Acidobacteria Phylum Sequences in Uranium-Contaminated Subsurface Sediments Greatly Expand the Known Diversity within the Phylum
TLDR
Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups.Abstract:
The abundance and composition of bacteria of the phylum Acidobacteria were surveyed in subsurface sediments from uranium-contaminated sites using amplification of 16S rRNA genes followed by clone/sequence analysis. Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups.read more
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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
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A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses
Ryan T. Jones,Michael S. Robeson,Christian L. Lauber,Micah Hamady,Rob Knight,Noah Fierer,Noah Fierer +6 more
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Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils
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Soil microbial community responses to multiple experimental climate change drivers
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References
More filters
Journal ArticleDOI
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
TL;DR: A protocol is described for rapidly generating large blocks of 16S rRNA sequence data without isolation of the 16 S rRNA or cloning of its gene, and its phylogenetic usefulness is evaluated by examination of several 17S rRNAs whose gene sequences are known.
Journal ArticleDOI
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
TL;DR: The authors' perspective on microbial diversity has improved enormously over the past few decades in large part due to molecular phylogenetic studies that objectively relate organisms.
Journal Article
Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity (vol 180, pg 4765, 1998)
Journal ArticleDOI
Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes
TL;DR: In 1909, H. Joel Conn expressed the hope that methods would soon be at hand by which the significance of the different bacteria present in any soil could be understood.
Journal ArticleDOI
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
James R. Cole,Benli Chai,Ryan J. Farris,Qiong Wang,S. A. Kulam,Donna M. McGarrell,George M. Garrity,James M. Tiedje +7 more
TL;DR: The Ribosomal Database Project (RDP-II) provides the research community with aligned and annotated rRNA gene sequences, along with analysis services and a phylogenetically consistent taxonomic framework for these data.
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