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Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay

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Abstract

Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.

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References

  1. RI Amann W Ludwig KH Schleifer (1995) ArticleTitlePhylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59(1) 143–169

    Google Scholar 

  2. CT Amemiya T Ota GW Litman (1996) Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. B Birren E Lal (Eds) Nonmammalian Genomic Analysis: A Practical Guide Academic Press New York 223–256

    Google Scholar 

  3. N Bano JT Hollibaugh (2002) ArticleTitlePhylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl Environ Microbiol 68(2) 505–518 Occurrence Handle10.1128/AEM.68.2.505-518.2002

    Article  Google Scholar 

  4. O Béjà L Aravind EV Koonin MT Suzuki A Hadd LP Nguyen SB Jovanovich CM Gates RA Feldman JL Spudich EN Spudich EF DeLong (2002) ArticleTitleBacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289(5486) 1902–1906

    Google Scholar 

  5. O Béjà EV Koonin L Aravind LT Taylor H Seitz JL Stein DC Bensen RA Feldmen RV Swanson EF DeLong (2002) ArticleTitleComparative genomic analysis of archeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 68(1) 335–345

    Google Scholar 

  6. O Béjà MT Suzuki JF Heidelberg WC Nelson CM Preston T Hamada JA Eisen CM Fraser EF DeLong (2002) ArticleTitleUnsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415(6872) 630–633

    Google Scholar 

  7. O Béjà MT Suzuki EV Koonin L Aravind A Hadd LP Nguyer R Villacorta M Amjadi C Garrigues SB Jovanovich RA Feldman EF DeLong (2000) ArticleTitleConstruction and analysis or bacterial artifical chromosome libraries from a marine microbial assemblage. Environ Microbiol 2(5) 516–529

    Google Scholar 

  8. J Borneman EW Triplett (1997) ArticleTitleMolecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl Environ Microbiol 63(7) 2647–2653

    Google Scholar 

  9. SF Brady CJ Chao J Handelsman J Clardy (2001) ArticleTitleConing and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett 3(13) 1981–1984 Occurrence Handle10.1021/ol015949k

    Article  Google Scholar 

  10. J Brosius TJ Dull DD Sleeter HF Noller (1981) ArticleTitleGene organization and primary, structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148 107–127 Occurrence Handle1:CAS:528:DyaL3MXltFSgtro%3D Occurrence Handle7028991

    CAS  PubMed  Google Scholar 

  11. SA Connon SJ Giovannoni (2002) ArticleTitleHigh-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 68(8) 3878–3885 Occurrence Handle10.1128/AEM.68.8.3878-3885.2002

    Article  Google Scholar 

  12. JR de la Torre LM Christianson O Beja MT Suzuki DM Karl J Heidelberg EF DeLong (2003) ArticleTitleProteorhodopsin genes are distributed among divergent marine bacterial taxa. Proc Natl Acad Sci USA 100(22) 12830–12835 Occurrence Handle10.1073/pnas.2133554100

    Article  Google Scholar 

  13. EF DeLong (1992) ArticleTitleArchaea in coastal marine environments. Proc Natl Acad Sci USA 89(12) 5685–5689

    Google Scholar 

  14. H Eilers J Pernthaler FO Glockner R Amann (2000) ArticleTitleCulturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 66(7) 3044–3051 Occurrence Handle10.1128/AEM.66.7.3044-3051.2000

    Article  Google Scholar 

  15. J Felsenstein (1989) ArticleTitlePHYLIP—phylogeny inference package (v3.5). Cladistics 5 164–166

    Google Scholar 

  16. KG Field D Gordon T Wright M Rappe E Urback K Vergin SJ Giovannoni (1997) ArticleTitleDiversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria. Appl Environ Microbiol 63(1) 63–70

    Google Scholar 

  17. MM Fisher EW Triplett (1999) ArticleTitleAutomated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65(10) 4630–4636

    Google Scholar 

  18. JA Fuhrman AA Davis (1997) ArticleTitleWidespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar Ecol Prog Ser 150(1–3) 275–285

    Google Scholar 

  19. J Garcia-Martinez SG Acinas AI Anton F Rodriguez-Valera (1999) ArticleTitleUse of the 16S–23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36(1–2) 55–64 Occurrence Handle10.1016/S0167-7012(99)00011-1

    Article  Google Scholar 

  20. J Garcia-Martinez F Rodriguez-Valera (2000) ArticleTitleMicrodiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol Ecol 9(7) 935–948 Occurrence Handle10.1046/j.1365-294x.2000.00953.x

    Article  Google Scholar 

  21. GM Garrity M Winters DB Seales (2001) Taxonomic Outline of the Prokaryotic Genera, 2nd ed., Bergeys Manual of Systematic Bacteriology Springer Verlag New York

    Google Scholar 

  22. DE Gillespie SF Brady AD Bettermann NP Cianciotto MR Liles MR Rondon J Clardy RM Goodman J Handelsman (2002) ArticleTitleIsolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68(9) 4301–4306 Occurrence Handle10.1128/AEM.68.9.4301-4306.2002

    Article  Google Scholar 

  23. SJ Giovannoni MS Rappé (2000) Evolution, diversity and molecular ecology of marine prokaryotes. DL Kirchman (Eds) Microbial Ecology of the Oceans Wiley New York 47–84

    Google Scholar 

  24. SJ Giovannoni MS Rappe KL Vergin NL Adair (1996) ArticleTitle16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the green non-sulfur bacteria. Proc Natl Acad Sci USA 93(15) 7979–7984 Occurrence Handle10.1073/pnas.93.15.7979

    Article  Google Scholar 

  25. JM Gonzalez R Simo R Massana JS Covert EO Casamayor C Pedros-Alio MA Moran (2000) ArticleTitleBacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom. Appl Environ Microbiol 66(10) 4237–4246 Occurrence Handle10.1128/AEM.66.10.4237-4246.2000

    Article  Google Scholar 

  26. DA Gordon SJ Giovannoni (1996) ArticleTitleDetection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans. Appl Environ Microbiol 62(4) 1171–1177

    Google Scholar 

  27. V Gurtler VA Stanisich (1996) ArticleTitleNew approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142(1) 3–16

    Google Scholar 

  28. A Hagstrom T Pommier F Rohwer K Simu W Stolte D Svensson UL Zweifel (2002) ArticleTitleUse of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl Environ Microbiol 68(7) 3628–3633 Occurrence Handle10.1128/AEM.68.7.3628-3633.2002

    Article  Google Scholar 

  29. DJ Lane (1991) 16S/23S rRNA sequencing. E Stackebrandt M Goodfellow (Eds) Nucleic Acid Techniques in Bacterial Systematics John Wiley & Sons New York 115–175

    Google Scholar 

  30. MR Liles BF Manske SB Bintrim J Handelsman RM Goodman (2003) ArticleTitleA census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69(5) 2684–2691 Occurrence Handle10.1128/AEM.69.5.2684-2691.2003

    Article  Google Scholar 

  31. W Ludwig O Strunk R Westram L Richter H Meier Y Kumar A Buchner T Lai S Steppi G Jobb W Förster I Brettske S Gerber AW Ginhart O Gross S Grumann S Hermann R Jost A König T Liss R Lüßmann M May B Nonhoff B Reichel R Strehlow AP Stamatakis N Stuckmann A Vilbig M Lenke T Ludwig A Bode KH Schleifer (2004) ArticleTitleARB: a software environment for sequence data. Nucleic Acids Res 32 1363–1371

    Google Scholar 

  32. IA MacNeil CL Tiong C Minor PR August TH Grossman KA Loiacond BA Lynch T Phillips S Narula R Sundaramoorthi A Tyler T Aldredge H Long M Gilman D Holt MS Osburne (2001) ArticleTitleExpression and isolation of antimicrobial small molecule from soil DNA libraries. J Mol Microbiol Biotechnol 3(2) 301–308

    Google Scholar 

  33. R Massana AE Murray CM Preston EF DeLong (1997) ArticleTitleVertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. Appl Environ Microbiol 63(1) 50–56

    Google Scholar 

  34. LR Moore G Rocap SW Chisholm (1998) ArticleTitlePhysiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature 393(6684) 464–467

    Google Scholar 

  35. A Quaiser T Ochsenreiter HP Klenk A Kletzin AH Treusch G Meurer J Eck CW Sensen C Schleper (2002) ArticleTitleFirst insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4(10) 603–611 Occurrence Handle10.1046/j.1462-2920.2002.00345.x

    Article  Google Scholar 

  36. MS Rappé SA Connon KL Vergin SJ Giovannoni (2002) ArticleTitleCultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418(6898) 630–633 Occurrence Handle10.1038/nature00917

    Article  Google Scholar 

  37. MS Rappé DA Gordon KL Vergin SJ Giovannoni (1999) ArticleTitlePhylogeny of actionbacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Sys Appl Microbiol 22(1) 106–112

    Google Scholar 

  38. MS Rappé PF Kemp SJ Giovannoni (1997) ArticleTitlePhylogenetic diversity of marine coastal picoplankton 16s rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina. Limnol Oceanogr 42(5) 811–826

    Google Scholar 

  39. G Rocap DL Diste JB Waterbury SW Chisholm (2002) ArticleTitleResolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl Environ Microbio 68(3) 1180–1191 Occurrence Handle10.1128/AEM.68.3.1180-1191.2002

    Article  Google Scholar 

  40. MR Rondon PR August AD Bettermann SF Brady TH Grossmann MR Lies KA Loiacono BA Lynch IA MacNeil C Minor CL Tiong M Gilman MS Osburne J Clardy J Handelsman RM Goodman (2000) ArticleTitleCloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66(6) 2541–2547 Occurrence Handle10.1128/AEM.66.6.2541-2547.2000

    Article  Google Scholar 

  41. G Sabehi R Massana JP Bielawski M Rosenberg EF DeLong O Beja (2003) ArticleTitleNovel Proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol 5(10) 842–849 Occurrence Handle10.1046/j.1462-2920.2003.00493.x

    Article  Google Scholar 

  42. C Schleper EF DeLong CM Preston RA Feldman KY Wu RV Swanson (1998) ArticleTitleGenomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 180(19) 5003–5009

    Google Scholar 

  43. C Schleper RV Swanson EJ Mathur EF DeLong (1997) ArticleTitleCharacterization of a DNA polymerase from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 179(24) 7803–7811

    Google Scholar 

  44. JL Stein H Felbeck (1993) ArticleTitleKinetic and physical properties of a recombinant RuBisCO2 from a chemoautotrophic endosymbiont. Mol Mar Biol Biotechnol 2(5) 280–290

    Google Scholar 

  45. JL Stein TL Marsh KY Wu H Shizuya EF DeLong (1996) ArticleTitleCharacterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178(3) 591–599

    Google Scholar 

  46. MT Suzuki O Beja LT Taylor EF DeLong (2001) ArticleTitlePhylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3(5) 323–331 Occurrence Handle10.1046/j.1462-2920.2001.00198.x

    Article  Google Scholar 

  47. MT Suzuki EF DeLong (2002) Marine prokaryotic diversity. JD Staley AL Reysenbach (Eds) Biodiversity of Microbial Life: Foundation of Earth’s Biosphere Wiley New York 209–234

    Google Scholar 

  48. MT Suzuki LT Taylor EF DeLong (2000) ArticleTitleQuantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66(11) 4605–4614 Occurrence Handle10.1128/AEM.66.11.4605-4614.2000

    Article  Google Scholar 

  49. TD Wright KL Vergin PW Boyd SJ Giovannoni (1997) ArticleTitleA novel ô-subdivision proteobacterial lineage from the lower ocean surface layer. Appl Environ Microbiol 63(4) 1441–1448

    Google Scholar 

  50. MV Zubkov BM Fuchs SD Archer RP Kiene R Amann PH Burkill (2001) ArticleTitleLinking the composition of bacterioplankton to rapid turnover of dissolved dimethylsulphonioprocionate in an algal bloom in the North Sea. Environ Microbiol 3(5) 304–311 Occurrence Handle10.1046/j.1462-2920.2001.00196.x

    Article  Google Scholar 

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Acknowledgments

We thank the captain and crews of the RV Point Lobos/ROV Ventana as well as Erich Rienecker, Lynne Christianson, Virginia Rich, and Mark Jeanette for their assistance during sampling. This work was supported by a grant from the David and Lucile Packard Foundation and NSF Microbial Observatory grant 0084211 to E.F.D. and John Heidelberg (TIGR). O. Béjà was supported by a long-term fellowship from the European Molecular Biology Organization and NSF grant OCE0001619 to E.F.D.

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Author notes

  1. O. Béjà

    Present address: Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel

  2. J.R. de la Torre

    Present address: Department of Microbiology, University of Washington, Seattle, WA 98195, USA

  3. G.F. Steward

    Present address: Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA

  4. E.F. DeLong

    Present address: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Authors and Affiliations

  1. Chesapeake Biological Laboratory, University of Maryland Center for Environmental Sciences, Solomons, MD 20688, USA

    M.T. Suzuki

  2. Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA

    C.M. Preston, O. Béjà, J.R. de la Torre, G.F. Steward & E.F. DeLong

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  1. M.T. Suzuki
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  2. C.M. Preston
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  3. O. Béjà
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Correspondence to E.F. DeLong.

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(M.T. Suzuki and C.M. Preston) These authors contributed equally to this paper.

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Suzuki, M., Preston, C., Béjà, O. et al. Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay. Microb Ecol 48, 473–488 (2004). https://doi.org/10.1007/s00248-004-0213-5

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