title: Lineages of acidophilic archaea revealed by community genomic analysis.
abstract: 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.
authors.affiliation: Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.
authors.forename: Brett J
authors.initials: BJ
authors.lastname: Baker
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
authors.forename: Richard I
authors.initials: RI
authors.lastname: Webb
authors.forename: Judith
authors.initials: J
authors.lastname: Flanagan
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Eric E
authors.initials: EE
authors.lastname: Allen
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D018441:Biofilms; D002140:California; D002462:Cell Membrane / Q000648:ultrastructure; D004251:DNA Transposable Elements; D019641:DNA, Archaeal; D030541:Databases, Genetic; D017753:Ecosystem; D019605:Euryarchaeota / Q000235:genetics / Q000502:physiology / Q000648:ultrastructure; D019766:Genes, Archaeal; D020459:Genes, rRNA; D020745:Genome, Archaeal; D006863:Hydrogen-Ion Concentration; D046529:Microscopy, Electron, Transmission; D008906:Mining; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes; D010802:Phylogeny; D011755:Pyrophosphatases / Q000235:genetics / Q000378:metabolism; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013696:Temperature
chemical_list: D004251:DNA Transposable Elements; D019641:DNA, Archaeal; D015345:Oligonucleotide Probes; D012336:RNA, Ribosomal, 16S; D011755:Pyrophosphatases