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

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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.

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References

  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 62:2138–2144

    PubMed  CAS  Google Scholar 

  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 89–118

    Google Scholar 

  3. Agostinho AA, Zalewski M (1996) A planicie alagavel do alto rio Paraná: Importancia e preservacao. EDUEM, Maringa

    Google Scholar 

  4. Bahr M, Hobbie JE, Sogin ML (1996) Bacterial diversity in an arctic lake—a freshwater SAR1 cluster. Aquat Microb Ecol 11:271–277

    Article  Google Scholar 

  5. Barreto SRG, Nozaki J, Barreto WJ (2003) Origin of dissolved organic carbon studied by UV–vis spectroscopy. Acta Hydrochimmica et Hydrobiologica 31:513–518

    Article  CAS  Google Scholar 

  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 71:609–620

    Article  PubMed  CAS  Google Scholar 

  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 62:1935–1943

    PubMed  CAS  Google Scholar 

  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 31:173–182

    Article  CAS  Google Scholar 

  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. 69:6550–6559

    Article  CAS  Google Scholar 

  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 510:67–74

    Article  CAS  Google Scholar 

  11. Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11:265–270

    Google Scholar 

  12. Crump BC, Baross JA (1996) Particle-attached bacteria and heterotrophic plankton in the Columbia River estuary. Mar Ecol Prog Ser 138:265–273

    Article  Google Scholar 

  13. Crump BC, Baross JA (2000) Characterization of the bacterially-active particle fraction in the Columbia River estuary. Mar Ecol Prog Ser 206:12–22

    Article  Google Scholar 

  14. Crump BC, Imenstad CA, Baross JA (1998) Particle-attached bacteria dominant the Columbia River estuary. Aquat Microb Ecol 14:7–18

    Article  Google Scholar 

  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 65:3192–3204

    PubMed  CAS  Google Scholar 

  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 69:2253–2268

    Article  PubMed  Google Scholar 

  17. Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (Eds) (2006) The prokaryotes, 3rd ed. Springer, NY

  18. Eiler A, Bertilsson S (2004) Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes. Environ Microbiol 6:1228–1243

    Article  PubMed  Google Scholar 

  19. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410

    Article  Google Scholar 

  20. Gine MF, Bergamin H, Zaggato EAG, Reis BF (1980) Simultaneous determination of nitrate and nitrite by flow-injection analysis. Analytica Chimica Acta 114:191–197

    Article  CAS  Google Scholar 

  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 65:3721–3726

    PubMed  Google Scholar 

  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 66:5053–5065

    Article  PubMed  Google Scholar 

  23. Golterman HL, Clymo RS, Ohmstad MAM (1978) Methods for physical and chemical analysis of fresh waters. Blackwell Scientific, Oxford, p 214

    Google Scholar 

  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 7:620–630

    Article  PubMed  CAS  Google Scholar 

  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 63:2957–2960

    CAS  Google Scholar 

  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. 106

  27. Knapp JS (1988) Historical perspectives and identification of Neisseria and related species. Clin Microbiol Rev 1:415–431

    PubMed  CAS  Google Scholar 

  28. Lane DJ (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goofellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  29. Lindström ES (2000) Bacterioplankton community composition in a boreal forest lake. FEMS Microbiol Ecol 27:163–174

    Google Scholar 

  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 39:380–388

    Article  PubMed  CAS  Google Scholar 

  31. Mackereth FYH, Heron J, Talling JJ (1978) Water analysis: some revised methods for limnologists. Freshwater Biological Association. Scientific Publication No. 36, Cumbria, p 120

  32. Maddison DR, Maddison WP (2001) MacClade analysis of phylogeny and character evolution, Ver. 4. Wayne P. Sinauer, Sunderland, MA

    Google Scholar 

  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 29:173–174

    Article  PubMed  CAS  Google Scholar 

  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 43:368–374

    Google Scholar 

  35. Methé BA, Zehr JP (1999) Diversity of bacterial communities in Adirondack lakes: do species assemblages reflect lake water chemistry? Hydrobiologia 401:77–96

    Article  Google Scholar 

  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 59:695–700

    PubMed  CAS  Google Scholar 

  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 64:1382–1388

    CAS  Google Scholar 

  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 34:608–617

    Article  CAS  Google Scholar 

  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 45:499–513

    Google Scholar 

  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 47–484

    Google Scholar 

  41. Sarkar N, Thornton JW, Planet PJ, Figurski DH, Schierwater D, DeSalle R (2002) An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24:388–399

    Article  PubMed  CAS  Google Scholar 

  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 3–43

    Google Scholar 

  43. Swofford DL (2002) Phylogenetic analysis using parsimony* version 4. Wayne P. Sinauer, Sunderland, MA

    Google Scholar 

  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 75–102

    Google Scholar 

  45. Thomaz S, Bini L, Bozelli R (2007) Floods increase similarity among aquatic habitats in river-flooplain systems. Hydrobiologia 579:1–13

    Article  Google Scholar 

  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 3:680–690

    Article  Google Scholar 

  47. Ward N, Rainey FA, Stackebrandt E, Schlesner H (1995) Unraveling the extent of diversity within the order Planctomycetales. Appl Environ Microbiol 61:2270–2275

    PubMed  CAS  Google Scholar 

  48. Warnecke R, Amann R, Pernthaler J (2004) Actinobacterial 16S rRNA genes from freshwater habitats cluster in four distinct lineages. Environ Microbiol 6:242–253

    Article  PubMed  CAS  Google Scholar 

  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 62:1998–2005

    CAS  Google Scholar 

  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 73:421–431

    Article  PubMed  CAS  Google Scholar 

  51. Zavarzin GA, Stackebrandt E, Murray RG (1991) A correlation of phylogenetic diversity in Proteobacteria with the influences of ecological forces. Can J Microbiol 37:1–6

    Article  PubMed  CAS  Google Scholar 

  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 28:141–155

    Article  Google Scholar 

  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 21:546–556

    PubMed  CAS  Google Scholar 

  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 25:159–169

    Article  CAS  Google Scholar 

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Acknowledgments

We thank Sidinei M. Thomas and the Universidade Estadual de Maringá, Núcleo de Pesquisas em Limnologia, Ictiologia e Aqüicultura, Maringá—PR—Brazil. We also thank A. M. Lemke, J. Bartletti, K. Kiehl, and A. K. da Silva Nakamura for field assistance, S. Paver for improvements to the manuscript, and boatmen A. Soares and Roberto. Brazil samples were collected under CNPq permit Portaria MCT no. 260/03, and work was partially supported by CNPq (Long Term Ecological Program, Brazilian site 6). Work at the American Museum of Natural History was supported by the Lewis and Dorothy Cullman Program in Molecular Systematics, with funding from the Sackler Institute of Comparative Genomics. E. K. Lienau and J. Rothe acknowledge financial assistance from the MacCracken Fellowship (NYU) and Hudson River Foundation, NY, respectively.

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Authors and Affiliations

  1. Biology Department, University of Illinois at Springfield, One University Plaza, Springfield, IL, 62703, USA

    Michael J. Lemke

  2. Department of Biology, New York University, New York, NY, 10011, USA

    E. Kurt Lienau

  3. Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA

    Jean Rothe, Jeff Rosenfeld & Rob DeSalle

  4. Departamento Acadêmico de Química e Biologia, Universidade Tecnológica Federal do Paraná, Curitiba, Paraná, Brazil

    Thomaz A. Pagioro

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  1. Michael J. Lemke
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Correspondence to Michael J. Lemke.

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Lemke, M.J., Lienau, E.K., Rothe, J. et al. Description of Freshwater Bacterial Assemblages from the Upper Paraná River Floodpulse System, Brazil. Microb Ecol 57, 94–103 (2009). https://doi.org/10.1007/s00248-008-9398-3

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