapy and Pharmacology 54, 1-6.
59. Quaiser, A., Ochsenreiter, T., Klenk, H.-P., Kletzin, A., Treusch, A.H., Meurer, G., Eck, J., Sensen, C.W. and Schleper, C. (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environmental Microbiology 4, 603-611.
60. Quaiser, A., Ochsenreiter, T., Lanz, C., Schuster, C., Treusch, A.H., Eck, J. and Schleper, C. (2003) Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology 50, 563-575.
61. Raaijmakers, J.M., Weller, D.M. and Thomashow, L.S. (1997) Frequency of antibiotic-producing Pseudomonas spp. in natural environments. Applied and Environmental Microbiology 63, 881-887.
62. Rhee, J.-K., Ahn, D.-G., Kim, Y.-G. and Oh, J.-W. (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Applied and Environmental Microbiology 71, 817-825.
63. Richardson, T.H., Tan, X., Frey, G., Callen, W., Cabell, M., Lam, D., Macomber, J., Short, J.M., Robertson, D.E. and Miller, C. (2002) A novel, high performance enzyme for starch liquification. Journal of Biological Chemistry 277, 26501-26507.
64. Riesenfeld, C.S., Goodman, R.M. and Handelsman, J. (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology 6, 981-989.
65. Rodríguez-Valera, F. (2002) Approaches to prokaryotic biodiversity: a population genetics perspective. Environmental Microbiology 4, 628-633.
66. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., Loiacono, K.A., Lynch, B.A., MacNeil, I.A., Minor, C., Tiong, C.L., Gilman, M., Osburne, M.S., Clardy, J., Handelsman, J. and Goodman, R.M. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and Environmental Microbiology 66, 2541-2547.
67. Sabehi, G., Loy, A., Jung, K.-H., Partha, R., Spudlich, J.L., Isaacson, T., Hirschberg, J., Wagner, W. and Béjà, O. (2005) New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLOS Biology 3, 1-9.
68. Schloss, P.D. and Handelsman, J. (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 71, 1501-1506.
69. Schloss, P.D., Larget, B.R. and Handelsman, J. (2004) Integration of microbial ecology and statistics: a test to compare gene libraries. Applied and Environmental Microbiology 70, 5485-5492.
70. Sebat, J.L., Colwell, F.S. and Crawford, R.L. (2003) Metagenomic profiling: microarray analysis of an environmental genomic library. Applied and Environmental Microbiology 69, 4927-4934.
71. Shaw, L.J. and Burns, R.G. (2005) Rhizodeposition and the enhanced mineralization of 2,4-dichlorophenoxyacetic acid in soil from the Trifolium pratense rhizosphere. Environmental Microbiology 7, 191-202.
72. Shen, B., Du, L., Sanchez, C., Edwards, D.J., Chen, M. and Murrell, J.M. (2002) Cloning and characterization of the bleomycin biosynthetic gene cluster from Streptomyces verticillus ATCC15003. Journal of Natural Products 65, 422-431.
73. Skoko, N., Vujovic, J., Savic, M., Papic, N., Vasiljevic, B. and Ljubijankic, G. (2005) Construction of Saccharomyces cerevisiae strain FAV20 useful in detection of immunosuppressants produced by soil actinomycetes. Journal of Microbiological Methods 61, 137-140.
74. Steele, H.L. and Streit, W.R. (2005) Metagenomics: advances in ecology and biotechnology. FEMS Microbiology Letters 247, 105-111.
75. Stein, J.L., Marsh, T.L., Wu, K.Y., Shizuya, H. and DeLong, E. (1996) Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. Journal of Bacteriology 178, 591-599.
76. Streit, W.R. and Schmitz, R.A. (2004) Metagenomics: the key to the uncultured microbes. Current Opinion in Microbiology 7, 492-498.
77. Streit, W.R., Daniel, R. and Jaeger, K.-E. (2004) Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Current Opinion in Biotechnology 15, 285-290.
78. Torsvik, V. and Oøvreås, L. (2002) Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology 5, 240-245.
79. Treusch, A.H., Kletzin, A., Raddatz, G., Ochsenreiter, T., Quaiser, A., Meurer, G., Schuster, S.C. and Schleper, C. (2004) Characterisation of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environmental Microbiology 6, 970-980.
80. Tringe, S.G., von Mering, C., Kobayashi, A., Salamov, A.A., Chen, K., Chang, H.W., Podar, M., Short, J.M., Mathur, E.J., Detter, J.C., Bork, P., Hugenholtz, P. and Rubin, E.M. (2005) Comparative metagenomics of microbial communities. Science 308, 554-557.
81. Tyson, G.W., Chapman, J., Hugenholtz, P., Allen, E.E., Ram, R.J., Richardson, P.M., Solovyev, V.V., Rubin, E.M., Rokhsar, D.S. and Banfield, J.F. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37-43.
82. Uchiyama, T., Abe, T., Ikemura, T. and Watanabe, K. (2005) Substrate-induced gene-expression screening of environmental metagenomic libraries for isolation of catabolic genes. Nature Biotechnology 23, 88-93.
83. Ullrich, R., Nüske, J., Scheibner, K., Spantzel, J. and Hofrichter, M. (2004) Novel haloperoxidase from the agaric basidiomycete Agrocybe aegerita oxidizes aryl alcohols and aldehydes. Applied and Environmental Microbiology 70, 4575-4581.
84. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., Fouts, D.E., Levy, S., Knap, A.H., Lomas, M.W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.-H. and Smith, H.O. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74.
85. Voget, S., Leggewie, C., Usebeck, A., Raasch, C., Jaeger, K.-E. and Streit, W.R. (2003) Prospecting for novel biocatalysts in the soil metagenome. Applied and Environmental Microbiology 69, 6235-6242.
86. Wallner, G., Fuchs, B., Spring, S., Beisker, W. and Amann, R. (1997) Flow sorting of microorganisms for molecular analysis. Applied and Environmental Microbiology 63, 4223-4231.
87. Wang, G.-Y.-S., Graziani, E., Waters, B., Pan, W., Li, X., McDermott, J., Meurer, G., Saxena, G., Andersen, R.J. and Davies, J. (2000) Novel natural products from soil DNA libraries in a streptomycete host. Organic Letters 2, 2401-2404.
88. Yun, J., Kang, S., Park, S., Yoon, H., Kim, M.-J., Heu, S. and Ryu, S. (2004) Characterisation of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Applied and Environmental Microbiology 70, 7229-7235.
89. Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E.J., Short, J.M. and Keller, M. (2002) Cultivating the uncultured. Proceedings of the National Academy of Sciences of the USA 99, 15681-15686.