title: Effects of abiotic factors on the phylogenetic diversity of bacterial communities in acidic thermal springs.
abstract: Acidic thermal springs offer ideal environments for studying processes underlying extremophile microbial diversity. We used a carefully designed comparative analysis of acidic thermal springs in Yellowstone National Park to determine how abiotic factors (chemistry and temperature) shape acidophile microbial communities. Small-subunit rRNA gene sequences were PCR amplified, cloned, and sequenced, by using evolutionarily conserved bacterium-specific primers, directly from environmental DNA extracted from Amphitheater Springs and Roaring Mountain sediment samples. Energy-dispersive X-ray spectroscopy, X-ray diffraction, and colorimetric assays were used to analyze sediment chemistry, while an optical emission spectrometer was used to evaluate water chemistry and electronic probes were used to measure the pH, temperature, and E(h) of the spring waters. Phylogenetic-statistical analyses found exceptionally strong correlations between bacterial community composition and sediment mineral chemistry, followed by weaker but significant correlations with temperature gradients. For example, sulfur-rich sediment samples contained a high diversity of uncultured organisms related to Hydrogenobaculum spp., while iron-rich sediments were dominated by uncultured organisms related to a diverse array of gram-positive iron oxidizers. A detailed analysis of redox chemistry indicated that the available energy sources and electron acceptors were sufficient to support the metabolic potential of Hydrogenobaculum spp. and iron oxidizers, respectively. Principal-component analysis found that two factors explained 95% of the genetic diversity, with most of the variance attributable to mineral chemistry and a smaller fraction attributable to temperature.
authors.affiliation: Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
authors.forename: Jayanti
authors.initials: J
authors.lastname: Mathur
authors.forename: Richard W
authors.initials: RW
authors.lastname: Bizzoco
authors.forename: Dean G
authors.initials: DG
authors.lastname: Ellis
authors.forename: David A
authors.initials: DA
authors.lastname: Lipson
authors.forename: Alexander W
authors.initials: AW
authors.lastname: Poole
authors.forename: Richard
authors.initials: R
authors.lastname: Levine
authors.forename: Scott T
authors.initials: ST
authors.lastname: Kelley
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000187:drug effects* / Q000235:genetics; D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D003124:Colorimetry; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D019015:Geologic Sediments / Q000382:microbiology*; D045482:Hot Springs / Q000737:chemistry* / Q000382:microbiology*; D008855:Microscopy, Electron, Scanning; D008903:Minerals / Q000032:analysis / Q000737:chemistry; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D013052:Spectrometry, X-Ray Emission; D013696:Temperature; D014481:United States; D014871:Water Microbiology; D014961:X-Ray Diffraction
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D008903:Minerals; D012336:RNA, Ribosomal, 16S