Novel division level bacterial diversity in a Yellowstone hot spring - PubMed (original) (raw)

Novel division level bacterial diversity in a Yellowstone hot spring

P Hugenholtz et al. J Bacteriol. 1998 Jan.

Abstract

A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), 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 (> or = 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 with 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.

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Figures

FIG. 1

FIG. 1

Scanning electron micrographs of glass slides colonized by microbial cells after immersion in OP for 1 week. Slides were fixed and prepared as described previously (37). Note the apparent succession of the primary colonizing rod morphotypes (left panel) by overlying filament morphotypes (center and right panels). Bar = 5 μm in all panels.

FIG. 2

FIG. 2

Evolutionary distance dendrogram of the bacterial domain and bacterial 16S rDNA sequence types obtained from OP sediment. Reference sequences were chosen to represent the broadest diversity of Bacteria. Sulfolobus acidocaldarius and Methanococcus vannielii were used as outgroups for the analysis. Division level groupings are bracketed at the right of the figure. Twelve novel candidate divisions determined in the present study are indicated as OP1 to OP12. Branch points supported (bootstrap values, ≥75%) by most or all phylogenetic analyses (see Materials and Methods) are indicated by filled circles; open circles indicate branch points supported by some analyses but only marginally supported (bootstrap, 50 to 74%), or not supported (bootstrap, <50%) by others. Branch points without circles are not resolved (bootstrap, <50%) as specific groups in different analyses.

FIG. 3

FIG. 3

Evolutionary distance dendrogram of the δ-Proteobacteria and associated OP sequence types. Rhodocyclus purpureus (β-Proteobacteria) and E. coli (γ-Proteobacteria) were used as outgroups for the analysis. Branch points supported (bootstrap values, ≥75%) by rate-corrected maximum likelihood, parsimony, and distance analyses are indicated by filled circles. Branch points without circles are not resolved (bootstrap, <50%) as specific groups in different analyses. SRB are indicated with asterisks.

FIG. 4

FIG. 4

Evolutionary distance dendrogram of the Thermus-Deinococcus division showing the OPB19 sequence type rDNA gene cluster. Branch points supported (bootstrap values, ≥75%) by maximum likelihood, parsimony, and distance analyses are indicated by filled circles.

FIG. 5

FIG. 5

Representative membrane hybridization of rDNAs PCR amplified with universal primers and E. coli rRNA, hybridized with a _Bacteria_-specific and an _Archaea-Eucarya_-specific probe. rDNAs were amplified from three hot spring communities including OP and representative organisms or clones. Reference archaeal pJP clone rDNAs were described in a previous study (7).

FIG. 6

FIG. 6

Diagrammatic radial representation of the known phylogenetic span of Bacteria in 1987 (inset [46]) and today. The figure is based directly on Fig. 2. Filled sectors indicate that two or more representative sequences fall within the indicated depth of branching. Twelve novel candidate divisions determined in the present study are indicated as OP1 to OP12.

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