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Chapter 11 : Soils—the Metagenomics Approach

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Abstract:

Metagenomics offers a new look by accessing the as-yet-unculturable microorganisms that represent the majority of life in soil. Metagenomic analysis of soil is challenging because soil is such a complex environment, containing diverse organisms in a dynamic matrix. The biological, chemical, and physical properties of soil all contribute to the technical difficulties of the analysis, and thus numerous obstacles to cloning and analyzing the metagenome of soil remain to be overcome. Discovery of metabolic networks and small molecules from the cultured microorganisms from soil has been unparalleled in any other environment, and therefore it is likely that the potential for discovery from the uncultured community is similarly enormous. Because most of the uncultured life forms in soil appear to be new species and many represent new genera, there is much to learn about the fundamental functioning of soil microbial communities, and these communities have already yielded new enzymes and antibiotics. Technical advances in DNA recovery, gene expression, and functional analysis will enhance the rate of discovery and make possible productive prospecting of soil for the medicinal, agricultural, and industrial chemicals.

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11

Key Concept Ranking

16s rRNA Sequencing
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Soil Microbial Communities
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Figures

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Figure 1

Microorganisms in soil, on minerals, and on plant surfaces.

(A) and (B) Scanning electron micrographs of the naturally occurring biofilm on sand grains in the clog mat of a septic system infiltration mound. The biofilm is composed of mineral particles, a variety of microorganisms, and a network of slime, or glycocalyx, that binds the microorganisms and particles together. Image (A) scale bar is 150 μm. Image (B) scale bar is 4.3 μm. Copyright Amy ? Lee Wong. Licensed for use, ASM MicrobeLibrary (linked to http://www.microbelibrary.org). (C) Unidentified bacterium attached to a feldspar surface by extracellular polymers. High-resolution, low-voltage cryoscanning electron micrograph of high-pressure frozen, freeze-fracture/sublimed culture sample. (D) Microbial soil assemblage consisting of extensive extracellular polymer networks (p), anhedral clay minerals (clay), quartz (qtz), bacteria (b), and fungi. Energy filtered transmission electron micrograph of ultrathin section of high-pressure frozen, freeze-substituted, undisturbed soil sample. (E) Microbial soil assemblage consisting of extensive extracellular polymer networks (P), anhedral clay minerals (clay), bacteria (B), and filamentous cyanobacteria (BGA). Energy-filtered transmission electron micrograph of ultrathin section of high-pressure frozen, freeze-substituted, undisturbed soil sample. (F) Diatoms (D), cyanobacteria (C), and fungal hyphae (F) inhabit the surface of a quartz grain from a spring seep sandstone outcrop near Mount Horeb, Wisconsin. High-resolution, low-voltage scanning electron micrograph. (G) (B) bound to euhedral kaolinite (K) by extracellular polysaccharides (arrows). High-resolution, low-voltage cryoscanning electron micrograph of high-pressure frozen, freeze-fracture/sublimed culture sample. (H) (B) attached to euhedral kaolinite (k) by f-type sex pili (P). Transmission electron micrograph of a propane cryojet-frozen, frceze-etch Pt replica. (Micrographs in panels ? to H courtesy of William W. Barker, The College of Letters and Science, University of Wisconsin-Madison.) (I) Micrograph of naturally occurring biofilm on a plant surface (alfalfa sprout hypocotyl). The size of the bacteria ranged from 0.4 μπι in diameter (cocci) to 0.2 × 1.7 μm (rods). Copyright Peter Cooke and William Fett. Licensed for use, ASM Microbe Library (linked to http://www.microbelibrary.org).

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11
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Image of Figure 2
Figure 2

Phylogenetic diversity of microbial life. Phyla that have been detected in soil are indicated by shading.

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11
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Figure 3

Strategy for metagenomic analysis.

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11
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Figure 4

Small molecules discovered in metagenomic libraries.

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11
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References

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Tables

Generic image for table
Table 1

Genes and gene products discovered in metagenomic libraries constructed with DNA extracted directly from soil

Citation: Handelsman J. 2004. Soils—the Metagenomics Approach, p 109-119. In Bull A (ed), Microbial Diversity and Bioprospecting. ASM Press, Washington, DC. doi: 10.1128/9781555817770.ch11

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