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Hydrogeology Journal

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01-09-2006 | Report

Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods

Authors: Nico Goldscheider, Daniel Hunkeler, Pierre Rossi

Published in: Hydrogeology Journal | Issue 6/2006

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Abstract

The current knowledge of microbial biocenoses (communities) in pristine aquifers is presented in a review, which also discusses their relevance for questions of groundwater protection. Aquifers are heterogeneous on all scales and structured in a variety of habitats. The void spaces in many aquifers are small. The biocenoses are thus predominantly composed of microorganisms and, often, microinvertebrates. Larger voids and macroorganisms occur in karst cavities. Due to the absence of light, the biocenoses depend on chemical energy resources, which are, however, scarce in non-contaminated groundwater. The microorganisms thus show small cell sizes, low population densities and reduced activity; they developed specific strategies to survive oligotrophic conditions. The review also discusses the impact of contamination on the biocenoses, and the potential use of the biocenoses or specific organisms as indicators for groundwater quality, and the limits of this approach. Bacteria are either planktonic or attached to aquifer material, which requires both fluid and solid phase sampling. Most groundwater bacteria are viable but non-culturable. Consequently, cultivation techniques give an incomplete picture of the biocenoses, while methods from molecular microbiology provide genetic fingerprints of the entire community. Different analytical methods are available to count microorganisms, identify species, characterise microbial diversity, and measure activity.

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Ackermann H-W, DuBow MS (1987) Viruses of prokaryotes: General properties of bacteriophages, 1. CRC Press, Boca Raton, Florida, 202 pp

Ahn IS, Lee CH (2003) Kinetic studies of attachment and detachment of microbial cells from soil. Environ Technol 24(4):411–418PubMed

Albrechtsen HJ (1994) Distribution of bacteria, estimated by a viable count method, and heterotrophic activity in different size fractions of aquifer sediment. Geomicrobiol J 12(4):253–264

Alfreider A, Krossbacher M, Psenner R (1997) Groundwater samples do not reflect bacterial densities and activity in subsurface systems. Water Res 31(4):832–840CrossRef

Amann R, Fuchs BM, Behrens S (2001) The identification of micro-organisms by fluorescence in situ hybridisation. Curr Opin Biotechnol 12(3):231–236CrossRefPubMed

Amann R, Kühl M (1998) In situ methods for assessment of micro-organisms and their activities. Curr Opin Microbiol 1(3):352–358CrossRefPubMed

Anderson RT, Lovley DR (1997) Ecology and biogeochemistry of in situ groundwater bioremediation. Adv Microbial Ecol 15:289–350

Auckenthaler A, Huggenberger P (ed) (2003) Pathogene Mikroorganismen im Grund- und Trinkwasser [pathogenic microorganisms in groundwater and drinking water]. Birkhäuser Verlag, Basel, 184 pp

Auckenthaler A, Raso G, Huggenberger P (2002) Particle transport in a karst aquifer: natural and artificial tracer experiments with bacteria, bacteriophages and microspheres. Water Sci Technol 46(3):131–138

Baker MA, Valett HM, Dahm CN (2000) Organic carbon supply and metabolism in a shallow groundwater ecosystem. Ecology 81(11):3133–3148

Balkwill DL, Ghiorse WC (1985) Characterization of subsurface bacteria associated with two shallow aquifers in Oklahoma. Appl Environ Microbiol 50(3):580–588PubMed

Balkwill DL, Murphy EM, Fair DM, Ringelberg DB, White DC (1998) Microbial communities in high and low recharge environments: implications for microbial transport in the vadose zone. Microbial Ecol 35(2):156–171CrossRef

Bast E (2001) Mikrobiologische Methoden [microbiological methods]. Spektrum Akademischer Verlag, Heidelberg, 429 pp

Batiot C, Emblanch C, Blavoux B (2003) Total organic carbon (TOC) and magnesium (Mg): two complementary tracers of residence time in karstic systems. Comptes Rendus Geosci 335(2):205–214CrossRef

Baur WH (2003) Gewässergüte bestimmen und beurteilen [determination and evaluation of water quality]. VFG, 209 pp

Beloin RM, Sinclair JL, Ghiorse WC (1988) Distribution and activity of micro-organisms in subsurface sediments of a pristine study site in Oklahoma. Microbial Ecol 16(1):85–97CrossRef

Bloom Y, Aravena R, Hunkeler D, Edwards E, Frape SK (2000) Carbon isotope fractionation during microbial dechlorination of trichloroethene, cis-1,2-dichloroethene, and vinyl chloride: implications for assessment of natural attenuation. Environ Sci Technol 34(13):2768–2772CrossRef

Boissier JM, Marmonier P, Claret C, Fontvieille D, Blanc P (1996) Comparison of solutes, nutrients and bacteria inputs from two types of groundwater to the Rhone River during an artificial drought. Hydrobiologia 319(1):65–72CrossRef

Bone TL, Balkwill DL (1988) Morphological and cultural comparison of micro-organisms in surface soil and subsurface sediments at a pristine study site in Oklahoma. Microbial Ecol 16:49–64CrossRef

Boon N, De Windt W, Verstraete W, Top EM (2002) Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol 39(2):101–112

Boulton AJ, Findlay S, Marmonier P, Stanley EH, Valett HM (1998) The functional significance of the hyporheic zone in streams and rivers. Ann Rev Ecol Syst 29:59–81CrossRef

Brockman FJ, Li SW, Fredrickson JK, Ringelberg DB, Kieft TL, Spadoni CM, White DC, McKinley JP (1998) Post-sampling changes in microbial community composition and activity in a subsurface paleosol. Microbial Ecol 36(2):152–164CrossRef

Brockman FJ, Murray CJ (1997) Subsurface microbiological heterogeneity: Current knowledge, descriptive approaches and applications. FEMS Microbiol Rev 20(3/4):231–247

Brooks T, Osicki RA, Springthorpe VS, Satter SA, Filion L, Abrial D, Riffard S (2004) Detection and infection of Legionella species from groundwaters. J Toxicol Environ Health A 67:1845–1859CrossRefPubMed

Bruggemann J, Stephen JR, Chang YJ, Macnaughton SJ, Kowalchuk GA, Kline E, White DC (2000) Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy. J Microbiol Methods 40(2):111–123CrossRefPubMed

Brunke M, Gonser T (1997) The ecological significance of exchange processes between rivers and groundwater [Review]. Freshwater Biol 37(1):1–33CrossRef

Bruns A, Cypionka H, Overmann J (2002) Cyclic AMP and Acyl Homoserine Lactones Increase the Cultivation Efficiency of Heterotrophic Bacteria from the Central Baltic Sea. Appl Environ Microbiol 68(8):3978–3987CrossRefPubMed

Byrd JJ, Xu HS, Colwell RR (1991) Viable but nonculturable bacteria in drinking-water. Appl Environ Microbiol 57(3):875–878PubMed

Capuano RM, Siringan MA, Jan RZ, Jurtshuk P (1995) Enhanced activity of oligotrophic endogenous bacteria in clay-rich sediments by nutrient injection. Geomicrobiol J 13(3):165–179

Casamayor EO, Pedros-Alio C, Muyzer G, Amann R (2002) Microheterogeneity in 16S ribosomal DNA-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. Appl Environ Microbiol 68(4):1706–1714CrossRefPubMed

Cassidy MB, Leung KT, Lee H, Trevors JT (2000) A comparison of enumeration methods for culturable Pseudomonas fluorescens cells marked with green fluorescent protein. J Microbiol Methods 40(2):135–145CrossRefPubMed

Chandler DP, Brockman FJ, Fredrickson JK (1997) Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol Rev 20(3/4):217–230

Chapelle FH (2001) Ground-water microbiology and geochemistry. Wiley , New York, 477 pp

Cho JC, Kim SJ (1999) Viable, but non-culturable, state of a green fluorescence protein-tagged environmental isolate of Salmonella typhi in groundwater and pond water. FEMS Microbiol Lett 170(1):257–264PubMed

Cho JC, Kim SJ (2000) Increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. Appl Environ Microbiol 66(3):956–965CrossRefPubMed

Church PE, Granato GE (1996) Bias in ground-water data caused by well-bore flow in long-screen wells. Ground Water 34(2):262–273CrossRef

Colwell FS, Stormberg GJ, Phelps TJ, Birnbaum SA, McKinley J, Rawson SA, Veverka C, Goodwin S, Long PE, Russell BF, Garland T, Thompson D, Skinner P, Grover S (1992) Innovative techniques for collection of saturated and unsaturated subsurface basalts and sediments for microbiological characterization. J Microbiol Methods 15(4):279–292CrossRef

Covich AP, Austen MC, Barlocher F, Chauvet E, Cardinale BJ, Biles CL, Inchausti P, Dangles O, Solan M, Gessner MO, Statzner B, Moss B (2004) The role of biodiversity in the functioning of freshwater and marine benthic ecosystems. Bioscience 54(8):767–775

Craun GF, Nwachuku N, Calderon RL, Craun MF (2002) Outbreaks in drinking-water systems, 1991–1998. J Environ Health 65(1):16–23

Culver DC, Christman MC, Sket B, Trontelj P (2004) Sampling adequacy in an extreme environment: species richness patterns in Slovenian caves. Biodivers Conserv 13(6):1209–1229CrossRef

Damgaard LR, Revsbech NP (1997) A microscale biosensor for methane containing methanotrophic bacteria and an internal oxygen reservoir. Anal Chem 69(13):2262–2267CrossRef

Damgaard LR, Revsbech NP, Reichardt W (1998) Use of an oxygen-insensitive microscale biosensor for methane to measure methane concentration profiles in a rice paddy. Appl Environ Microbiol 64(3):864–870PubMed

Danielopol DL, Griebler C, Gunatilaka A, Notenboom J (2003) Present state and future prospects for groundwater ecosystems. Environ Conserv 30(2):104–130CrossRef

Danielopol DL, Pospisil P (2001) Hidden biodiversity in the groundwater of the Danube Flood Plain National Park (Austria). Biodivers Conserv 10(10):1711–1721CrossRef

de Beer D, Glud A, Epping E, Kühl M (1997) A fast-responding CO₂ microelectrode for profiling sediments, microbial mats, and biofilms. Limnol Oceanogr 42(7):1590–1600

de Lipthay JR, Johnsen K, Albrechtsen HJ, Rosenberg P, Aamand J (2004) Bacterial density and community structure of a sub-surface aquifer exposed to realistic low herbicide concentrations. FEMS Microbiol Ecol 49:59–69CrossRef

DeBorde DC, Woessner WW, Lauerman B, Ball PN (1998) Virus occurrence and transport in a school septic system and unconfined aquifer. Ground Water 36(5):825–834CrossRef

DeLeo PC, Baveye P (1997) Factors affecting protozoan predation of bacteria clogging laboratory aquifer microcosms. Geomicrobiol J 14(2):127–149

Dewettinck T, Hulsbosch W, Van Hege K, Top EM, Verstraete W (2001) Molecular fingerprinting of bacterial populations in groundwater and bottled mineral water. Appl Microbiol Biotechnol 57(3):412–418CrossRefPubMed

Doig F, Lollar BS, Ferris FG (1995) Microbial communities in deep Canadian Shield groundwaters—an in-situ biofilm experiment. Geomicrobiol J 13(2):91–102

Dollhopf SL, Hashsham SA, Tiedje JM (2001) Interpreting 16S rDNA T-RFLP Data: Application of self-organizing maps and principal component analysis to describe community dynamics and convergence. Microbial Ecol 42:495–505CrossRef

Drever JI (ed) (1997) The geochemistry of natural waters—surface and groundwater environments. Prentice Hall, Upper Saddle River, NJ, 436 pp

Dröge M, Pühler A, Selbitschka W (1999) Horizontal gene transfer among bacteria in terrestrial and aquatic habitats as assessed by microcosm and field studies. Biol Fertil Soils 29:221–245CrossRef

Dumas P, Bou C, Gibert J (2001) Groundwater macrocrustaceans as natural indicators of the Ariege alluvial aquifer. Int Rev Hydrobiol 86(6):619–633CrossRef

Dumont MG, Murrell JC (2005) Stable isotope probing linking microbial identity to function. Nat Rev Microbiol 3(6):499–504CrossRefPubMed

EC (2000) Directive 2000/60/EC of the European Parliament and of the Council of 23 October 2000 establishing a framework for Community action in the field of water policy

Edberg SC, LeClerc H, Robertson J (1997) Natural protection of spring and well drinking water against surface microbial contamination: II. Indicators and monitoring parameters for parasites. Crit Rev Microbiol 23(2):179–206PubMed

Ekendahl S, Arlinger J, Stahl F, Pedersen K (1994) Characterization of attached bacterial-populations in deep granitic groundwater from the stripa research mine by 16s ribosomal-RNA gene sequencing and scanning electron-microscopy. Microbiol UK 140:1575–1583

Farnleitner AH, Wilhartitz I, Ryzinska G, Kirschner AKT, Stadler H, Burtscher MM, Hornek R, Szewzyk U, Herndl G, Mach RL (2005) Bacterial dynamics in spring water of alpine karst aquifers indicates the presence of stable autochthonous microbial endokarst communities. Environ Microbiol 7(8):1248–1259CrossRefPubMed

Fernandez A, Huang SY, Seston S, Xing J, Hickey R, Criddle C, Tiedje J (1999) How stable is stable? Function versus community composition. Appl Environ Microbiol 65(8):3697–3704PubMed

Flanigan D, Rodgers M (2003) A method to detect viable Helicobacter pylori bacteria in groundwater. Acta Hydrochim Et Hydrobiol 31(1):45–48CrossRef

Flynn R (2003) Virus transport and attenuation in perialpine gravel aquifers. PhD Thesis, University of Neuchâtel, Switzerland, 178 pp

Franklin RB, Taylor DR, Mills AL (2000) The distribution of microbial communities in anaerobic and aerobic zones of a shallow coastal plain aquifer. Microbial Ecol 38(4):377–386CrossRef

Fredrickson JK, Li SW, Brockman FJ, Haldeman DL, Amy PS, Balkwill DL (1995) Time-dependent changes in viable numbers and activities of aerobic heterotrophic bacteria in subsurface samples. J Microbiol Methods 21(3):253–265CrossRef

Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M, Rossi P (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4(11):634–643PubMed

Gabrovsek F, Menne B, Dreybrodt W (2000) A model of early evolution of karst conduits affected by subterranean CO₂ sources. Environ Geol 39(6):531–543CrossRef

Galassi DMP (2001) Groundwater copepods: diversity patterns over ecological and evolutionary scales. Hydrobiologia 453(1–3):227–253CrossRef

Gavrieli I, Burg A, Guttman J (2002) Transition from confined to phreatic conditions as the factor controlling salinization and change in redox state, Upper subaquifer of the Judea Group, Israel. Hydrogeol J 10(4):483–494CrossRef

Gayraud S, Herouin E, Philippe M (2002) The clogging of stream beds: A review of mechanisms and consequences on habitats and macroinvertebrate communities. Bulletin francais de la peche et de la pisciculture (365/366):339–355

Ghiorse WC, Miller DN, Sandoli RL, Siering PL (1996) Applications of laser scanning microscopy for analysis of aquatic microhabitats. Microsc Res Tech 33(1):73–86CrossRefPubMed

Gillham RW, Starr RC, Millar D (1990) A device for in situ determination of geochemical transport parameters, 2. Biochemical reactions. Ground Water 28(6):858–862CrossRef

Gobat JM, Aragno M, Matthey W (2004) The Living Soil. Fundamentals of Soil Science and Soil Biology. Science Publishers, 602 pp

Golas I, Filipkowska Z, Lewandowska D, Zmyslowska I (2002) Potentially pathogenic bacteria from the family Enterobacteriaceae, Pseudomonas sp. and Aeromonas sp. in waters designated for drinking and household purposes. Pol J Environ Stud 11(4):325–330

Griebler C, Mindl B, Slezak D, Geiger-Kaiser M (2002) Distribution patterns of attached and suspended bacteria in pristine and contaminated shallow aquifers studied with an in situ sediment exposure microcosm. Aquat Microbial Ecol 28(2):117–129

Griebler C, Mösslacher F (2003) Grundwasser-Ökologie [ground-water ecology]. Facultas UTB, Vienna, 495 pp

GSchV (1998) Water Protection Ordinance, SR 814.201, Swiss Federal Law, Bern

Haack SK, Bekins B (2000) Microbial populations in contaminant plumes. Hydrogeol J 8:63–76CrossRef

Hahn HJ, Friedrich E (1999) Brauchen wir ein faunistisch begründetes Grundwassermonitoring und was kann es leisten? [Do we need a fauna-based groundwater monitoring, and what is its potential?] Grundwasser 4:147–154CrossRef

Hakenkamp CC, Palmer MA, James BR (1994) Metazoans from a sandy aquifer - dynamics across a physically and chemically heterogeneous groundwater system. Hydrobiologia 287(2):195–206

Haldeman DL, Amy PS, White DC, Ringelberg DB (1994) Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C. Appl Environ Microbiol 60(8):2697–2703PubMed

Hancock PJ, Boulton AJ, Humphreys WF (2005) Aquifers and hyporheic zones: Towards an ecological understanding of groundwater. Hydrogeol J 13(1):98–111CrossRef

Harvey RW, Smith RL, George L (1984) Effect of organic contamination upon microbial distributions and heterotrophic uptake in a Cape Cod, Mass., Aquifer. Appl Environ Microbiol 48(6):1197–1202PubMed

Haveman SA, Pedersen K (2002) Distribution of culturable micro-organisms in Fennoscandian Shield groundwater. FEMS Microbiol Ecol 39(2):129–137

Hazen TC, Jimenez L, Devictoria GL, Fliermans CB (1991) Comparison of bacteria from deep subsurface sediment and adjacent groundwater. Microbial Ecol 22(3):293–304

Herwaldt BL, Craun GF, Stokes SL, Juranek DD (1992) Outbreaks of waterborne disease in the United-States - 1989–90. J Am Water Works Assoc 84(4):129–135

Hohener P, Hunkeler D, Hess A, Bregnard T, Zeyer J (1998) Methodology for the evaluation of engineered in situ bioremediation: lessons from a case study. J Microbiol Methods 32(2):179–192CrossRef

Hollibaugh JT (1994) Relationship between thymidine metabolism, bacterioplankton community metabolic capabilities, and sources of organic-matter. Microbial Ecol 28(2):117–131CrossRef

Holliger C, Gaspard S, Glod G, Heijman C, Schumacher W, Schwarzenbach R, Vazquez F (1995) Contaminated environments in the subsurface and bioremediation: organic contaminants. Curr Opin Biotechnol 6(3):347–351CrossRef

Holm PE, Nielsen PH, Albrechtsen HJ, Christensen TH (1992) Importance of unattached bacteria and attached bacteria to sediment in determining potentials for degradation of xenobiotic organic contaminants in an aerobic aquifer. Appl Environ Microbiol 58:3020–3026PubMed

Hunkeler D, Anderson N, Aravena R, Bernasconi SM, Butler BJ (2001) Hydrogen and carbon isotope fractionation during aerobic biodegradation of benzene. Environ Sci Technol 35(17):3462–3467CrossRefPubMed

Hunkeler D, Aravena R, Parker BL, Cherry JA, Diao X (2003) Monitoring oxidation of chlorinated ethenes by permanganate in groundwater using stable isotopes: Laboratory and field studies. Environ Sci Technol 37(4):798–804CrossRefPubMed

Hunkeler D, Goldscheider N, Rossi P, Burn C (2006) Biozönosen im Grundwasser - Grundlagen und Methoden der Charakterisierung von mikrobiellen Gemeinschaften [Biocenoses in groundwater - basics and methods to characterise microbial communities]. Umwelt-Wissen, Swiss Federal Office for the Environment (FOEN), Berne

Hunkeler D, Hohener P, Bernasconi S, Zeyer J (1999) Engineered in situ bioremediation of a petroleum hydrocarbon-contaminated aquifer: assessment of mineralization based on alkalinity, inorganic carbon and stable carbon isotope balances. J Contam Hydrol 37(3/4):201–223CrossRef

Hurst CJ, Crawford RL, Knudsen GR, McInerney MJ, Stetzenbach LD (2002) Manual of environmental microbiology, 2nd edn. ASM Press, 1158 pp

Istok JD, Humphrey MD, Schroth MH, Hyman MR, Oreilly KT (1997) Single-well, “push-pull” test for in situ determination of microbial activities. Ground Water 35(4):619–631CrossRef

Jean JS, Tsai CL, Ju SH, Tsao CW, Wang SM (2002) Biodegradation and transport of benzene, toluene, and xylenes in a simulated aquifer: comparison of modelled and experimental results. Hydrol Process 16(16):3151–3168CrossRef

Kell DB, Kaprelyants AS, Weichart DH, Harwood CR, Barer MR (1998) Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 73(2):169–187CrossRef

Kent AD, Triplett EW (2002) Microbial communities and their interactions in soil and rhizosphere ecosystems. Annu Rev Microbiol 56:211–236CrossRefPubMed

Kirchman D, Knees E, Hodson R (1985) Leucine incorporation and its potential as a measure of protein-synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49(3):599–607PubMed

Klimant I, Holst G, Kühl M (1997) A simple fiberoptic sensor to detect the penetration of microsensors into sediments and other biogeochemical systems. Limnol Oceanogr 42(7):1638–1643

Konopka A, Turco R (1991) Biodegradation of organic-compounds in vadose zone and aquifer sediments. Appl Environ Microbiol 57(8):2260–2268PubMed

Kota S, Borden RC, Barlaz MA (1999) Influence of protozoan grazing on contaminant biodegradation. FEMS Microbiol Ecol 29(2):179–189

Krumholz LR, McKinley JP, Ulrich FA, Suflita JM (1997) Confined subsurface microbial communities in Cretaceous rock. Nature 386(6620):64–66CrossRef

Lawrence JG (2002) Gene transfer in bacteria: speciation without species? Theor Popul Biol 61(4):449–460CrossRefPubMed

Lebaron P, Servais P, Baudoux AC, Bourrain M, Courties C, Parthuisot N (2002) Variations of bacterial-specific activity with cell size and nucleic acid content assessed by flow cytometry. Aquat Microbial Ecol 28(2):131–140

Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer KH, Wagner M (1999) Combination of fluorescent in situ hybridization and microautoradiography–-a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 65(3):1289–1297PubMed

Lehloesa LJ, Muyima NYO (2000) Evaluation of the impact of household treatment procedures on the quality of groundwater supplies in the rural community of the Victoria district, Eastern Cape. Water SA 26(2):285–290

Lehman RM (2001) Attached and unattached microbial communities in a simulated basalt aquifer under fracture- and porous-flow conditions. Appl Environ Microbiol 67(6)

Lehman RM, Roberto FF, Earley D, Bruhn DF, Brink SE, O’Connell SP, Delwiche ME, Colwell FS (2001) Attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer. Appl Environ Microbiol 67(5):2095–2106CrossRefPubMed

Lerner DN, Teutsch G (1995) Recommendations for level-determined sampling in wells. J Hydrol 171(3/4):355–377CrossRef

Li BL, Loehle C, Malon D (1996) Microbial transport through heterogeneous porous media: random walk, fractal, and percolation approaches. Ecol Model 85(2/3):285–302CrossRef

Lillis TO, Bissonnette GK (2001) Detection and characterization of filterable heterotrophic bacteria from rural groundwater supplies. Lett Appl Microbiol 32(4):268–272CrossRefPubMed

Lisle JT, Rose JB (1995) Cryptosporidium contamination of water in the USA and UK—a minireview. J Water Supply: Res Technol - AQUA 44(3):103–117

Loaiciga HA, Charbeneau RJ, Everett LG, Fogg GE, Hobbs BF, Rouhani S (1992) Review of groundwater quality monitoring network design. J Hydraulic Eng - Asce 118(1):11–37

Madigan MT, Martinko JM, Parker J (2000) Brock - biology of micro-organisms, 9th edn. Prentice-Hall, New York, 991 pp

Mahler BJ, Personne JC, Lods GF, Drogue C (2000) Transport of free and particulate-associated bacteria in karst. J Hydrol 238(3/4):179–193CrossRef

Maier RM, Pepper IL, Gerba CP (2000) Environmental microbiology. Academic: 585 pp

Malard F, Gibert J, Laurent R, Reygrobellet JL (1994) A new method for sampling the fauna of deep karstic aquifers. C R Acad Sci 317(10):955–966

Malard F, Hervant F (1999) Oxygen supply and the adaptations of animals in groundwater. Freshwater Biol 41(1):1–30CrossRef

Malard F, Mathieu J, Reygrobellet JL, Lafont M (1996a) Biomotoring groundwater contamination: application to a karst area in Southern France. Aquat Sci 58(2):158–187CrossRef

Malard F, Plenet S, Gibert J (1996b) The use of invertebrates in ground water monitoring: a rising research field. Ground Water Monit Remediation 16(2):103–113

Malard F, Tockner K, Dole-Olivier MJ, Ward JV (2002) A landscape perspective of surface-subsurface hydrological exchanges in river corridors. Freshwater Biol 47(4):621–640CrossRef

Marmonier P, Vervier P, Gibert J, Doleolivier MJ (1993) Biodiversity in ground waters. Trends Ecol Evol 8(11):392–395CrossRef

Martin K (2002) Ökologie der Biozönosen [ecology of biocenoses]. Springer-Lehrbuch

Marxsen J (1988) Investigations into the number of respiring bacteria in groundwater from sandy and gravelly deposits. Microbial Ecol 16(1):65–72CrossRef

Marxsen J (1996) Measurement of bacterial production in stream-bed sediments via leucine incorporation. FEMS Microbiol Ecol 21(4):313–325

Mathieu J, Essafichergui K, Culver DC (1992) Variations in the structure of stygobiont crustacean populations (Niphargus-Rhenorhodanensis and Proasellus Valdensis) within the sediments of a karst outflow. Hydrobiologia 231(1):41–49CrossRef

Mauclaire L, Pelz O, Thullner M, Abraham WR, Zeyer J (2003) Assimilation of toluene carbon along a bacteria-protist food chain determined by C-13-enrichment of biomarker fatty acids. J Microbiol Methods 55(3):635–649CrossRefPubMed

McMahon PB, Chapelle FH (1991) Geochemistry of dissolved inorganic carbon in a coastal plain aquifer. 2. Modeling carbon sources, sinks, and δ¹³C evolution. J Hydrol 127:109–135CrossRef

Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (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(8):3518–3525PubMed

Murphy EM, Ginn TR, Chilakapati A, Resch CT, Phillips JL, Wietsma TW, Spadoni CM (1997) The influence of physical heterogeneity on microbial degradation and distribution in porous media. Water Resour Res 33(5):1087–1103CrossRef

Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2(3):317–322CrossRefPubMed

Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek Int J Gen Mol Microbiol 73(1):127–141CrossRef

Nasser AM, Tchorch Y, Fattal B (1993) Comparative survival of Escherichia coli, F+bacteriophages, HAV and poliovirus-1 in waste-water and groundwater. Water Sci Technol 27(3/4):401–407

Nebbache S, Loquet M, Vinceslas-Akpa M, Feeny V (1997) Turbidity and micro-organisms in a karst spring. Eur J Soil Biol 33(2):89–103

Neff JC, Asner GP (2001) Dissolved organic carbon in terrestrial ecosystems: synthesis and a model. Ecosystems 4(1):29–48CrossRef

Nielsen JL, Nielsen PH (2002) Quantification of functional groups in activated sludge by microautoradiography. Water Sci Technol 46(1–2):389–395

Niemi RM, Niemi JS (1991) Bacterial pollution of waters in pristine and agricultural lands. J Environ Qual 20(3):620–627CrossRef

Northup DE, Lavoie KH (2001) Geomicrobiology of caves: a review. Geomicrobiol J 18(3):199–222CrossRef

Olson GJ, Dockins WS, McFeters GA, Iverson WP (1981) Sulfate-reducing and methanogenic bacteria from deep aquifers in Montana. Geomicrobiol J 2(4):327–340

Overmann J (2003) Principles of enrichment, isolation, cultivation, and preservation of prokaryotes, Release 3.12. In: Dworkin M (ed) The Prokaryotes: an evolving electronic resource for the microbiological community, http://141.150.157.117:8080/ prokPUB/index.htm (cited September 2005), Springer, Berlin Heidelberg New York

Pabich WJ, Valiela I, Hemond HF (2001) Relationship between DOC concentration and vadose zone thickness and depth below water table in groundwater of Cape Cod, USA. Biogeochemistry 55(3):247–268CrossRef

Pedersen K, Arlinger J, Ekendahl S, 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(4):249–262

Pickup RW, Rhodes G, Alamillo ML, Mallinson HEH, Thornton SF, Lerner DN (2001) Microbiological analysis of multi-level borehole samples from a contaminated groundwater system. J Contam Hydrol 53(3/4):269–284CrossRefPubMed

Pipan T, Brancelj A (2004) Distribution patterns of copepods (Crustacea: Copepoda) in percolation water of the Postojnska Jama Cave system (Slovenia). Zool Stud 43(2):206–210

Plenet S, Gibert J (1995) Comparison of surface-water groundwater interface zones in fluvial and karstic systems. Comptes Rendus De L Academie Des Sciences Serie Iii-Sciences De La Vie-Life Sciences 318(4):499–509

Plenet S, Hugueny H, Gibert J (1996) Invertebrate community responses to physical and chemical factors at the river aquifer interaction zone. 2. Downstream from the city of Lyon. Archiv für Hydrobiologie 136(1):65–88

Pombo SA, Pelz O, Schroth MH, Zeyer J (2002) Field-scale C-13-labeling of phospholipid fatty acids (PLFA) and dissolved inorganic carbon: tracing acetate assimilation and mineralization in a petroleum hydrocarbon-contaminated aquifer. FEMS Microbiol Ecol 41(3):259–267

Preuss G, Schminke HK (2004) A global ecosystem–-groundwater is alive! Chemie in unserer Zeit 38(5):340–347CrossRef

Pronk M, Goldscheider N, Zopfi J (in press) Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system. Hydrogeol J, published online. DOI: 10.1007/s10040-005-0454-5

Puhakka JA, Jarvinen KT, Langwaldt JH, Melin ES, Mannisto MK, Salminen JM, Sjolund MT (2000) On-site and in situ bioremediation of wood-preservative contaminated groundwater. Water Sci Technol 42(5/6):371–376

Rapp MC, Fulda C, Schafer W, Kinzelbach W (1998) The Dual Pumping Technique (DPT) for level-determined sampling in fully screened groundwater wells. J Hydrol 207(3/4):220–235CrossRef

Richardson JS, Kiffney PM (2000) Responses of a macroinvertebrate community from a pristine, southern British Columbia, Canada, stream to metals in experimental mesocosms. Environ Toxicol Chem 19(3):736–743CrossRef

Rogers JR, Bennett PC (2004) Mineral stimulation of subsurface micro-organisms: release of limiting nutrients from silicates. Chem Geol 203(1/2):91–108CrossRef

Röling WFM, van Verseveld HW (2002) Natural attenuation: What does the subsurface have in store? Biodegradation 13(1):53–64CrossRefPubMed

Ross N, Villemur R, Marcandella E, Deschenes L (2001) Assessment of changes in biodiversity when a community of ultramicrobacteria isolated from groundwater is stimulated to form a biofilm. Microbial Ecol 42(1):56–68

Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67CrossRefPubMed

Rossi P, Dorfliger N, Kennedy K, Muller I, Aragno M (1998) Bacteriophages as surface and ground water tracers. Hydrol Earth Syst Sci 2(1):101–110CrossRef

Roszak DB, Colwell RR (1987) Survival strategies of bacteria in the natural environment. Microbiol Rev 51(3):365–379PubMed

Rouch R, Danielopol DL (1997) Species richness of microcrustacea in subterranean freshwater habitats. Comparative analysis and approximate evaluation. Internationale Revue der gesamten Hydrobiologie 82(2):121–145

Ruiz-Aguilar GML, Fernandez-Sanchez JM, Kane SR, Kim D, Alvarez PJJ (2002) Effect of ethanol and methyl-tert-butyl ether on monoaromatic hydrocarbon biodegradation: Response variability for different aquifer materials under various electron-accepting conditions. Environ Toxicol Chem 21(12):2631–2639CrossRefPubMed

Russell CE, Jacobson R, Haldeman DL, Amy PS (1994) Heterogeneity of deep subsurface micro-organisms and correlations to hydrogeological and geochemical parameters. Geomicrobiol J 12(1):37–51

Rusterholtz KJ, Mallory LM (1994) Density, activity, and diversity of bacteria indigenous to a karstic aquifer. Microbial Ecol 28(1):79–99CrossRef

Ryan M, Meiman J (1996) An examination of short-term variations in water quality at a karst spring in Kentucky. Ground Water 34(1):23–30CrossRef

Santegoeds CM, Damgaard LR, Hesselink C, Zopfi J, Lens P, Muyzer G, De Beer D (1999) Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analyses. Appl Environ Microbiol 65(10):4618–4629PubMed

Santegoeds CM, Muyzer G, de Beer D (1998) Biofilm dynamics studied with microsensors and molecular techniques. Water Sci Technol 37(4/5):125–129CrossRef

Schaffter N, Parriaux A (2002) Pathogenic-bacterial water contamination in mountainous catchments. Water Res 36(1):131–139CrossRefPubMed

Schaffter N, Zumstein J, Parriaux A (2004): Factors influencing the bacteriological water quality in mountainous surface and groundwaters. Acta Hydrochim Hydrobiol 32:225–234CrossRef

Schlegel HG (1993) General Microbiology, 7th ed. Cambridge University Press, 673 pp

Schmitter-Soto JJ, Comin FA, Escobar-Briones E, Herrera-Silveira J, Alcocer J, Suarez-Morales E, Elias-Gutierrez M, Diaz-Arce V, Marin LE, Steinich B (2002) Hydrogeochemical and biological characteristics of cenotes in the Yucatan Peninsula (SE Mexico). Hydrobiologia 467(1–3):215–228CrossRef

Schubert R (1991) Lehrbuch der Ökologie [Introduction to ecology]. Spektrum Akademischer Verlag: 657 pp

Schulze-Makuch D, Kennedy JF (2000) Microbiological and chemical characterization of hydrothermal fluids at Tortugas Mountain Geothermal Area, southern New Mexico, USA. Hydrogeol J 8(3):295–309CrossRef

Sekar R, Fuchs BM, Amann R, Pernthaler J (2004) Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl Environ Microbiol 70(10):6210–6219CrossRefPubMed

Severson KJ, Johnstone DL, Keller CK, Wood BD (1991) Hydrogeologic parameters affecting vadose-zone microbial distributions. Geomicrobiol J 9(4):197–216

Sievert SM, Brinkhoff T, Muyzer G, Ziebis V, Kuever J (1999) Spatial heterogeneity of bacterial populations along an environmental gradient at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl Environ Microbiol 65(9):3834–3842PubMed

Sinclair JL, Alexander M (1989) Effect of protozoan predation on relative abundance of fast- growing and slow-growing bacteria. Can J Microbiol 35(5):578–582CrossRef

Sinclair JL, Randtke SJ, Denne JE, Hathaway LR, Ghiorse WC (1990) Survey of microbial-populations in buried-valley aquifer sediments from Northeastern Kansas. Ground Water 28(3):369–377CrossRef

Sket B (1999) High biodiversity in hypogean waters and its endangerment - the situation in Slovenia, the Dinaric Karst, and Europe. Crustaceana 72:767–779CrossRef

Smets BF, Siciliano SD, Verstraete W (2002) Natural attenuation: extant microbial activity forever and ever? Environ Microbiol 4(6):315–317CrossRefPubMed

Smith H, Wood PJ (2002) Flow permanence and macroinvertebrate community variability in limestone spring systems. Hydrobiologia 487(1):45–58CrossRef

Swiger RR, Tucker JD (1996) Fluorescence in situ hybridization: A brief review. Environ Mol Mutagen 27: 245–254

Szewzyk U, Szewzyk R, Manz W, Schleifer KH (2000) Microbiological safety of drinking water. Annu Rev Microbiol 54:81–127CrossRefPubMed

Thomas JM, Ward CH (1992) Subsurface microbial ecology and bioremediation. J Hazard Mater 32(2/3):179–194CrossRef

Ultee A, Souvatzi N, Maniadi K, König H (2004) Identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Germany. J Appl Microbiol 96:560–568CrossRefPubMed

Vachee A, Vincent P, Struijk CB, Mossel DAA, Leclerc H (1997) A study of the fate of the autochtonous bacterial flora of still mineral waters by analysis of restriction fragment length polymorphism of genes coding for rRNA. Syst Appl Microbiol 20(3):492–503

Ventullo RM, Ladd TI, Costerton JW (1983) Distribution and activity of particle-bound and free-living suspended bacteria in groundwater. Abstracts of Papers of the American Chemical Society, 186(AUG): 105-ENVR

Vervier P, Gibert J (1991) Dynamics of surface-water groundwater ecotones in a karstic aquifer. Freshwater Biol 26(2):241–250

Vervier P, Gibert J, Marmonier P, Doleolivier MJ (1992) A perspective on the permeability of the surface fresh-water-groundwater ecotone. J N Am Benthological Soc 11(1):93–102

Vives-Rego J, Lebaron P, Nebe-von Caron G (2000) Current and future applications of flow cytometry in aquatic microbiology. FEMS Microbiol Rev 24(4):429–448PubMed

Wackett LP (2004) Stable isotope probing in biodegradation research. Trends Biotechnol 22(4):153–154CrossRefPubMed

Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6(3):302–309CrossRefPubMed

Ward JV, Palmer MA (1994) Distribution patterns of interstitial fresh-water meiofauna over a range of spatial scales, with emphasis on alluvial river aquifer systems. Hydrobiologia 287(1):147–156CrossRef

Williams DD (1993) Changes in fresh-water meiofauna communities along the groundwater-hyporheic water ecotone. Trans Am Microsc Soc 112(3):181–194

Wilson MS, Bakermans C, Madsen EL (1999) In situ, real-time catabolic gene expression: Extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl Environ Microbiol 65(1):80–87PubMed

Winding A (1994) Fingerprinting bacterial soil communities using Biolog microtitre plates. In: Ritz K, Dighton J, Giller KE (eds), Beyond the biomass. Wiley, New York, pp 85–94

Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271PubMed

Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95(16):9710–9710

Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97(15):8392–8396CrossRefPubMed

Wood PJ, Gunn J, Perkins J (2002) The impact of pollution on aquatic invertebrates within a subterranean ecosystem—out of sight out of mind. Archiv für Hydrobiologie 155(2):223–237

Zhang CL, Palumbo AV, Phelps TJ, Beauchamp JJ, Brockman FJ, Murray CJ, Parsons BS, Swift DJP (1998) Grain size and depth constraints on microbial variability in coastal plain subsurface sediments. Geomicrobiol J 15(3):171–185CrossRef

Zhou JZ, Xia BC, Treves DS, Wu LY, Marsh TL, O'Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68(1):326–334CrossRefPubMed

Title: Review: Microbial biocenoses in pristine aquifers and an assessment of investigative methods
Authors: Nico Goldscheider
Daniel Hunkeler
Pierre Rossi
Publication date: 01-09-2006
Publisher: Springer-Verlag
Published in: Hydrogeology Journal / Issue 6/2006
Print ISSN: 1431-2174
Electronic ISSN: 1435-0157
DOI: https://doi.org/10.1007/s10040-005-0009-9

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