The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains

PLoS One. 2013;8(3):e58209. doi: 10.1371/journal.pone.0058209. Epub 2013 Mar 7.

Abstract

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Betaproteobacteria / classification*
  • Betaproteobacteria / genetics*
  • Betaproteobacteria / growth & development
  • Betaproteobacteria / metabolism
  • Biomass
  • Ecosystem*
  • Fresh Water / microbiology*
  • Genetic Variation*
  • Molecular Sequence Data
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics

Substances

  • RNA, Ribosomal, 16S

Associated data

  • GENBANK/HE600660
  • GENBANK/HE600661
  • GENBANK/HE600662
  • GENBANK/HE600663
  • GENBANK/HE600664
  • GENBANK/HE600665
  • GENBANK/HE600666
  • GENBANK/HE600667
  • GENBANK/HE600668
  • GENBANK/HE600669
  • GENBANK/HE600670
  • GENBANK/HE600671
  • GENBANK/HE600672
  • GENBANK/HE600673
  • GENBANK/HE600674
  • GENBANK/HE600675
  • GENBANK/HE600676
  • GENBANK/HE600677
  • GENBANK/HE600678
  • GENBANK/HE600679
  • GENBANK/HE600680
  • GENBANK/HE600681
  • GENBANK/HE600682
  • GENBANK/HE600683
  • GENBANK/HE600684
  • GENBANK/HE600685
  • GENBANK/HE600686
  • GENBANK/HE600687
  • GENBANK/HE600688
  • GENBANK/HE600689
  • GENBANK/HE600690
  • GENBANK/HE600691
  • GENBANK/HE600692

Grant support

This study was largely supported by the Grant Agency of the Czech Republic under research grants 206/08/0015 (granted to KS) and P504/10/0566 (granted to JJ), the institutional project of the ASCR No. AV0Z 60170517. The authors also profited from the Czech-Austrian mobility found KONTAKT projects MEB 060602/CZ 05-2007 (granted to KS and MWH) and MEB 060901/WTZ project 406600 (granted to JJ and MWH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.