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The interaction of protozoa with their potential prey bacteria in the rhizosphere.

Extensive colonization of the rhizosphere by beneficial bacteria is desirable but it is not yet clear whether the feeding patterns of protozoa exert any ecological impact on the competence of bacteria in the rhizosphere. To determine whether the successful colonization of the rhizosphere by bacteria can be explained by inherent abilities of the bacteria to resist predation, six bacteria categorized as poor, mediocre or good rhizosphere colonists were tested. The populations of protozoa in the rhizosphere consistently increased to a maximum density in two days but then declined to a stable level. Grazing by protozoa increased the doubling time of all of the test bacteria but did not significantly affect the final densities of bacteria in the rhizosphere. The differences in the colonization ability of the six bacteria tested were not attributable to inherent differences in their susceptibility to predation by protozoa.

Acanthamoeba↗
PubMed1999

Flagellate predation on a bacterial model community: interplay of size-selective grazing, specific bacterial cell size, and bacterial community composition.

The influence of grazing by the bacterivorous nanoflagellate Ochromonas sp. strain DS on the taxonomic and morphological structures of a complex bacterial community was studied in one-stage chemostat experiments. A bacterial community, consisting of at least 30 different strains, was fed with a complex carbon source under conditions of low growth rate (0.5 day(-1) when nongrazed) and low substrate concentration (9 mg liter(-1)). Before and after the introduction of the predator, the bacterial community composition was studied by in situ techniques (immunofluorescence microscopy and fluorescent in situ hybridization), as well as by cultivation on agar media. The cell sizes of nonspecifically stained and immunofluorescently labeled bacteria were measured by image analysis. Grazing by the flagellate caused a bidirectional change in the morphological structure of the community. Medium-size bacterial cells, which dominated the nongrazed community, were largely replaced by smaller cells, as well as by cells contained in large multicellular flocs. Cell morphological changes were combined with community taxonomic changes. After introduction of the flagellate, the dominating strains with medium-size cells were largely replaced by single-celled strains with smaller cells on the one hand and, on the other hand, by Pseudomonas sp. strain MWH1, which formed the large, floc-like forms. We assume that size-selective grazing was the major force controlling both the morphological and the taxonomic structures of the model community.

Aeromonas↗
PubMed2000

Monitoring bacterial transport by stable isotope enrichment of cells.

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 (delta(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 delta(13)C values of the samples, allowing specific and sensitive detection and enumeration of the bacteria of interest. We demonstrate the ability to produce highly (13)C-enriched bacteria, present data indicating that results obtained with this approach accurately represent intact introduced bacteria, and include field data on the use of this stable isotope approach to monitor in situ bacterial transport. This detection strategy allows sensitive detection of an introduced, unmodified bacterial strain in the presence of the indigenous bacterial community, including itself in its unenriched form.

Arthrobacter↗
PubMed2001

Evidence for detachment of indigenous bacteria from aquifer sediment in response to arrival of injected bacteria.

Two bacterial strains isolated from the aquifer underlying Oyster, Va., were recently injected into the aquifer and monitored using ferrographic capture, a high-resolution immunomagnetic technique. Injected cells were enumerated on the basis of a vital fluorescence stain, whereas total cell numbers (stained target cells plus unstained target and antigenically similar indigenous bacteria) were identified by cell outlines emanating from fluorophore-conjugated antibodies to the two target strains. The arrival of injected bacteria at the majority of monitored sampling ports was accompanied by simultaneous temporary increases in unstained cell counts that outnumbered the injected bacteria by 2- to 100-fold. The origin and mechanism of appearance of the unstained cells are considered.

Bacterial Adhesion↗
PubMed2006

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole.

A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing pK(a) models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50-0.76 ppm/pK(a) unit, suggesting a bond shortening of 0.02 A/pK(a) unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (DeltaDeltaG = -0.2 kcal/mol/pK(a) unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (DeltaDeltaH = -2.0 kcal/mol/pK(a) unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of 300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution.

Anions↗
PubMed2002

Bioreactor design studies for a hydrogen-producing bacterium.

Carbon monoxide (CO) can be metabolized by a number of microorganisms along with water to produce hydrogen (H2) and carbon dioxide. National Renewable Energy Laboratory researchers have isolated a number of bacteria that perform this so-called water-gas shift reaction at ambient temperatures. We performed experiments to measure the rate of CO conversion and H2 production in a trickle-bed reactor (TBR). The liquid recirculation rate and the reactor support material both affected the mass transfer coefficient, which controls the overall performance of the reactor. A simple reactor model taken from the literature was used to quantitatively compare the performance of the TBR geometry at two different size scales. Good agreement between the two reactor scales was obtained.

Bicarbonates↗