Microbial Ecology

, Volume 57, Issue 1, pp 94–103 | Cite as

Description of Freshwater Bacterial Assemblages from the Upper Paraná River Floodpulse System, Brazil

  • Michael J. Lemke
  • E. Kurt Lienau
  • Jean Rothe
  • Thomaz A. Pagioro
  • Jeff Rosenfeld
  • Rob DeSalle
Original Article

Abstract

Bacteria were identified from a large, seasonally flooded river (Paraná River, Brazil) and two floodplain habitats that were part of the same river system yet very different in nature: clearwater Garças Lagoon and the highly humic waters of Patos Lagoon. Bacterioplankton were collected during mid-summer (Jan. 2002) from water samples (2 l) filtered first through a 1.2-μm filter then a 0.2-μm membrane filter representing the particle-attached and free-living sub-communities, respectively. DNA was extracted from filters and purified and a 16S rRNA clone library established for each habitat. Over 300 clones were sequenced and checked for similarity to existing 16S sequences in GenBank using the BLAST algorithm with default parameters. Further classification of clones was done using a species “backbone” attachment followed by parsimony analysis. The majority (85%) of sequences, referred to here as operational taxonomic units (OTUs), were most similar to uncultured bacterium 16S sequences. OTUs from each Proteobacteria sub-phylum (α, β, γ, δ, ɛ) were present in the Upper Paraná River system, as well as members of the Bacteroidetes. The microbial assemblage from Patos Lagoon was least like other samples in that it had no Firmicutes present and was dominated by Actinobacteria. Verrucomicrobia OTUs were only found in the free-living assemblage. This study documents the presence of globally distributed phyla in Upper Paraná River and taxa unique to habitat and particle attachment.

Supplementary material

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References

  1. 1.
    Alfreider A, Pernthaler J, Amann R, Sattler B, Glockner F, Wille A, Psenner R (1996) Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl Environ Microbiol 62:2138–2144PubMedGoogle Scholar
  2. 2.
    Agostinho AA, Thomaz SM, Minte-Vera CV, Winemiller KO (2000) Biodiversity in the High River Paraná floodplain. In: Gopal B, Junk WJ, Davis JA (eds) Biodiversity in wetlands: assessment, function and conservation. Backhuys, Leiden, pp 89–118Google Scholar
  3. 3.
    Agostinho AA, Zalewski M (1996) A planicie alagavel do alto rio Paraná: Importancia e preservacao. EDUEM, MaringaGoogle Scholar
  4. 4.
    Bahr M, Hobbie JE, Sogin ML (1996) Bacterial diversity in an arctic lake—a freshwater SAR1 cluster. Aquat Microb Ecol 11:271–277CrossRefGoogle Scholar
  5. 5.
    Barreto SRG, Nozaki J, Barreto WJ (2003) Origin of dissolved organic carbon studied by UV–vis spectroscopy. Acta Hydrochimmica et Hydrobiologica 31:513–518CrossRefGoogle Scholar
  6. 6.
    Besemer KM, Moeseneder M, Arrieta JM, Herndl GJ, Peduzzi P (2005) Complexity of bacterial communities in a river-floodplain system (Danube, Austria). Appl Environ Microbiol 71:609–620PubMedCrossRefGoogle Scholar
  7. 7.
    Borneman J, Skroch PW, O’Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943PubMedGoogle Scholar
  8. 8.
    Bosshard PP, Santini Y, Grütter D, Stettler R, Bachofen R (2000) Bacterial diversity and community composition in the chemocline of the meromictic alpine Lake Cadagno as revealed by 16S rDNA analysis. FEMS Microbial Ecol 31:173–182CrossRefGoogle Scholar
  9. 9.
    Bukert U, Warnecke F, Babenzien D, Zwirnmann E, Pernthaler J (2003) Members of a readily enriched β-proteobacterial clade are common in surface waters of a humic lake. Appl Environ Microbio. 69:6550–6559CrossRefGoogle Scholar
  10. 10.
    Carvalho P, Thomaz SM, Bini LM (2003) Effects of water level, abiotic and biotic factors on bacterioplankton abundance in lagoons of a tropical flooplain (Paraná River, Brazil). Hydrobiologia 510:67–74CrossRefGoogle Scholar
  11. 11.
    Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270Google Scholar
  12. 12.
    Crump BC, Baross JA (1996) Particle-attached bacteria and heterotrophic plankton in the Columbia River estuary. Mar Ecol Prog Ser 138:265–273CrossRefGoogle Scholar
  13. 13.
    Crump BC, Baross JA (2000) Characterization of the bacterially-active particle fraction in the Columbia River estuary. Mar Ecol Prog Ser 206:12–22CrossRefGoogle Scholar
  14. 14.
    Crump BC, Imenstad CA, Baross JA (1998) Particle-attached bacteria dominant the Columbia River estuary. Aquat Microb Ecol 14:7–18CrossRefGoogle Scholar
  15. 15.
    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
  16. 16.
    Crump BC, Kling GW, Bahr M, Hobbie JE (2003) Bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. Appl Environ Microbiol 69:2253–2268PubMedCrossRefGoogle Scholar
  17. 17.
    Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (Eds) (2006) The prokaryotes, 3rd ed. Springer, NYGoogle Scholar
  18. 18.
    Eiler A, Bertilsson S (2004) Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ Microbiol 6:1228–1243PubMedCrossRefGoogle Scholar
  19. 19.
    Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410CrossRefGoogle Scholar
  20. 20.
    Gine MF, Bergamin H, Zaggato EAG, Reis BF (1980) Simultaneous determination of nitrate and nitrite by flow-injection analysis. Analytica Chimica Acta 114:191–197CrossRefGoogle Scholar
  21. 21.
    Glöckner FO, Fuchs BM, Amann R (1999) Bacterioplankton compositions of lakes and oceans: A first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65:3721–3726PubMedGoogle Scholar
  22. 22.
    Glöckner FO, Zaichikov E, Belkova N, Denissova L, Pernthaler J, Pernthaler A, Amann R (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of Actinobacteria. Appl Environ Microbiol 66:5053–5065PubMedCrossRefGoogle Scholar
  23. 23.
    Golterman HL, Clymo RS, Ohmstad MAM (1978) Methods for physical and chemical analysis of fresh waters. Blackwell Scientific, Oxford, p 214Google Scholar
  24. 24.
    Haukka K, Heikkinen E, Kairesalo T, Karjaiainen H, Sivoneh K (2005) Effect of humic material on the bacterioplankton community composition in boreal lakes and mesocosms. Environ Microbiol 7:620–630PubMedCrossRefGoogle Scholar
  25. 25.
    Hiorns WD, Methe BA, Nierzwicki-Bauer SA, Zehr JP (1997) Bacterial diversity in Adirondack mountain lakes as reveled by 16S rRNA gene sequences. Appl Environ Microiol 63:2957–2960Google Scholar
  26. 26.
    Junk WJ, Bayley PB, Sparks RE (1989) The floodpluse concept in river-floodplain systems. In: Dodge DP (ed) Proceedings of the International Large River Symposium, pp 110–127. Can. Spec. Publ. Fish. Aquat. Sci. 106Google Scholar
  27. 27.
    Knapp JS (1988) Historical perspectives and identification of Neisseria and related species. Clin Microbiol Rev 1:415–431PubMedGoogle Scholar
  28. 28.
    Lane DJ (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goofellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175Google Scholar
  29. 29.
    Lindström ES (2000) Bacterioplankton community composition in a boreal forest lake. FEMS Microbiol Ecol 27:163–174Google Scholar
  30. 30.
    Lyautey E, Lacoste B, Ten-Hage L, Rols J-L, Garabetian F (2005) Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: Methodological settings and fingerprints interpretation. Water Res 39:380–388PubMedCrossRefGoogle Scholar
  31. 31.
    Mackereth FYH, Heron J, Talling JJ (1978) Water analysis: some revised methods for limnologists. Freshwater Biological Association. Scientific Publication No. 36, Cumbria, p 120Google Scholar
  32. 32.
    Maddison DR, Maddison WP (2001) MacClade analysis of phylogeny and character evolution, Ver. 4. Wayne P. Sinauer, Sunderland, MAGoogle Scholar
  33. 33.
    Maidak BL, Cole JR, Liburn TG, Parker CT, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acid Res 29:173–174PubMedCrossRefGoogle Scholar
  34. 34.
    Methé BA, Hiorns WD, Zehr JP (1998) Contrasts between marine and freshwater bacterial community composition—analyses of communities in Lake George and six other Adirondack lakes. Limnol Oceanogr 43:368–374Google Scholar
  35. 35.
    Methé BA, Zehr JP (1999) Diversity of bacterial communities in Adirondack lakes: do species assemblages reflect lake water chemistry? Hydrobiologia 401:77–96CrossRefGoogle Scholar
  36. 36.
    Muyzer G, De Waal ED, Uitterlindiden 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
  37. 37.
    Nakatsu CH, Torsvik V, Øveås L (2000) Soil community analysis using DGGE of 16S rDNA polymerase chain reaction products. Soil Sci Soc Am J 64:1382–1388Google Scholar
  38. 38.
    Oliveira JL, Boroski M, Azevedo JCR, Nozaki J (2006) Spectroscopic investigation of humic substances in a tropical lake during a complete hydrological cycle. Acta Hydrochimmica et Hydrobiologica 34:608–617CrossRefGoogle Scholar
  39. 39.
    Rodrigues LC, Train S, do C, Roberto M, Pagioro TA (2002) Seasonal fluctuation of some limnological variables on a floodplain lake (Patos lagoon) of the Upper Paraná River, Mato Grosso do Sul State, Brazil. Brazilian Arch of Biol Tech 45:499–513Google Scholar
  40. 40.
    Simestad CA, Morgan CA, Cordell JR, Baross JA (1994) Flux, passive retention, and active residence of zooplankton in Columbia River estuarine turbidity maxima. In: Dyer KR, Orth BJ (eds) Changes in fluxes in estuaries: implications from science to management (ECSA22/ERF symposium, Plymouth, September 1992). Olsen and Olsen, Fredensborg, Denmark, pp 47–484Google Scholar
  41. 41.
    Sarkar N, Thornton JW, Planet PJ, Figurski DH, Schierwater D, DeSalle R (2002) An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24:388–399PubMedCrossRefGoogle Scholar
  42. 42.
    Souza FEE, Stevaux JC (1997) Geolgia e geomorfologia do complex rio Baia, Corutuba, Ivinhema. In: Vazzoler AEAM, Agostinho AA, Hahn NS (eds) A Planicie de inundacao do alto rio Paraná: Aspectos Fisico Biologicos e socioeconomicos. EDUEM, Maringa, pp 3–43Google Scholar
  43. 43.
    Swofford DL (2002) Phylogenetic analysis using parsimony* version 4. Wayne P. Sinauer, Sunderland, MAGoogle Scholar
  44. 44.
    Thomaz SM, Pagioro TA, Bini LM, do Roberto CM, de Araújo Rocha RR (2004) Chapter 4: Limnological characterization of the aquatic environments and the influence of hydrometric levels. In: Thomaz SM, Agostinho AA, Hahn NS (eds) The upper Paraná River and its flooplain: physical aspects, ecology and conservation. Backhuys, Leiden, The Netherlands, pp 75–102Google Scholar
  45. 45.
    Thomaz S, Bini L, Bozelli R (2007) Floods increase similarity among aquatic habitats in river-flooplain systems. Hydrobiologia 579:1–13CrossRefGoogle Scholar
  46. 46.
    Van der Gucht K, Sabbe K, De Meester L, Vloemans N, Zwart G, Gillis M, Vyverman W (2001) Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes. Environ Microbiol 3:680–690CrossRefGoogle Scholar
  47. 47.
    Ward N, Rainey FA, Stackebrandt E, Schlesner H (1995) Unraveling the extent of diversity within the order Planctomycetales. Appl Environ Microbiol 61:2270–2275PubMedGoogle Scholar
  48. 48.
    Warnecke R, Amann R, Pernthaler J (2004) Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ Microbiol 6:242–253PubMedCrossRefGoogle Scholar
  49. 49.
    Weiss P, Schweitzer B, Amann R, Simon M (1996) Identification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow). Appl Envion Microbiol 62:1998–2005Google Scholar
  50. 50.
    Winter C, Hein T, Kavka G, Mach RL, Farnleitner AH (2007) Longitudinal changes in the bacterial community composition of the Danube River: a whole-river approach. Appl Environ Microbiol 73:421–431PubMedCrossRefGoogle Scholar
  51. 51.
    Zavarzin GA, Stackebrandt E, Murray RG (1991) A correlation of phylogenetic diversity in Proteobacteria with the influences of ecological forces. Can J Microbiol 37:1–6PubMedCrossRefGoogle Scholar
  52. 52.
    Zwart G, Crump BC, Kamst-van Agterveld M, Hagen F, Han S-K (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microbial Ecol 28:141–155CrossRefGoogle Scholar
  53. 53.
    Zwart G, Hiorns WD, Methe BA, van Agterveld MP, Huismans R, Nold SC, Zehr JP, Laanbroek HJ (1998) Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 21:546–556PubMedGoogle Scholar
  54. 54.
    Zwart G, Huismans R, van Agterveld MP, Van de Peer Y, De Rijk P, Eenhorrn H, Muyzer G, van Hannen EJ, Gons HJ, Laanbroek HJ (1998) Divergent members of the bacterial division Verrucomicrobiales in a temperate freshwater lake. FEMS Microbiol Ecol 25:159–169CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Michael J. Lemke
    • 1
  • E. Kurt Lienau
    • 2
  • Jean Rothe
    • 3
  • Thomaz A. Pagioro
    • 4
  • Jeff Rosenfeld
    • 3
  • Rob DeSalle
    • 3
  1. 1.Biology DepartmentUniversity of Illinois at SpringfieldSpringfieldUSA
  2. 2.Department of BiologyNew York UniversityNew YorkUSA
  3. 3.Division of Invertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
  4. 4.Departamento Acadêmico de Química e BiologiaUniversidade Tecnológica Federal do ParanáCuritibaBrazil

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