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Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds.
- Source :
-
Environmental microbiology [Environ Microbiol] 2011 May; Vol. 13 (5), pp. 1138-52. Date of Electronic Publication: 2010 Dec 22. - Publication Year :
- 2011
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Abstract
- Ribosomal tag libraries based on DNA and RNA in coral reef sediment from Hawaii show the microbial community to be dominated by the bacterial phyla Proteobacteria, Firmicutes and Actinobacteria, the archaeal order Nitrosopumilales and the uncultivated divisions Marine Group III (Euryarchaeota) and Marine Benthic Group C (Crenarchaeota). Operational taxonomic units (OTUs) number in the high thousands, and richness varies with site, presence or absence of porewater sulfide (sediment depth), and nucleotide pool. Rank abundance curves of DNA-based libraries, but not RNA-based libraries, possess a tail of low abundance taxa, supporting the existence of an inactive 'rare' biosphere. While bacterial libraries from two oxic samples differ markedly, those from two anoxic (sulfidic) samples are similar. The four dominant bacterial OTUs are members of genera that include pathogens, but are found in marine environments, and include facultative anaerobes, i.e. dissimilatory nitrate reducers and denitrifiers. This may explain their abundance in both oxic and anoxic samples. A numerous archaeon is closely related to the lithoautotrophic ammonia oxidizer Nitrosopumilus maritimus. Known bacterial ammonia oxidizers are essentially absent, but bacterial nitrite oxidizers are abundant. Although other studies of this reef found evidence for anaerobic ammonia oxidizers, primer bias rendered that clade invisible to this study.<br /> (© 2010 Society for Applied Microbiology and Blackwell Publishing Ltd.)
- Subjects :
- Archaea genetics
Bacteria genetics
DNA, Archaeal genetics
DNA, Bacterial genetics
DNA, Ribosomal genetics
Hawaii
Nitrogen metabolism
Phylogeny
RNA, Archaeal genetics
RNA, Bacterial genetics
RNA, Ribosomal, 16S genetics
Sequence Analysis, DNA methods
Sequence Analysis, RNA methods
Archaea classification
Bacteria classification
Coral Reefs
Gene Library
Metagenome
Subjects
Details
- Language :
- English
- ISSN :
- 1462-2920
- Volume :
- 13
- Issue :
- 5
- Database :
- MEDLINE
- Journal :
- Environmental microbiology
- Publication Type :
- Academic Journal
- Accession number :
- 21176054
- Full Text :
- https://doi.org/10.1111/j.1462-2920.2010.02392.x