title: Diverse uncultivated ultra-small bacterial cells in groundwater.
abstract: Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a ~0.2-μm filter reveals a wide diversity of bacteria from the WWE3, OP11 and OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation, cells consistently have small cell size (0.009±0.002 μm(3)). Ultrastructural features potentially related to cell and genome size minimization include tightly packed spirals inferred to be DNA, few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions that compensate for biosynthetic capacities inferred to be missing from genomic data. The results suggest that extremely small cell size is associated with these relatively common, yet little known organisms.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Birgit
authors.initials: B
authors.lastname: Luef
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Kyle R
authors.initials: KR
authors.lastname: Frischkorn
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.affiliation: Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Hoi-Ying N
authors.initials: HY
authors.lastname: Holman
authors.affiliation: Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Birarda
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Andrea
authors.initials: A
authors.lastname: Singh
authors.affiliation: Geophysics Department Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors.forename: Cristina E
authors.initials: CE
authors.lastname: Siegerist
authors.affiliation: Department of Energy (DOE), Joint Genome Institute, Walnut Creek, California 94598, USA.
authors.forename: Susannah G
authors.identifier: 0000000164798427
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Structural Biology and Imaging Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Downing
authors.affiliation: Structural Biology and Imaging Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Luis R
authors.initials: LR
authors.lastname: Comolli
authors.affiliation: 1] Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA [2] Geophysics Department Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [3] Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000648:ultrastructure*; D001483:Base Sequence; D020285:Cryoelectron Microscopy; D005374:Filtration; D059646:Genome Size / Q000235:genetics; D060587:Groundwater / Q000382:microbiology*; D064307:Microbiota / Q000235:genetics*; D008969:Molecular Sequence Data; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S