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 16S 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 16S 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.
1 Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.
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
