Microbiological Comparison of Core and Groundwater Samples Collected from a Fractured Basalt Aquifer with that of Dialysis Chambers Incubated In Situ

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 .
   Web of Science ®Google Scholar
• Altschul , SF , Gish , W , Miller , W , Myers , EW and Lipman , DJ. 1990 . Basic local alignment search tool . J Mol Biol , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Atlas , RM. 1993 . Handbook of Microbiological Media , Boca Raton, FL : CRC Press .
   Google Scholar
• Balkwill , DL and Ghiorse , WC. 1985 . Characterization of subsurface bacteria associated with two shallow aquifers in Oklahoma . Appl Environ Microbiol , 50 : 580 – 588 .
   PubMed Web of Science ®Google Scholar
• Bekins , BA , Godsy , EM and Warren , E. 1999 . Distribution of microbial physiologic types in an aquifer contaminated by crude oil . Microb Ecol , 37 : 263 – 275 .
   PubMed Web of Science ®Google Scholar
• Boone , D , Liu , Y , Zhao , Z , Balkwill , D , Drake , G , Stevens , T and Aldrich , H. 1995 . Bacillus infernus sp nov, an Fe(III)- and Mn(IV)-reducing anaerobe from the deep terrestrial subsurface . Int J System Bacteriol , 45 : 441 – 448 .
   PubMedGoogle Scholar
• Bowman , JP , Jimenez , L , Rosario , I , Hazen , TC and Sayler , GS. 1993 . Characterization of the methanotrophic bacterial community present in a trichloroethylene-contaminated subsurface groundwater site . Appl Environ Microbiol , 59 : 2380 – 2387 .
   PubMed Web of Science ®Google Scholar
• Brockman , FJ and Murray , CJ. 1997 . Subsurface microbiological heterogeneity: current knowledge, descriptive approaches and applications . FEMS Microbiol Rev , 20 : 231 – 247 .
   Web of Science ®Google Scholar
• Demezas , DH and Bottomley , PJ. 1986 . Autecology in rhizospheres and nodulating behavior of indigenous. Rhizobium trifolii . Appl Environ Microbiol , 52 : 1014 – 1019 .
   PubMed Web of Science ®Google Scholar
• Doong , R-A , Chen , T-F and Wu , Y-W . 1997 . Anaerobic dechlorination of carbon tetrachloride by free-living and attached bacteria under various electron-donor conditions . Appl Microbiol Biotechnol , 47 : 317 – 323 .
   Google Scholar
• Franklin , RB , Taylor , DR and Mills , AL. 1999 . The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer . Microb Ecol , 38 ( 4 ) : 377 – 386 .
   PubMed Web of Science ®Google Scholar
• Fredrickson , JK and Phelps , TJ. 1997 . “ Subsurface drilling and sampling ” . In Manual of Environmental Microbiology , Edited by: Hurst , CJ , Knudsen , GR , McInerney , MJ , Stetzenbach , LD and Walter , MV . p 526 – 540 . Washington, DC : ASM Press .
   Google Scholar
• Garland , JL. 1996 . Analytical approaches to the characterization of samples of microbial communities using patterns of potential C source utilization . Soil Biol Biochem , 28 : 213 – 221 .
   Web of Science ®Google Scholar
• Garland , JL. 1997 . Analysis and interpretation of community-level physiological profiles in microbial ecology . FEMS Microbiol Ecol , 24 : 289 – 300 .
   Web of Science ®Google Scholar
• Garland , JL and Mills , AL. 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 .
   PubMed Web of Science ®Google Scholar
• Ghiorse , WC and Wilson , JT. 1988 . Microbial ecology of the terrestrial subsurface . Adv Appl Microbiol , 33 : 107 – 173 .
   PubMed Web of Science ®Google Scholar
• Godsy , EM , Goerlitz , DF and Grbic Galic , D. 1992 . Methanogenic biodegradation of creosote contaminants in natural and simulated groundwater ecosystems . Ground Water , 30 : 232 – 242 .
   Web of Science ®Google Scholar
• Gordon , DA and Giovannoni , SJ. 1996 . Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans . Appl Environ Microbiol , 62 : 1171 – 1177 .
   PubMed Web of Science ®Google Scholar
• Gounot , AM. 1994 . “ Microbial ecology of groundwaters ” . In Groundwater Ecology , Edited by: Gibert , J , Danielopol , DL and Stanford , JA . p 189 – 207 . New York : Academic Press .
   Google Scholar
• Griffin , WT , Phelps , TJ , Colwell , FS and Long , PE. 1997 . “ Methods for obtaining deep subsurface microbiological samples by drilling ” . In The Microbiology of the Terrestrial Deep Subsurface , Edited by: Amy , PS and Haldeman , DL . p 23 – 44 . Boca Raton, FL : CRC Press .
   Google Scholar
• Guerin , WF and Boyd , SA. 1997 . Bioavailability of naphthalene associated with natural and synthetic sorbents . Water Res , 31 : 1504 – 1512 .
   Web of Science ®Google Scholar
• Harvey , RW , Smith , RL 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 .
   PubMed Web of Science ®Google Scholar
• Hazen , TC , Jimenez , L , de Victoria , GL and Fliermans , CB. 1991 . Comparison of bacteria from deep subsurface sediment and adjacent groundwater . Microb Ecol , 22 : 293 – 304 .
   PubMed Web of Science ®Google Scholar
• Hirsch , P and Rades-Rohkohl , E. 1988 . Some special problems in the determination of viable counts of groundwater microorganisms . Microb Ecol , 16 : 99 – 113 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Holm , PE , Nielsen , PH , Albrechtsen , H-J and Christensen , TH. 1992 . Importance of unattached bacterial and bacteria attached to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer . Appl Environ Microbiol , 58 : 3020 – 3026 .
   PubMedGoogle Scholar
• Kepner , RL and Pratt , JR. 1994 . Use of fluorochromes for direct enumeration of total bacteria in environmental samples: past and present . Microbiology , 58 : 603 – 615 .
   Google Scholar
• Kieft , TL , Fredrickson , JK , McKinley , JP , Bjornstad , BN , Rawson , SA , Phelps , TJ , Brockman , FJ and Pfiffner , SM. 1995 . Microbiological comparisons within and across contiguous lacustrine, paleosol, and fluvial subsurface sediments . Appl Environ Microbiol , 61 : 749 – 757 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Lehman , RM , Roberto , FF , Earley , D , Bruhn , DF , Brink , SE , O'Connell , SP , Delwiche , ME and Colwell , FS. 2001 . Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer . Applied and Environ Microbiol , 67 : 2095 – 2106 .
   PubMed Web of Science ®Google Scholar
• Lovley , DR and Phillips , EJP. 1986 . Organic-matter mineralization with reduction of ferric iron in anaerobic sediments . Appl Environ Microbiol , 51 : 683 – 689 .
   PubMed Web of Science ®Google Scholar
• Marshall , KC. 1992 . “ Planktonic versus sessile life of prokaryotes ” . In The Prokaryotes: a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications , Edited by: Balows , A , Truper , HG , Dworkin , M , Harder , W and Schleifer , KH . p 262 – 275 . New York : Springer-Verlag .
   Google Scholar
• McKinley , JP and Colwell , FS. 1996 . Application of perfluorocarbon tracers to microbial sampling in subsurface environments using mud-rotary and air-rotary drilling techniques . J Microbiol Meth , 26 : 1 – 9 .
   Web of Science ®Google Scholar
• Murphy , EM , Ginn , TR , Chilakapati , A , Resch , CT , Phillips , JL , Wietsma , TW and Spadoni , CM. 1997 . The influence of physical heterogeneity on microbial degradation and distribution in porous media . Water Res Res , 33 : 1087 – 1103 .
   Web of Science ®Google Scholar
• Muyzer , G , DeWaal , EC and Uitterlinden , AG. 1993 . Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA . Appl Environ Microbiol , 59 : 695 – 700 .
   PubMed Web of Science ®Google Scholar
• O'Connell , S , Lawson , RD , Watwood , ME and Lehman , RM. 2000 . BASIC program for reduction of data from community-level physiological profiling using Biolog microplates: rationale and critical interpretation of data . J Microbiol Meth , 40 : 213 – 220 .
   PubMed Web of Science ®Google Scholar
• Pedersen , K. 2000 . Exploration of deep intraterrestrial microbial life: current perspectives . FEMS Microbiol Lett , 185 : 9 – 16 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Pedersen , K and Ekendahl , S. 1990 . Distribution and activity of bacteria in deep granitic groundwaters of southeastern Sweden . Microb Ecol , 20 : 37 – 52 .
   PubMed Web of Science ®Google Scholar
• 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 .
   PubMed Web of Science ®Google Scholar
• Reasoner , DJ and Geldreich , EE. 1985 . A new medium for the enumeration and subculture of bacteria from potable water . Appl Environ Microbiol , 49 : 1 – 7 .
   PubMed Web of Science ®Google Scholar
• Rolleke , S , Muyzer , G , Wawer , C , Wanner , G and Lubitz , W. 1996 . Identification of bacteria in a biodegraded wall painting by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA . Appl Environ Microbiol , 62 : 2059 – 2065 .
   PubMed Web of Science ®Google Scholar
• 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 .
   Web of Science ®Google Scholar
• Rosswall , T and Kvillner , E. 1978 . Principal-Components and Factor Analysis for the Description of Microbial Populations , New York : Plenum Press .
   Google Scholar
• Russell , BF , Phelps , TJ , Griffin , WT and Sargent , KA. 1992 . Procedures for sampling deep subsurface microbial communities in unconsolidated sediments . Ground Water Monitor Rev , 12 : 96 – 104 .
   Web of Science ®Google Scholar
• Shati , MR , Ronen , D and Mandelbaum , R. 1996 . Method for in situ study of bacterial activity in aquifers . Environ Sci Technol , 30 : 2646 – 2653 .
   Google Scholar
• Shuter , E and Pemberton , RR. 1978 . “ Inflatable straddle packers and associated equipment for hydraulic fracturing and hydraulic testing ” . In USGS Water-Investigations , 78 – 55 . Denver : USGS Water Resources Division .
   Google Scholar
• Thomas , JM , Lee , MD and Ward , CH. 1987 . Use of ground water in assessment of biodegradation potential in the subsurface . Environ Toxicol Chem , 6 : 607 – 614 .
   Web of Science ®Google Scholar
• Van Loosdrecht , MCM , Lyklema , J , Norde , W and Zehnder , AJB. 1990 . Influence of interfaces on microbial activity . Microbiol Rev , 54 : 75 – 87 .
   PubMedGoogle Scholar
• Vetriani , C , Jannasch , HW , MacGregor , BJ , Stahl , DA and Reysenbach , A-I . 1999 . Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments . Appl Environ Microbiol , 65 : 4375 – 4384 .
   PubMed Web of Science ®Google Scholar
• White , DC. 1979 . “ Lipid analysis of sediments for microbial biomass and community structure ” . In Methodology for Biomass Determinations and Microbial Activities in Sediments, Vol ASTM, STP 673 , Edited by: Litchfield , CD and Seyfreid , PL . p 87 – 103 . Philadelphia : American Society for Testing and Materials .
   Google Scholar
• Wood , WW and Low , WH. 1986 . Aqueous geochemistry and diagenesis in the eastern Snake River Plain aquifer system, Idaho . Geol Soc Amer Bull , 97 : 1456 – 1466 .
   Google Scholar