REFERENCES
- Alfreider , A , Krossbacher , M and Psenner , R . 1997 . Groundwater samples do not reflect bacterial densities and activity in subsurface systems . Water Res , 31 : 832 – 840 .
- Almas , A R , Mulder , J and Bakken , L R . 2005 . Trace metal exposure of soil bacteria depends on their position in the soil matrix . Environ Sci Technol , 39 : 5927 – 5932 .
- Amy , P S , Haldeman , D L , Ringelberg , D , Hall , D H and Russell , C . 1992 . Comparison of identification systems for classification of bacteria isolated from water and endolithic habitats within the deep subsurface . Appl Environ Microbiol , 58 : 3367 – 3373 .
- Anderson , R T and Lovley , D R . 1999 . Ecology and biogeochemistry of in situ groundwater bioremediation . Adv Microb Ecol , 15 : 289 – 350 .
- Barcelona , M J and Xie , G . 2001 . In situ lifetimes and kinetics of a reductive whey barrier and an oxidative ORC barrier in the subsurface . Environ Sci Technol , 35 : 3378 – 3385 .
- Bekins , B A , Godsy , E M and Warren , E . 1999 . Distribution of microbial physiologic types in an aquifer contaminated by crude oil . Microb Ecol , 37 : 263 – 275 .
- Blackwelder , D B and Radtke , C W . Meso-scale treatability study using field deployable, flow-through microcosms . Proceedings of the 8th In Situ and On-Site Bioremediation Symposium . June 6–9 . Edited by: Alleman , B C and Kelley , M E . Baltimore, MD : Battelle Press .
- Crump , B C , Armbrust , E V and Baross , J A . 1999 . Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary, and the adjacent coastal ocean . Appl Environ Microbiol , 65 : 3192 – 3204 .
- Cullimore , D R . 1993 . Practical Groundwater Microbiology , Boca Raton : Lewis Publishers .
- Davis , J P . 1967 . Petroleum Microbiology , New York : Elsevier .
- Dodds , W K , Randel , C A and Edler , C C . 1996 . Microcosms for aquifer research: application to colonization of various sized particles by ground-water microorganisms . Ground Water , 34 ( 4 ) : 756 – 759 .
- Ekendahl , S , Arlinger , J , Stahl , F and Pedersen , K . 1994 . Characterization of attached bacterial populations in deep granitic groundwater from the Stripa research mine by 16S rRNA gene sequencing and scanning electron microscopy . Microbiology , 140 : 1575 – 1583 .
- Ekendahl , S and Pedersen , K . 1994 . Carbon transformations by attached bacterial populations in granitic groundwater from deep crystalline bed-rock of the Stripa research mine . Microbiology , 140 : 1565 – 1573 .
- Erwin , D P , Erickson , I K , Delwiche , M E , Colwell , F S , Strap , J L and Crawford , R L . 2005 . Diversity of oxygenase genes from the methane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain aquifer . Appl Environ Microbiol , 71 : 2016 – 2025 .
- Fennell , D E , Carroll , A B , Gossett , J M and Zinder , S H . 2001 . Assessment of indigenous reductive dechlorinating potential at a TCE-contaminated site using microcosms, polymerase chain reaction analysis, and site data . Environ Sci Technol , 35 : 1830 – 1839 .
- Garland , J L and Mills , A L . 1991 . Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-cource utilization . Appl Environ Microbiol , 57 : 2351 – 2359 .
- Gerba , C P and Bitton , G . 1984 . “ Microbial pollutants—their survival and transport pattern to groundwater ” . In Groundwater Pollution Microbiology , Edited by: Bitton , G and Gerba , C P . 65 – 88 . New York : John Wiley and Sons .
- Ghiorse , W C . 1997 . Subterranean life . Science , 275 : 789 – 790 .
- Ghiorse , W C and Wilson , J T . 1988 . Microbial ecology of the terrestrial subsurface . Adv Appl Microbiol , 33 : 107 – 173 .
- Gillham , R W , Starr , R C and Miller , D J . 1990 . A device for in situ determination of geochemical transport parameters, 2. biochemical reactions . Ground Water , 28 : 858 – 862 .
- Godsy , E M , Goerlitz , D F and Grbic Galic , D . 1992 . Methanogenic biodegradation of creosote contaminants in natural and simulated groundwater ecosystems . Ground Water , 30 : 232 – 242 .
- Goldscheider , N , Hunkeler , D and Rossi , P . 2006 . Review: microbial biocenosis in pristine aquifers and an assessment of investigative methods . Hydrogeol J , 14 : 926 – 941 .
- Griebler , C , Mindl , B , Slezak , D and Geiger-Kaiser , M . 2002 . Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microocosm . Aquat Microb Ecol , 28 : 117 – 129 .
- Griffin , W T , Phelps , T J , Colwell , F S and Long , P E . 1997 . “ Methods for obtaining deep subsurface microbiological samples by drilling ” . In The Microbiology of the Terrestrial Deep Subsurface , Edited by: Amy , P S and Haldeman , D L . 23 – 44 . Boca Raton : CRC Press .
- Harvey , R W , Smith , R L and George , L . 1984 . Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., aquifer . Appl Environ Microbiol , 48 : 1197 – 1202 .
- Hazen , T C , Jimenez , L , de Victoria , G L and Fliermans , C B . 1991 . Comparison of bacteria from deep subsurface sediment and adjacent groundwater . Microb Ecol , 22 : 293 – 304 .
- Hendrickx , B , Dejonghe , W , Boenne , W , Brennerova , M , Cernik , M , Lederer , T , Bucheli-Witschel , M , Bastiaens , L , Verstraete , W and Top EM and others . 2005 . Dynamics of oligtrophophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ microcosm study . Appl Environ Microbiol , 71 : 3815 – 3825 .
- Hirsch , P and Rades-Rohkohl , E . 1988 . Some special problems in the determination of viable counts of groundwater microorganisms . Microb Ecol , 16 : 99 – 113 .
- Hirsch , P and Rades-Rohkohl , E . 1990 . Microbial colonization of aquifer sediment exposed in a groundwater well in northern germany . Appl Environ Microbiol , 56 : 2963 – 2966 .
- Holm , P E , Nielsen , P H , Albrechtsen , H-J and Christensen , T H . 1992 . Importance of unattached bacteria and bacteria attached to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer . Appl and Environ Microbiol , 58 : 3020 – 3026 .
- Keswick , B H . 1984 . “ Sources of groundwater pollution ” . In Groundwater Pollution Microbiology , Edited by: Bitton , G and Gerba , C P . 39 – 64 . New York : Wiley-Interscience .
- Kolbel-Boelke , J , Anders , E-M and Nehrkorn , A . 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 .
- Kovacik , W P , Takai , K , Mormile , M R , McKinley , J P , Brockman , F J , Fredrickson , J K and Holben , W E . 2006 . Molecular analysis of deep subsurface Cretaceous rock indicates abundant Fe(III)- and S0-reducing bacteria in a sulfate-rich environment . Environ Microbiol , 8 : 141 – 155 .
- Krumholz , L R , McKinley , J P , Ulrich , G A and Suflita , J M . 1997 . Confined subsurface microbial communities in Cretaceous rock . Nature , 386 : 64 – 66 .
- Lehman , R M , Colwell , F S and Bala , G A . 2001a . Attached and unattached microbial communities in a simulated basalt aquifer under fracture- and porous-flow conditions . Appl Environ Microbiol , 67 : 2799 – 2809 .
- Lehman , R M and O'Connell , S P . 2002 . Comparison of extracellular enzyme activities and community composition of attached and free-living bacteria in porous media columns . Appl Environ Microbiol , 68 : 1569 – 1575 .
- Lehman , R M , O'Connell , S P , Banta , A , Fredrickson , J K , Reysenbach , A-L , Kieft , T L and Colwell , F S . 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 .
- Lehman , R M , Roberto , F F , Earley , D , Bruhn , D F , Brink , S E , O'Connell , S P , Delwiche , M E and Colwell , F S . 2001b . Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer . Appl Environ Microbiol , 67 : 2095 – 2106 .
- Ludvigsen , L , Albrechtsen , H , Ringelberg , D B , Ekelund , F and Christensen , T H . 1999 . Distribution and composition of microbial populations in a landfill leachate contaminated aquifer (Grindsted, Denmark) . Microb Ecol , 37 ( 3 ) : 197 – 207 .
- Madsen , E . 1998 . Epistemology of environmental microbiology . Environ Sci Technol , 32 : 429 – 439 .
- Madsen , E L . 1991 . Determining in situ biodegradation . Environ Sci Technol , 25 : 1663 – 1673 .
- Mandelbaum , R T , Shati , M R and Ronen , D . 1997 . In situ microcosms in aquifer bioremediation studies . FEMS Microbiol Rev , 20 : 489 – 502 .
- Murphy , E M and Ginn , T R . 2000 . Modeling of microbial processes in porous media . Hydrogeol J , 8 : 142 – 158 .
- Nielsen , P H , Bjerg , P L , Nielsen , P , Smith , P and Christensen , T H . 1996a . In situ and laboratory determined first order degradation rate constants of specific organic compounds in an aerobic aquifer . Environ Sci Technol , 30 : 31 – 37 .
- Nielsen , P H , Christensen , T H , Albrechtsen , H J and Gillham , R W . 1996b . Performance of the in situ microcosm technique for measuring the degradation of organic chemicals in aquifers . Ground Water Monitor Remed , 16 : 130 – 140 .
- Nielsen , P H , Holm , P E and Christensen , T H . 1992 . A field method for determination of groundwater and groundwater-sediment associated potentials for degradation of xenobiotic organic compounds . Chemosphere , 25 : 449 – 462 .
- Peacock , A D , Chang , Y-J , Istok , J D , Krumholz , L , Geyer , R , Kinsall , B , Watson , D , Sublette , K L and White , D C . 2004 . Utilization of microbial biofilms as monitors of bioremediation . Microb Ecol , 47 : 284 – 292 .
- Pedersen , K , Arlinger , J , Ekendahl , S and Hallbeck , L . 1996 . 16S rRNA gene diversity of attached and unattached bacteria in boreholes along the access tunnel to the Aspo hard rock laboratory, Sweden . FEMS Microbiol Ecol , 19 : 249 – 262 .
- Pedersen , K and Ekendahl , S . 1990 . Distribution and activity of bacteria in deep granitic groundwaters of southeastern Sweden . Microb Ecol , 20 : 37 – 52 .
- Pedersen , K and Ekendahl , S . 1992 . Assimilation of CO2 and introduced organic compounds by bacterial communities in groundwater from southeastern Sweden deep crystalline bedrock . Microb Ecol , 23 : 1 – 14 .
- Phelps , T J and Fredrickson , J K . 2002 . “ Drilling, Coring, and Sampling Subsurface Environments ” . In Manual of Environmental Microbiology. , 2 ed. , Edited by: Hurst , C J , Crawford , R L , Knudsen , G R , McInerney , M J and Stetzenbach , L D . 526 – 540 . Washington, DC : ASM Press .
- Reardon , C L , Cummings , D E , Petzke , L M , Kinsall , B L , Watson , D B , Peyton , B M and Geesey , G G . 2004 . Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer . Appl Environ Microbiol , 70 : 6037 – 6046 .
- Roling , W FM , van Breukelen , B M , Braster , M , Lin , B and van Verseveld , H W . 2001 . Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer . Appl Environ Microbiol , 67 : 4619 – 4629 .
- Ronen , D , Magaritz , M and Levy , Y . 1986 . A multi-layer sampler for the study of detailed hydrochemical profiles in groundwater . Water Res , 20 : 311 – 315 .
- Smith , D C , Simon , M , Alldredge , A L and Azam , F . 1992 . Intense hydrolytic enzyme activity on marine aggregates and implications for rapid particle dissolution . Nature , 359 : 139 – 142 .
- Stevens , T O , McKinley , J P and Fredrickson , J K . 1993 . Bacterial associated with deep, alkaline, anaerobic groundwaters in southeast Washington . Microb Ecol , 25 : 35 – 50 .
- Takai , K , Mormile , M R , McKinley , J P , Brockman , F J , Holben , W E , Kovacik , W P and Fredrickson , J K . 2003 . Shifts in Archaeal communities associated with lithological and geochemical variations in subsurface Cretaceous rock . Environ Microbiol , 5 : 309 – 320 .
- Thomas , J M , Lee , M D and Ward , C H . 1987 . Use of ground water in assessment of biodegradation potential in the subsurface . Environ Toxicol Chem , 6 : 607 – 614 .
- Winding , A . 1994 . “ Fingerprinting bacterial soil communities using Biolog microtitre plates ” . In Beyond the Biomass: Compositional and Functional Analysis of Soil Microbial Communities , Edited by: Ritz , K , Dighton , J and Giller , K E . 85 – 94 . Chichester : John Wiley and Sons .