Novel division level bacterial diversity in a Yellowstone hot spring

Hugenholtz, P., Pitulle, C., Hershberger, K. L. and Pace, N. R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. Journal of Bacteriology, 180 2: 366-376.

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Author Hugenholtz, P.
Pitulle, C.
Hershberger, K. L.
Pace, N. R.
Title Novel division level bacterial diversity in a Yellowstone hot spring
Journal name Journal of Bacteriology   Check publisher's open access policy
ISSN 0021-9193
1098-5530
Publication date 1998-01-01
Year available 1998
Sub-type Article (original research)
Open Access Status File (Publisher version)
Volume 180
Issue 2
Start page 366
End page 376
Total pages 11
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Language eng
Abstract A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OF), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal diversity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609-1613 1994). Small-subunit rRNA genes (rDNA) were amplified directly from OP sediment DNA by PCR with universally conserved or Bacteria-specific rDNA primers and cloned. Unique rDNA types among >300 clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (greater than or equal to 98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial divisions (main phyla; kingdoms); 30% were unaffiliated with recognized bacterial divisions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, division level lineages termed candidate divisions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium, or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing delta-Proteobacteria. The occurrence of such organisms is consistent,vith the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of amplified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial diversity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of division level bacterial phylogenetic diversity is collated and summarized.
Keyword Ribosomal-rna genes
Polymerase chain-reaction
Phylogenetic position
Sp-nov
Marine picoplankton
Archaeal diversity
National-park
Community
Amplification
Field
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

 
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