Chapter 14
Targeting Major Soil-Borne Bacterial Lineages Using Large-Insert Metagenomic Approaches
Anna M. Kielak,
George A. Kowalchuk,
Anna M. Kielak
Netherlands Institute of Ecology, Heteren, The Netherlands
University of Groningen, The Netherlands
Search for more papers by this authorGeorge A. Kowalchuk
Netherlands Institute of Ecology, Heteren, The Netherlands
Free University Amsterdam, Amsterdam, The Netherlands
Search for more papers by this authorAnna M. Kielak,
George A. Kowalchuk,
Anna M. Kielak
Netherlands Institute of Ecology, Heteren, The Netherlands
University of Groningen, The Netherlands
Search for more papers by this authorGeorge A. Kowalchuk
Netherlands Institute of Ecology, Heteren, The Netherlands
Free University Amsterdam, Amsterdam, The Netherlands
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorFirst published: 16 September 2011
Summary
This chapter contains sections titled:
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Introduction
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Metagenomic Approaches
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Application of Large-Insert Metagenomic Approaches in Soil Environments
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Metagenomic Analysis of Important, Yet Difficult to Culture, Soil-Borne Microorganisms
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Concluding Remarks
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References
REFERENCES
- Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. 2005. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res. 12: 281–290.
- Abulentia CB, Wyborski DL, Garcia JA, Podar M, Chen WQ, etal. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 72: 3291–3301.
- Barns SM, Takala SL, Kuske CR. 1999. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 65: 1731–1737.
- Barns SM, Cain EC, Sommerville L, Kuske CR. 2007. Acidobactetia phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 73: 3113–3116.
- Beja O, Suzuki MT, Koonin EV, Aravind L, Hadd A, et al. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2: 516–529.
- Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411: 786–789.
- Bellgard M, Schibeci D, Trifonov E, Gojobori T. 2001. Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. J. Mol. Evol. 53: 465–468.
- Bentley SD, Parkhill J. 2004. Comparative genomic structure of prokaryotes. Annu. Rev. Genet. 38: 771–792.
- Bork P. 1993. Hundreds of ankyrin-like repeats in functionally diverse proteins—Mobile modules that cross phyla horizontally. Proteins 17: 363–374.
- Bryant DA, Costas AMG, Maresca JA, Chew AGM, Klatt CG, et al. 2007. Candidatus Chloracidobacterium thermophilum: An aerobic phototrophic acidobacterium. Science 317: 523–526.
- Buckley DH, Schmidt TM. 2001. Environmental factors influencing the distribution of rRNA from Verrucomicrobia in soil. FEMS Micro-biol. Ecol. 35: 105–112.
- Courtois S, Cappellano CM, Ball M, Francou F-X, Normand P. et al. 2003. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl. Environ. Microbiol. 69: 49–55.
- Curtis TP, Sloan WT. 2004. Prokaryotic diversity and its limits: Microbial community structure in nature and implications for microbial ecology. Curr. Opin. Microbiol. 7: 221–226.
- Daniel R. 2004. The soil metagenome—A rich resource for the discovery of novel natural products. Curr. Opin. Biotechnol. 15: 199–204.
- Daniel R. 2005. The metagenomics of soil. Nat. Rev. Microbiol. 3: 470–478.
- Dunbar J, Barns SM, Ticknor LO, Kuske CR. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68: 3035–3045.
-
Eichorst SA, Breznak JA, Schmidt TM. 2007. Isolation and characterization of soil bacteria that define Teniglobus gen. nov., in the phylum Acidobacteria. Appl. Environ. Microbiol. 73: 2708–2717.
10.1128/AEM.02140-06 Google Scholar
- George I, Agathos SN. 2009. Cultivation of fastitious microorganisms: The case of Acidobacteria. BAGECO 10 Bacterial Genetics and Ecology—Coexisting on a Changing Planet. 15–19 June, 2009, Uppsala, Sweden. Book of Abstracts, p. 168.
- Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem. Biol. 5: R245–R249.
- Hansel CM, Fendorf S, Jardine PM, Francis CA. 2008. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl. Environ. Microbiol. 74: 1620–1633.
- Hardeman F, Sjoling S. 2007. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol. Ecol. 59: 524–534.
- Henne A, Daniel R, Schmitz RA, Gottschalk G. 1999. 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.
- Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765–4774.
- Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, et al. 2007. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc. Natl. Acad. Sci. USA 104: 18217–18222.
- Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Micro-biol. 72: 1719–1728.
- Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3: 442–453.
- Kanokratana P, Chanapan S, Pootanakit K, Eurwilaichitr L. 2004. Diversity and abundance of Bacteria and Archaea in the Bor Khlueng hot spring in Thailand. J. Basic Microbiol. 44: 430–444.
- Karlin S, Campbell AM, Mrazek J. 1998. Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32: 185–225.
- Kielak AM, van Veen JA, Kowalchuk GA. 2010. Comparative analysis of acidobacterial genomic fragments from terrestrial and aquatic metagenomic libraries, with emphasis on acidobacteria subdivision 6. Appl. Environ. Microbiol. 76: 6769–6777.
- Kielak A, Pijl AS, van Veen JA, Kowalchuk GA. 2008. Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol. Ecol. 63: 372–382.
- Kielak A, Pijl AS, van Veen JA, Kowalchuk GA. 2009. Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J. 3: 378–382.
- Kielak A, Rodrigues JLM, Kuramae EE, Chain PSG, van Veen JA, Kowalchuk GA. 2010. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol. Ecol. 71: 23–33.
- Kim YJ, Choi GS, Kim SB, Yoon GS, Kim YS, Ryu YW. 2006. Screening and characterization of a novel esterase from a metagenomic library. Protein Expr. Purif. 45: 315–323.
-
Kowalchuk GA, Drigo B, Yergeau E, van Veen JA. 2006. Molecular approaches to assess the structure of bacterial and fungal communities in soil—the use of rRNA and other gene markers. InNannipieri P, Smalla K, eds. Nucleic Acids and Proteins in Soil. Heidelberg: Springer, pp. 159–188.
10.1007/3-540-29449-X_8 Google Scholar
- Kowalchuk GA, Speksnijder A, Zhang K, Goodman RM, van Veen JA. 2007. Finding the needles in the metagenome haystack. Microb. Ecol. 53: 475–485.
- Kuske CR, Barns SM, Busch JD. 1997. Diverse uncultivated bacterial groups from soils of the arid southwestern United States that are present in many geographic regions. Appl. Environ. Microbiol. 63: 3614–3621.
-
Leveau JHJ, Gerards S, de Boer W, van Veen JA. 2004. Phylogeny-function analysis of (meta)genomic libraries: Screening for expression of ribosomal RNA genes by large-insert library fluorescent in situ hybridization (LIL-FISH). Environ. Microbiol. 6: 990–998.
10.1111/j.1462-2920.2004.00673.x Google Scholar
- Li YG, Wexler M, Richardson DJ, Bond PL, Johnston AWB. 2005. Screening a wide host-range, waste-water metagenomic library in tryptophan auxotrophs of Rhizobium leguminosarum and of Escherichia coli reveals different classes of cloned trp genes. Environ. Microbiol. 7: 1927–1936.
- Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM. 2003. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69: 2684–2691.
- Lopez-Garcia P, Brochier C, Moreira D, Rodriguez-Valera F. 2004. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ. Microbiol. 6: 19–34.
- Lorenz P, Eck J. 2005. Metagenomics and industrial applications. Nat. Rev. Microbiol. 3: 510–516.
- Martinez A, Kolvek SJ, Yip CLT, Hopke J, Brown KA, et al. 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. Appl. Environ. Microbiol. 70: 2452–2463.
- Nei M, Gojobori T. 1986. Simple Methods for Estimating the Numbers of Synonymous and Nonsynonymous Nucleotide Substitutions, Vol. 3. SMBE, pp. 418–426.
- Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
- Park SJ, Kang CH, Chae JC, Rhee SK. 2008. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol. Lett. 284: 28–34.
- Podar M, Abulentia CB, Walcher M, Hutchison D, Zengler K, et al. 2007. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73: 3205–3214.
- Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. 2003. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13: 145–158.
- Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, et al. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: Evidence from environmental genomics. Mol. Microbiol. 50: 563–575.
- Quaiser A, Lopez-Garcia P, Zivanovic Y, Henn MR, Rodriguez-Valera F, Moreira D. 2008. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ. Microbiol. 10: 2704–2717.
- Quince C, Curtis TP, Sloan WT. 2008. The rational exploration of microbial diversity. The ISME J. 2: 997–1006.
- Riaz K, Elmerich C, Moreira D, Raffoux A, Dessaux Y, Faure D. 2008. A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases. Environ. Microbiol. 10: 560–570.
- Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM, et al. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1: 283–290.
- Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, et al. 2000. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541–2547.
- Sait M, Hugenholtz P, Janssen PH. 2002. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ. Microbiol. 4: 654–666.
- Stevenson BS, Schmidt TM. 2004. Life history implications of rRNA gene copy number in Escherichia coli. Appl. Environ. Microbiol. 70: 6670–6677.
- Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85: 2653–2657.
- Torsvik V, Ovreas L. 2002. Microbial diversity and function in soil: From genes to ecosystems. Curr. Opin. Microbiol. 5: 240–245.
- Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. 2005. Comparative metagenomics of microbial communities. Science 308: 554–557.
- Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43.
- van Elsas JD, Speksnijder A, van Overbeek LS. 2008. A procedure for the metagenomics exploration of disease-suppressive soils. J. Microbiol. Methods 75: 515–522.
- Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D. et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74.
- Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, et al. 2009. TerraGenome: A consortium for the sequencing of a soil metagenome. Nat. Rev. Microbiol. 7: 252.
- Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, et al. 2009. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils. Appl. Environ. Microbiol. 75: 2046–2056.
- Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms—Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87: 4576–4579.
- Yim LC, Jing HM, Aitchison JC, Pointing SB. 2006. Highly diverse community structure in a remote central Tibetan geothermal spring does not display monotonic variation to thermal stress. FEMS Micro-biol. Ecol. 57: 80–91.
- Yun J, Kang S, Park S, Yoon H, Kim MJ, et al. 2004. Characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. Appl. Environ. Microbiol. 70: 7229–7235.
- Yung PY, Burke C, Lewis M, Egan S, Kjelleberg S, Thomas T. 2009. Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion. Nucleic Acids Res. 37(21): e144.
