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An oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental RNA.
- Source :
-
Environmental microbiology [Environ Microbiol] 2008 Apr; Vol. 10 (4), pp. 836-50. Date of Electronic Publication: 2008 Jan 30. - Publication Year :
- 2008
-
Abstract
- An oligonucleotide microarray that monitors prokaryotic diversity in extremely acidic environments has been developed. The oligonucleotide probes target most known acidophilic microorganisms, including members of the Nitrospira phylum, Acidithiobacillus genus, acidobacteria, sulfur reducing bacteria, Actinobacteria and Archaea of the Ferroplasma and Thermoplasma genera. The probes were tested for their specificity against the corresponding type strain by microarray hybridization using PCR-amplified fluorescent DNA of the 16S rRNA genes. The microarray was tested and validated against well-established molecular ecology techniques such as molecular cloning and sequencing and FISH by using samples obtained from a natural extremely acidic environment, the Río Tinto (SW Spain). Also, fluorescent labelled total environmental RNA from Río Tinto samples were used as targets for microarray hybridizations. This approach allowed the detection of the most metabolically active prokaryotes of the ecosystem by simultaneously checking probes against 16S and 23S rRNAs as well as other functional genes. Seasonal and spatial variations in the relative expression of specific rRNA genes have been detected between two sampling sites that differ in several physicochemical parameters, mainly iron and sulfur content.
- Subjects :
- Acids
Archaea classification
Archaea genetics
Bacteria classification
Bacteria genetics
Biodiversity
Phylogeny
RNA genetics
RNA, Archaeal genetics
RNA, Bacterial genetics
RNA, Ribosomal, 16S genetics
RNA, Ribosomal, 23S genetics
Seasons
Sensitivity and Specificity
Spain
Archaea isolation & purification
Bacteria isolation & purification
Environmental Microbiology
Oligonucleotide Array Sequence Analysis methods
Subjects
Details
- Language :
- English
- ISSN :
- 1462-2920
- Volume :
- 10
- Issue :
- 4
- Database :
- MEDLINE
- Journal :
- Environmental microbiology
- Publication Type :
- Academic Journal
- Accession number :
- 18248453
- Full Text :
- https://doi.org/10.1111/j.1462-2920.2008.01477.x