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Chapter 14 : Spatial Segregation: The Deep Subsurface Story

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Abstract:

This chapter focuses on the physical and chemical characteristics of the terrestrial subsurface that are most likely to influence microbial evolution, with emphasis on the spatial segregation issue, and suggests possible directions for future research. Subsurface environments are any terrestrial environments situated beneath the topsoil zone of the Earth's crust. Microorganisms are present in many different types of subsurface environments. Some subsurface microbes may be physically isolated from other microorganisms because they are surrounded by layers of dense, impermeable material. Spatial segregation could even be an important issue within some kinds of geological formations, especially those with very low porosity, in which the movement of groundwater, chemicals, and microbial cells is greatly restricted. Phylogenetic analysis of 16S rRNA gene sequences may provide evidence for long-term spatial segregation of microbes in some types of subsurface environments. Physical characteristics like permeability may affect spatial segregation of microbes in the subsurface by determining whether microbes, water, and nutrients can move from one location to another. Microbes and microbial communities in ultra-deep environments may have evolved unique combinations of traits in response to long-term spatial segregation. Analysis of antibiotic resistance traits of subsurface microbes might provide preliminary evidence for gene transfer in some kinds of subsurface environments. Sometimes the physical nature of the environment leads to spatial segregation, such that subsurface microbes may be physically isolated from those at the surface for very long periods.

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14

Key Concept Ranking

Environmental Microbiology
0.519819
16s rRNA Sequencing
0.48427516
Microbial Communities in Environment
0.47721794
0.519819
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Figures

Image of FIGURE 1
FIGURE 1

Simplified representation of Atlantic Coastal Plain sediments at the U.S. Department of Energy's Savannah River Site in Aiken, SC. Regional aquifers composed mostly of sands are separated by relatively low-permeability aquatards composed mostly of clay. Arrow indicates principal direction of groundwater flow through this system. Depths below land surface (at right) are approximate.

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14
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Image of FIGURE 2
FIGURE 2

Lithographic and stratigraphic column of the Ringold Formation sediments examined at the Hanford Site. The areas from which core samples were taken are indicated, along with their respective sediment sample identities. Reprinted from Applied and Environmental Microbiology ( ) with permission of the publisher.

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14
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Image of FIGURE 3
FIGURE 3

Phylogenetic tree based on parsimony analysis of 16S rRNA gene sequences for deep-subsurface and type strains of species. For the deep-subsurface strains, the sediment sample identifier and stratum from which they originate are indicated. FG and , fluvial gravel; FS and Δ, fluvial sand; LC and ■, lacustrine; LP and ★, lower paleosol; UL and ○, upper lacustrine; UP and ▲, upper paleosol. The tree is rooted using as an outgroup. Numbers at the nodes indicate the percentages of occurrence in 100 bootstrapped trees; only values that are 50% or greater are shown. Reprinted from ( ) with permission of the publisher.

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14
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References

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1. Balkwill, D. L.,, G. R. Drake,, R. H. Reeves,, J. K. Fredrickson,, D. C. White,, D. B. Ringelberg,, D. P. Chandler,, M. F. Romine,, D. W. Kennedy,, and C. M. Spadoni. 1997a. Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov. Int. J. Syst. Bacteriol. 47:191201.
2. Balkwill, D. L.,, R. H. Reeves,, G. R. Drake,, J. Y. Reeves,, F. H. Crocker, M. B. King, and D. R. Boone. 1997b. Phylogenetic characterization of bacteria in the Subsurface Microbial Culture Collection. FEMS Microbiol. Rev. 20:201216.
3. Boone, D. R.,, Y. Liu,, Z. Zhao,, D. L. Balkwill,, G. R. Drake,, T. O. Stevens,, and H. C. Aldrich. 1995. Bacillus infernus sp. nov., an Fe(III)-and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface. Int. J. Syst. Bacteriol. 45:441448.
4. Kim, E.,, P. J. Aversano,, M. F. Romine,, R. P. Schneider,, and G. L. Zylstra. 1996. Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface Sphingomonas strains. Appl. Environ. Microbiol. 62:14671470.
5. Romine, M. F.,, L. C. Stillwell,, K.-K. Wong,, S. J. Thurston,, E. C. Sisk,, C. Sensen,, T. Gaasterland,, J. K. Fredrickson,, and J. D. SafFer. 1999. Complete sequence of a 184-kilo-base catabolic plasmid from Sphingomonas aromaticivorans F199. J. Bacteriol. 181:15851602.
6. van Waasbergen, L. G.,, D. L. Balkwill,, F. H. Crocker,, B. N. Bjonstad,, and R. V. Miller. 2000. Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences. Appl. Environ. Microbiol. 66:34543463.
7. Amy, P. S.,, and D. L. Haldeman (ed.). 1997. The Microbiology of the Terrestrial Deep Subsurface. CRC Lewis Publishers, New York, N.Y.
8. Bachofen, R. (ed.). 1997. Proceedings of the 1996 Internal Symposium on Subsurface Microbiology (ISSM-96). FEMS Microbiol. Rev. 20:179638. (Special issue.)
9. Fredrickson, J. K.,, and M. Fletcher (ed.). 2001. Subsurface Microbiology and Biogeochemistry. John Wiley & Sons, New York, N.Y.
10. Ghiorse, W. C. (ed.). 1989. Special issue on deep subsurface microbiology. Geomicrobiol. J. 7:1130.
11. Ghiorse, W. C.,, and J. T. Wilson. 1988. Microbial ecology of the terrestrial subsurface. Adv. Appl. Microbiol. 33:107172.
12. Pedersen, K., 2002. Igneous rock aquifers microbial communities, p. 16611673. In G. Bitton (ed.), Encyclopedia of Environmental Microbiology, vol. 3. John Wiley & Sons, New York, N.Y.
13. Wilson, J. T.,, J. F. McNabb,, D. L. Balkwill,, and W. C. Ghiorse. 1983. Enumeration and characterization of bacteria indigenous to a shallow water-table aquifer. Ground Water 21:134142.

Tables

Generic image for table
TABLE 1

Percentages of subsurface bacterial isolates from different sample sites possessing resistance to antibiotics

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14
Generic image for table
TABLE 2

Percentages of subsurface bacterial isolates from different sites possessing resistance to specific antibiotics

Citation: Balkwill D. 2004. Spatial Segregation: The Deep Subsurface Story, p 214-230. In Miller R, Day M (ed), Microbial Evolution. ASM Press, Washington, DC. doi: 10.1128/9781555817749.ch14

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