Linked Life Data

10877803

Source:http://linkedlifedata.com/resource/pubmed/id/10877803

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
7
pubmed:dateCreated
2000-9-7
pubmed:abstractText
rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% +/- 3.7% [mean +/- standard deviation]) relative to direct DAPI (4',6'-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r(2) = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-10831421, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-2275539, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-2448289, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-2466341, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-2480344, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-7504429, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-7506896, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-7524446, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-7535888, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-7683186, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-8636045, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-8787391, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-8890483, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-8919801, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-9055434, http://linkedlifedata.com/resource/pubmed/commentcorrection/10877803-9327553
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
0099-2240
pubmed:author
pubmed:issnType
Print
pubmed:volume
66
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
3037-43
pubmed:dateRevised
2010-9-14
pubmed:meshHeading
pubmed:year
2000
pubmed:articleTitle
Whole-cell versus total RNA extraction for analysis of microbial community structure with 16S rRNA-targeted oligonucleotide probes in salt marsh sediments.
pubmed:affiliation
Skidaway Institute of Oceanography, Savannah, Georgia 31411, USA. frischer@skio.peachnet.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S.