Skip to main content
PMC home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1996 Apr;62(4):1171–1177. doi: 10.1128/aem.62.4.1171-1177.1996

Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans.

D A Gordon 1, S J Giovannoni 1
PMCID: PMC167883  PMID: 8919778

Abstract

A gene lineage (SAR406) related to Chlorobium and Fibrobacter species was found in 16S rRNA gene clone libraries prepared from samples from two oceans. The clone libraries were constructed from total picoplankton genomic DNA to assess bacterial diversity in the lower surface layer. The samples were collected by filtration from a depth of 80 m at a site in the western Sargasso Sea and from a depth of 120 m at a site in the Pacific Ocean, approximately 70 km from the Oregon coast. The PCR and primers which amplified nearly full-length 16S rRNA genes were used to prepare the clone libraries. Among the diverse gene clones in these libraries were two related clones (SAR406 and OCS307) which could not be assigned to any of the major bacterial phyla. Phylogenetic analyses demonstrated that these genes were distant relatives of the genus Fibrobacter and the green sulfur bacterial phylum, which includes the genus Chlorobium. The inclusion of SAR406 in phylogenetic trees inferred by several methods resulted in support from bootstrap replicates for the conclusion that Fibrobacter and Chlorobium species and SAR406 are a monophyletic group. An oligonucleotide probe that selectively hybridized to clone SAR406 was used to examine the distribution of this gene lineage in vertical profiles from the Atlantic and Pacific Oceans and in monthly time series at 0 and 200 m in the Atlantic Ocean. During stratified periods, the genes were most abundant slightly below the deep chlorophyll layer. Seasonal changes in the surface abundance of SAR406 rDNA were highly correlated with chlorophyll a levels (r = 0.75).

Full Text

The Full Text of this article is available as a PDF (354.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Amann R. I., Ludwig W., Schleifer K. H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995 Mar;59(1):143–169. doi: 10.1128/mr.59.1.143-169.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barns S. M., Fundyga R. E., Jeffries M. W., Pace N. R. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1609–1613. doi: 10.1073/pnas.91.5.1609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. DeLong E. F. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685–5689. doi: 10.1073/pnas.89.12.5685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Farrelly V., Rainey F. A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol. 1995 Jul;61(7):2798–2801. doi: 10.1128/aem.61.7.2798-2801.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368–376. doi: 10.1007/BF01734359. [DOI] [PubMed] [Google Scholar]
  6. Fuhrman J. A., McCallum K., Davis A. A. Novel major archaebacterial group from marine plankton. Nature. 1992 Mar 12;356(6365):148–149. doi: 10.1038/356148a0. [DOI] [PubMed] [Google Scholar]
  7. Fuhrman J. A., McCallum K., Davis A. A. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 1993 May;59(5):1294–1302. doi: 10.1128/aem.59.5.1294-1302.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Giovannoni S. J., Britschgi T. B., Moyer C. L., Field K. G. Genetic diversity in Sargasso Sea bacterioplankton. Nature. 1990 May 3;345(6270):60–63. doi: 10.1038/345060a0. [DOI] [PubMed] [Google Scholar]
  9. Lee S., Fuhrman J. A. DNA hybridization to compare species compositions of natural bacterioplankton assemblages. Appl Environ Microbiol. 1990 Mar;56(3):739–746. doi: 10.1128/aem.56.3.739-746.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. The Ribosomal Database Project. Nucleic Acids Res. 1994 Sep;22(17):3485–3487. doi: 10.1093/nar/22.17.3485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci. 1994 Feb;10(1):41–48. doi: 10.1093/bioinformatics/10.1.41. [DOI] [PubMed] [Google Scholar]
  12. Robison-Cox J. F., Bateson M. M., Ward D. M. Evaluation of nearest-neighbor methods for detection of chimeric small-subunit rRNA sequences. Appl Environ Microbiol. 1995 Apr;61(4):1240–1245. doi: 10.1128/aem.61.4.1240-1245.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Salama M., Sandine W., Giovannoni S. Development and application of oligonucleotide probes for identification of Lactococcus lactis subsp. cremoris. Appl Environ Microbiol. 1991 May;57(5):1313–1318. doi: 10.1128/aem.57.5.1313-1318.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Sgaramella V., Khorana H. G. CXII. Total synthesis of the structural gene for an alanine transfer RNA from yeast. Enzymic joining of the chemically synthesized polydeoxynucleotides to form the DNA duplex representing nucleotide sequence 1 to 20. J Mol Biol. 1972 Dec 28;72(2):427–444. doi: 10.1016/0022-2836(72)90155-6. [DOI] [PubMed] [Google Scholar]
  15. Shuldiner A. R., Nirula A., Roth J. Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res. 1989 Jun 12;17(11):4409–4409. doi: 10.1093/nar/17.11.4409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Suzuki M. T., Giovannoni S. J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol. 1996 Feb;62(2):625–630. doi: 10.1128/aem.62.2.625-630.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Woese C. R., Mandelco L., Yang D., Gherna R., Madigan M. T. The case for relationship of the flavobacteria and their relatives to the green sulfur bacteria. Syst Appl Microbiol. 1990;13:258–262. doi: 10.1016/s0723-2020(11)80196-7. [DOI] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES