Mechanical limits to microbial activity in deep sediments

Geochemistry, Geophysics, Geosystems

Volumn 7, Issue 11, 2006, Pages

  Rebata Landa, Verónica ^a   Santamarina, J Carlos ^a  

^a Georgia Institute of Technology   (United States)

Author keywords

Mechanical stress; Microorganisms; Porosity; Sediments; Soils; Survivability

Indexed keywords

EID: 34948857324     PISSN: 15252027     EISSN: 15252027     Source Type: Journal    
DOI: 10.1029/2006GC001355     Document Type: Article

References (70)

1. Abu-Ashour, J., D. M. Joy, H. Lee, H. R. Whiteley, and S. Zelin (1994), Transport of microorganisms through soil, Water Air Soil Pollut., 75(1-2), 141-158.
2. Agnelli, A., J. Ascher, G. Corti, M. T. Ceccherini, P. Nannipieri, and G. Pietramellara (2004), Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA, Soil Biol. Biochem., 36(5), 859-868.
3. Ahmed, S., C. W. Lovell, and S. Diamond (1974), Pore sizes and strength of compacted clay, J. Geotech. Eng. Div. Am. Soc. Civ. Eng., GT4, 407-425.
4. AlMukhtar, M., N. Belanteur, D. Tessier, and S. K. Vanapalli (1996), The fabric of a clay soil under controlled mechanical and hydraulic stress states, Appl. Clay Sci., 11(2-4), 99-115.
5. Astumian, R. D., and P. Hanggi (2002), Brownian motors, Phys. Today, 55(11), 33-39.
6. Bennett, R. H., W. R. Bryant, and M. H. Hulbert (1991), The Microstructure of Fine-Grained Sediments, From Mud to Shale, vol. xxii, 582 pp., Springer, New York.
7. Bird, D. F., S. K. Juniper, M. Ricciardi-Rigault, P. Martineu, Y. T. Prairie, and S. E. Calvert (2001), Subsurface viruses and bacteria in Holocene/Late Pleistocene sediments of Saanich Inlet, BC: ODP Holes 1033B and 1034B, Leg 169S, Mar. Geol., 174(1-4), 227-239.
8. Blume, E., M. Bischoff, J. M. Reichert, T. Moorman, A. Konopka, and R. F. Turco (2002), Surface and subsurface microbial biomass, community structure and metabolic activity as a function of soil depth and season, Appl. Soil Ecol., 20(3), 171-181.
9. Boivin-Jahns, V., R. Ruimy, A. Bianchi, S. Daumas, and R. Christen (1996), Bacterial diversity in a deep-subsurface clay environment, Appl. Environ. Microbiol., 62(9), 3405-3412.
10. Bolton, A. J., A. J. Maltman, and Q. Fisher (2000), Anisotropic permeability and bimodal pore-size distributions of finegrained marine sediments, Mar. Petrol. Geol., 17(6), 657-672.
11. Boulbitch, A., B. Quinn, and D. Pink (2000), Elasticity of the rod-shaped Gram-negative eubacteria, Phys. Rev. Lett., 85(24), 5246-5249.
12. Chen, C. R., Z. H. Xu, T. J. Blumfield, and J. M. Hughes (2003), Soil microbial biomass during the early establishment of hoop pine plantation: Seasonal variation and impacts of site preparation, Forest Ecol. Manage., 186(1-3), 213-225.
13. Cragg, B. A., R. J. Parkes, J. C. Fry, A. J. Weightman, P. A. Rochelle, and J. R. Maxwell (1996), Bacterial populations and processes in sediments containing gas hydrates (ODP Leg 146: Cascadia Margin), Earth Planet. Sc. Lett., 139(3-4), 497-507.
14. Cuisinier, O., and L. Laloui (2004), Fabric evolution during hydromechanical loading of a compacted silt, Int. J. Numer. Anal. Meteorol., 28(6), 483-499.
15. Delage, P., and G. Lefebvre (1984), Study of the structure of a sensitive Champlain clay and of its evolution during consolidation, Can. Geotech. J., 21(1), 21-35.
16. Delage, P., M. Audiguier, Y. J. Cui, and M. D. Howat (1996), Microstructure of a compacted silt, Can. Geotech. J., 33(1), 150-158.
17. Dewhurst, D., A. Aplin, J. Sarda, and Y. Yang (1998), Compaction- driven evolution of porosity and permeability in natural mudstones: An experimental study, J. Geophys. Res., 103(B1), 651-661.
18. Dewhurst, D. N., A. C. Aplin, and J. P. Sarda (1999), Influence of clay fraction on pore-scale properties and hydraulic conductivity of experimentally compacted mudstones, J. Geophys. Res., 104(B12), 29,261-29,274.
19. D'Hondt, S., et al. (2004), Distributions of microbial activities in deep subseafloor sediments, Science, 306(5705), 2216-2221.
20. Diamond, S. (1971), Microstructure and pore structure of impact/compacted clays, Clay Clay Miner., 19(4), 239-249.
21. Dodds, W. K., M. K. Banks, C. S. Clenan, C. W. Rice, D. Sotomayor, E. A. Strauss, and W. Yu (1996), Biological properties of soil and subsurface sediments under abandoned pasture and cropland, Soil Biol. Biochem., 28(7), 837-846.
22. Edwards, G. (1990), Biology the Easy Way, 2nd ed., Barron's Educ. Ser., New York.
23. Ehrlich, H. L. (1996), Geomicrobiology, 3rd ed., vol. xix, 719 pp., CRC Press, Boca Raton, Fla.
24. Fierer, N., J. P. Schimel, and P. A. Holden (2003), Variations in microbial community composition through two soil depth profiles, Soil Biol. Biochem., 35(1), 167-176.
25. Fredrickson, J. K., D. L. Balkwill, J. M. Zachara, S. M. W. Li, F. J. Brockman, and M. A. Simmons (1991), Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the Atlantic Coastal Plain, Appl. Environ. Microbiol., 57(2), 402-411.
26. Fredrickson, J. K., et al. (1997), Pore-size constraints on the activity and survival of subsurface bacteria in a late Cretaceous shale-sandstone sequence, northwestern New Mexico, Geomicrobiol. J., 14(3), 183-202.
27. Garcia-Bengochea, I., C. W. Lovell, and A. G. Altschaeffl (1979), Pore distribution and permeability of silty clays, J. Geotech. Eng. Div. Am. Soc. Civ. Eng., 105(7), 839-856.
28. Griffiths, F. J., and R. C. Joshi (1989), Change in pore-size distribution due to consolidation of clays, Geotechnique, 39(1), 159-167.
29. Griffiths, F. J., and R. C. Joshi (1990), Clay fabric response to consolidation, Appl. Clay Sci., 5, 37-66.
30. Hattori, T. (1973), Microbial Life in the Soil: An Introduction, vol. vi, 427 pp., CRC Press, Boca Raton, Fla.
31. Heling, D. (1970), Micro-fabrics of shales and their rearrangement by compaction, Sedimentology, 15(3-4), 247-260.
32. Hicher, P. Y., H. Wahyudi, and D. Tessier (2000), Microstructural analysis of inherent and induced anisotropy in clay, Mech. Cohesive Frictional Mater., 5(5), 341-371.
33. Horsrud, P., E. F. Sonstebo, and R. Boe (1998), Mechanical and petrophysical properties of north sea shales, Int. J. Rock Mech. Min. Sci., 35(8), 1009-1020.
34. Howard-Jones, M. H., V. D. Ballard, A. E. Allen, M. E. Frischer, and P. G. Verity (2002), Distribution of bacterial biomass and activity in the marginal ice zone of the central Barents Sea during summer, J. Mar. Syst., 38(1-2), 77-91.
35. Juang, C. H., and R. D. Holtz (1986), Fabric, pore-size distribution, and permeability of sandy soils, J. Geotech. Eng., 112(9), 855-868.
36. Katz, A., A. Alimova, M. Xu, E. Rudolph, M. K. Shah, H. E. Savage, R. B. Rosen, S. A. McCormick, and R. R. Alfano (2003), Bacteria size determination by elastic light scattering, IEEE J. Selected Topics in Quantum Electron., 9(2), 277-287.
37. Kieft, T. L., et al. (1998), Microbial transport, survival, and succession in a sequence of buried sediments, Microbial Ecol., 36(3), 336-348.
38. Lapierre, C., S. Leroueil, and J. Locat (1990), Mercury intrusion and permeability of Louiseville clay, Can. Geotech. J., 27(6), 761-773.
39. Lohnes, R. A., E. R. Tuncer, and T. Demirel (1976), Pore structure of selected Hawaiian soils, in Subsidence Over Mines and Caverns, Moisture and Frost Actions, and Classification, Trans. Res. Rec. 612, pp. 76-79, Transp. Res. Board, Washington, D. C.
40. Marchesi, J. R., A. J. Weightman, B. A. Cragg, R. J. Parkes, and J. C. Fry (2001), Methanogen and bacterial diversity and distribution in deep gas hydrate sediments from the Cascadia Margin as revealed by 16S rRNA molecular analysis, FEMS Microbiol. Ecol., 34(3), 221-228.
41. McDowell, G. R., and M. D. Bolton (1998), On the micromechanics of crushable aggregates, Geotechnique, 48(5), 667-679.
42. Mitchell, J. K. (1993), Fundamentals of Soil Behavior, 2nd ed., vol. xiii, 437 pp., John Wiley, Hoboken, N. J.
43. Miyata, M., W. S. Ryu, and H. C. Berg (2002), Force and velocity of Mycoplasma mobile gliding, J. Bacteriol., 184(7), 1827-1831.
44. Negre, M., P. Leone, J. Trichet, C. Defarge, V. Boero, and M. Gennari (2004), Characterization of model soil colloids by cryo-scanning electron microscopy, Geoderma, 121(1-2), 1-16.
45. Newberry, C. J., G. Webster, B. A. Cragg, R. J. Parkes, A. J. Weightman, and J. C. Fry (2004), Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190, Environ. Microbiol., 6(3), 274-287. (Pubitemid 38261026)
46. Parkes, R. J., B. A. Cragg, S. J. Bale, J. M. Getliff, K. Goodman, P. A. Rochelle, J. C. Fry, A. J. Weightman, and S. M. Harvey (1994), Deep bacterial biosphere in Pacific Ocean sediments, Nature, 371(6496), 410-413.
47. Parkes, R. J., B. A. Cragg, and P. Wellsbury (2000), Recent studies on bacterial populations and processes in subseafloor sediments: A review, Hydrogeol. J, 8(1), 11-28.
48. Penumadu, D., and J. Dean (2000), Compressibility effect in evaluating the pore-size distribution of kaolin clay using mercury intrusion porosimetry, Can. Geotech. J., 37(2), 393-405.
49. Phelps, T. J., S. M. Pfiffner, K. A. Sargent, and D. C. White (1994), Factors influencing the abundance and metabolic capacities of microorganisms in eastern coastal-plain sediments, Microbial Ecol., 28(3), 351-364.
50. Santamarina, J. C., K. A. Klein, and M. A. Fam (2001), Soils and Waves: Particulate Materials Behavior, Characterization and Process Monitoring, vol. xix, 488 pp., John Wiley, Hoboken, N. J.
51. Simms, P. H., and E. K. Yanful (2001), Measurement and estimation of pore shrinkage and pore distribution in a clayey till during soil-water characteristic curve tests, Can. Geotech. J., 38(4), 741-754.
52. Simms, P. H., and E. K. Yanful (2004), A discussion of the application of mercury intrusion porosimetry for the investigation of soils, including an evaluation of its use to estimate volume change in compacted clayey soils, Geotechnique, 54(6), 421-426.
53. Sinclair, J. L., and W. C. Ghiorse (1989), Distribution of aerobic bacteria, protozoa, algae, and fungi in deep subsurface sediments, Geomicrobiol. J., 7(1-2), 15-31.
54. Sinclair, J. L., S. J. Randtke, J. E. Denne, L. R. Hathaway, and W. C. Ghiorse (1990), Survey of microbial populations in buried valley aquifer sediments from northeastern Kansas, Ground Water, 28(3), 369-377.
55. Sridharan, A., and A. G. Altschaeffl (1971), Pore size distribution studies, J. Soil Mech. Found. Div. Am. Soc. Civ. Eng., SM5, 771-787.
56. Sun, Y., K. T. Wan, K. P. Roberts, J. C. Bischof, and B. J. Nelson (2003), Mechanical property characterization of mouse zona pellucida, IEEE Trans. Nanobiosci., 2(4), 279-286.
57. Tanaka, H., D. R. Shiwakoti, N. Omukai, F. Rito, J. Locat, and M. Tanaka (2003), Pore size distribution of clayey soils measured by mercury intrusion porosimetry and its relation to hydraulic conductivity, Soils Found., 43(6), 63-73.
58. Thwaites, J. J., and U. C. Surana (1991), Mechanical properties of Bacillus subtilis cell walls-ffects of removing residual culture medium, J. Bacteriol., 173(1), 197-203.
59. Thwaites, J. J., U. C. Surana, and A. M. Jones (1991), Mechanical properties of Bacillus subtilis cell walls-Effects of ions and lysozyme, J. Bacteriol., 173(1), 204-210.
60. Treves, D. S., B. Xia, J. Zhou, and J. M. Tiedje (2003), A twospecies test of the hypothesis that spatial isolation influences microbial diversity in soil, Microbial Ecol., 45(1), 20-28.
61. Updegraff, D. M. (1982), Plugging and penetration of reservoir rock by microorganisms, paper presented at International Conference in Microbial Enhancement of Oil Recovery, U.S. Dept. of Energy, Bartlesville, Okla.
62. Vasseur, G., I. Djeranmaigre, D. Grunberger, G. Rousset, D. Tessier, and B. Velde (1995), Evolution of structural and physical parameters of clays during experimental compaction, Mar. Petrol. Geol., 12(8), 941-954.
63. Wellsbury, P., R. A. Herbert, and R. J. Parkes (1996), Bacterial activity and production in near-surface estuarine and freshwater sediments, FEMS Microbiol. Ecol., 19(3), 203-214.
64. Wellsbury, P., I. Mather, and R. J. Parkes (2002), Geomicrobiology of deep, low organic carbon sediments in the Woodlark Basin, Pacific Ocean, FEMS Microbiol. Ecol., 42(1), 59-70.
65. Yang, Y. L., and A. C. Aplin (1998), Influence of lithology and compaction on the pore size distribution and modelled permeability of some mudstones from the Norwegian margin, Mar. Petrol. Geol., 15(2), 163-175.
66. Yao, X., M. Jericho, D. Pink, and T. Beveridge (1999), Thickness and elasticity of gram-negative murein sacculi measured by atomic force microscopy, J. Bacteriol., 181(22), 6865-6875.
67. Zhang, C. L., A. V. Palumbo, T. J. Phelps, J. J. Beauchamp, F. J. Brockman, C. J. Murray, B. S. Parsons, and D. J. P. Swift (1998), Grain size and depth constraints on microbial variability in coastal plain subsurface sediments, Geomicrobiol. J., 15(3), 171-185.
68. Zhou, J. Z., B. C. Xia, D. S. Treves, L. Y. Wu, T. L. Marsh, R. V. O'Neill, A. V. Palumbo, and J. M. Tiedje (2002), Spatial and resource factors influencing high microbial diversity in soil, Appl. Environ. Microbiol., 68(1), 326-334.
69. Zhou, J. Z., B. C. Xia, H. Huang, A. V. Palumbo, and J. M. Tiedje (2004), Microbial diversity and heterogeneity in sandy subsurface soils, Appl. Environ. Microbiol., 70(3), 1723-1734.
70. Zweifel, U. L., and A. Hagstrom (1995), Total counts of marine- bacteria include a large fraction of non-nucleoid-containing bacteria (ghosts), Appl. Environ. Microbiol., 61(6), 2180-2185.