PMID- 14602652
OWN - NLM
STAT- MEDLINE
DCOM- 20040220
LR  - 20210526
IS  - 0099-2240 (Print)
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Linking)
VI  - 69
IP  - 11
DP  - 2003 Nov
TI  - The isotope array, a new tool that employs substrate-mediated labeling of rRNA 
      for determination of microbial community structure and function.
PG  - 6875-87
AB  - A new microarray method, the isotope array approach, for identifying 
      microorganisms which consume a (14)C-labeled substrate within complex microbial 
      communities was developed. Experiments were performed with a small microarray 
      consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing 
      bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas 
      eutropha grown in the presence of [(14)C]bicarbonate. After fluorescence labeling 
      of the RNA and microarray hybridization, scanning of all probe spots for 
      fluorescence and radioactivity revealed that specific signals were obtained and 
      that the incorporation of (14)C into rRNA could be detected unambiguously. 
      Subsequently, we were able to demonstrate the suitability of the isotope array 
      approach for monitoring community composition and CO(2) fixation activity of AOB 
      in two nitrifying activated-sludge samples which were incubated with 
      [(14)C]bicarbonate for up to 26 h. AOB community structure in the 
      activated-sludge samples, as predicted by the microarray hybridization pattern, 
      was confirmed by quantitative fluorescence in situ hybridization (FISH) and 
      comparative amoA sequence analyses. CO(2) fixation activities of the AOB 
      populations within the complex activated-sludge communities were detectable on 
      the microarray by (14)C incorporation and were confirmed independently by 
      combining FISH and microautoradiography. AOB rRNA from activated sludge incubated 
      with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of 
      AOB activity showed no incorporation of (14)C and thus was not detectable on the 
      radioactivity scans of the microarray. These results suggest that the isotope 
      array can be used in a PCR-independent manner to exploit the high parallelism and 
      discriminatory power of microarrays for the direct identification of 
      microorganisms which consume a specific substrate in the environment.
FAU - Adamczyk, Justyna
AU  - Adamczyk J
AD  - Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D-85350 Freising, 
      Germany.
FAU - Hesselsoe, Martin
AU  - Hesselsoe M
FAU - Iversen, Niels
AU  - Iversen N
FAU - Horn, Matthias
AU  - Horn M
FAU - Lehner, Angelika
AU  - Lehner A
FAU - Nielsen, Per Halkjaer
AU  - Nielsen PH
FAU - Schloter, Michael
AU  - Schloter M
FAU - Roslev, Peter
AU  - Roslev P
FAU - Wagner, Michael
AU  - Wagner M
LA  - eng
SI  - GENBANK/AY367275
SI  - GENBANK/AY367276
SI  - GENBANK/AY367277
PT  - Evaluation Study
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
RN  - 0 (Bicarbonates)
RN  - 0 (Carbon Radioisotopes)
RN  - 0 (DNA, Ribosomal)
RN  - 0 (RNA, Ribosomal, 16S)
RN  - 0 (Sewage)
RN  - 7664-41-7 (Ammonia)
RN  - EC 1.- (Oxidoreductases)
RN  - EC 1.7.3.- (ammonia monooxygenase)
SB  - IM
MH  - Ammonia/*metabolism
MH  - Autoradiography
MH  - Bacteria/enzymology/genetics
MH  - Bicarbonates/*metabolism
MH  - Carbon Radioisotopes/*metabolism
MH  - DNA, Ribosomal/analysis
MH  - Ecosystem
MH  - In Situ Hybridization, Fluorescence
MH  - Molecular Sequence Data
MH  - Nitrosomonas/genetics/*metabolism
MH  - Oligonucleotide Array Sequence Analysis/*methods
MH  - Oxidation-Reduction
MH  - Oxidoreductases/genetics
MH  - RNA, Ribosomal, 16S/genetics/*metabolism
MH  - Sequence Analysis, DNA
MH  - Sewage/microbiology
MH  - Waste Disposal, Fluid/methods
PMC - PMC262286
EDAT- 2003/11/07 05:00
MHDA- 2004/02/21 05:00
PMCR- 2003/11/01
CRDT- 2003/11/07 05:00
PHST- 2003/11/07 05:00 [pubmed]
PHST- 2004/02/21 05:00 [medline]
PHST- 2003/11/07 05:00 [entrez]
PHST- 2003/11/01 00:00 [pmc-release]
AID - 0769 [pii]
AID - 10.1128/AEM.69.11.6875-6887.2003 [doi]
PST - ppublish
SO  - Appl Environ Microbiol. 2003 Nov;69(11):6875-87. doi: 
      10.1128/AEM.69.11.6875-6887.2003.