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


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.


Total Organic Carbon Proteobacteria Actinobacteria Firmicutes Bacteroidetes 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.

Supplementary material

248_2008_9398_MOESM1_ESM.pdf (24 kb)
ESM (PDF 23.6 kb)


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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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