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Biomedical subjects

R M Atlas

Publications and source records attributed to R M Atlas.

At least 55 records · Page 3Linked to original sources
PubMed1988

Recovery of DNA from soils and sediments.

Experiments were performed to evaluate the effectiveness of two different methodological approaches for recovering DNA from soil and sediment bacterial communities: cell extraction followed by lysis and DNA recovery (cell extraction method) versus direct cell lysis and alkaline extraction to recover DNA (direct lysis method). Efficiency of DNA recovery by each method was determined by spectrophotometric absorbance and using a tritiated thymidine tracer. With both procedures, the use of polyvinylpolypyrrolidone was important for the removal of humic compounds to improve the purity of the recovered DNA; without extensive purification, various restriction enzymes failed to cut added target DNA. Milligram quantities of high-purity DNA were recovered from 100-g samples of both soils and sediments by the direct lysis method, which was a greater than 1-order-of-magnitude-higher yield than by the cell extraction method. The ratio of labeled thymidine to total DNA, however, was higher in the DNA recovered by the cell extraction method. than by the direct lysis method, suggesting that the DNA recovered by the cell extraction method came primarily from active bacterial cells, whereas that recovered by the direct lysis method may have contained DNA from other sources.

Cell Separation↗
PubMed1988

Mineralization of the dibenzothiophene biodegradation products 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone.

Dibenzothiophene is degraded to 3-hydroxy-2-formyl benzothiophene by various bacteria, including a strain of Pseudomonas putida that also forms dibenzothiophene sulfone via an alternate pathway. By using these end products as substrates, mixed enrichment cultures that could degrade 3-hydroxy-2-formyl benzothiophene and dibenzothiophene sulfone with the formation of CO2 were established.

Biodegradation, Environmental↗
PubMed1988

DNA amplification to enhance detection of genetically engineered bacteria in environmental samples.

The polymerase chain reaction (PCR) was performed to amplify a 1.0-kilobase (kb) probe-specific region of DNA from the herbicide-degrading bacterium Pseudomonas cepacia AC1100 in order to increase the sensitivity of detecting the organism by dot-blot analysis. The 1.0-kb region was an integral portion of a larger 1.3-kb repeat sequence which is present as 15 to 20 copies on the P. cepacia AC1100 genome. PCR was performed by melting the target DNA, annealing 24-base oligonucleotide primers to unique sequences flanking the 1.0-kb region, and performing extension reactions with DNA polymerase. After extension, the DNA was again melted, and the procedure was repeated for a total of 25 to 30 cycles. After amplification the reaction mixture was transferred to nylon filters and hybridized against radiolabeled 1.0-kb fragment probe DNA. Amplified target DNA was detectable in samples initially containing as little as 0.3 pg of target. The addition of 20 micrograms of nonspecific DNA isolated from sediment samples did not hinder amplification or detection of the target DNA. The detection of 0.3 pg of target DNA was at least a 10(3)-fold increase in the sensitivity of detecting gene sequences compared with dot-blot analysis of nonamplified samples. PCR performed after bacterial DNA was isolated from sediment samples permitted the detection of as few as 100 cells of P. cepacia AC1100 per 100 g of sediment sample against a background of 10(11) diverse nontarget organisms; that is, P. cepacia AC1100 was positively detected at a concentration of 1 cell per g of sediment. This represented a 10(3)-fold increase in sensitivity compared with nonamplified samples.

Bacteria↗
PubMed1988

Plasmid frequency fluctuations in bacterial populations from chemically stressed soil communities.

The frequency of plasmids in chemically stressed bacterial populations was investigated by individually adding various concentration of kanamycin, ampicillin, and mercuric chloride to soil samples. Viable bacterial populations were enumerated, soil respiration was monitored for up to 6 weeks as an indicator of physiological stress, and bacterial isolates from stressed and control soils were screened for the presence of plasmids. Low levels of the chemical stress factors did not for the most part significantly alter population viability, soil respiration, or plasmid frequency. Exposure to high stress levels of mercury and ampicillin, however, resulted in altered numbers of viable organisms, soil respiration, and plasmid frequency. Plasmid frequency increased in response to ampicillin exposure but was not significantly changed after exposure to kanamycin. In mercuric chloride-stressed soils, there was a decrease in plasmid frequency despite an increase in overall mercury resistance of the isolates, suggesting that mercury resistance in these populations is largely, if not completely, chromosome encoded. Chemical stress did not cause an increase in plasmid-mediated multiple resistance. A genetic response (change in plasmid frequency) was not found unless a physiological (phenotypic) response (change in viable cells and respiratory activity) was also observed. The results indicate that a change in plasmid frequency is dependent on both the amount and type of chemical stress.

Journal Article↗
PubMed1988

Biodegradation of nitriles in shale oil.

Enrichment cultures were obtained, after prolonged incubation on a shale oil as the sole source of nitrogen, that selectively degraded nitriles. Capillary gas chromatographic analyses showed that the mixed microbial populations in the enrichments degraded the homologous series of aliphatic nitriles but not the aliphatic hydrocarbons, aromatic hydrocarbons, or heterocyclic-nitrogen compounds found in this oil. Time course studies showed that lighter nitriles were removed more rapidly than higher-molecular-weight nitriles. A Pseudomonas fluorescens strain isolated from an enrichment, which was able to completely utilize the individual nitriles undecyl cyanide and undecanenitrile as sole sources of carbon and nitrogen, was unable to attack stearonitrile when provided alone as the growth substrate. A P. aeruginosa strain, also isolated from one of the enrichments, used nitriles but not aliphatic or aromatic hydrocarbons when the oil was used as a sole nitrogen source. However, when the shale oil was used as the sole source of carbon, aliphatic hydrocarbons in addition to nitriles were degraded but aromatic hydrocarbons were still not attacked by this P. aeruginosa strain.

Journal Article↗
PubMed1987

Measurement of the effects of cadmium stress on protozoan grazing of bacteria (bacterivory) in activated sludge by fluorescence microscopy.

The effect of cadmium stress on protozoan bacterivory in sewage sludge was measured by experimentally exposing sludge communities to 0 to 150 mg of Cd per liter for up to 6 h and then determining the rates of protozoan grazing on bacteria, using a double-staining technique and epifluorescence microscopy. Bacterivory was measured by incubating the sludge with fluorescently labeled bacterium-sized latex beads and directly observing ingestion of the beads and bacterial cells in the sludge by epifluorescence microscopy of preserved samples. Staining with 4',6-diamidino-2-phenylindole and acridine orange permitted the simultaneous determination of protozoan numbers and bacterivory activity as estimated by the number of bacterial cells and bacterium-sized latex beads ingested by the representative ciliate Aspidisca costata. Enumeration with latex beads proved to be an effective way of estimating bacterivory in sludges subjected to heavy-metal stress. This technique should prove useful for determining the effects of other chemical stresses on protozoan numbers and bacterivory in organic-rich environments. Although the number of protozoa declined significantly only after exposure to 100 mg of Cd per liter for 4 h, grazing, as indicated by bead ingestion, was significantly inhibited by Cd concentrations of greater than 25 mg/liter in less than 1 h, and exposure to 100 mg of Cd per liter effectively stopped protozoan grazing within 1 h of exposure. Protozoan ingestion of latex beads and bacteria was inversely correlated to Cd concentration and exposure time. The reduction of protozoan bacterivory by Cd provides a possible explanation for the increase in suspended bacteria in the effluents of metal-stressed treatment facilities.

Analysis of Variance↗
PubMed1984

Bacteria associated with crabs from cold waters with emphasis on the occurrence of potential human pathogens.

A diverse array of bacterial species, including several potential human pathogens, was isolated from edible crabs collected in cold waters. Crabs collected near Kodiak Island, Alaska, contained higher levels of bacteria than crabs collected away from regions of human habitation. The bacteria associated with the crabs collected near Kodiak included Yersinia enterocolitica, Klebsiella pneumoniae, and coagulase-negative Staphylococcus species; the pathogenicity of these isolates was demonstrated in mice. Although coliforms were not found, the bacterial species associated with the tissues of crabs collected near Kodiak indicate possible fecal contamination that may have occurred through contact with sewage. Compared with surrounding waters and sediments, the crab tissues contained much higher proportions of gram-positive cocci. As revealed by indirect plate counts and direct scanning electron microscopic observations, muscle and hemolymph tissues contained much lower levels of bacteria than shell and gill tissues. After the death of a crab, however, the numbers of bacteria associated with hemolymph and muscle tissues increased significantly. Microcosm studies showed that certain bacterial populations, e.g., Vibrio cholerae, can be bioaccumulated in crab gill tissues. The results of this study indicate the need for careful review of waste disposal practices where edible crabs may be contaminated with microorganisms that are potential human pathogens and the need for surveillance of shellfish for pathogenic microorganisms that naturally occur in marine ecosystems.

Alaska↗
PubMed1981

Denitrification and nitrogen fixation in alaskan continental shelf sediments.

Rates of nitrogen fixation and denitrification were measured in Alaskan continental shelf sediments. In some regions, rates of nitrogen fixation and denitrification appeared to be equal; in other areas, rates were significantly different. Potential rates of denitrification were found to be limited primarily by the available nitrate substrate. Major regional differences in rates of denitrification were not statistically significant, but significant differences were found for nitrogen fixation rates in different regions of the Alaskan continental shelf. Estimated net losses of nitrogen from Bering Sea sediments were calculated as 1.8 x 10 g of N/yr. Experimental exposure of continental shelf sediments to petroleum hydrocarbons reduced rates of nitrogen fixation and denitrification in some cases but not others. Long-term exposure was necessary before a reduction in nitrogen fixation rates was observed; unamended rates of denitrification but not potential denitrification rates (NO(3) added) were depressed after exposure to hydrocarbons.

Journal Article↗
PubMed1978

Distribution of hydrocarbon-utilizing microorganisms and hydrocarbon biodegradation potentials in Alaskan continental shelf areas.

Hydrocarbon-utilizing microorganisms were enumerated from Alaskan continental shelf areas by using plate counts and a new most-probable-number procedure based on mineralization of (14)C-labeled hydrocarbons. Hydrocarbon utilizers were ubiquitously distributed, with no significant overall concentration differences between sampling regions or between surface water and sediment samples. There were, however, significant seasonal differences in numbers of hydrocarbon utilizers. Distribution of hydrocarbon utilizers within Cook Inlet was positively correlated with occurrence of hydrocarbons in the environment. Hydrocarbon biodegradation potentials were measured by using (14)C-radiolabeled hydrocarbon-spiked crude oil. There was no significant correlation between numbers of hydrocarbon utilizers and hydrocarbon biodegradation potentials. The biodegradation potentials showed large seasonal variations in the Beaufort Sea, probably due to seasonal depletion of available nutrients. Non-nutrient-limited biodegradation potentials followed the order hexadecane > naphthalene >> pristane > benzanthracene. In Cook Inlet, biodegradation potentials for hexadecane and naphthalene were dependent on availability of inorganic nutrients. Biodegradation potentials for pristane and benzanthracene were restricted, probably by resistance to attack by available enzymes in the indigenous population.

Alaska↗
PubMed1977

Continuous open flow-through system as a model for oil degradation in the arctic ocean.

A continuous flow-through system incubated in situ was used to model oil biodegradation in Arctic coastal waters. High numbers of oil-degrading microorganisms were found in the Arctic coastal waters examined in this study. The microbial community underlying oil slicks increased and showed a population shift to a greater percentage of hydrocarbon-utilizing microorganisms. Microbial populations and oil biodegradation were increased by the addition of nitrogen and phosphorus. Both abiotic and biodegradative losses were lower than expected, perhaps due to the unusually harsh, ice-dominated Arctic summer, during which these tests were conducted. Chromatographic and spectrometric analyses showed that residual oils contained similar percentages of individual components and classes of hydrocarbons, regardless of the amount of degradation, indicating that most components of the oil were being degraded at similar rates.

Journal Article↗
PubMed1977

Response of microorganisms to an accidental gasoline spillage in an arctic freshwater ecosystem.

The response of microorganisms to an accidental spillage of 55,000 gallons of leaded gasoline into an Arctic freshwater lake was studied. Shifts in microbial populations were detected after the spillage, reflecting the migration pattern of the gasoline, enrichment for hydrocarbon utilizers, and selection for leaded-gasoline-tolerant microorganisms. Ratios of gasoline-tolerant/utilizing heterotrophs to "total" heterotrophs were found to be a sensitive indicator of the degree of hydrocarbon contamination. Respiration rates were elevated in the highly contaminated area, but did not reflect differences between moderately and lightly contaminated areas. Hydrocarbon biodegradation potential experiments showed that indigenous microorganisms could extensively convert hydrocarbons to CO(2). In situ measurement of gasoline degradation showed that, if untreated, sediment samples retained significant amounts of gasoline hydrocarbons including "volatile components" at the time the lake froze for the winter. Nutrient addition and bacterial inoculation resulted in enhanced biodegradative losses, significantly reducing the amount of residual hydrocarbons. Enhanced biodegradation, however, resulted in the appearance of compounds not detected in the gasoline. Since the contaminated lake serves as a drinking water supply, treatment to enhance microbial removal of much of the remaining gasoline still may be advisable.

Alaska↗
PubMed1977

Response of microbial populations in arctic tundra soils to crude oil.

Experimental crude oil spillages of 5 and 12 litre/m2 were established on the four major topographically distinguished soils of Arctic coastal polygonized tundra. The response of microbial populations to contaminating oil was found to depend on soil type and depth. Increases in numbers of heterotrophs were initially restricted to the top 2 cm of the soils. Increase in oil-degrading populations were found in oil-treated soils. Increases in microbial populations in subsurface soils paralleled downward migration of the oil. Some of the observed population increases probably resulted from input of plant residues and products from oil biodegradation.

Arctic Regions↗
PubMed1975

Effects of temperature and crude oil composition on petroleum biodegradation.

The biodegradability of seven different crude oils was found to be highly dependent on their composition and on incubation temperature. At 20 C lighter oils had greater abiotic losses and were more susceptible to biodegradation than heavier oils. These light crude oils, however, possessed toxic volatile components which evaporated only slowly and inhibited microbial degradation of these oils at 10 C. No volatile toxic fraction was associated with the heavier oils tested. Rates of oil mineralization for the heavier oils were significantly lower at 20 C than for the lighter ones. Similar relative degradation rates were found with a mixed microbial community, using CO2 evolution as the measure, and with a Pseudomonas isolate from the Arctic, using O2 consumption as the measure. The paraffinic, aromatic, and asphaltic fractions were subject to biodegradation. Some preference was shown for paraffin degradation, especially at low temperatures. Branched paraffins, such as pristane, were degraded at both 10 and 20 C. At best, a 20% residue still remained after 42 days of incubation. Oil residues generally had a lower relative percentage of paraffins and higher percentage of asphaltics than fresh or weathered oil.

Alkanes↗
PubMed1974

Hydrocarbon metabolism by Brevibacterium erythrogenes: normal and branched alkanes.

Branched- and straight-chain alkanes are metabolized by Brevibacterium erythrogenes by means of two distinct pathways. Normal alkanes (e.g., n-pentadecane) are degraded, after terminal oxidation, by the beta-oxidation system operational in fatty acid catabolism. Branched alkanes like pristane (2,6,10,14-tetramethylpentadecane) and 2-methylundecane are degraded as dicarboxylic acids, which also undergo beta-oxidation. Pristane-derived intermediates are observed to accumulate, with time, as a series of dicarboxylic acids. This dicarboxylic acid pathway is not observed in the presence of normal alkanes. Release of (14)CO(2) from [1-(14)C]pristane is delayed, or entirely inhibited, in the presence of n-hexadecane, whereas CO(2) release from n-hexadecane remains unaffected. These results suggest an inducible dicarboxylic acid pathway for degradation of branched-chain alkanes.

Alkanes↗