ArticleApplied and environmental microbiology2003
The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function.
Article in Applied and environmental microbiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 221 citations in OpenAlex.
- Nitrifying Communities in Biological Nitrogen Removal Processes at Tropical Municipal Wastewater Treatment Plants.Microbes and environments · 2025Article
- Quantification of depth-dependent microbial growth in encapsulated systems.Microbial biotechnology · 2023Article
- A Multicolor FluorescenceFrontiers in microbiology · 2019Article
- Nitrite oxidizing bacteria (NOB) dominating in nitrifying community in full-scale biological nutrient removal wastewater treatment plants.AMB Express · 2017Article
- Microbial Population Dynamics and Ecosystem Functions of Anoxic/Aerobic Granular Sludge in Sequencing Batch Reactors Operated at Different Organic Loading Rates.Frontiers in microbiology · 2017Article
- Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis.Frontiers in microbiology · 2015Article
- Agreement between amoA gene-specific quantitative PCR and fluorescence in situ hybridization in the measurement of ammonia-oxidizing bacteria in activated sludge.Applied and environmental microbiology · 2014Article
- The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems.Journal of the science of food and agriculture · 2014Review
- Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds.Marine drugs · 2014Review
- Application of a novel functional gene microarray to probe the functional ecology of ammonia oxidation in nitrifying activated sludge.PloS one · 2013Article
- Microbial diversity in the era of omic technologies.BioMed research international · 2013Review
- Identification of nitrite-reducing bacteria using sequential mRNA fluorescence in situ hybridization and fluorescence-assisted cell sorting.Microbial ecology · 2012Article
- High-throughput isotopic analysis of RNA microarrays to quantify microbial resource use.The ISME journal · 2012Article
- A commensal symbiotic interrelationship for the growth of Symbiobacterium toebii with its partner bacterium, Geobacillus toebii.BMC research notes · 2011Article
- Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens.Microarrays (Basel, Switzerland) · 2011Review
- Shotgun isotope array for rapid, substrate-specific detection of microorganisms in a microbial community.Applied and environmental microbiology · 2011Article
- Enumeration of methanogens with a focus on fluorescence in situ hybridization.Die Naturwissenschaften · 2011Review
- mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization.Applied and environmental microbiology · 2011Article
- Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils.Applied and environmental microbiology · 2010Article
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Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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