Insights Into Variability of Actinorhodopsin Genes of the LG1 Cluster in Two Different Freshwater Habitats

PLoS One. 2013 Jul 2;8(7):e68542. doi: 10.1371/journal.pone.0068542. Print 2013.

Abstract

Actinorhodopsins (ActRs) are recently discovered proteorhodopsins present in Actinobacteria, enabling them to adapt to a wider spectrum of environmental conditions. Frequently, a large fraction of freshwater bacterioplankton belongs to the acI lineage of Actinobacteria and codes the LG1 type of ActRs. In this paper we studied the genotype variability of the LG1 ActRs. We have constructed two clone libraries originating from two environmentally different habitats located in Central Europe; the large alkaline lake Mondsee (Austria) and the small humic reservoir Jiřická (the Czech Republic). The 75 yielded clones were phylogenetically analyzed together with all ActR sequences currently available in public databases. Altogether 156 sequences were analyzed and 13 clusters of ActRs were distinguished. Newly obtained clones are distributed over all three LG1 subgroups--LG1-A, B and C. Eighty percent of the sequences belonged to the acI lineage (LG1-A ActR gene bearers) further divided into LG1-A1 and LG1-A2 subgroups. Interestingly, the two habitats markedly differed in genotype composition with no identical sequence found in both samples of clones. Moreover, Jiřická reservoir contained three so far not reported clusters, one of them LG1-C related, presenting thus completely new, so far undescribed, genotypes of Actinobacteria in freshwaters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinobacteria / classification
  • Actinobacteria / genetics*
  • Actinobacteria / growth & development
  • Austria
  • Bacterial Proteins / classification
  • Bacterial Proteins / genetics*
  • Czech Republic
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • Ecosystem*
  • Fresh Water / microbiology*
  • Genetic Variation
  • Geography
  • In Situ Hybridization, Fluorescence
  • Molecular Sequence Data
  • Multigene Family / genetics
  • Phylogeny
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA

Substances

  • Bacterial Proteins
  • DNA, Bacterial

Associated data

  • GENBANK/KC601681
  • GENBANK/KC601682
  • GENBANK/KC601683
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  • GENBANK/KC601754
  • GENBANK/KC601755

Grant support

This study was financially supported by the Czech Grant Agency project EEF/10/E011 awarded to Jan Jezbera. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.