Nucleic Acids Research, 2005, Vol. 33, Database issue D294-D296
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
1 Center for Microbial Ecology and 2 Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
* To whom correspondence should be addressed. Tel: +1 517 432 4998; Fax: +1 517 353 8957; Email: rdpstaff{at}msu.edu
Received September 14, 2004; Revised and Accepted September 24, 2004
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ABSTRACT |
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 TOP ABSTRACT DESCRIPTIONRDP-II ACCESS AND CONTACTREFERENCES |
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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. Updated monthly, these services are made available through the RDP-II website (http://rdp.cme.msu.edu/). RDP-II release 9.21 (August 2004) contains 101 632 bacterial small subunit rRNA gene sequences in aligned and annotated format. High-throughput tools for initial taxonomic placement, identification of related sequences, probe and primer testing, data navigation and subalignment download are provided. The RDP-II email address for questions or comments is rdpstaff{at}msu.edu.
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DESCRIPTION |
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TOPABSTRACTDESCRIPTIONRDP-II ACCESS AND CONTACTREFERENCES |
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Release 9 introduces substantial changes to the Ribosomal Database Project (RDP). These changes are in response to the rapidly increasing number of available ribosomal RNA gene sequences (rRNA sequences) and the trend toward high-throughput rRNA sequencing with the concomitant need for high volume rRNA analysis tools. This paper describes changes since the 2003 description (1). Details about the data and analysis services can be found at the RDP-II website (http://rdp.cme.msu.edu/).
Sequences. The RDP obtains bacterial rRNA sequences from the International Nucleotide Sequence Databases (INSD: GenBank/EMBL/DDBJ) on a monthly basis. These sequences are aligned against a general bacterial rRNA model using a modified version of RNACAD (2), a Stochastic Context Free Grammar (SCFG)-based rRNA aligner that directly incorporates rRNA secondary structure information into its internal model. This aligner is trained on a set of high-quality hand-aligned sequences and incorporates the conserved bacterial secondary structure model of Gutell and co-workers (3). As of release 9.21 (August 2004), the database contained 101 632 total small subunit bacterial rRNA sequences. Of these, 39 772 were near full-length (
1200 bases), 54 316 came from uncultured organisms and 4431 were from type strains of validly named bacterial species.
Taxonomy. All Release 9 tools use a new hierarchical framework (RDP Hierarchy) differing significantly from the hierarchy provided with previous RDP releases. The RDP Hierarchy is based on the new phylogenetically consistent higher-order bacterial taxonomy proposed by Garrity et al. (4) (http://dx.doi.org/10.1007/bergeysoutline). This hierarchy provides order to the collection. It provides a phylogenetic framework into which to place results of the RDP analysis functions, and it provides an entry point for users looking for sequences from specific groups of organisms. New sequences are placed into the RDP Hierarchy using the RDP Classifier (see below).
Analysis services
The RDP analysis services have been completely revised to support the emerging trend toward high-throughput rRNA sequence analysis in microbial ecology and related disciplines. Three of the tools listed below incorporate the concept of data filters. The user can choose to apply up to three data filters on the view or analysis. By applying the three filters, the user can (i) include only environmental clone or only isolate sequences; (ii) include only sequences 1200 bases in length (near full-length) or only shorter sequences; and (iii) include only sequences from type strains or only non-type strain sequences. The latter filter is of special importance since type strains act as a link between rRNA-based phylogeny and taxonomy. A more detailed description of each analysis service can be found at the RDP website.
Hierarchy Browser allows rapid navigation through the RDP sequence data. The browser presents views of the RDP sequences placed either in the RDP Hierarchy, or optionally in the NCBI taxonomy hierarchy (5). While navigating, the browser automatically expands an appropriate number of hierarchical levels to fit the display. At any time, the user can select for later download of both individual sequences and those of entire taxa. Data filters can be applied at any time to limit the display to specific data subsets. In addition, the user can quickly search for words or phrases in the sequence definition line. This includes the organism name and strain designation (if available), culture collection identifiers and INSD nucleic acid accession identifiers.
RDP Classifier places sequences into the RDP Hierarchy. Optimized for large query sets, it can be used to give an initial taxonomic placement for a single sequence or hundreds of sequences. The first result page summarizes the assignments on an interactive display similar to that of the Hierarchy Browser. Each node in the hierarchy lists the number of user queries assigned to that taxonomic rank. A confidence estimate is generated for each assignment, and the assignments are displayed only when the estimate is above a user-specified confidence threshold. At any time, the user can switch to a detail view showing the detailed taxonomic assignments and confidence scores for any subset of query sequences. These assignment details can also be downloaded in a file suitable for import into popular spreadsheet programs.
Sequence Match is a complete re-implementation of the original Sequence Match method (1). Sequence Match finds sequences similar to a user's query sequences using a word matching strategy not requiring prior alignment. Sequence Match is more accurate than BLAST (6) at finding closely related rRNA sequences (Table 1). The related sequences returned by Sequence Match serve as a good starting point for more detailed examination of relatedness by classical phylogenetic or other methods. The initial result page presents a k-nearest neighbor (k-NN) classifier assignment of the query sequences. A query is assigned to the lowest taxonomic rank that includes the k highest scoring database sequences. The value of k, as well as the three data filters can be changed at will in this view. The user can switch from the summary k-NN view to a detailed results view for any query sequence. In this view, the top k database matches to the query are displayed in the RDP Hierarchy. In this mode, any subset of the matches can be selected for transfer to the Hierarchy Browser and later download. A third view presents sets of results in a format suitable for download.
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Probe Match is a complete re-implementation of our previous Probe Match program (1). It uses a more efficient algorithm that is better suited to the amount of rRNA data available today and in the foreseeable future. The new Probe Match accepts a candidate primer/probe, optionally with ambiguity codons, of up to 64 bases in length. While our previous version searched for hits within a specified number of mismatches (Hamming distance), the new version finds hits with a combination of mismatches and insertion/deletions (edit distance). Since some single insertion/deletion may be no more deleterious than a single mismatch, this new capability offers a significant improvement in the detection of potential cross-hybridization. In our previous implementation, the high percentage of partial sequences in the database limited the program's utility; it was difficult to determine if database entries failed to match simply because the sequence was incomplete in the target region. In this new version, the users can restrict analysis to database entries containing sequence data for the candidate probe target region of the rRNA molecule. (However, the search is not limited to this region of the molecule.) Similar to the other new programs, the results are displayed in an interactive version of the RDP Hierarchy. Each taxonomic rank lists the total number of sequences searched and the number matching within a user-specified edit distance. This maximum edit distance can be changed on the fly. For any hierarchy node, users can switch to a detail view listing the matching sequences. A third format is suitable for download and import into spreadsheet or other programs.
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RDP-II ACCESS AND CONTACT |
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TOPABSTRACTDESCRIPTIONRDP-II ACCESS AND CONTACTREFERENCES |
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The RDP-II data and analysis services can be found at http://rdp.cme.msu.edu/. The RDP's mission includes user support. The address for email support is rdpstaff{at}msu.edu. Telephone support is available (+1 517 432 4998). The RDP-II staff may also be contacted via fax (+1 517 353 8957 Attn:RDP) or regular mail.
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ACKNOWLEDGEMENTS |
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We thank several individuals for their past contributions: Robin Gutell (and his colleagues), Chuck Parker, Paul Saxman, Bonnie Maidak, Tim Lilburn, Niels Larsen, Tom Macke, Michael J. McCaughey, Ross Overbeek, Sakti Pramanik, Scott Dawson, Mitch L. Sogin, Gary Olsen and Carl Woese. The RDP is supported through US DOE OBER/NIH grant DE-FG02-99ER62848 and NSF grant DBI-0328255.
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Notes |
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The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
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REFERENCES |
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TOPABSTRACTDESCRIPTIONRDP-II ACCESS AND CONTACTREFERENCES |
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- Cole,J.R., Chai,B., Marsh,T.L., Farris,R.J., Wang,Q., Kulam,S.A., Chandra,S., McGarrell,D.M., Schmidt,T.M., Garrity,G.M. et al. ( (2003) ) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res., , 31, , 442–443.
[Abstract/Free Full Text] . - Brown,M.P.S. ( (2000) ) Small subunit ribosomal RNA modeling using stochastic context-free grammar. In: Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000), San Diego, CA, pp. 57–66. .
- Cannone,J.J., Subramanian,S., Schnare,M.N., Collett,J.R., D'Souza,L.M., Du,Y., Feng,B., Lin,N., Madabusi,L.V., Muller,K.M. et al. ( (2002) ) The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed. Central Bioinformatics, , 3, , 2.[CrossRef][Medline] .
- Garrity,G.M., Bell,J.A. and Lilburn,T.G. ( (2004) ) Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology, 2nd edn. Release 5.0, May 2004. Springer-Verlag, NY. .
- Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. ( (2000) ) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., , 28, , 10–14.
[Abstract/Free Full Text] . - Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. ( (1997) ) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., , 25, , 3389–3402.
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B. C. Crump, C. Peranteau, B. Beckingham, and J. C. Cornwell Respiratory Succession and Community Succession of Bacterioplankton in Seasonally Anoxic Estuarine Waters Appl. Envir. Microbiol., November 1, 2007; 73(21): 6802 - 6810. [Abstract] [Full Text] [PDF]
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C. Militon, S. Rimour, M. Missaoui, C. Biderre, V. Barra, D. Hill, A. Mone, G. Gagne, H. Meier, E. Peyretaillade, et al. PhylArray: phylogenetic probe design algorithm for microarray Bioinformatics, October 1, 2007; 23(19): 2550 - 2557. [Abstract] [Full Text] [PDF]
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J. Song and J.-C. Cho Methylibium aquaticum sp. nov., a betaproteobacterium isolated from a eutrophic freshwater pond Int J Syst Evol Microbiol, September 1, 2007; 57(9): 2125 - 2128. [Abstract] [Full Text] [PDF]
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N. Guimaraes, N. F. Azevedo, C. Figueiredo, C. W. Keevil, and M. J. Vieira Development and Application of a Novel Peptide Nucleic Acid Probe for the Specific Detection of Helicobacter pylori in Gastric Biopsy Specimens J. Clin. Microbiol., September 1, 2007; 45(9): 3089 - 3094. [Abstract] [Full Text] [PDF]
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R. A. Luna, L. R. Fasciano, S. C. Jones, B. L. Boyanton Jr., T. T. Ton, and J. Versalovic DNA Pyrosequencing-Based Bacterial Pathogen Identification in a Pediatric Hospital Setting J. Clin. Microbiol., September 1, 2007; 45(9): 2985 - 2992. [Abstract] [Full Text] [PDF]
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J. Clardy and S. F. Brady Cyclic AMP Directly Activates NasP, an N-Acyl Amino Acid Antibiotic Biosynthetic Enzyme Cloned from an Uncultured {beta}-Proteobacterium J. Bacteriol., September 1, 2007; 189(17): 6487 - 6489. [Abstract] [Full Text] [PDF]
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Q. Wang, G. M. Garrity, J. M. Tiedje, and J. R. Cole Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy Appl. Envir. Microbiol., August 15, 2007; 73(16): 5261 - 5267. [Abstract] [Full Text] [PDF]
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E. Harth, J. Romero, R. Torres, and R. T. Espejo Intragenomic heterogeneity and intergenomic recombination among Vibrio parahaemolyticus 16S rRNA genes Microbiology, August 1, 2007; 153(8): 2640 - 2647. [Abstract] [Full Text] [PDF]
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M. S. Elshahed, N. H. Youssef, Q. Luo, F. Z. Najar, B. A. Roe, T. M. Sisk, S. I. Buhring, K.-U. Hinrichs, and L. R. Krumholz Phylogenetic and Metabolic Diversity of Planctomycetes from Anaerobic, Sulfide- and Sulfur-Rich Zodletone Spring, Oklahoma Appl. Envir. Microbiol., August 1, 2007; 73(15): 4707 - 4716. [Abstract] [Full Text] [PDF]
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A. M. Spain, A. D. Peacock, J. D. Istok, M. S. Elshahed, F. Z. Najar, B. A. Roe, D. C. White, and L. R. Krumholz Identification and Isolation of a Castellaniella Species Important during Biostimulation of an Acidic Nitrate- and Uranium-Contaminated Aquifer Appl. Envir. Microbiol., August 1, 2007; 73(15): 4892 - 4904. [Abstract] [Full Text] [PDF]
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K. Besemer, G. Singer, R. Limberger, A.-K. Chlup, G. Hochedlinger, I. Hodl, C. Baranyi, and T. J. Battin Biophysical Controls on Community Succession in Stream Biofilms Appl. Envir. Microbiol., August 1, 2007; 73(15): 4966 - 4974. [Abstract] [Full Text] [PDF]
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D. Nord, E. Torrents, and B.-M. Sjoberg A Functional Homing Endonuclease in the Bacillus anthracis nrdE Group I Intron J. Bacteriol., July 15, 2007; 189(14): 5293 - 5301. [Abstract] [Full Text] [PDF]
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R. E. Collins and G. Rocap REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis Nucleic Acids Res., July 13, 2007; 35(suppl_2): W58 - W62. [Abstract] [Full Text] [PDF]
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H. Kasai, A. Katsuta, H. Sekiguchi, S. Matsuda, K. Adachi, K. Shindo, J. Yoon, A. Yokota, and Y. Shizuri Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum 'Verrucomicrobia' Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1630 - 1634. [Abstract] [Full Text] [PDF]
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K. Lee, Y.-J. Choo, S. J. Giovannoni, and J.-C. Cho Maritimibacter alkaliphilus gen. nov., sp. nov., a genome-sequenced marine bacterium of the Roseobacter clade in the order Rhodobacterales Int J Syst Evol Microbiol, July 1, 2007; 57(7): 1653 - 1658. [Abstract] [Full Text] [PDF]
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P. M. LeBlanc, R. C. Hamelin, and M. Filion Alteration of Soil Rhizosphere Communities following Genetic Transformation of White Spruce Appl. Envir. Microbiol., July 1, 2007; 73(13): 4128 - 4134. [Abstract] [Full Text] [PDF]
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L. Zhang, Z. Xu, and B. K. C. Patel Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest Int J Syst Evol Microbiol, June 1, 2007; 57(6): 1177 - 1182. [Abstract] [Full Text] [PDF]
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G. Xie, D. C. Bruce, J. F. Challacombe, O. Chertkov, J. C. Detter, P. Gilna, C. S. Han, S. Lucas, M. Misra, G. L. Myers, et al. Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsonii Appl. Envir. Microbiol., June 1, 2007; 73(11): 3536 - 3546. [Abstract] [Full Text] [PDF]
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V. Corby-Harris, A. C. Pontaroli, L. J. Shimkets, J. L. Bennetzen, K. E. Habel, and D. E. L. Promislow Geographical Distribution and Diversity of Bacteria Associated with Natural Populations of Drosophila melanogaster Appl. Envir. Microbiol., June 1, 2007; 73(11): 3470 - 3479. [Abstract] [Full Text] [PDF]
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D. H. Buckley, V. Huangyutitham, S.-F. Hsu, and T. A. Nelson Stable Isotope Probing with 15N2 Reveals Novel Noncultivated Diazotrophs in Soil Appl. Envir. Microbiol., May 15, 2007; 73(10): 3196 - 3204. [Abstract] [Full Text] [PDF]
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L. Zhang, Z. Xu, and B. K. C. Patel Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage Int J Syst Evol Microbiol, May 1, 2007; 57(5): 974 - 978. [Abstract] [Full Text] [PDF]
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S. M. Barns, E. C. Cain, L. Sommerville, and C. R. Kuske Acidobacteria Phylum Sequences in Uranium-Contaminated Subsurface Sediments Greatly Expand the Known Diversity within the Phylum Appl. Envir. Microbiol., May 1, 2007; 73(9): 3113 - 3116. [Abstract] [Full Text] [PDF]
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J. P. Allen, E. A. Atekwana, E. A. Atekwana, J. W. Duris, D. D. Werkema, and S. Rossbach The Microbial Community Structure in Petroleum-Contaminated Sediments Corresponds to Geophysical Signatures Appl. Envir. Microbiol., May 1, 2007; 73(9): 2860 - 2870. [Abstract] [Full Text] [PDF]
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S. A. Eichorst, J. A. Breznak, and T. M. Schmidt Isolation and Characterization of Soil Bacteria That Define Terriglobus gen. nov., in the Phylum Acidobacteria Appl. Envir. Microbiol., April 15, 2007; 73(8): 2708 - 2717. [Abstract] [Full Text] [PDF]
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D. L. Bedard, K. M. Ritalahti, and F. E. Loffler The Dehalococcoides Population in Sediment-Free Mixed Cultures Metabolically Dechlorinates the Commercial Polychlorinated Biphenyl Mixture Aroclor 1260 Appl. Envir. Microbiol., April 15, 2007; 73(8): 2513 - 2521. [Abstract] [Full Text] [PDF]
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K. Rudi, M. Zimonja, B. Kvenshagen, J. Rugtveit, T. Midtvedt, and M. Eggesbo Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space Appl. Envir. Microbiol., April 15, 2007; 73(8): 2727 - 2734. [Abstract] [Full Text] [PDF]
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S. W. Rogers, T. B. Moorman, and S. K. Ong Fluorescent In Situ Hybridization and Micro-autoradiography Applied to Ecophysiology in Soil Soil Sci. Soc. Am. J., March 12, 2007; 71(2): 620 - 631. [Abstract] [Full Text] [PDF]
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K. Adachi, A. Katsuta, S. Matsuda, X. Peng, N. Misawa, Y. Shizuri, R. M. Kroppenstedt, A. Yokota, and H. Kasai Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae Int J Syst Evol Microbiol, February 1, 2007; 57(2): 297 - 301. [Abstract] [Full Text] [PDF]
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K. Katoh and H. Toh PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences Bioinformatics, February 1, 2007; 23(3): 372 - 374. [Abstract] [Full Text] [PDF]
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J. R. Cole, B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data Nucleic Acids Res., January 12, 2007; 35(suppl_1): D169 - D172. [Abstract] [Full Text] [PDF]
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Y. Li, Y. Ge, D. Saxena, and P. W. Caufield Genetic Profiling of the Oral Microbiota Associated with Severe Early-Childhood Caries J. Clin. Microbiol., January 1, 2007; 45(1): 81 - 87. [Abstract] [Full Text] [PDF]
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C. M. Anderson and M. G. Haygood {alpha}-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora Appl. Envir. Microbiol., January 1, 2007; 73(1): 303 - 311. [Abstract] [Full Text] [PDF]
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M. L. Marco, R. S. Bongers, W. M. de Vos, and M. Kleerebezem Spatial and Temporal Expression of Lactobacillus plantarum Genes in the Gastrointestinal Tracts of Mice Appl. Envir. Microbiol., January 1, 2007; 73(1): 124 - 132. [Abstract] [Full Text] [PDF]
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C. Winter, T. Hein, G. Kavka, R. L. Mach, and A. H. Farnleitner Longitudinal Changes in the Bacterial Community Composition of the Danube River: a Whole-River Approach Appl. Envir. Microbiol., January 1, 2007; 73(2): 421 - 431. [Abstract] [Full Text] [PDF]
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J. A. McGarvey, W. G. Miller, R. Zhang, Y. Ma, and F. Mitloehner Bacterial Population Dynamics in Dairy Waste during Aerobic and Anaerobic Treatment and Subsequent Storage Appl. Envir. Microbiol., January 1, 2007; 73(1): 193 - 202. [Abstract] [Full Text] [PDF]
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I. Letunic and P. Bork Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation Bioinformatics, January 1, 2007; 23(1): 127 - 128. [Abstract] [Full Text] [PDF]
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Y. Matsuo, A. Katsuta, S. Matsuda, Y. Shizuri, A. Yokota, and H. Kasai Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov. Int J Syst Evol Microbiol, December 1, 2006; 56(12): 2837 - 2842. [Abstract] [Full Text] [PDF]
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K. P. Drees, J. W. Neilson, J. L. Betancourt, J. Quade, D. A. Henderson, B. M. Pryor, and R. M. Maier Bacterial Community Structure in the Hyperarid Core of the Atacama Desert, Chile Appl. Envir. Microbiol., December 1, 2006; 72(12): 7902 - 7908. [Abstract] [Full Text] [PDF]
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J. Waldeck, G. Daum, B. Bisping, and F. Meinhardt Isolation and Molecular Characterization of Chitinase-Deficient Bacillus licheniformis Strains Capable of Deproteinization of Shrimp Shell Waste To Obtain Highly Viscous Chitin Appl. Envir. Microbiol., December 1, 2006; 72(12): 7879 - 7885. [Abstract] [Full Text] [PDF]
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M. Hartmann and F. Widmer Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices Appl. Envir. Microbiol., December 1, 2006; 72(12): 7804 - 7812. [Abstract] [Full Text] [PDF]
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A. Dinoto, T. M. Marques, K. Sakamoto, S. Fukiya, J. Watanabe, S. Ito, and A. Yokota Population Dynamics of Bifidobacterium Species in Human Feces during Raffinose Administration Monitored by Fluorescence In Situ Hybridization-Flow Cytometry Appl. Envir. Microbiol., December 1, 2006; 72(12): 7739 - 7747. [Abstract] [Full Text] [PDF]
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L. Sheneman, J. Evans, and J. A. Foster Clearcut: a fast implementation of relaxed neighbor joining Bioinformatics, November 15, 2006; 22(22): 2823 - 2824. [Abstract] [Full Text] [PDF]
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C. Canchaya, M. J. Claesson, G. F. Fitzgerald, D. van Sinderen, and P. W. O'Toole Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology, November 1, 2006; 152(Pt 11): 3185 - 3196. [Abstract] [Full Text] [PDF]
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C. Piccini, D. Conde, C. Alonso, R. Sommaruga, and J. Pernthaler Blooms of single bacterial species in a coastal lagoon of the southwestern atlantic ocean. Appl. Envir. Microbiol., October 1, 2006; 72(10): 6560 - 6568. [Abstract] [Full Text] [PDF]
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