PMID- 19638289
OWN - NLM
STAT- MEDLINE
DCOM- 20091117
LR  - 20090928
IS  - 1872-8359 (Electronic)
IS  - 0167-7012 (Linking)
VI  - 79
IP  - 1
DP  - 2009 Oct
TI  - Detection of iron-depositing Pedomicrobium species in native biofilms from the 
      Odertal National Park by a new, specific FISH probe.
PG  - 37-43
LID - 10.1016/j.mimet.2009.07.014 [doi]
AB  - Iron-depositing bacteria play an important role in technical water systems (water 
      wells, distribution systems) due to their intense deposition of iron oxides and 
      resulting clogging effects. Pedomicrobium is known as iron- and 
      manganese-oxidizing and accumulating bacterium. The ability to detect and 
      quantify members of this species in biofilm communities is therefore desirable. 
      In this study the fluorescence in situ hybridization (FISH) method was used to 
      detect Pedomicrobium in iron and manganese incrusted biofilms. Based on 
      comparative sequence analysis, we designed and evaluated a specific 
      oligonucleotide probe (Pedo 1250) complementary to the hypervariable region 8 of 
      the 16S rRNA gene for Pedomicrobium. Probe specificities were tested against 3 
      different strains of Pedomicrobium and Sphingobium yanoikuyae as non-target 
      organism. Using optimized conditions the probe hybridized with all tested strains 
      of Pedomicrobium with an efficiency of 80%. The non-target organism showed no 
      hybridization signals. The new FISH probe was applied successfully for the in 
      situ detection of Pedomicrobium in different native, iron-depositing biofilms. 
      The hybridization results of native bioflims using probe Pedo_1250 agreed with 
      the results of the morphological structure of Pedomicrobium bioflims based on 
      scanning electron microscopy.
FAU - Braun, Burga
AU  - Braun B
AD  - Department of Environmental Microbiology, Berlin University of Technology, 
      Franklinstrasse 29, 10587 Berlin, Germany. burga.braun@tu-berlin.de
FAU - Richert, Inga
AU  - Richert I
FAU - Szewzyk, Ulrich
AU  - Szewzyk U
LA  - eng
SI  - GENBANK/FM886836
SI  - GENBANK/FM886849
SI  - GENBANK/FM886854
SI  - GENBANK/FM886881
SI  - GENBANK/FM886896
SI  - GENBANK/FM886902
SI  - GENBANK/FM886904
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20090725
PL  - Netherlands
TA  - J Microbiol Methods
JT  - Journal of microbiological methods
JID - 8306883
RN  - 0 (DNA, Bacterial)
RN  - 0 (DNA, Ribosomal)
RN  - 0 (Oligonucleotide Probes)
RN  - 0 (RNA, Ribosomal, 16S)
SB  - IM
MH  - *Biofilms
MH  - Cluster Analysis
MH  - DNA, Bacterial/chemistry/*genetics
MH  - DNA, Ribosomal/chemistry/genetics
MH  - Hyphomicrobiaceae/genetics/*isolation & purification
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Molecular Sequence Data
MH  - Oligonucleotide Probes/*genetics
MH  - Phylogeny
MH  - RNA, Ribosomal, 16S/genetics
MH  - Sensitivity and Specificity
MH  - Sequence Analysis, DNA
MH  - *Water Microbiology
EDAT- 2009/07/30 09:00
MHDA- 2009/11/18 06:00
CRDT- 2009/07/30 09:00
PHST- 2009/06/05 00:00 [received]
PHST- 2009/07/16 00:00 [revised]
PHST- 2009/07/18 00:00 [accepted]
PHST- 2009/07/30 09:00 [entrez]
PHST- 2009/07/30 09:00 [pubmed]
PHST- 2009/11/18 06:00 [medline]
AID - S0167-7012(09)00226-7 [pii]
AID - 10.1016/j.mimet.2009.07.014 [doi]
PST - ppublish
SO  - J Microbiol Methods. 2009 Oct;79(1):37-43. doi: 10.1016/j.mimet.2009.07.014. Epub 
      2009 Jul 25.