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  • Review Article
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The metagenomics of soil

Nature Reviews Microbiology volume 3, pages 470–478 (2005)Cite this article

Key Points

  • Soil is probably the most complex and heterogeneous microbial habitat on earth. The diversity of soil microbial communities exceeds that of other environments.

  • Soil metagenomics is a cultivation-independent molecular approach to explore and exploit the enormous diversity of soil microbial communities. This technology comprises isolation of soil DNA and production and screening of clone libraries.

  • The protocols for isolation of high-quality DNA from soil samples are based either on the recovery of cells and subsequent lysis, or on the direct lysis of cells in the sample followed by DNA purification.

  • Purified soil DNA is used to construct small-insert libraries in plasmid vectors or large-insert libraries in cosmid, fosmid or BAC (bacterial artificial chromosome) vectors. Small-insert libraries are useful to identify single genes or small operons that encode new metabolic functions, and large-insert libraries to recover complex pathways encoded by gene clusters and to characterize genomic fragments of uncultured soil microorganisms.

  • The screening strategies for metagenomic soil libraries are based either on activities of the library clones or on sequence similarities with known genes.

  • Screening of metagenomic soil libraries, especially by activity-based approaches, has led to the identification of various novel biomolecules, including enzymes and antibiotics of industrial importance. To increase gene detection frequencies, enrichment steps for soil microorganisms harbouring the desired traits can be used prior to library construction.

Abstract

Phylogenetic surveys of soil ecosystems have shown that the number of prokaryotic species found in a single sample exceeds that of known cultured prokaryotes. Soil metagenomics, which comprises isolation of soil DNA and the production and screening of clone libraries, can provide a cultivation-independent assessment of the largely untapped genetic reservoir of soil microbial communities. This approach has already led to the identification of novel biomolecules. However, owing to the complexity and heterogeneity of the biotic and abiotic components of soil ecosystems, the construction and screening of soil-based libraries is difficult and challenging. This review describes how to construct complex libraries from soil samples, and how to use these libraries to unravel functions of soil microbial communities.

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Figure 1: Essential steps to explore and exploit the genomic diversity of soil microbial communities by metagenomics.
Figure 2: Examples of activity-based screens.

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References

  1. Richter, D. D. & Markewitz, D. How deep is soil? Bioscience 45, 600–609 (1995).

    Article  Google Scholar 

  2. Paul, E. A. & Clark, F. E. Soil microbiology and biochemistry (Academic Press, San Diego, 1989).

    Book  Google Scholar 

  3. Torsvik, V., Daae, F. L., Sandaa, R. -A. & Øvreås, L. Microbial diversity and function in soil: from genes to ecosystems. Curr. Opin. Microbiol. 5, 240–245 (2002).

    Article  CAS  PubMed  Google Scholar 

  4. Torsvik, V., Daae, F. L., Sandaa, R.-A. & Øvreås, L. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotech. 64, 53–62 (1998).

    Article  CAS  Google Scholar 

  5. Torsvik, V., Sorheim, R. & Goksoyr, J. Total bacterial diversity in soil and sediment communities. J. Ind. Microbiol. 17, 170–178 (1996).

    CAS  Google Scholar 

  6. Doolittle, W. Phylogenic classification and the universal tree. Science 284, 2124–2128 (1999).

    Article  CAS  PubMed  Google Scholar 

  7. Hassink, J., Bouwman, L. A., Zwart, K. B. & Brussaard, L. Relationship between habitable pore space, soil biota, and mineralization rates in grassland soils. Soil. Biol. Biochem. 25, 47–55 (1993).

    Article  Google Scholar 

  8. Foster, R. C. Microenvironments of soil microorganisms. Biol. Fertil. Soils 6, 189–203 (1988).

    Article  Google Scholar 

  9. Kieft, T. L., Soroker, E. & Firestone, M. R. Microbial biomass response to a rapid change increase in water potential when dry soil is wetted. Soil Biol. Biochem. 19, 119–126 (1987).

    Article  Google Scholar 

  10. Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Osburne, M. S., Grossmann, T. H., August, P. R. & MacNeil, I. A. Tapping into microbial diversity for natural products drug discovery. ASM News 66, 411–417 (2000).

    Google Scholar 

  12. Amann, R. I., Ludwig, W. & Schleifer, K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Torsvik, V., Goksoyr, J. & Daae, F. L. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56, 782–787 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Joseph, S. J., Hugenholtz, P., Sangwan, P., Osborne, C. A. & Janssen, P. H. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl. Environ. Microbiol. 69, 7210–7215 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Kaeberlein, T., Lewis, K. & Epstein, S. Isolating “uncultivable” microorganisms in a simulated natural environment. Science 296, 1127–1129 (2002).

    Article  CAS  PubMed  Google Scholar 

  16. Zengler, K. et al. Cultivating the uncultured. Proc. Natl Acad. Sci. USA 99, 15684–15686 (2002).

    Article  CAS  Google Scholar 

  17. Handelsman, J., Rondon, M. R., Brady, S. F, Clardy, J. & Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5, R245–R249 (1998).

    Article  CAS  PubMed  Google Scholar 

  18. Rondon, M. R., Goodman, R. M. & Handelsman, J. The earth's bounty: assessing and accessing soil microbial diversity. TIBTECH 17, 403–409 (1999).

    Article  CAS  Google Scholar 

  19. Ogram, A., Sayler, G. S. & Barkay, T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7, 57–66 (1987).

    Article  CAS  Google Scholar 

  20. Holben, W. E., Jansson, J. K., Chelm, B. K. & Tiedje, J. M. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54, 703–711 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Steffan, R. J., Goksoyr, J., Bej, A. K. & Atlas, R. M. Recovery of DNA from soils and sediments. Appl. Environ. Microbiol. 54, 2908–2915 (1988).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Jacobsen, C. S. & Rasmussen, O. F. Development and application of a new method to extract bacterial DNA from soil based on separation of bacteria from soil with cation-exchange resin. Appl. Environ. Microbiol. 58, 2458–2462 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Lindahl, V. & Bakken, L. R. Evaluation of methods for extraction of bacteria from soil. FEMS Microbiol. Ecol. 16, 135–142 (1995).

    Article  CAS  Google Scholar 

  24. Zhou, J. M., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Miller, D. N., Bryant, J. E., Madsen, E. L. & Ghiorse, W. C. Evaluation and optimization of DNA extraction for soil and sediment samples. Appl. Environ. Microbiol. 65, 4715–4724 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Hurt, R. A. et al. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67, 4495–4503 (2001). Development of a method for direct nucleic acid isolation from soils of various compositions.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Lloyd-Jones, G. & Hunter, D. W. F. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol. Biochem. 33, 2053–2059 (2001).

    Article  CAS  Google Scholar 

  28. Dunbar, J., Takala, S., Barns, S. M., Davis, J. A. & Kuske, C. R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65, 1662–1669 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Øvreås, L. Population and community level approaches for analysing microbial diversity in natural environments. Ecol. Letts. 3, 236–251 (2000).

    Article  Google Scholar 

  30. Dunbar, J., Barns, S. M., Ticknor, L. O. & Kuske, C. R. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68, 3035–3045 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Zhou, J. et al. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68, 326–334 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Yeager, C. M. et al. Diazotrophic community structure and function in two successional stages of biological soil crusts from the Colorado plateau and Chihuahuan desert. Appl. Environ. Microbiol. 70, 973–983 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Yap, W. H., Li, X., Soong, T. W. & Davies, J. E. Genetic diversity of soil microorganisms assessed by analysis of hsp70 (dnaK) sequences. J. Industr. Microbiol. 17, 179–184 (1996).

    Article  CAS  Google Scholar 

  34. Webster, G., Embley, T. M. & Posser, J. L. Grassland management regimens reduce small-scale heterogeneity and species diversity of β-proteobacterial ammonia oxidisers. Appl. Environ. Microbiol. 68, 20–30 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Henne, A., Daniel, R., Schmitz, R. A. & Gottschalk, G. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate. Appl. Environ. Microbiol. 65, 3901–3907 (1999). First report on the isolation of biocatalysts from soil-derived plasmid libraries.

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Brady, S. F. & Clardy, J. Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J. Am. Chem. Soc. 122, 12903–12904 (2000). First isolation of antibiotics from a soil-based cosmid library.

    Article  CAS  Google Scholar 

  37. Rondon, M. R. et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66, 2541–2547 (2000). Generation of a large-insert soil-derived BAC library and illustration of the potential of this type of library for soil-based gene discovery.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Henne, A., Schmitz, R. A., Bömeke, M., Gottschalk, G. & Daniel, R. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66, 3113–3116 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Lee, S. -W. et al. Screening for novel lipolytic enzymes from uncultured soil microorganisms. Appl. Microbiol. Biotechnol. 65, 720–726 (2004).

    Article  CAS  PubMed  Google Scholar 

  40. Lorenz, P. & Schleper, C. Metagenome — a challenging source of enzyme discovery. J. Mol. Catal. B Enzym. 19, 13–19 (2002).

    Article  Google Scholar 

  41. Gupta, R., Berg, Q. K. & Lorenz, P. Bacterial alkaline proteases: molecular approaches and industrial applications. Appl. Microbiol. Biotechnol. 59, 15–32 (2002).

    Article  CAS  PubMed  Google Scholar 

  42. Santosa, D. A. Rapid extraction and purification of environmental DNA for molecular cloning applications and molecular diversity studies. Mol. Biotechnol. 17, 59–64 (2001).

    Article  CAS  PubMed  Google Scholar 

  43. Knietsch, A., Waschkowitz, T., Bowien, S., Henne, A. & Daniel, R. Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J. Mol. Microbiol. Biotechnol. 5, 46–56 (2003).

    Article  CAS  PubMed  Google Scholar 

  44. Richardson, T. H. et al. A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable α-amylase. J. Biol. Chem. 277, 26501–26507 (2002).

    Article  CAS  PubMed  Google Scholar 

  45. Yun, J. et al. Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl. Environ. Microbiol. 70, 7229–7235 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Wang, G. Y. et al. Novel natural products from soil DNA libraries in a streptomycete host. Org. Lett. 2, 2401–2404 (2000). First report on the use of a non- E. coli host for screening of metagenomic libraries.

    Article  CAS  PubMed  Google Scholar 

  47. MacNeil, I. A. et al. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol. 3, 301–308 (2001).

    CAS  PubMed  Google Scholar 

  48. Gillespie, D. E. et al. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68, 4310–4306 (2002).

    Article  CAS  Google Scholar 

  49. Courtois, S. et al. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl. Environ. Microbiol. 69, 49–55 (2003). Strategy for increasing the screening efficiency of large-insert metagenomic libraries by using a cosmid shuttle vector.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Riesenfeld, C. S., Goodman, R. M. & Handelsman, J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6, 981–989 (2004). References 50 and 51 illustrate the immense power of activity-based screening strategies using host strains or mutants of host strains that require heterologous complementation for growth under selective conditions.

    Article  CAS  PubMed  Google Scholar 

  51. Majernik, A., Gottschalk, G. & Daniel, R. Screening of environmental DNA libraries for the presence of genes conferring Na+(Li+)/H+ antiporter activity on Escherichia coli:characterization of the recovered genes and the corresponding gene products. J. Bacteriol. 183, 6645–6653 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Liesack, W. & Stackebrandt, E. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174, 5072–5078 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Martin-Laurent, F. et al. DNA extractions from soils: old bias for new microbial diversity analysis methods. Appl. Environ. Microbiol. 67, 2354–2359 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Tebbe, C. C. & Vahjen, W. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and yeast. Appl. Environ. Microbiol. 59, 2657–2665 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Tsai, Y. -L., & Olson, B. H. Detection of low numbers of bacterial cells in soils and sediments. Appl. Environ. Microbiol. 58, 754–757 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Courtois, S. et al. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3, 431–439 (2001).

    Article  CAS  PubMed  Google Scholar 

  57. Gabor, E. M., de Vries, E. J. & Janssen, D. B. Efficient recovery of environmental DNA for expression cloning by indirect methods. FEMS Microbiol. Ecol. 44, 153–163 (2003). References 57 and 58 compare direct cell lysis with cell separation approaches with respect to species representation and content of eukaryotic DNA in the isolated soil DNA.

    Article  CAS  PubMed  Google Scholar 

  58. Treusch, A. H. et al. Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea. Environ Microbiol. 6, 970–980 (2004).

    Article  CAS  PubMed  Google Scholar 

  59. Stach, J. E. M., Bathe, S., Clapp, J. P. & Burns, R. G. PCR–SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol. Ecol. 36, 139–151 (2001).

    Article  CAS  PubMed  Google Scholar 

  60. Leff, L. G., Dana, J. R., McArthur, J. V. & Shimkets, L. J. Comparison of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61, 1141–1143 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Brady, S. F., Chao, C. J. & Clardy, J. Long-chain N-acyltyrosine synthases from environmental DNA. Appl. Environ. Microbiol. 70, 46865–46870 (2004).

    Article  CAS  Google Scholar 

  62. Martinez, A. et al. Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl. Environ. Microbiol. 70, 2452–2463 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Gabor, E. M., de Vries, E. J. & Janssen, D. B. Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ. Microbiol. 6, 948–958 (2004).

    Article  CAS  PubMed  Google Scholar 

  64. Brady, S. F., Chao, C. J., Handelsman, J. & Clardy, J. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org. Lett. 3, 1981–1984 (2001).

    Article  CAS  PubMed  Google Scholar 

  65. Quaiser, A. et al. First insight into the genome of an uncultivated crenarchaeota from soil. Environ. Microbiol. 4, 603–611 (2002).

    Article  CAS  PubMed  Google Scholar 

  66. Quaiser, A. et al. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50, 563–575 (2003). Partial genomic characterization of uncultivated Acidobacteria.

    Article  CAS  PubMed  Google Scholar 

  67. Ginolhac, A. et al. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl. Environ. Microbiol. 70, 5522–5527 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Riesenfeld, C. S., Schloss, P. D. & Handelsman, J. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38, 525–552 (2004).

    Article  CAS  PubMed  Google Scholar 

  69. Liles, M. R., Manske, B. F., Bintrim, S. B., Handelsman, J. & Goodman, R. M. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69, 2684–2691 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Robertson, D. E. et al. Exploring nitrilase sequence for enantioselective catalysis. Appl. Environ. Microbiol. 70, 2429–2436 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Gray, K. A., Richardson, T. H., Robertson, D. E., Swanson, P. E. & Subramanian, M. V. Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications. Adv. Appl. Microbiol. 52, 1–27 (2003).

    Article  CAS  PubMed  Google Scholar 

  72. Brady, S. F. & Clardy, J. Synthesis of long-chain fatty acid enol esters isolated from an environmental DNA clone. Org. Lett. 5, 121–124 (2003).

    Article  CAS  PubMed  Google Scholar 

  73. Brady, S. F., Chao, C. J. & Clardy, J. New natural product families from an environmental DNA (eDNA) gene cluster. J. Am. Chem. Soc. 124, 9968–9969 (2002).

    Article  CAS  PubMed  Google Scholar 

  74. Borneman, J. & Triplett, E. W. Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63, 2647–2653 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Seow, K. -T. et al. A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms. J. Bacteriol. 179, 7360–7368 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Eschenfeldt, W. H. et al. DNA from uncultured organisms as a source of 2,5-diketo-D-gluconic acid reductases. Appl. Environ. Microbiol. 67, 4206–4214 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Precigou, S., Goulas, P. & Duran, R. Rapid and specific identification of nitrile hydratase (Nhase)-encoding genes. FEMS Microbiol. Lett. 204, 155–161 (2001).

    Article  CAS  PubMed  Google Scholar 

  78. Knietsch, A., Bowien, S., Whited, G., Gottschalk, G. & Daniel, R. Identification and characterization of genes encoding coenzyme B12-dependent glycerol and diol dehydratases from metagenomic DNA libraries derived from enrichment cultures. Appl. Environ. Microbiol. 69, 3048–3060 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Stokes, H. W. et al. Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl. Environ. Microbiol. 67, 5240–5246 (2001). Library-independent approach for recovery of novel genes from environmental samples.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Wu, L. et al. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67, 5780–5790 (2001). One of the first reports on using DNA microarray technology for assessing functional gene diversity in soil microbial communities.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Zhou, J. & Thompson, D. K. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13, 204–207 (2002).

    Article  CAS  PubMed  Google Scholar 

  82. Cho, J. -C. & Tiedje, J. M. Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68, 1425–1430 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Denef, V. J. et al. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5, 933–943 (2003).

    Article  CAS  PubMed  Google Scholar 

  84. Sebat, J. L., Colwell, F. S. & Crawford, R. L. Metagenomic profiling: microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 69, 4927–4934 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Knietsch, A., Waschkowitz, T., Bowien, S., Henne, A. & Daniel, R. Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl. Environ. Microbiol. 69, 1408–1416 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Entcheva, P., Liebl, W., Johann, A., Hartsch, T. & Streit, W. Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl. Environ. Microbiol. 67, 89–99 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Voget, S. et al. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69, 6235–6242 (2003). The library derived from an agarolytic microbial consortium enriched from soil harbours a large number of genes encoding industrially relevant biocatalysts.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Daniel, R. The soil metagenome — a rich resource for the discovery of novel natural products. Curr. Opin. Microbiol. 15, 199–204 (2004).

    CAS  Google Scholar 

  89. Radajewski, S., McDonald, I. R. & Murrell, J. C. Stable-isotope probing of nucleic acids: a window to the function of uncultured microorganisms. Curr. Opin. Biotechnol. 14, 296–302 (2003).

    Article  CAS  PubMed  Google Scholar 

  90. Wellington, E. M. H., Berry, A. & Krsek, M. Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotope probing. Curr. Opin. Microbiol. 6, 295–301 (2003).

    Article  CAS  PubMed  Google Scholar 

  91. Yin, B., Crowley, D., Sparovek, G., De Melo, W. J. & Borneman, J. Bacterial functional redundancy along a soil reclamation gradient. Appl. Environ. Microbiol. 66, 4361–4365 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Schloss, P. D., Larget, B. R. & Handelsman, J. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70, 5485–5492 (2004). A statistical approach for comparing gene libraries is described.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Uchiyama, T., Abe, T., Ikemura, T. & Watanabe, K. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nature Biotechnol. 23, 88–93 (2005). This strategy for screening of metagenomic libraries has enormous potential for soil-based gene discovery.

    Article  CAS  Google Scholar 

  94. Venter, J. C. et al. Environmental shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

R.D. is supported by funds of the Competence Network Göttingen 'Genome Research on Bacteria', financed by the German Federal Ministry of Education and Research and by a European Commission grant.

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  1. Abteilung Angewandte Mikrobiologie, Institut für Mikrobiologie und Genetik der Georg-August-Universität, Grisebachstrasse 8, Göttingen, 37077, Germany

    Rolf Daniel

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∫–LIBSHUFF

Glossary

BIOTA

The organisms that occupy an ecosystem.

HUMUS

A complex of heteropolymeric substances, including humic acids, humin and fulvic acids.

ABIOTIC

Non-living objects, substances or processes.

SUBSURFACE

The geological zone below the surface of the Earth. It is not exposed to the Earth's surface.

CONSORTIUM

Physical association between cells of two or more types of microorganisms. Such an association might be advantageous to at least one of the microorganisms.

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Daniel, R. The metagenomics of soil. Nat Rev Microbiol 3, 470–478 (2005). https://doi.org/10.1038/nrmicro1160

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