Microbial Ecology

, Volume 66, Issue 1, pp 84–95 | Cite as

Diversity of Planktonic and Attached Bacterial Communities in a Phenol-Contaminated Sandstone Aquifer

  • Athanasios Rizoulis
  • David R. Elliott
  • Stephen A. Rolfe
  • Steven F. Thornton
  • Steven A. Banwart
  • Roger W. Pickup
  • Julie D. Scholes
Environmental Microbiology

Abstract

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.

Supplementary material

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ESM 1(PDF 249 kb)

References

  1. 1.
    Alfreider A, Vogt C (2007) Bacterial diversity and aerobic biodegradation potential in a BTEX-contaminated aquifer. Water Air Soil Pollut 183:415–426CrossRefGoogle Scholar
  2. 2.
    Thornton SF, Quigley S, Spence MJ, Banwart SA, Bottrell S, Lerner DN (2001) Processes controlling the distribution and natural attenuation of dissolved phenolic compounds in a deep sandstone aquifer. J Contam Hydrol 53:233–267PubMedCrossRefGoogle Scholar
  3. 3.
    Prommer H, Tuxen N, Bjerg PL (2006) Fringe-controlled natural attenuation of phenoxy acids in a landfill plume: integration of field-scale processes by reactive transport modeling. Environ Sci Technol 40:4732–4738PubMedCrossRefGoogle Scholar
  4. 4.
    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 53:269–284PubMedCrossRefGoogle Scholar
  5. 5.
    Anneser B, Einsiedl F, Meckenstock RU, Richters L, Wisotzky F, Griebler C (2008) High-resolution monitoring of biogeochemical gradients in a tar oil-contaminated aquifer. Appl Geochem 23:1715–1730CrossRefGoogle Scholar
  6. 6.
    Winderl C, Anneser B, Griebler C, Meckenstock RU, Lueders T (2008) Depth-resolved quantification of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl Environ Microbiol 74:792–801PubMedCrossRefGoogle Scholar
  7. 7.
    Wilson RD, Thornton SF, Mackay DM (2004) Challenges in monitoring the natural attenuation of spatially variable plumes. Biodegradation 15:359–369PubMedCrossRefGoogle Scholar
  8. 8.
    Kappler A, Emerson D, Edwards K, Amend JP, Gralnick JA, Grathwohl P, Hoehler T, Straub KL (2005) Microbial activity in biogeochemical gradients—new aspects of research. Geobiology 3:229–233CrossRefGoogle Scholar
  9. 9.
    Hazen TC, Jiménez L, de Victoria GL, Fliermans CB (1991) Comparison of bacteria from deep subsurface sediment and adjacent groundwater. Microb Ecol 22:293–304CrossRefGoogle Scholar
  10. 10.
    Holm PE, Nielsen PH, Albrechtsen HJ, Christensen TH (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 58:3020–3026PubMedGoogle Scholar
  11. 11.
    Wilhartitz IC, Kirschner AKT, Stadler H, Herndl GJ, Dietzel M, Latal C, Mach RL, Farnleitner AH (2009) Heterotrophic prokaryotic production in ultraoligotrophic alpine karst aquifers and ecological implications. FEMS Microbiol Ecol 68:287–299PubMedCrossRefGoogle Scholar
  12. 12.
    DeLong EF, Franks DG, Alldredge AL (1993) Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr 38:924–934CrossRefGoogle Scholar
  13. 13.
    Crump BC, Armbrust EV, Baross JA (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 65:3192–3204PubMedGoogle Scholar
  14. 14.
    Bakermans C, Madsen EL (2002) Diversity of 16S rDNA and naphthalene dioxygenase genes from coal tar waste contaminated aquifer waters. Microb Ecol 44:95–106PubMedCrossRefGoogle Scholar
  15. 15.
    Rooney-Varga JN, Anderson RT, Fraga JL, Ringelberg D, Lovley DR (1999) Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65:3056–3063PubMedGoogle Scholar
  16. 16.
    Reardon CL, Cummings DE, Petzke LM, Kinsall BL, Watson DB, Peyton BM, Geesey GG (2004) Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer. Appl Environ Microbiol 70:6037–6046PubMedCrossRefGoogle Scholar
  17. 17.
    Vrionis HA, Anderson RT, Ortiz-Bernad I, O'Neill KR, Resch CT, Peacock AD, Dayvault R, White DC, Long PE, Lovley DR (2005) Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl Environ Microbiol 71:6308–6318PubMedCrossRefGoogle Scholar
  18. 18.
    Williams GM, Pickup RW, Thornton SF, Lerner DN, Mallinson HEH, Moore Y, White C (2001) Biogeochemical characterisation of a coal tar distillate plume. J Contam Hydrol 53:175–197PubMedCrossRefGoogle Scholar
  19. 19.
    Thornton SF, Lerner DN, Banwart SA (2001) Assessing the natural attenuation of organic contaminants in aquifers using plume-scale electron and carbon balances: model development with analysis of uncertainty and parameter sensitivity. J Contam Hydrol 53:199–232PubMedCrossRefGoogle Scholar
  20. 20.
    Manefield M, Griffiths RI, Leigh MB, Fisher R, Whiteley AS (2005) Functional and compositional comparison of two activated sludge communities remediating coking effluent. Environ Microbiol 7:715–722PubMedCrossRefGoogle Scholar
  21. 21.
    Cortés-Lorenzo C, Molina-Muñoz ML, Gómez-Villalba B, Vilchez R, Ramos A, Rodelas B, Hontoria E, González-López J (2006) Analysis of community composition of biofilms in a submerged filter system for the removal of ammonia and phenol from industrial wastewater. Biochem Soc Trans 34:165–168PubMedCrossRefGoogle Scholar
  22. 22.
    Padmanabhan P, Padmanabhan S, DeRito C, Gray A, Gannon D, Snape JR, Tsai CS, Park W, Jeon C, Madsen EL (2003) Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Appl Environ Microbiol 69:1614–1622PubMedCrossRefGoogle Scholar
  23. 23.
    DeRito CM, Pumphrey GM, Madsen EL (2005) Use of field-based stable isotope probing to identify adapted populations and track carbon flow through a phenol-degrading soil microbial community. Appl Environ Microbiol 71:7858–7865PubMedCrossRefGoogle Scholar
  24. 24.
    Baker KM, Bottrell SH, Thornton SF, Peel KE, Spence MJ (2012) Effect of contaminant concentration on in situ bacterial sulfate reduction and methanogenesis in phenol-contaminated groundwater. Appl Geochem 27:2010–2018CrossRefGoogle Scholar
  25. 25.
    Elliott DR, Scholes JD, Thornton SF, Rizoulis A, Banwart SA, Rolfe SA (2010) Dynamic changes in microbial community structure and function in phenol-degrading microcosms inoculated with cells from a contaminated aquifer. FEMS Microbiol Ecol 71:247–259PubMedCrossRefGoogle Scholar
  26. 26.
    Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ (2000) Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488–5491PubMedCrossRefGoogle Scholar
  27. 27.
    Whiteley AS, Bailey MJ (2000) Bacterial community structure and physiological state within an industrial phenol bioremediation system. Appl Environ Microbiol 66:2400–2407PubMedCrossRefGoogle Scholar
  28. 28.
    Muyzer G, Dewaal EC, 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 59:695–700PubMedGoogle Scholar
  29. 29.
    Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Aust J Ecol 18:117–143CrossRefGoogle Scholar
  30. 30.
    Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175Google Scholar
  31. 31.
    Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734–5741PubMedCrossRefGoogle Scholar
  32. 32.
    Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541PubMedCrossRefGoogle Scholar
  33. 33.
    Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145PubMedCrossRefGoogle Scholar
  34. 34.
    Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  35. 35.
    Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  36. 36.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  37. 37.
    Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic, New York, pp 21–132Google Scholar
  38. 38.
    Aamand J, Jørgensen C, Arvin E, Jensen BK (1989) Microbial adaptation to degradation of hydrocarbons in polluted and unpolluted groundwater. J Contam Hydrol 4:299–312CrossRefGoogle Scholar
  39. 39.
    Crosby LD, Criddle CS (2003) Understanding bias in microbial community analysis techniques due to rrn operon copy number heterogeneity. Biotechniques 34:790–802PubMedGoogle Scholar
  40. 40.
    Wintzingerode FV, Göbel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229CrossRefGoogle Scholar
  41. 41.
    Rabus R, Widdel F (1995) Anaerobic degradation of ethylbenzene and other aromatic hydrocarbons by new denitrifying bacteria. Arch Microbiol 163:96–103PubMedCrossRefGoogle Scholar
  42. 42.
    Schulze R, Spring S, Amann R, Huber I, Ludwig W, Schleifer KH, Kampfer P (1999) Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov. Syst Appl Microbiol 22:205–214PubMedCrossRefGoogle Scholar
  43. 43.
    Mechichi T, Stackebrandt E, Gad'on N, Fuchs G (2002) Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromatica sp. nov., and Azoarcus buckelii sp. nov. Arch Microbiol 178:26–35PubMedCrossRefGoogle Scholar
  44. 44.
    Manefield M, Whiteley AS, Griffiths RI, Bailey MJ (2002) RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 68:5367–5373PubMedCrossRefGoogle Scholar
  45. 45.
    Heinaru E, Truu J, Stottmeister U, Heinaru A (2000) Three types of phenol and p-cresol catabolism in phenol- and p-cresol-degrading bacteria isolated from river water continuously polluted with phenolic compounds. FEMS Microbiol Ecol 31:195–205PubMedCrossRefGoogle Scholar
  46. 46.
    Whiteley AS, Wiles S, Lilley AK, Philp J, Bailey MJ (2001) Ecological and physiological analyses of pseudomonad species within a phenol remediation system. J Microbiol Methods 44:79–88PubMedCrossRefGoogle Scholar
  47. 47.
    Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJP, Gorby YA, Goodwin S (1993) Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 159:336–344PubMedCrossRefGoogle Scholar
  48. 48.
    Bak F, Widdel F (1986) Anaerobic degradation of phenol and phenol derivatives by Desulfobacterium phenolicum sp. nov. Arch Microbiol 146:177–180CrossRefGoogle Scholar
  49. 49.
    Franzmann PD, Robertson WJ, Zappia LR, Davis GB (2002) The role of microbial populations in the containment of aromatic hydrocarbons in the subsurface. Biodegradation 13:65–78PubMedCrossRefGoogle Scholar
  50. 50.
    Liu A, Garcia-Dominguez E, Rhine ED, Young LY (2004) A novel arsenate respiring isolate that can utilize aromatic substrates. FEMS Microbiol Ecol 48:323–332PubMedCrossRefGoogle Scholar
  51. 51.
    Ramamoorthy S, Sass H, Langner H, Schumann P, Kroppenstedt RM, Spring S, Overmann J, Rosenzweig RF (2006) Desulfosporosinus lacus sp. nov., a sulfate-reducing bacterium isolated from pristine freshwater lake sediments. Int J Syst Evol Microbiol 56:2729–2736PubMedCrossRefGoogle Scholar
  52. 52.
    Watson IA, Oswald SE, Mayer KU, Wu YX, Banwart SA (2003) Modeling kinetic processes controlling hydrogen and acetate concentrations in an aquifer-derived microcosm. Environ Sci Technol 37:3910–3919PubMedCrossRefGoogle Scholar
  53. 53.
    Watson IA, Oswald SE, Banwart SA, Crouch RS, Thornton SF (2005) Modeling the dynamics of fermentation and respiratory processes in a groundwater plume of phenolic contaminants interpreted from laboratory- to field-scale. Environ Sci Technol 39:8829–8839PubMedCrossRefGoogle Scholar
  54. 54.
    Wartiainen I, Hestnes AG, McDonald IR, Svenning MM (2006) Methylobacter tundripaludum sp. nov., a methane-oxidizing bacterium from Arctic wetland soil on the Svalbard islands, Norway (78°N). Int J Syst Evol Microbiol 56:109–113PubMedCrossRefGoogle Scholar
  55. 55.
    Wartiainen I, Hestnes AG, McDonald IR, Svenning MM (2006) Methylocystis rosea sp. nov., a novel methanotrophic bacterium from Arctic wetland soil, Svalbard, Norway (78°N). Int J Syst Evol Microbiol 56:541–547PubMedCrossRefGoogle Scholar
  56. 56.
    Watanabe K, Kodama Y, Hamamura N, Kaku N (2002) Diversity, abundance, and activity of archaeal populations in oil-contaminated groundwater accumulated at the bottom of an underground crude oil storage cavity. Appl Environ Microbiol 68:3899–3907PubMedCrossRefGoogle Scholar
  57. 57.
    Chen CL, Wu JH, Liu WT (2008) Identification of important microbial populations in the mesophilic and thermophilic phenol-degrading methanogenic consortia. Water Res 42:1963–1976PubMedCrossRefGoogle Scholar
  58. 58.
    Yagi JM, Neuhauser EF, Ripp JA, Mauro DM, Madsen EL (2010) Subsurface ecosystem resilience: long-term attenuation of subsurface contaminants supports a dynamic microbial community. ISME J 4:131–143PubMedCrossRefGoogle Scholar
  59. 59.
    Boll M, Fuchs G, Heider J (2002) Anaerobic oxidation of aromatic compounds and hydrocarbons. Curr Opin Chem Biol 6:604–611PubMedCrossRefGoogle Scholar
  60. 60.
    Davey ME, O'Toole GA (2000) Microbial biofilms: from ecology to molecular genetics. Microbiol Mol Biol Rev 64:847–867PubMedCrossRefGoogle Scholar
  61. 61.
    Stewart PS, Franklin MJ (2008) Physiological heterogeneity in biofilms. Nat Rev Microbiol 6:199–210PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Athanasios Rizoulis
    • 1
    • 5
  • David R. Elliott
    • 1
    • 6
  • Stephen A. Rolfe
    • 1
  • Steven F. Thornton
    • 2
  • Steven A. Banwart
    • 3
  • Roger W. Pickup
    • 4
  • Julie D. Scholes
    • 1
  1. 1.Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
  2. 2.Groundwater Protection and Restoration Group, Kroto Research InstituteUniversity of SheffieldSheffieldUK
  3. 3.Cell-Mineral Research Centre, Kroto Research InstituteUniversity of SheffieldSheffieldUK
  4. 4.Biomedical and Life Sciences Division, Faculty of Health and MedicineLancaster UniversityLancasterUK
  5. 5.School of Earth, Atmospheric and Environmental SciencesThe University of ManchesterManchesterUK
  6. 6.School of Science and the EnvironmentManchester Metropolitan UniversityManchesterUK

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