Development of a 16S rRNA-targeted probe set for Verrucomicrobia and its application for fluorescence in situ hybridization in a humic lake.
Members of the highly diverse bacterial phylum Verrucomicrobia are globally distributed in various terrestrial and aquatic habitats. They are key players in soils, but little is known about their role in aquatic systems. Here, we report on the design and evaluation of a 16S rRNA-targeted probe set for the identification of Verrucomicrobia and of clades within this phylum. Subsequently, the probe set was applied to a study concerning the seasonal abundance of Verrucomicrobia in waters of the humic lake Grosse Fuchskuhle (Germany) by catalyzed reporter deposition fluorescence in situ hybridization. The lake hosted diverse Verrucomicrobia clades in all seasons. Either Spartobacteria (up to 19%) or Opitutus spp. (up to 7%) dominated the communities, whereas Prosthecobacter spp. were omnipresent in low numbers (<1%). Verrucomicrobial abundance and community composition varied between the seasons, and between more and less humic basins, but were rather stable in oxic and seasonally anoxic waters.
Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Celsiusstrasse 1, 28359 Bremen, Germany.
Julia
J
Arnds
Katrin
K
Knittel
Ulrike
U
Buck
Matthias
M
Winkel
Rudolf
R
Amann
D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D044822:Biodiversity; D015169:Colony Count, Microbial / Q000379:methods; D005618:Fresh Water / Q000382:microbiology*; D005858:Germany; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012621:Seasons
D015345:Oligonucleotide Probes; D012336:RNA, Ribosomal, 16S