Attached and suspended microbial communities in a pristine confined aquifer

Water Resources Research

Volumn 44, Issue 7, 2008, Pages

  Flynn, Theodore M ^a   Sanford, Robert A ^a   Bethke, Craig M ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DIGITAL SIGNAL PROCESSING; GROUNDWATER; HYDROGEOLOGY; POPULATION STATISTICS; SEDIMENTATION; UNDERGROUND RESERVOIRS; WELLS;

COMMUNITY OR; CONFINED AQUIFERS; GEOBACTER; ILLINOIS; IN-SITU; IRON-REDUCING BACTERIA; MICROBIAL COMMUNITIES; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

GROUNDWATER RESOURCES;

BACTERIUM; CLONE; COMPARATIVE STUDY; CONFINED AQUIFER; FILTRATION; IN SITU MEASUREMENT; MICROBIAL COMMUNITY; MULTIVARIATE ANALYSIS; POLYMORPHISM; PRISTINE ENVIRONMENT;

ILLINOIS; MAHOMET AQUIFER; NORTH AMERICA; UNITED STATES;

BACTERIA (MICROORGANISMS); GEOBACTER; GEOTHRIX;

EID: 53649099233     PISSN: 00431397     EISSN: None     Source Type: Journal    
DOI: 10.1029/2007WR006633     Document Type: Article

References (70)

1. Alfreider, A., M. Krössbacher, and R. Psenner (1997), Groundwater samples do not reflect bacterial densities and activity in subsurface systems, Water Res., 31, 832-840, doi:10.1016/S0043-1354(96)00311-9.
2. Bekins, B. A., E. M. Godsy, and E. Warren (1999), Distribution of microbial physiologic types in an aquifer contaminated by crude oil, Microb. Ecol., 37, 263-275, doi:10.1007/s002489900149.
3. Bent, S. J., J. D. Pierson, L. J. Forney, R. Danovaro, G. M. Luna, A. Dell'Anno, and B. Pietrangeli (2007), Measuring species richness based on microbial community fingerprints: The emperor has no clothes, Appl. Environ. Microbiol., 73, 2399-2401, doi:10.1128/AEM.02383-06.
4. Bitton, G., and C. P. Gerba (1984), Groundwater pollution microbiology: The emerging issue, in Groundwater Pollution Microbiology, edited by G. Bitton and C. P. Gerba, pp. 65-88, John Wiley, New York.
5. Blackwood, C. B., D. Hudleston, D. R. Zak, and J. S. Buyer (2007), Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: Insights from simulated microbial communities, Appl. Environ. Microbiol., 73, 5276-5283, doi:10.1128/AEM.00514-07.
6. Bray, J. R., and J. T. Curtis (1957), An ordination of the upland forest communities of southern Wisconsin, Ecol. Monogr., 27, 326-349, doi:10.2307/1942268.
7. Burch, S. L. (2005), Development of an observation well network in the Mahomet aquifer of east-central Illinois, Data/Case Study 2005-01, 33 pp., Cent. for Groundwater Sci., Ill. State Water Surv., Champaign, Ill.
8. Caccavo, F., Jr., and A. Das (2002), Adhesion of dissimilatory Fe(III)-reducing bacteria to Fe(III) minerals, Geomicrobiol. J., 19, 161-177, doi:10.1080/01490450252864262.
9. Chapelle, F. H. (2000), The significance of microbial processes in hydrogeology and geochemistry, Hydrogeol. J., 8, 41-46, doi:10.1007/PL00010973.
10. Chapelle, F. H. (2001), Ground-Water Microbiology and Geochemistry, 2nd ed., 477 pp., John Wiley, New York.
11. Chapelle, F. H., and D. R. Lovley (1992), Competitive exclusion of sulfate reduction by Fe(III)-reducing bacteria: A mechanism for producing discrete zones of high-iron ground water, Ground Water, 30, 29-36, doi:10.1111/j.1745-6584.1992.tb00808.x.
12. Clarke, K. R., and R. M. Warwick (2001), Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd ed., 172 pp., PRIMER-E, Ltd., Plymouth, U. K.
13. Cole, J. R., B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje (2007), The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data, Nucleic Acids Res., 35, D169-D172, doi:10.1093/nar/gkl889.
14. Cozzarelli, I. M., and J. V. Weiss (2007), Biogeochemistry of aquifer systems, in Manual of Environmental Microbiology, edited by C. J. Hurst et al., pp. 843-859, ASM Press, Washington, D. C.
15. DeLong, E. F., and N. R. Pace (2001), Environmental diversity of Bacteria and Archaea, Syst. Biol., 50, 470-478, doi:10.1080/106351501750435040.
16. Dunbar, J., L. O. Ticknor, and C. R. Kuske (2000), Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis, Appl. Environ. Microbiol., 66, 2943-2950, doi:10.1128/AEM.66.7.2943-2950.2000.
17. Fierer, N., and R. B. Jackson (2006), The diversity and biogeography of soil bacterial communities, Proc. Natl. Acad. Sci. U. S. A., 103, 626-631, doi:10.1073/pnas.0507535103.
18. Fierer, N., C. B. Blackwood, D. R. Zak, and J. S. Buyer (2007), Tilting at windmills: A response to a recent critique of terminal restriction fragment length polymorphism data, Appl. Environ. Microbiol., 73, 8041-8042, doi:10.1128/AEM.02140-07.
19. Forney, L. J., X. Zhou, and C. J. Brown (2004), Molecular microbial ecology: Land of the one-eyed king, Curr. Opin. Microbiol., 7, 210-220, doi:10.1016/j.mib.2004.04.015.
20. Griebler, C., B. Mindl, D. Slezak, and M. Geiger-Kaiser (2002), Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm, Aquat. Microb.Ecol., 28, 117-129, doi:10.3354/ame028117.
21. Guha, H. (2004), Biogeochemical influence on transport of chromium in manganese sediments: Experimental and modeling approaches, J. Contam. Hydrol., 70, 1-36, doi:10.1016/j.jconhyd.2003.08.012.
22. Hackley, K. C. (2002), A chemical and isotopic investigation of the groundwater in the Mahomet Bedrock Valley aquifer: Age, recharge and geochemical evolution of the groundwater, Ph.D. thesis, 152 pp., Univ. of Ill. at Urbana-Champaign, Urbana.
23. Hartmann, M., and F. Widmer (2008), Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling, FEMS Microbiol. Ecol., 63, 249-260.
24. Harvey, R. W., R. L. Smith, and L. George (1984), Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., aquifer, Appl. Environ. Microbiol., 48, 1197-1202.
25. Hazen, T. C., L. Jiménez, G. López de Victoria, and C. B. Fliermans (1991), Comparison of bacteria from deep subsurface sediment and adjacent groundwater, Microb. Ecol., 22, 293-304, doi:10.1007/BF02540231.
26. Hirsch, P., and E. Rades-Rohkohl (1990), Microbial colonization of aquifer sediment exposed in a groundwater well in northern Germany, Appl. Environ. Microbiol., 56, 2963-2966.
27. Hirsch, P., E. Rades-Rohkohl, J. Kolbel-Boelke, A. Nehrkorn, R. Schweisfurth, F. Selenka, and A. Hack (1992), Methods of studying ground water microbiology: Critical evaluations and method suggestions, in Progress in Hydrogeochemistry, edited by G. Matthess et al., pp. 325-333, Springer, Heidelberg, Germany.
28. Holm, P. E., P. H. Nielsen, H. J. Albrechtsen, and T. H. Christensen (1992), Importance of unattached bacteria and bacteria attached to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer, Appl. Environ. Microbiol., 58, 3020-3026.
29. Hugenholtz, P., B. M. Goebel, and N. R. Pace (1998), Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J. Bacteriol., 180, 4765-4774.
30. Jarman, S. N. (2006), Cleaver: Software for identifying taxon specific restriction endonuclease recognition sites, Bioinformatics, 22, 2160-2161, doi:10.1093/bioinformatics/btl330.
31. Kelly, W. R., T. R. Holm, S. D. Wilson, and G. S. Roadcap (2005), Arsenic in glacial aquifers: Sources and geochemical controls, Ground Water, 43, 500-510, doi:10.1111/j.1745-6584.2005.0058.x.
32. Kieft, T. L., T. J. Phelps, and J. K. Fredrickson (2007), Drilling, coring, and sampling subsurface environments, in Manual of Environmental Microbiology, edited by C. J. Hurst et al., pp. 799-817, ASM Press, Washington, D. C.
33. Kirk, M. F., T. R. Holm, J. Park, Q. Jin, R. A. Sanford, B. W. Fouke, and C. M. Bethke (2004), Bacterial sulfate reduction limits natural arsenic contamination in groundwater, Geology, 32, 953-956, doi:10.1130/G20842.1.
34. Klaus, J. S., I. Janse, J. M. Heikoop, R. A. Sanford, and B. W. Fouke (2007), Coral microbial communities, zooxanthellae and mucus along gradients of seawater depth and coastal pollution, Environ. Microbiol., 9, 1291-1305.
35. Kölbel-Boelke, J., E. M. Anders, and A. Nehrkorn (1988), Microbial communities in the saturated groundwater environment II: Diversity of bacterial communities in a Pleistocene sand aquifer and their in vitro activities, Microb. Ecol., 16, 31-48, doi:10.1007/BF02097403.
36. Kruskal, J. ( 1964), Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis, Psychometrika, 29, 1-27, doi:10.1007/BF02289565.
37. Lehman, R. M., F. F. Roberto, D. Earley, D. F. Bruhn, S. E. Brink, S. P. O'Connell, M. E. Delwiche, and F. S. Colwell (2001), Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer, Appl. Environ. Microbiol., 67, 2095-2106, doi:10.1128/AEM.67.5. 2095-2106.2001.
38. Lehman, R. M., S. P. O'Connell, A. Banta, J. K. Fredrickson, A. L. Reysenbach, T. L. Kieft, and F. S. Colwell (2004), Microbiological comparison of core and groundwater samples collected from a fractured basalt aquifer with that of dialysis chambers incubated in situ, Geomicrobiol. J., 21, 169-182, doi:10.1080/01490450490275848.
39. Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney (1997), Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA, Appl. Environ. Microbiol., 63, 4516-4522.
40. Lovley, D. R. (1997), Potential for anaerobic bioremediation of BTEX in petroleum-contaminated aquifers, J. Ind. Microbiol. Biotechnol., 18, 75-81, doi:10.1038/sj.jim.2900246.
41. Lovley, D. R., D. E. Holmes, and K. P. Nevin (2004), Dissimilatory Fe(III) and Mn(IV) reduction, Adv. Microb. Physiol., 49, 219-286, doi:10.1016/S0065-2911(04)49005-5.
42. Madsen, E. L. (2000), Nucleic-acid characterization of the identity and activity of subsurface microorganisms, Hydrogeol. J., 8, 112-125, doi:10.1007/s100400050012.
43. Marsh, T. L. (2005), Culture-independent microbial community analysis with terminal restriction fragment length polymorphism, Methods Enzymol., 397, 308-329, doi:10.1016/S0076-6879(05)97018-3.
44. Marshall, K. C. (2006), Planktonic versus sessile life of prokaryotes, in The Prokaryotes, edited by M. Dworkin et al., pp. 3-15, Springer, New York.
45. Martin-Laurent, F., L. Philippot, S. Hallet, R. Chaussod, J. C. Germon, G. Soulas, and G. Catroux (2001), DNA extraction from soils: Old bias for new microbial diversity analysis methods, Appl. Environ. Microbiol., 67, 2354-2359, doi:10.1128/AEM.67.5.2354-2359.2001.
46. Marxsen, J. (1982), A new method for the investigation of bacterial occurrence in groundwater-bearing sandy sediments, Arch. Hydrobiol., 95, 221-233.
47. Mauck, B. S., and J. A. Roberts (2007), Mineralogic control on abundance and diversity of surface-adherent microbial communities, Geomicrobiol. J., 24, 167-177, doi:10.1080/01490450701457162.
48. McGuinness, L. M., M. Salganik, L. Vega, K. D. Pickering, and L. J. Kerkhof (2006), Replicability of bacterial communities in denitrifying bioreactors as measured by PCR/T-RFLP analysis, Environ. Sci. Technol., 40, 509-515, doi:10.1021/es0509001.
49. Mehnert, E., K. C. Hackley, T. H. Larson, S. V. Panno, A. Pugin, H. A. Wehrmann, T. R. Holm, G. S. Roadcap, S. D. Wilson, and K. L. Warner (2004), The Mahomet aquifer: Recent advances in our knowledge, Open File Ser. 2004-16, Ill. State Geol. Surv., Champaign.
50. Moeseneder, M. M., J. M. Arrieta, G. Muyzer, C. Winter, and G. J. Herndl (1999), Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis, Appl. Environ. Microbiol., 65, 3518-3525.
51. Mohn, W. W., and J. M. Tiedje (1992), Microbial reductive dehalogenation, Microbiol. Mol Biol. Rev., 56, 482-507.
52. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl (1986), Microbial ecology and evolution: A ribosomal RNA approach, Annu. Rev. Microbiol., 40, 337-365, doi:10.1146/annurev.mi.40.100186.002005.
53. Osborn, A. M., E. R. B. Moore, and K. N. Timmis (2000), An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics, Environ. Microbiol., 2, 39-50, doi:10.1046/j.1462-2920.2000.00081.x.
54. Panno, S. V., K. C. Hackley, K. Cartwright, and C. L. Liu (1994), Hydrochemistry of the Mahomet Bedrock Valley aquifer, east-central Illinois: Indicators of recharge and ground-water flow, Ground Water, 32, 591-604, doi:10.1111/j.1745-6584.1994.tb00895.x.
55. Park, J., R. A. Sanford, and C. M. Bethke (2006), Geochemical and microbiological zonation of the Middendorf aquifer, South Carolina, Chem. Geol., 230, 88-104, doi:10.1016/j.chemgeo.2005.12.001.
56. Parkinson, D., T. R. G. Gray, and S. T. Williams (1971), Methods for Studying the Ecology of Soil Microorganisms, Blackwell Sci., Oxford, U. K.
57. Peacock, A. D., Y.-J. Chang, J. D. Istok, L. Krumholz, R. Geyer, B. Kinsall, D. Watson, K. L. Sublette, and D. C. White (2004), Utilization of microbial biofilms as monitors of bioremediation, Microb. Ecol., 47, 284-292, doi:10.1007/s00248-003-1024-9.
58. Pedersen, K., J. Arlinger, S. Ekendahl, and L. Hallbeck (1996), 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Äspö Hard Rock Laboratory, Sweden, FEMS Microbiol Ecol., 19, 249-262.
59. Reardon, C. L., D. E. Cummings, L. M. Petzke, B. L. Kinsall, D. B. Watson, B. M. Peyton, and G. G. Geesey (2004), Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer, Appl. Environ. Microbiol., 70, 6037-6046, doi:10.1128/AEM.70.10.6037-6046.2004.
60. Rees, G. N., D. S. Baldwin, G. O. Watson, S. Perryman, and D. L. Nielsen (2004), Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: Application of multivariate statistics, Antonie van Leeuwenhoek, 86, 339-347, doi:10.1007/s10482-004-0498-x.
61. Roden, E. E. (2006), Geochemical and microbiological controls on dissimilatory iron reduction, C. R. Geosci., 338, 456-467, doi:10.1016/j.crte.2006.04.009.
62. Rossi, G. M., S. Riccardo, G. Gesué, M. Stanganelli, and T. K. Wang (1936), Direct microscopic and bacteriological examination of the soil, Soil Sci., 41, 53-66, doi:10.1097/00010694-193601000-00007.
63. Senko, J. M., J. D. Istok, J. M. Suflita, and L. R. Krumholz (2002), In-situ evidence for uranium immobilization and remobilization, Environ. Sci. Technol., 36, 1491-1496, doi:10.1021/es011240x.
64. Sipos, R., A. J. Székely, M. Palatinszky, S. Révész, K. Márialigeti, and M. Nikolausz (2007), Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targeting bacterial community analysis, FEMS Microbiol. Ecol., 60, 341-350, doi:10.1111/j.1574-6941.2007.00283.x.
65. Stahl, D. A., M. Hullar, and S. Davidson (2006), The structure and function of microbial communities, in The Prokaryotes, edited by M. Dworkin et al., pp. 299-327, Springer, New York.
66. Tiedje, J. M., S. Asuming-Brempong, K. Nüsslein, T. L. Marsh, and S. J. Flynn (1999), Opening the black box of soil microbial diversity, Appl. Soil Ecol., 13, 109-122, doi:10.1016/S0929-1393(99)00026-8.
67. Tsai, Y. L., and B. H. Olson (1991), Rapid method for direct extraction of DNA from soil and sediments, Appl. Environ. Microbiol., 57, 1070-1074.
68. von Mering, C., P. Hugenholtz, J. Raes, S. G. Tringe, T. Doerks, L. J. Jensen, N. Ward, and P. Bork (2007), Quantitative phylogenetic assessment of microbial communities in diverse environments. Science, 315, 1126-1130, doi:10.1126/science.1133420.
69. Woese, C. R. (1987), Bacterial evolution, Microbiol. Rev., 51, 221-271.
70. Wolsing, M., and A. Priemé (2004), Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments, FEMS Microbiol. Ecol., 48, 261-271, doi:10.1016/j.femsec.2004.02.002.