American Academy of Microbiology (2008)
A Merican, S Ociety, For M Icrobiology, N Ational, S Cience, F Oundation, ...
This report is based on a colloquium sponsored by the American Academy of
Louis A. Kaplan, Karen M. Hogan, Paul M. Berube, David A. Stahl
• The initial survey of microbial communities in streambed sediments from the Peruvian Amazon indicates that the ammonia oxidizer community is primarily composed of Archaea and not Bacteria. (i)...
Paul M. Berube, Ram Samudrala, David A. Stahl
The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition...
Starke, E Michelle L, Smoot, James C, Smoot, Laura M, Liu, Wen-Tso, Chandler, Darrell P, Lee, Hyun H, ...
Abstract The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the...
Functional marker genes for identification of sulfate-reducing prokaryotes (2005)
Wagner, Michael, Loy, Alexander, Klein, Michael, Lee, Natuschka, Ramsing, Niels B., Stahl, David A., ...
Thesis (M.S. in Biology)--University of Wisconsin-Oshkosh, 2004.
Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin (2003)
Dhillon, Ashita, Teske, Andreas, Dillon, Jesse, Stahl, David A., Sogin, Mitchell L.
Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive...
Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin (2003)
Dhillon, Ashita, Teske, Andreas, Dillon, Jesse, Stahl, David A., Sogin, Mitchell L.
Author Posting. © American Society for Microbiology, 2003. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive...
Biofilm Structure and Diversity (2003)
To develop molecular measures of the identity, activity, and spatial distribution of microbial populations making up natural (multispecies) biofilms. To use biofilm bioreactors to characterize the...
Thesis (M.S.E.E.)--University of Washington, 1999.
Characterization of Biofilm Community Structure by Ribosomal RNA Sequences. (1998)
The general objectives of this project are to develop molecular techniques, based upon comparative ribosomal RNA sequencing, for the explicit identification and localization of individual...
Analysis of GI Community Shifts in Response to Dietary Fiber (1998)
Stahl, David A., Davidson, Seana K., Ziemer, Cherie
To enhance survivability of military personnel with limited provisions, it may be possible to alter human gut bacterial populations to increase energy yield from plant fiber. To enable development of...
Biofilm Structure and Activity. (1997)
To develop molecular measures of the identity, activity, and spatial distribution of microbial populations mailing up natural (multispecies) biofilms. To use biofilm bioreactors to characterize the...
Stahl, David A., Luehrsent, Kenneth R., Woese, Carl R., Pace, Norman R.
The nucleotide sequence of the 5S ribosomal RNA of the thermoacidophilie archaebacterium Sulfolobus acidocaldarius was determined. The high degree of evident secondary structure in the molecule has...
Secondary structure model for 23S ribosomal RNA (1981)
Noller, Harry F., Kop, JoAnn, Wheaton, Virginia, Brosius, Jürgen, Gutell, Robin R., Kopylov, Alexei M., ...
A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and...
Nielsen, Alex T., Liu, Wen-Tso, Filipe, Carlos, Grady, Leslie, Molin, Søren, Stahl, David A.
The microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. The reactor was fed with media containing acetate and...
Vetriani, Costantino, Jannasch, Holger W., MacGregor, Barbara J., Stahl, David A., Reysenbach, Anna-Louise
During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic...
Minz, Dror, Fishbain, Susan, Green, Stefan J., Muyzer, Gerard, Cohen, Yehuda, Rittmann, Bruce E., ...
The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with...
Minz, Dror, Flax, Jodi L., Green, Stefan J., Muyzer, Gerard, Cohen, Yehuda, Wagner, Michael, ...
Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline microbial mat and to evaluate their distribution in relation...
Becker, Jennifer G., Stahl, David A., Rittmann, Bruce E.
Biotransformation of 2-chlorophenol by a methanogenic sediment community resulted in the transient accumulation of phenol and benzoate. 3-Chlorobenzoate was a more persistent product of...
Seasonal and Spatial Variability in Lake Michigan Sediment Small-Subunit rRNA Concentrations
MacGregor, Barbara J., Moser, Duane P., Baker, Brett J., Alm, Elizabeth W., Maurer, Max, Nealson, Kenneth H., ...
We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
The response of a complex methanogenic sediment community to 2-chlorophenol (2-CP) was evaluated by monitoring the concentrations of this model contaminant and important metabolic intermediates and...
Klein, Michael, Friedrich, Michael, Roger, Andrew J., Hugenholtz, Philip, Fishbain, Susan, Abicht, Heike, ...
A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing...
Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration
Wagner, Michael, Roger, Andrew J., Flax, Jodi L., Brusseau, Gregory A., Stahl, David A.
Microorganisms that use sulfate as a terminal electron acceptor for anaerobic respiration play a central role in the global sulfur cycle. Here, we report the results of comparative sequence analysis...
Urakawa, Hidetoshi, Noble, Peter A., El Fantroussi, Said, Kelly, John J., Stahl, David A.
The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (Td) and signal intensity of short DNA duplexes were determined by using oligonucleotide...
Koizumi, Yoshikazu, Kelly, John J., Nakagawa, Tatsunori, Urakawa, Hidetoshi, El-Fantroussi, Saïd, Al-Muzaini, Saleh, ...
A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by...
Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays
Urakawa, Hidetoshi, El Fantroussi, Said, Smidt, Hauke, Smoot, James C., Tribou, Erik H., Kelly, John J., ...
The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting...
Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin†
Dhillon, Ashita, Teske, Andreas, Dillon, Jesse, Stahl, David A., Sogin, Mitchell L.
The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse...
El Fantroussi, Said, Urakawa, Hidetoshi, Bernhard, Anne E., Kelly, John J., Noble, Peter A., Smidt, H., ...
Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study...
Fishbain, Susan, Dillon, Jesse G., Gough, Heidi L., Stahl, David A.
Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular...
Bavykin, Sergei G., Lysov, Yuri P., Zakhariev, Vladimir, Kelly, John J., Jackman, Joany, Stahl, David A., ...
In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species...
Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries
Nielsen, Jeppe L., Schramm, Andreas, Bernhard, Anne E., Van Den Engh, Gerrit J., Stahl, David A.
A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting-assisted cloning, was...
Lateral Gene Transfer of Dissimilatory (Bi)Sulfite Reductase Revisited
Zverlov, Vladimir, Klein, Michael, Lücker, Sebastian, Friedrich, Michael W., Kellermann, Josef, Stahl, David A., ...
In contrast to previous findings, we demonstrate that the dissimilatory (bi)sulfite reductase genes (dsrAB) of Desulfobacula toluolica were vertically inherited. Furthermore, Desulfobacterium anilini...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
Stable associations of syntrophic fermentative organisms and populations that consume fermentation products play key roles in the anaerobic biodegradation of chlorinated organic contaminants. The...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
Lengthy adaptation periods in laboratory studies evaluating the potential for contaminant biodegradation in natural or engineered environments may indicate that the native microbial communities are...
Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats
Hullar, Meredith A. J., Kaplan, Louis A., Stahl, David A.
Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations...
Transmission of Nephridial Bacteria of the Earthworm Eisenia fetida
Davidson, Seana K., Stahl, David A.
The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the...
Bavykin, Sergei G., Lysov, Yuri P., Zakhariev, Vladimir, Kelly, John J., Jackman, Joany, Stahl, David A., ...
Nielsen, Alex T., Liu, Wen-Tso, Filipe, Carlos, Grady, Leslie, Molin, Søren, Stahl, David A.
The microbial diversity of a deteriorated biological phosphorus removal reactor was investigated by methods not requiring direct cultivation. The reactor was fed with media containing acetate and...
Vetriani, Costantino, Jannasch, Holger W., MacGregor, Barbara J., Stahl, David A., Reysenbach, Anna-Louise
During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic...
Minz, Dror, Fishbain, Susan, Green, Stefan J., Muyzer, Gerard, Cohen, Yehuda, Rittmann, Bruce E., ...
The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with...
Minz, Dror, Flax, Jodi L., Green, Stefan J., Muyzer, Gerard, Cohen, Yehuda, Wagner, Michael, ...
Sequence analysis of genes encoding dissimilatory sulfite reductase (DSR) was used to identify sulfate-reducing bacteria in a hypersaline microbial mat and to evaluate their distribution in relation...
Becker, Jennifer G., Stahl, David A., Rittmann, Bruce E.
Biotransformation of 2-chlorophenol by a methanogenic sediment community resulted in the transient accumulation of phenol and benzoate. 3-Chlorobenzoate was a more persistent product of...
Seasonal and Spatial Variability in Lake Michigan Sediment Small-Subunit rRNA Concentrations
MacGregor, Barbara J., Moser, Duane P., Baker, Brett J., Alm, Elizabeth W., Maurer, Max, Nealson, Kenneth H., ...
We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
The response of a complex methanogenic sediment community to 2-chlorophenol (2-CP) was evaluated by monitoring the concentrations of this model contaminant and important metabolic intermediates and...
Klein, Michael, Friedrich, Michael, Roger, Andrew J., Hugenholtz, Philip, Fishbain, Susan, Abicht, Heike, ...
A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing...
Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration
Wagner, Michael, Roger, Andrew J., Flax, Jodi L., Brusseau, Gregory A., Stahl, David A.
Microorganisms that use sulfate as a terminal electron acceptor for anaerobic respiration play a central role in the global sulfur cycle. Here, we report the results of comparative sequence analysis...
Urakawa, Hidetoshi, Noble, Peter A., El Fantroussi, Said, Kelly, John J., Stahl, David A.
The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (Td) and signal intensity of short DNA duplexes were determined by using oligonucleotide...
Koizumi, Yoshikazu, Kelly, John J., Nakagawa, Tatsunori, Urakawa, Hidetoshi, El-Fantroussi, Saïd, Al-Muzaini, Saleh, ...
A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by...
Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays
Urakawa, Hidetoshi, El Fantroussi, Said, Smidt, Hauke, Smoot, James C., Tribou, Erik H., Kelly, John J., ...
The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting...
Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin†
Dhillon, Ashita, Teske, Andreas, Dillon, Jesse, Stahl, David A., Sogin, Mitchell L.
The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse...
El Fantroussi, Said, Urakawa, Hidetoshi, Bernhard, Anne E., Kelly, John J., Noble, Peter A., Smidt, H., ...
Oligonucleotide microarrays were used to profile directly extracted rRNA from environmental microbial populations without PCR amplification. In our initial inspection of two distinct estuarine study...
Fishbain, Susan, Dillon, Jesse G., Gough, Heidi L., Stahl, David A.
Diversity, habitat range, and activities of sulfate-reducing prokaryotes within hot springs in Yellowstone National Park were characterized using endogenous activity measurements, molecular...
Bavykin, Sergei G., Lysov, Yuri P., Zakhariev, Vladimir, Kelly, John J., Jackman, Joany, Stahl, David A., ...
In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species...
Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries
Nielsen, Jeppe L., Schramm, Andreas, Bernhard, Anne E., Van Den Engh, Gerrit J., Stahl, David A.
A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting-assisted cloning, was...
Lateral Gene Transfer of Dissimilatory (Bi)Sulfite Reductase Revisited
Zverlov, Vladimir, Klein, Michael, Lücker, Sebastian, Friedrich, Michael W., Kellermann, Josef, Stahl, David A., ...
In contrast to previous findings, we demonstrate that the dissimilatory (bi)sulfite reductase genes (dsrAB) of Desulfobacula toluolica were vertically inherited. Furthermore, Desulfobacterium anilini...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
Stable associations of syntrophic fermentative organisms and populations that consume fermentation products play key roles in the anaerobic biodegradation of chlorinated organic contaminants. The...
Becker, Jennifer G., Berardesco, Gina, Rittmann, Bruce E., Stahl, David A.
Lengthy adaptation periods in laboratory studies evaluating the potential for contaminant biodegradation in natural or engineered environments may indicate that the native microbial communities are...
Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats
Hullar, Meredith A. J., Kaplan, Louis A., Stahl, David A.
Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations...
Transmission of Nephridial Bacteria of the Earthworm Eisenia fetida
Davidson, Seana K., Stahl, David A.
The lumbricid earthworms (annelid family Lumbricidae) harbor gram-negative bacteria in their excretory organs, the nephridia. Comparative 16S rRNA gene sequencing of bacteria associated with the...
Bavykin, Sergei G., Lysov, Yuri P., Zakhariev, Vladimir, Kelly, John J., Jackman, Joany, Stahl, David A., ...
Metabolic modeling of a mutualistic microbial community
Stolyar, Sergey, Van Dien, Steve, Hillesland, Kristina Linnea, Pinel, Nicolas, Lie, Thomas J, Leigh, John A, ...
The rate of production of methane in many environments depends upon mutualistic interactions between sulfate-reducing bacteria and methanogens. To enhance our understanding of these relationships, we...
Berube, Paul M., Samudrala, Ram, Stahl, David A.
The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition...
Dillon, Jesse G., Fishbain, Susan, Miller, Scott R., Bebout, Brad M., Habicht, Kirsten S., Webb, Samuel M., ...
The importance of sulfate respiration in the microbial mat found in the low-sulfate thermal outflow of Mushroom Spring in Yellowstone National Park was evaluated using a combination of molecular,...
Starke, E Michelle L, Smoot, James C, Smoot, Laura M, Liu, Wen-Tso, Chandler, Darrell P, Lee, Hyun H, ...
The human oral cavity contains a complex microbial community that, until recently, has not been well characterized. Studies using molecular tools have begun to enumerate and quantify the species...
Response of Desulfovibrio vulgaris to Alkaline Stress▿ †
Stolyar, Sergey, He, Qiang, Joachimiak, Marcin P., He, Zhili, Yang, Zamin Koo, Borglin, Sharon E., ...
The response of exponentially growing Desulfovibrio vulgaris Hildenborough to pH 10 stress was studied using oligonucleotide microarrays and a study set of mutants with genes suggested by microarray...
Schouten, Stefan, Hopmans, Ellen C., Baas, Marianne, Boumann, Henry, Standfest, Sonja, Könneke, Martin, ...
In this study we analyzed the membrane lipid composition of “Candidatus Nitrosopumilus maritimus,” the only cultivated representative of the cosmopolitan group I crenarchaeota and the only...
Biome-Level Biogeography of Streambed Microbiota▿
Findlay, Robert H., Yeates, Christine, Hullar, Meredith A. J., Stahl, David A., Kaplan, Louis A.
A field study was conducted to determine the microbial community structures of streambed sediments across diverse geographic and climatic areas. Sediment samples were collected from three adjacent...
Identification of a Repressor of a Truncated Denitrification Pathway in Moraxella catarrhalis▿
Wang, Wei, Richardson, Anthony R., Martens-Habbena, Willm, Stahl, David A., Fang, Ferric C., Hansen, Eric J.
Growth of Moraxella catarrhalis in a biofilm resulted in marked upregulation of two open reading frames (ORFs), aniA and norB, predicted to encode a nitrite reductase and a nitric oxide reductase,...
Lateral Transfer of Genes for Hexahydro-1,3,5-Trinitro-1,3,5-Triazine (RDX) Degradation▿ †
Andeer, Peter F., Stahl, David A., Bruce, Neil C., Strand, Stuart E.
Recent studies demonstrated that degradation of the military explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by species of Rhodococcus, Gordonia, and Williamsia is mediated by a novel...