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23 results on '"Macur, Richard E"'

2. Molecular analysis of surfactant-driven microbial population shifts in hydrocarbon-contaminated soil

Author

Colores, Gregory M., Macur, Richard E., Ward, David M., and Inskeep, William P.

Subjects
Microbiological research -- Analysis, Hydrocarbons -- Analysis, Microorganisms -- Research, Bioavailability -- Analysis, Biological sciences
Abstract

Research has been conducted on the hydrocarbon-degrading microbial population shifts in soil. The effect of surfactant addition on these shifts has been investigated.

Published
2000

7. Geomicrobiology of sublacustrine thermal vents in Yellowstone Lake: geochemical controls on microbial community structure and function

Author

Inskeep, William P., primary, Jay, Zackary J., additional, Macur, Richard E., additional, Clingenpeel, Scott, additional, Tenney, Aaron, additional, Lovalvo, David, additional, Beam, Jacob P., additional, Kozubal, Mark A., additional, Shanks, W. C., additional, Morgan, Lisa A., additional, Kan, Jinjun, additional, Gorby, Yuri, additional, Yooseph, Shibu, additional, and Nealson, Kenneth, additional

Published
2015
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8. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

Author

Inskeep, William P, Jay, Zackary J, Herrgard, Markus, Kozubal, Mark A, Rusch, Douglas B, Tringe, Susannah G, Macur, Richard E, Jennings, Ryan deM, Boyd, Eric S, Spear, John R, Roberto, Francisco F, Inskeep, William P, Jay, Zackary J, Herrgard, Markus, Kozubal, Mark A, Rusch, Douglas B, Tringe, Susannah G, Macur, Richard E, Jennings, Ryan deM, Boyd, Eric S, Spear, John R, and Roberto, Francisco F

Abstract

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40-45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP.

Published
2013

9. Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages.

Author

Takacs-Vesbach, Cristina, Inskeep, William P, Jay, Zackary J, Herrgard, Markus, Rusch, Douglas B, Tringe, Susannah G, Kozubal, Mark A, Hamamura, Natsuko, Macur, Richard E, Fouke, Bruce W, Reysenbach, Anna-Louise, McDermott, Timothy R, Jennings, Ryan deM, Hengartner, Nicolas W, Xie, Gary, Takacs-Vesbach, Cristina, Inskeep, William P, Jay, Zackary J, Herrgard, Markus, Rusch, Douglas B, Tringe, Susannah G, Kozubal, Mark A, Hamamura, Natsuko, Macur, Richard E, Fouke, Bruce W, Reysenbach, Anna-Louise, McDermott, Timothy R, Jennings, Ryan deM, Hengartner, Nicolas W, and Xie, Gary

Abstract

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal "filamentous streamer" communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellowstone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae) populations, whereas the circum-neutral pH (6.5-7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse-TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl). The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl-CoA synthetase (Ccs), and citryl-CoA lyase (Ccl). All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I) involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2) have resulted in niche specialization among members of the Aquificales.

Published
2013

11. Yellowstone Lake Nanoarchaeota

Author

Clingenpeel, Scott, primary, Kan, Jinjun, additional, Macur, Richard E., additional, Woyke, Tanja, additional, Lovalvo, Dave, additional, Varley, John, additional, Inskeep, William P., additional, Nealson, Kenneth, additional, and McDermott, Timothy R., additional

Published
2013
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12. Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

Author

Takacs-Vesbach, Cristina, primary, Inskeep, William P., additional, Jay, Zackary J., additional, Herrgard, Markus J., additional, Rusch, Douglas B., additional, Tringe, Susannah G., additional, Kozubal, Mark A., additional, Hamamura, Natsuko, additional, Macur, Richard E., additional, Fouke, Bruce W., additional, Reysenbach, Anna-Louise, additional, McDermott, Timothy R., additional, Jennings, Ryan deM., additional, Hengartner, Nicolas W., additional, and Xie, Gary, additional

Published
2013
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13. Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

Author

Inskeep, William P., primary, Jay, Zackary J., additional, Herrgard, Markus J., additional, Kozubal, Mark A., additional, Rusch, Douglas B., additional, Tringe, Susannah G., additional, Macur, Richard E., additional, Jennings, Ryan deM., additional, Boyd, Eric S., additional, Spear, John R., additional, and Roberto, Francisco F., additional

Published
2013
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15. Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

Author

Kozubal, Mark A., primary, Macur, Richard E., additional, Jay, Zackary J., additional, Beam, Jacob P., additional, Malfatti, Stephanie A., additional, Tringe, Susannah G., additional, Kocar, Benjamin D., additional, Borch, Thomas, additional, and Inskeep, William P., additional

Published
2012
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16. Archaea in Yellowstone Lake

Author

Kan, Jinjun, primary, Clingenpeel, Scott, additional, Macur, Richard E, additional, Inskeep, William P, additional, Lovalvo, Dave, additional, Varley, John, additional, Gorby, Yuri, additional, McDermott, Timothy R, additional, and Nealson, Kenneth, additional

Published
2011
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17. Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

Author

Inskeep, William P., primary, Rusch, Douglas B., additional, Jay, Zackary J., additional, Herrgard, Markus J., additional, Kozubal, Mark A., additional, Richardson, Toby H., additional, Macur, Richard E., additional, Hamamura, Natsuko, additional, Jennings, Ryan deM., additional, Fouke, Bruce W., additional, Reysenbach, Anna-Louise, additional, Roberto, Frank, additional, Young, Mark, additional, Schwartz, Ariel, additional, Boyd, Eric S., additional, Badger, Jonathan H., additional, Mathur, Eric J., additional, Ortmann, Alice C., additional, Bateson, Mary, additional, Geesey, Gill, additional, and Frazier, Marvin, additional

Published
2010
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23. Bacterial Populations Associated with the Oxidation and Reduction of Arsenic in an Unsaturated Soil.

Author

Macur, Richard E., Jackson, Colin R., Botero, Lina M., McDermott, Timothy R., and Inskeep, William P.

Subjects
*BACTERIAL growth, *OXIDATION, *ARSENIC, *HETEROTROPHIC bacteria, *AGROBACTERIUM, *OXIDIZING agents, *ELECTROPHORESIS, *SOILS
Abstract

Microbial populations responsible for the oxidation and reduction of As were examined in unsaturated (aerobic) soil columns treated with 75 μM arsenite [As(III)] or 250 μM arsenate [As(V)]. Arsenite [As(III)] was rapidly oxidized to As(V) via microbial activity, whereas no apparent reduction of As(V) was observed in the column experiments. Eight aerobic heterotrophic bacteria with varying As redox phenotypes were isolated from the same columns. Three isolates, identified as Agrobacterium tumefaciens-, Pseudomonas fluorescens-, and Variovorax paradoxus-like organisms (based on 16S sequence), were As(III) oxidizers, and all were detected in community DNA fingerprints generated by PCR coupled with denaturing gradient gel electrophoresis. The five other isolates were identified (16S gene sequence) as A. tumefaciens, Flavobacterium sp., Microbacterium sp., and two Arthrobactersp.-like organisms and were shown to rapidly reduce As(V) under aerobic conditions. Although the two A. tumefaciens-like isolates exhibited opposite As redox activity, their l6s rDNA sequences (∼1400 bp) were 100% identical, and both were shown to contain putative arsC genes. Our results support the hypothesis that bacteria capable of either oxidizing As(III) or reducing As(V) coexist and are ubiquitous in soil environments, suggesting that the relative abundance and metabolic activity of specific microbial populations plays an important role in the speciation of inorganic As in soil pore waters. [ABSTRACT FROM AUTHOR]

Published
2004
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