ORCID Profile
0000-0002-8590-5129
Current Organisation
University of Colorado at Boulder
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Publisher: Springer Science and Business Media LLC
Date: 26-07-2012
Publisher: American Society for Microbiology
Date: 15-01-1998
DOI: 10.1128/JB.180.2.366-376.1998
Abstract: A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable archaeal ersity (S. M. Barns, R. E. Fundyga, M. W. Jeffries, and N. R. Page, Proc. Natl. Acad. Sci. USA 91:1609–1613, 1994). Small-subunit rRNA genes (rDNA) were lified directly from OP sediment DNA by PCR with universally conserved or Bacteria -specific rDNA primers and cloned. Unique rDNA types among clones were identified by restriction fragment length polymorphism, and 122 representative rDNA sequences were determined. These were found to represent 54 distinct bacterial sequence types or clusters (≥98% identity) of sequences. A majority (70%) of the sequence types were affiliated with 14 previously recognized bacterial isions (main phyla kingdoms) 30% were unaffiliated with recognized bacterial isions. The unaffiliated sequence types (represented by 38 sequences) nominally comprise 12 novel, ision level lineages termed candidate isions. Several OP sequences were nearly identical to those of cultivated chemolithotrophic thermophiles, including the hydrogen-oxidizing Calderobacterium and the sulfate reducers Thermodesulfovibrio and Thermodesulfobacterium , or belonged to monophyletic assemblages recognized for a particular type of metabolism, such as the hydrogen-oxidizing Aquificales and the sulfate-reducing δ- Proteobacteria . The occurrence of such organisms is consistent with the chemical composition of OP (high in reduced iron and sulfur) and suggests a lithotrophic base for primary productivity in this hot spring, through hydrogen oxidation and sulfate reduction. Unexpectedly, no archaeal sequences were encountered in OP clone libraries made with universal primers. Hybridization analysis of lified OP DNA with domain-specific probes confirmed that the analyzed community rDNA from OP sediment was predominantly bacterial. These results expand substantially our knowledge of the extent of bacterial ersity and call into question the commonly held notion that Archaea dominate hydrothermal environments. Finally, the currently known extent of ision level bacterial phylogenetic ersity is collated and summarized.
Publisher: Elsevier BV
Date: 06-2011
DOI: 10.1016/0167-7799(96)10025-1
Abstract: Our knowledge of microbial bio ersity has been severely limited by relying on microorganisms that have been cultured these represent only a tiny fraction of the microbial ersity in the environment. Recently, however, recombinant DNA and molecular phylogenetic techniques have provided methods for characterizing natural microbial communities without the need to cultivate organisms. These techniques have allowed a glimpse of the complexity of microbial communities and the huge, largely untapped, biotechnological resource that they represent.
Publisher: Elsevier BV
Date: 10-1989
DOI: 10.1016/0378-1119(89)90031-0
Abstract: The most incisive a priori approach to inferring the higher order structure of large RNAs has proven to be the use of phylogenetic comparisons. This article provides guidelines to the method, using as an illustration the elucidation of the secondary structure of the catalytic RNA subunit of ribonuclease P (RNase P). The resultant structure is compared to the possibilities that are predicted thermodynamically for the RNase P RNA sequences of nine eubacteria.
Publisher: American Society for Microbiology
Date: 15-09-1998
Location: United States of America
Location: United States of America
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