Lineages of Acidophilic Archaea Revealed by Community Genomic Analysis
Brett J. Baker,1
Gene W. Tyson,2
Richard I. Webb,3
Judith Flanagan,2*
Philip Hugenholtz,2
Eric E. Allen,2
Jillian F. Banfield1,2
Novel, low-abundance microbial species can be easily overlooked
in standard polymerase chain reaction (PCR)–based surveys.
We used community genomic data obtained without PCR or cultivation
to reconstruct DNA fragments bearing unusual 16
S ribosomal RNA
(rRNA) and protein-coding genes from organisms belonging to
novel archaeal lineages. The organisms are minor components
of all biofilms growing in pH 0.5 to 1.5 solutions within the
Richmond Mine, California. Probes specific for 16
S rRNA showed
that the fraction less than 0.45 micrometers in diameter is
dominated by these organisms. Transmission electron microscope
images revealed that the cells are pleomorphic with unusual
folded membrane protrusions and have apparent volumes of <0.006
cubic micrometer.
2 Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.
3 Centre for Microscopy and Microanalysis and Department of Microbiology and Parasitology, University of Queensland, Brisbane 4072, Australia.
* Present address: University of California, San Francisco, CA 94143, USA.
Present address: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
Present address: University of California, San Diego, La Jolla, CA 92093, USA.
To whom correspondence should be addressed. E-mail: jill{at}eps.berkeley.edu
