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Title: Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray

Abstract

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.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director. Office of Science. Chemical and BiologicalNational Security Program NN-22. Department of Energy and HazardousMaterials Response Unit of the FBI Work
OSTI Identifier:
862074
Report Number(s):
LBNL-57331
Journal ID: ISSN 0378-1097; FMLED7; R&D Project: G4W049; BnR: 400403209; TRN: US200601%%311
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
FEMS Microbiology Letters
Additional Journal Information:
Journal Volume: 245; Journal Issue: 2; Related Information: Journal Publication Date: 04/15/2005; Journal ID: ISSN 0378-1097
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; AEROSOLS; CLASSIFICATION; DNA; GENES; HYBRIDIZATION; PROBES; RIBOSOMAL RNA; 16S rRNA gene microarray oligonucleotide aerosol probe DNAextraction bioaerosol

Citation Formats

DeSantis, Todd Z, Stone, Carol E, Murray, Sonya R, Moberg, Jordan P, and Andersen, Gary L. Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray. United States: N. p., 2005. Web. doi:10.1016/j.femsle.2005.03.016.
DeSantis, Todd Z, Stone, Carol E, Murray, Sonya R, Moberg, Jordan P, & Andersen, Gary L. Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray. United States. doi:10.1016/j.femsle.2005.03.016.
DeSantis, Todd Z, Stone, Carol E, Murray, Sonya R, Moberg, Jordan P, and Andersen, Gary L. Tue . "Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray". United States. doi:10.1016/j.femsle.2005.03.016.
@article{osti_862074,
title = {Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray},
author = {DeSantis, Todd Z and Stone, Carol E and Murray, Sonya R and Moberg, Jordan P and Andersen, Gary L},
abstractNote = {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.},
doi = {10.1016/j.femsle.2005.03.016},
journal = {FEMS Microbiology Letters},
issn = {0378-1097},
number = 2,
volume = 245,
place = {United States},
year = {2005},
month = {2}
}