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Microbial Ecology

, Volume 66, Issue 1, pp 5–18 | Cite as

Structure and Community Composition of Sprout-Like Bacterial Aggregates in a Dinaric Karst Subterranean Stream

  • Rok Kostanjšek
  • Lejla Pašić
  • Holger Daims
  • Boris Sket
Microbiology of Aquatic Systems

Abstract

The Vjetrenica cave in the Dinaric Karst hosts a worldwide extraordinarily high cave biodiversity. Beside a diverse and specialized cave fauna, sprout-like formations attached to the bed of the cave stream were observed and described, but not further characterized, almost a century ago. Here we investigated these sprout-like microbial aggregates by the rRNA approach and detailed microscopy. Based on fluorescence in situ hybridization and ultrastructural analysis, the sprout-like formations are morphologically highly organized, and their core consists of a member of a novel deep-branching lineage in the bacterial phylum Nitrospirae. This organism displays an interesting cellular ultrastructure with different kinds of cytoplasmic inclusions and is embedded in a thick extracellular matrix, which contributes to the stability and shape of the aggregates. This novel bacterium has been provisionally classified as “Candidatus Troglogloea absoloni.” The surface of the sprout-like aggregates is more diverse than the core. It is colonized by a bacterial biofilm consisting primarily of filamentous Betaproteobacteria, whereas other microbial populations present in the crust include members of the Bacteriodetes, Gammaproteobacteria, Actinombacteria, Alphaproteobacteria, and Planctomycetes, which are intermingled with mineral inclusions. This study represents the first thorough molecular and ultrastructural characterization of the elusive sprout-like bacterial aggregates, which are also found in other cave systems of the Dinaric Karst. The discovery of Ca. Troglogloea absoloni contributes to the known biodiversity of subterranean ecosystems and especially of macroscopic structures formed in caves by microorganisms, whose composition and ecological function often remain enigmatic.

Keywords

Clone Library Betaproteobacteria Periplasmic Space Nitrite Oxidizer Karst Cave 
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.

Notes

Acknowledgments

We are grateful to D. Bakšić for the photography of the sprout-like formations in their natural environment, J. Jugovic for the assistance in the sampling and measurements on field, B. Papić for the assistance in clone library preparation, R. Ozimec for providing scientific literature, and J. Dolinšek for the constructive suggestions on hybridization procedures. This work was financed by the Slovenian Research Agency (ARRS), research programs no. P1-0184 and P1-0198.

Supplementary material

248_2012_172_Fig9_ESM.jpg (41 kb)
Supplementary Fig. 1

ML phylogenetic tree showing the positions of phylotypes recovered from sprout-like microbial community clone libraries and belonging to a classes Gammaproteobacteria and Alphaproteobacteria of Proteobacteria and b Bacteroidetes, Actinobacteria, and Planctomycetes. Names in italics correspond to cultivated species, while the rest correspond to 16S rRNA gene clones. Names in bold correspond to the clones obtained in this study. The bullets indicate that the ML and MP bootstrap values and Bayesian posterior probabilities were ≥75 % (JPEG 41.1 kb)

248_2012_172_MOESM1_ESM.tif (2.3 mb)
High resolution image (TIFF 2.33 mb)
248_2012_172_MOESM2_ESM.docx (15 kb)
ESM 2 (DOCX 14.8 kb)

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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Rok Kostanjšek
    • 1
  • Lejla Pašić
    • 1
  • Holger Daims
    • 2
  • Boris Sket
    • 1
  1. 1.Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
  2. 2.Department of Microbial Ecology, Ecology CentreUniversity of ViennaViennaAustria

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