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Comparison of Bacterial Communities in New England Sphagnum Bogs Using Terminal Restriction Fragment Length Polymorphism (T-RFLP)

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Abstract

Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.

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References

  1. CB Blackwood, TL Marsh, S-H Kim and EA Paul, Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69 (2003) 926-932

    Article  PubMed  CAS  Google Scholar 

  2. G Braker, HL Ayala del Río, AH Devol, A Fesefeldt and JM Tiedje, Community structure of denitrifiers, bacteria and Archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 67 (2001) 1893-1901

    Article  PubMed  CAS  Google Scholar 

  3. JE Brofft, JV McArthur and LJ Shimkets, Recovery of novel bacterial diversity from a forested wetland impacted by reject coal. Environ Microbiol 4 (2002) 764-769

    Article  PubMed  CAS  Google Scholar 

  4. DH Buckley and TM Schmidt, Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ Microbiol 5 (2003) 441-452

    Article  PubMed  Google Scholar 

  5. HF Castro, NH Williams and A Ogram, Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31 (2000) 1-9

    PubMed  CAS  Google Scholar 

  6. DE Cummings, AW March, B Bostick, S Spring, F Caccavo Jr, S Fendorf and RF Rosenzweig, Evidence for microbial Fe(III) reduction in anoxic, mining-impacted lake sediments (Lake Coeur d’Alene, Idaho). Appl Environ Microbiol 66 (2000) 154-162

    Article  PubMed  CAS  Google Scholar 

  7. SN Dedysh, NS Panikov, W Liesack, R Großkopf, J Zhou and JM Tiedje, Isolation of acidophilc methane-oxidizing bacteria from Northern peat wetlands. Science 282 (1998) 281-284

    Article  PubMed  CAS  Google Scholar 

  8. A Dhillon, A Teske, J Dillon, DA Stahl and ML Sogin, Molecular characterization of sulfate-reducing bacteria in the Guaymas basin. Appl Environ Microbiol 69 (2003) 2765-2772

    Article  PubMed  CAS  Google Scholar 

  9. JM Dunbar, LO Ticknor and CR Kuske, Assessment of microbial diversity in four Southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66 (2000) 2943-2950

    Article  PubMed  CAS  Google Scholar 

  10. B Duval, Methane production and release from two New England peatlands. Int Microbiol 3 (2000) 89-95

    PubMed  CAS  Google Scholar 

  11. AM Ellison and NJ Gotelli, Nitrogen availability alters the expression of carnivory in the northern pitcher plant, Sarracenia purpuea. PNAS 99 (2002) 4409-4412

    Article  PubMed  CAS  Google Scholar 

  12. TM Embley and E Stackebrandt, The molecular phylogeny and systematics of the actinomycetes. Annu Rev Microbiol 48 (1994) 257-289

    PubMed  CAS  Google Scholar 

  13. KW Farrish and DF Grigal, Decomposition in an ombrotrophic bog and a minerotrophic fen in Minnesota. Soil Sci 145 (1988) 353-358

    Article  Google Scholar 

  14. MM Fisher, JM Graham and LE Graham, Bacterial abundance and activity across sites within two Northern Wisconsin Sphagnum bogs. Microb Ecol 36 (1998) 259-269

    Article  PubMed  Google Scholar 

  15. JA Fuerst, The Planctomycetes: emerging models for microbial ecology, evolution and cell biology. Microbiology 141 (1995) 1493-1506

    Article  PubMed  CAS  Google Scholar 

  16. PE Galand, H Fritze and K Yrjälä, Microsite-dependant changes in methanogenic populations in a boreal oligotrophic fen. Environ Microbiol 5 (2003) 1133-1143

    Article  PubMed  Google Scholar 

  17. S Goodwin and G Zeikus, Ecophysiological adaptations of anaerobic bacteria to low pH: analysis of anaerobic digestion in acidic bog sediments. Appl Environ Microbiol 53 (1987) 57-64

    PubMed  CAS  Google Scholar 

  18. NJ Gotelli and AM Ellison, Biogeography at a regional scale: determinants of ant species density in New England bogs and forests. Ecology 83 (2002) 1604-1609

    Article  Google Scholar 

  19. TC Gsell, WE Holben and RM Ventullo, Characterization of the sediment bacterial community in groundwater discharge zones of an Alkaline Fen: a seasonal study. Appl Environ Microbiol 63 (1997) 3111-3118

    PubMed  CAS  Google Scholar 

  20. Bergey’s Manual of Determinative Bacteriology. Baltimore, MD: Williams and Wilkins (2000).

    Google Scholar 

  21. LC Johnson, WH Damman and N Malmer, Sphagnum macrostructure as an indicator of decay and compaction in peat cores from an ombrotrophic South Swedish peat bog. J Ecol 78 (1990) 633-647

    Article  Google Scholar 

  22. CW Kaplan and CL Kitts, Variation between observed and true terminal restriction fragment length is dependant on true TRF length and purine content. J Microbiol Methods 54 (2003) 121-125

    Article  PubMed  CAS  Google Scholar 

  23. AD Kent, DJ Smith, BJ Benson and EW Triplett, Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 69 (2003) 6768-6776

    Article  PubMed  CAS  Google Scholar 

  24. Y Koizumi, H Kojima, K Oguri, H Kitazato and M Fukui, Vertical and temporal shifts in microbial communities in the water column and sediment of saline meromictic Lake Kaiike (Japan), asdetermined by a 16S rDNA-based analysis, and related to physicochemical gradients. Environ Microbiol 6 (2004) 622-637

    Article  PubMed  CAS  Google Scholar 

  25. CR Kuske, LO Ticknor, ME Miller, JM Dunbar, JA Davis, SM Barns and J Belnap, Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68 (2002) 1854-1863

    Article  PubMed  CAS  Google Scholar 

  26. MG LaMontagne, I Leifer, S Bergmann, LC Werfhorst Van De and PA Holden, Bacterial diversity in marine hydrocarbon seep sediments. Environ Microbiol 6 (2004) 799

    Article  PubMed  Google Scholar 

  27. W-T Liu, TL Marsh, H Cheng and LJ Forney, Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63 (1997) 4516-4522

    PubMed  CAS  Google Scholar 

  28. A Loy, K Küsel, A Lehner, HL Drake and M Wagner, Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal coocurrence of recognized and novel lineages. Appl Environ Microbiol 70 (2004) 6998-7009

    Article  PubMed  CAS  Google Scholar 

  29. MT Madigan, JM Martinko and J Parker, Brock Biology of Microorganisms. Englewood, NJ: Prentice-Hall (2003).

    Google Scholar 

  30. WJ Mitsch and JG Gosselink, Wetlands. New York: Wiley (2000).

    Google Scholar 

  31. Mouser, PJ, Hession, WC, Rizzo, DM, Gotelli, NJ (2005) Hydrology and geostatistics of a Vermont, USA kettlehole peatland. J Hydrol 301: 250–266

    Article  CAS  Google Scholar 

  32. S Rendulic, P Jagtap, A Rosinus, M Eppinger, C Baar, C Lanz, H Keller, C Lambert, J Evans, A Goesmann, F Meyer, RE Sockett and SC Schuster, A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science 303 (2004) 689-692

    Article  PubMed  CAS  Google Scholar 

  33. M Sait, P Hugenholtz and PH Janssen, Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 4 (2002) 654

    Article  PubMed  CAS  Google Scholar 

  34. Sciarini, SM, Michel, F (2002) tRFLP Fragment Sorter. [2.5b3]. Computer Program

  35. MV Sizova, NS Panikov, TP Tourova and PW Flanagan, Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol Ecol 45 (2003) 301-315

    Article  CAS  PubMed  Google Scholar 

  36. M Strous, JG Kuenen, JA Fuerst, M Wagner and MS Jetten, The anammox case—a new experimental manifesto for microbiological eco-physiology. Antonie Van Leeuwenhoek 81 (2002) 693-702

    Article  PubMed  CAS  Google Scholar 

  37. M Upton, B Hill, C Edwards, JR Saunders, DA Ritchie and D Lloyd, Combined molecular ecological and confocal laser scanning microscopic analysis of peat bog methanogen populations. FEMS Microbiol Lett 193 (2000) 275-281

    Article  PubMed  CAS  Google Scholar 

  38. LA Niftrik van, JA Fuerst, JSS Damsté, JG Kuenen, MSM Jetten and M Strous, The anammoxosome: an intracytoplasmic compartment in anammox bacteria. FEMS Microbiol Lett 233 (2004) 7-13

    Article  PubMed  CAS  Google Scholar 

  39. JTA Verhoeven, E Maltby and MB Schmitz, Nitrogen and phosphorous mineralization in fens and bogs. J Ecol 78 (1990) 713-726

    Article  Google Scholar 

  40. RT Williams and RL Crawford, Effects of various physiochemical factors on microbial activity in peatlands: aerobic biodegradative processes. Can J Microbiol 29 (1983) 1430-1437

    Article  Google Scholar 

  41. RT Williams and RL Crawford, Microbial diversity of Minnesota peatlands. Microb Ecol 9 (1983) 201-214

    Article  CAS  Google Scholar 

  42. H Yamamoto, A Hiraishi, K Kato, HX Chiura, Y Maki and A Shimizu, Phylogenetic evidence for the existence of novel thermophilic bacteria in hot sulfur-turf microbial mats in Japan. Appl Environ Microbiol 64 (1998) 1680-1687

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by funding from NSF (EPS-0082977). The authors would like to thank Aaron M. Ellison for sharing data as well as his extensive knowledge of bog ecology and geography. We are grateful to Don Stratton for assistance with the statistical analysis and Carol Tudhope and Grant Henderson for sample preparation and data organization. Kevin Penn is thanked for performing DNA sequencing and analysis.

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Authors and Affiliations

  1. Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT, 05405, USA

    Sergio E. Morales & Thomas A. Lewis

  2. Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, 05405, USA

    Paula J. Mouser

  3. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD, 20850, USA

    Naomi Ward

  4. Center of Marine Biotechnology, 701 E. Pratt St, Baltimore, MD, 21202, USA

    Naomi Ward

  5. Department of Biology, University of Vermont, Burlington, VT, 05405, USA

    Stephen P. Hudman & Nicholas J. Gotelli

  6. Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA

    Donald S. Ross

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  1. Sergio E. Morales
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  2. Paula J. Mouser
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  3. Naomi Ward
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  4. Stephen P. Hudman
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  5. Nicholas J. Gotelli
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  7. Thomas A. Lewis
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Correspondence to Thomas A. Lewis.

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Morales, S.E., Mouser, P.J., Ward, N. et al. Comparison of Bacterial Communities in New England Sphagnum Bogs Using Terminal Restriction Fragment Length Polymorphism (T-RFLP). Microb Ecol 52, 34–44 (2006). https://doi.org/10.1007/s00248-005-0264-2

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  • DOI: https://doi.org/10.1007/s00248-005-0264-2

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