Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray

A microarray has been designed using 62,358 probes matched to both prokaryotic and eukaryotic small-subunit ribosomal RNA genes. The array categorized environmental DNA to specific phylogenetic clusters in under 9 h. To a background of DNA generated from natural outdoor aerosols, known quantities of...

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Bibliographic Details
Published in:FEMS microbiology letters 2005-04, Vol.245 (2), p.271-278
Main Authors: DeSantis, Todd Z., Stone, Carol E., Murray, Sonya R., Moberg, Jordan P., Andersen, Gary L.
Format: Article
Language:English
Subjects:
Aerosol
Bacillus
Bacteria - classification
Bacteria - genetics
Bacteriology
Biological and medical sciences
Burkholderia
Clostridiales
Community composition
Correlation analysis
Deoxyribonucleic acid
Disruption
DNA
DNA - genetics
DNA - isolation & purification
DNA microarrays
DNA Probes
DNA, Bacterial - genetics
DNA, Bacterial - isolation & purification
DNA, Fungal - genetics
DNA, Fungal - isolation & purification
Environmental DNA
Environmental Microbiology
Eukaryotic Cells - classification
Extraction
Fundamental and applied biological sciences. Psychology
Fungi - classification
Fungi - genetics
Genes, rRNA
Genetics
Hybridization
Microarray
Microbiology
Microorganisms
Mycoplasmatales
Nucleic Acid Hybridization - methods
Oligonucleotide
Oligonucleotide Array Sequence Analysis
Phaeophyceae - classification
Phaeophyceae - genetics
Phylogeny
Probe
rRNA
Systematics
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Description
Summary:A microarray has been designed using 62,358 probes matched to both prokaryotic and eukaryotic small-subunit ribosomal RNA genes. The array categorized environmental DNA to specific phylogenetic clusters in under 9 h. To a background of DNA generated from natural outdoor aerosols, known quantities of rRNA gene copies from distinct organisms were added producing corresponding hybridization intensity scores that correlated well with their concentrations ( r = 0.917). Reproducible differences in microbial community composition were observed by altering the genomic DNA extraction method. Notably, gentle extractions produced peak intensities for Mycoplasmatales and Burkholderiales, whereas a vigorous disruption produced peak intensities for Vibrionales, Clostridiales, and Bacillales.
ISSN:0378-1097
1574-6968
DOI:10.1016/j.femsle.2005.03.016