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 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.
DeSantis
Todd Z
TZ
Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 70A-3317, Berkeley, CA 94720, USA.
Stone
Carol E
CE
Murray
Sonya R
SR
Moberg
Jordan P
JP
Andersen
Gary L
GL
D001419:Bacteria / Q000145:classification* / Q000235:genetics; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D015342:DNA Probes; D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification; D004271:DNA, Fungal / Q000235:genetics / Q000302:isolation & purification; D004783:Environmental Microbiology; D005057:Eukaryotic Cells / Q000145:classification*; D005658:Fungi / Q000145:classification / Q000235:genetics; D020459:Genes, rRNA; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D000459:Phaeophyceae / Q000145:classification / Q000235:genetics; D010802:Phylogeny
D015342:DNA Probes; D004269:DNA, Bacterial; D004271:DNA, Fungal; D004247:DNA