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Research Interests: Biology and Microbiome
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Exploring the residence time of allelochemicals released by plants into different soils, episodic exposure of plants to allelochemicals, and the effects of allelochemicals in the field has the potential to improve our understanding of... more
Exploring the residence time of allelochemicals released by plants into different soils, episodic exposure of plants to allelochemicals, and the effects of allelochemicals in the field has the potential to improve our understanding of interactions among plants. We conducted experiments in India and the USA to understand the dynamics of soil concentrations and phytotoxicity of (+/-)-catechin, an allelopathic compound exuded from the roots of Centaurea maculosa, to other plants in vitro and in soil. Experiments with single and pulsed applications into soil were conducted in the field. Experimental application of (+/-)-catechin to soils always resulted in concentrations that were far lower than the amounts added but within the range of reported natural soil concentrations. Pulses replenished (+/-)-catechin levels in soils, but consistently at concentrations much lower than were applied, and even pulsed concentrations declined rapidly. Different natural soils varied substantially in the...
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We report several novel environmental sequences of archaea from the kingdom Crenarchaeota, recovered from anaerobic freshwater-lake sediments in Michigan. A nested PCR approach with Archaea- and Crenar-chaeota-specific primers was used to... more
We report several novel environmental sequences of archaea from the kingdom Crenarchaeota, recovered from anaerobic freshwater-lake sediments in Michigan. A nested PCR approach with Archaea- and Crenar-chaeota-specific primers was used to amplify partial Small-subunit ribosomal DNAs. Phylogenetic analysis of seven sequences shows that these DNAs represent a monophyletic lineage diverging prior to all recently identified crenarchaeotal phylotypes isolated from temperate environments. Including our lineage, all uncultured crenarchaeotal sequences recovered from moderate or cold environments form a distinct, monophyletic group separate from the "genuine" thermophilic crenarchaeota. Our finding extends the emerging picture that crenarchaeota, thought until recently to be solely extreme thermophiles, have radiated into an unexpectedly large variety of ecologically important, temperate environments.
Research Interests: Evolutionary Biology, Biology, Life Sciences, Medicine, Multidisciplinary, and 15 moreArchaea, Applied Environmental Microbiology, Bacteria, Michigan, Molecular phylogenetics, Ecosystem, Marine Environment, Fresh water, Monophyly, Base Sequence, Marine Invertebrate, Environmental DNA, Microbial community, Crenarchaeota, and Molecular Sequence Data
A DNA-based, direct method for initial characterization of the total bacterial community in ileum and cecum of the chicken gastrointestinal (GI) tract was developed. The efficiencies of bacterial extraction and lysis were >95 and... more
A DNA-based, direct method for initial characterization of the total bacterial community in ileum and cecum of the chicken gastrointestinal (GI) tract was developed. The efficiencies of bacterial extraction and lysis were >95 and >99%, respectively, and therefore the DNA recovered should accurately reflect the bacterial communities of the ileal and cecal digesta. Total bacterial DNA samples were fractionated according to their percent G+C content. The profiles reflecting the composition of the bacterial community were reproducible within each compartment, but different between the compartments of the GI tract. This approach is independent of the culturability of the bacteria in the consortium and can be used to improve our understanding of how diet and other variables modulate the microbial communities of the GI tracts of animals.
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Soils with a history of 2,4-dichlorophenoxyacetic acid (2,4-D) treatment at field application rates and control soils with no prior exposure to 2,4-D were amended with 2,4-D in the laboratory. Before and during these treatments, the... more
Soils with a history of 2,4-dichlorophenoxyacetic acid (2,4-D) treatment at field application rates and control soils with no prior exposure to 2,4-D were amended with 2,4-D in the laboratory. Before and during these treatments, the populations of 2,4-D-degrading bacteria were monitored by most-probable-number (MPN) enumeration and hybridization analyses, using probes for the tfd genes of plasmid pJP4, which encode enzymes for 2,4-D degradation. Data obtained by these alternate methods were compared. Several months after the most recent field application of 2,4-D (approximately 1 ppm), soils with a 42-year history of 2,4-D treatment did not have significantly higher numbers of 2,4-D-degrading organisms than did control soils with no prior history of treatment. In response to laboratory amendments with 2,4-D, both the previously treated soils and those with no prior history of exposure exhibited a dramatic increase in the number of 2,4-D-metabolizing organisms. The MPN data indicate ...
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RNA polymerase initiating at Escherichia coli ribosomal RNA promoter-leader regions can efficiently read through factor rho-dependent termination signals. Dissection of the promoter-leader region reveals that the ability to read through... more
RNA polymerase initiating at Escherichia coli ribosomal RNA promoter-leader regions can efficiently read through factor rho-dependent termination signals. Dissection of the promoter-leader region reveals that the ability to read through termination signals is conferred independently by both promoter and leader regions. Events in the leader also affect the transcription rate of structural genes downstream of the leader. When cells are grown in rich medium, the rrnC leader reduces transcription by a factor of approximately 4 when downstream of the rrnC promoters and by a factor of 2 when downstream of the lac promoter.
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Research Interests: Earth Sciences, Chemistry, Environmental Chemistry, Mining, Medicine, and 15 moreQuantitative PCR, Biological Sciences, Seasonality, Environmental Sciences, IDAHO, Iron, Sulfate, Sediment, Environmental quality, Fresh water, Industrial Waste, Environment Quality, Geologic Sediments, Pore Water, and Most Probable Number
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Research Interests: Geography, Environmental Science, Biology, Environmental Monitoring, Environmental Chemistry, and 15 moreMedicine, Multidisciplinary, Environmental science and technology, Heavy metals, Montana, Bacteria, Community Structure, Contamination, Ecosystem, Fluvial, Hyporheic Zone, Environmental, Geologic Sediments, Hyporheic microbial ecology, and Microbial community
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Understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation. The ability to reliably track and... more
Understanding the transport and behavior of bacteria in the environment has broad implications in diverse areas, ranging from agriculture to groundwater quality, risk assessment, and bioremediation. The ability to reliably track and enumerate specific bacterial populations in the context of native communities and environments is key to developing this understanding. We report a novel bacterial tracking approach, based on altering the stable carbon isotope value (δ 13 C) of bacterial cells, which provides specific and sensitive detection and quantification of those cells in environmental samples. This approach was applied to the study of bacterial transport in saturated porous media. The transport of introduced organisms was indicated by mass spectrometric analysis of groundwater samples, where the presence of 13 C-enriched bacteria resulted in increased δ 13 C values of the samples, allowing specific and sensitive detection and enumeration of the bacteria of interest. We demonstrate...
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Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a... more
Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was observed ( R 2 = 0.02, P = 0.83). However, denaturing gradient gel electrophoresis pattern analysis indicated a strong and consistent linear relationship between the difference in microbial community composition (populations present) and th...
Research Interests: Environmental Science, Biology, Life Sciences, Hydrobiology, Medicine, and 15 moreMicrobial Population Biology, Montana, Applied, Applied Environmental Microbiology, Heavy Metal, Community Structure, Contamination, Heavy Metal Contamination, Ecosystem, Fresh water, Base Sequence, Hyporheic Zone, Microbial Community Structure, Geologic Sediments, and Hyporheic microbial ecology
Vestimentiferan tubeworms thriving in sulfidic deep-sea hydrothermal vents and cold seeps are constrained by their nutritional reliance on chemoautotrophic endosymbionts. In a recent phylogenetic study using 16S ribosomal DNA, we found... more
Vestimentiferan tubeworms thriving in sulfidic deep-sea hydrothermal vents and cold seeps are constrained by their nutritional reliance on chemoautotrophic endosymbionts. In a recent phylogenetic study using 16S ribosomal DNA, we found that endosymbionts from vent and seep habitats form two distinct clades with little variation within each clade. In the present study, we used two different approaches to assess the genetic variation among biogeographically distinct vestimentiferan symbionts. DNA sequences were obtained for the noncoding, internal transcribed spacer (ITS) regions of the rRNA operons of symbionts associated with six different genera of vestimentiferan tubeworms. ITS sequences from endosymbionts of host genera collected from different habitats and widely distributed vent sites were surprisingly conserved. Because the ITS region was not sufficient for distinguishing endosymbionts from different habitats or locations, we used a DNA fingerprinting technique, repetitive-ext...
Research Interests: Biology, Life Sciences, Medicine, Multidisciplinary, Phylogeny, and 15 morePolychaeta, Applied, Animals, Applied Environmental Microbiology, Bacteria, Polymerase Chain Reaction, DNA fingerprinting, Cold Seep, Phylogenetic Tree, Genetic variation, Base Sequence, Environmental DNA, DNA sequence, Molecular Sequence Data, and Internal transcribed spacer
The aim of the present work was to compare the efficacies and levels of selectivity of different culture-dependent and -independent methods for analyzing bifidobacteria in human stool samples. The three different culture media used here... more
The aim of the present work was to compare the efficacies and levels of selectivity of different culture-dependent and -independent methods for analyzing bifidobacteria in human stool samples. The three different culture media used here significantly differed from each other, particularly with regard to the recovery of Bifidobacterium adolescentis . Bifidobacterium medium failed to recover B. adolescentis ; Beerens medium recovered some B. adolescentis organisms (17% of total bifidobacteria), whereas tomato-Eugon medium recovered mainly B. adolescentis organisms (58% of total bifidobacteria). A culture-independent method that combines GC fractionation of bacterial community DNA and 16S rRNA sequencing indicated that B. adolescentis organisms accounted for 85% of all bifidobacteria. Methodological biases, such as those described in this paper, should be taken into account in interpreting earlier studies and designing future experiments.
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Inulin is a well-known fructose-based prebiotic which has been shown to stimulate the growth of bifidobacteria, a bacterial group generally considered beneficial for intestinal health. In the present study, we analyzed inulin-associated... more
Inulin is a well-known fructose-based prebiotic which has been shown to stimulate the growth of bifidobacteria, a bacterial group generally considered beneficial for intestinal health. In the present study, we analyzed inulin-associated shifts in the total bacterial community of wild-type mice and mice carrying a genetically inactivated adenomatous polyposis coli tumor suppressor gene by using DNA-based approaches independent of bacterial culturability. Mice were fed a high-fat, nonfiber diet with or without inulin inclusion at a 10% (wt/wt) concentration. Cecal contents were analyzed after 0, 3, and 9 weeks on the experimental diets. Inulin inclusion significantly affected the total bacterial community structure of the cecum as determined by both a nonselective percent-guanine-plus-cytosine-based profiling analysis and a more specific 16S ribosomal DNA sequence analysis. The shifts included stimulation of bifidobacteria and suppression of clostridia, but sequence comparison reveale...
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The diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmids in the microbial community of an agricultural soil was examined by complementation. This technique involved mixing a suitable Alcaligenes eutrophus (Rifr)... more
The diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmids in the microbial community of an agricultural soil was examined by complementation. This technique involved mixing a suitable Alcaligenes eutrophus (Rifr) recipient strain with the indigenous microbial populations extracted from soil. After incubation of this mixture, Rifr recipient strains which grow with 2,4-D as the only C source were selected. Two A. eutrophus strains were used as recipients: JMP228 (2,4-D-), which was previously derived from A. eutrophus JMP134 by curing of the 2,4-D-degradative plasmid pJP4, and JMP228 carrying pBH501aE (a plasmid derived from pJP4 by deletion of a large part of the tfdA gene which encodes the first step in the mineralization of 2,4-D). By using agricultural soil that had been treated with 2,4-D for several years, transconjugants were obtained with both recipients. However, when untreated control soil was used, no transconjugants were isolated. The various transconjug...
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Research Interests: Biology, Life Sciences, Medicine, Multidisciplinary, Genetic Engineering, and 15 moreDNA, Applied Environmental Microbiology, Pseudomonas, Bacteria, Soils, Sol, Genome, Plasmids, Soil Microbiology, Plasmid, DNA probes, Molecular Probe, Restriction Mapping, Nucleotide sequence, and Chromosome deletion
We characterized the gene required to initiate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the soil bacterium Burkholderia sp. strain TFD6, which hybridized to the tfdA gene of the canonical 2,4-D catabolic plasmid pJP4... more
We characterized the gene required to initiate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the soil bacterium Burkholderia sp. strain TFD6, which hybridized to the tfdA gene of the canonical 2,4-D catabolic plasmid pJP4 under low-stringency conditions. Cleavage of the ether bond of 2,4-D by cell extracts of TFD6 proceeded by an (alpha)-ketoglutarate-dependent reaction, characteristic of TfdA (F. Fukumori and R. P. Hausinger, J. Bacteriol. 175:2083-2086, 1993). The TFD6 tfdA gene was identified in a recombinant plasmid which complemented a tfdA transposon mutant of TFD6 created by chromosomal insertion of Tn5. The plasmid also expressed TfdA activity in Escherichia coli DH5(alpha), as evidenced by enzyme assays with cell extracts. Sequence analysis of the tfdA gene and flanking regions from strain TFD6 showed 99.5% similarity to a tfdA gene cloned from the chromosome of a different Burkholderia species (strain RASC) isolated from a widely separated geographical area....
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We developed a protocol which yields purified bacterial DNA from the soil bacterial community. The bacteria were first dispersed and separated from soil particles in the presence of polyvinylpolypyrrolidone, which removes humic acid... more
We developed a protocol which yields purified bacterial DNA from the soil bacterial community. The bacteria were first dispersed and separated from soil particles in the presence of polyvinylpolypyrrolidone, which removes humic acid contaminants by adsorption to this insoluble polymer. The soil bacteria were then collected by centrifugation and lysed by using a comprehensive protocol designed to maximize disruption of the various types of bacteria present. Total bacterial DNA was purified from the cell lysate and remaining soil contaminants by using equilibrium density gradients. The isolated DNA was essentially pure as determined by UV spectral analysis, was at least 48 kilobases long, and was not subject to degradation, which indicated that there was no contaminating nuclease activity. The isolated DNA was readily digested by exogenously added restriction endonucleases and successfully analyzed by slot blot and Southern blot hybridizations. Using single-stranded, 32 P-labeled DNA ...
Research Interests: Bioinformatics, Biology, Life Sciences, Multidisciplinary, DNA, and 15 moreIdentification, Biomedical Research, Beta decay, Applied, Method, Applied Environmental Microbiology, Bacteria, Humic acid, Chemical Analysis, Density gradient, Organic Compound, Nucleic Acid, DNA sequence, Dry Weight, and Molecular Probe
Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil... more
Here we show that a commercial blocking reagent (G2) based on modified eukaryotic DNA significantly improved DNA extraction efficiency. We subjected G2 to an inter-laboratory testing, where DNA was extracted from the same clay subsoil using the same batch of kits. The inter-laboratory extraction campaign revealed large variation among the participating laboratories, but the reagent increased the number of PCR-amplified16S rRNA genes recovered from biomass naturally present in the soils by one log unit. An extensive sequencing approach demonstrated that the blocking reagent was free of contaminating DNA, and may therefore also be used in metagenomics studies that require direct sequencing.
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Research Interests: Land management, Biology, Agriculture, Medicine, Biological Sciences, and 15 moreEnvironmental Sciences, Land Use, Denitrification, Bacteria, Nitrogen, Greenhouse Gas Emissions, Greenhouse Gas, Nitrite Reductase, Greenhouse gases, Greenhouse Effect, Nitrous Oxide, Functional Group, Long Term Ecological Research, Microbial community, and isme
Research Interests: Technology, Soil, Biology, Medicine, Gene expression, and 15 moreBiological Sciences, real time PCR, Environmental Sciences, Bacteria, Soil Microbiology, Model System, Structural Similarity Index, Soil Amendment, Soil Pollutants, Agricultural Soil, Transition Temperature, Molecular Sequence Data, reverse transcriptase polymerase chain reaction, Structural similarity, and isme
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The Escherichia coli lac and ara promoters and rrnC ribosomal RNA promoter-leader region were fused to lacZYA. Transcription termination signals were introduced into the lac genes of these fusions by Tn9 and IS1 insertions. Measurement of... more
The Escherichia coli lac and ara promoters and rrnC ribosomal RNA promoter-leader region were fused to lacZYA. Transcription termination signals were introduced into the lac genes of these fusions by Tn9 and IS1 insertions. Measurement of lac enzymes from upstream and downstream of the insertions showed that termination signals resulting from these insertions are very efficient when transcription begins at lac or ara promoters but are very inefficient when transcription begins at the rrnC promoter-leader region. The rrnC promoter-leader region must, therefore, modify RNA polymerase to enable it to read through transcription termination signals.