Cited by 167Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesProtist diversity and phylogeny

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Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

Suzuki, Marcelino T., Béjà, Oded, Taylor, Lance T., DeLong, Edward F.·2001·Environmental Microbiology

DOI 10.1046/j.1462-2920.2001.00198.x

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Abstract

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.

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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
Nucleic acid techniques in bacterial systematics
Stackebrandt, E. S., & Goodfellow, M. (1991) · Wiley eBooks · Cited by 9,460
Phylogenetic identification and in situ detection of individual microbial cells without cultivation
Amann, R., Ludwig, W., & SCHLEIFER, K. H. (1995) · Microbiological Reviews · doi:10.1128/mr.59.1.143-169.1995 · Cited by 9,218
Archaea in coastal marine environments.
DeLong, E. F. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.12.5685 · Cited by 2,758
Self-citation
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
Liu, W., Marsh, T. L., Cheng, H. H., & Forney, L. J. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.11.4516-4522.1997 · Cited by 2,252
The RDP (Ribosomal Database Project)
Maidak, B. L., Olsen, G. J., Larsen, N. E., Overbeek, R., McCaughey, M. J., & Woese, C. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.109 · Cited by 2,018
Genetic diversity in Sargasso Sea bacterioplankton
Giovannoni, S. J., Britschgi, T. B., Moyer, C. L., & Field, K. G. (1990) · Nature · doi:10.1038/345060a0 · Cited by 1,676
High abundance of viruses found in aquatic environments
Bergh, Ø., Børsheim, K. Y., Bratbak, G., & Heldal, M. (1989) · Nature · doi:10.1038/340467a0 · Cited by 1,650
Quantitative Analysis of Small-Subunit rRNA Genes in Mixed Microbial Populations via 5′-Nuclease Assays
Suzuki, M. T., Taylor, L. T., & DeLong, E. F. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.11.4605-4614.2000 · Cited by 1,194
Self-citation
Phylogenetic diversity of aggregate‐attached vs. free‐living marine bacterial assemblages
DeLong, E. F., Franks, D. G., & Alldredge, A. L. (1993) · Limnology and Oceanography · doi:10.4319/lo.1993.38.5.0924 · Cited by 1,094
Self-citation

Show all 39 references

Research works printed but not linked: 3

10.1016/S0022-2836(05)80360-2 · DOI · Paper page
Ausubel F.A. Brent R. Kingston R.E. Moore D.D. Smith J.A. Seidman J.G. Struhl K.(1988) Current protocols in molecular biology. New York:John Wiley & Sons.
Lane D.J., 1991, Nucleic Acid Techniques in Bacterial Systematics., 115

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Authors: Suzuki, M. T., Béjà, O., Taylor, L. T., & DeLong, E. F.
Affiliations: Monterey Bay Aquarium Research Institute (US)
Corresponding author: DeLong, Edward F.
ORCID: Suzuki, Marcelino T.
Béjà, Oded
DeLong, Edward F.
Venue: Environmental Microbiology
Publisher: Wiley
Published: 2001-05
Volume: 3
Issue: 5
Pages: 323-331
ISSN: 1462-2912 (ISSN-L)
1462-2920
DOI: 10.1046/j.1462-2920.2001.00198.x
OpenAlex: W2170844353
Cited by: 167
References: 39
Citations by year: 2026: 2 · 2025: 3 · 2024: 2 · 2023: 3 · 2022: 5 · 2021: 11 · 2020: 7 · 2019: 5 · 2018: 4 · 2017: 6 · 2016: 3 · 2015: 4 · 2014: 7 · 2013: 8 · 2012: 4
FWCI: 10.57
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor, 233 d)
Locations: Environmental Microbiology (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation
David and Lucile Packard Foundation
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
Keywords: rRNA operons, small subunit rRNA gene, 28S rDNA, ITS region, uncultured bacteria, SAR11 clade, homologous recombination, phylogenetic relationships, bacterial diversity
MeSH terms: Bacteria, Base Sequence, Cloning, Molecular, DNA, Ribosomal, Marine Biology, Molecular Sequence Data, Operon, Phylogeny, RNA, Ribosomal, RNA, Transfer, Water Microbiology

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Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton

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