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At least 955 records · Page 53Linked to original sources
PubMed1997

Efficiency of indigenous and inoculated cold-adapted soil microorganisms for biodegradation of diesel oil in alpine soils.

Biodegradation of diesel oil (5 g(middot)kg [soil dry weight](sup-1)) was investigated in five alpine subsoils, differing in soil type and bedrock, in laboratory experiments during 20 days at 10(deg)C. The biodegradation activities of the indigenous soil microorganisms and of a psychrotrophic diesel oil-degrading inoculum and the effect of biostimulation by inorganic fertilization (C/N/P ratio = 100:10:2) were determined. Fertilization significantly enhanced diesel oil biodegradation activity of the indigenous soil microorganisms. Biostimulation by fertilization enhanced diesel oil biodegradation to a significantly greater degree than bioaugmentation with the psychrotrophic inoculum. In none of the five soils did fertilization plus inoculation result in a higher decontamination than fertilization alone. A total of 16 to 23% of the added diesel oil contamination was lost by abiotic processes. Total decontamination without and with fertilization was in the range of 16 to 31 and 27 to 53%, respectively.

Journal Article↗
PubMed1997

Distribution of microorganisms in deep-sea hydrothermal vent chimneys investigated by whole-cell hybridization and enrichment culture of thermophilic subpopulations.

The microbial community structure of hydrothermal vent chimneys was evaluated by the combined use of enrichment cultures and whole-cell hybridizations with fluorescently labeled 16S rRNA-based oligonucleotide probes. Chimneys were collected during the Microsmoke cruise on the Mid-Atlantic Ridge and were subsampled on board and stored under reduced conditions or fixed. For estimation of culturable thermophiles, selective media were inoculated by dilution series of the samples and incubated at 65, 80, and 95(deg)C. To analyze the microbial diversity of the samples, cells were extracted from the fixed chimney structure samples and hybridized with domain- and kingdom-specific probes. Quantification of the extracted cells was assessed by whole-cell hybridization on membrane filters. By both methods, the largest amounts of microorganisms were found in the upper and outer parts of the chimneys, although even the inner parts contained culturable and detectable amounts of cells. Different morphotypes of thermophilic and hyperthermophilic microorganisms were enriched and detected in samples. Our data clearly indicate that the morphological diversity observed by using whole-cell hybridization is much larger than that assessed by use of culture-based enrichments. This new approach, including culture-independent and -dependent methods to study hydrothermal vent chimneys, showed an uneven distribution of a diverse microbial community. Application of lower-level specific probes for known families and genera within each domain by our approach will be useful to reveal the real extent and nature of the chimney microbial diversity and to support cultivation attempts.

Journal Article↗
PubMed1997

Aerobic biodegradation of biphenyl and polychlorinated biphenyls by Arctic soil microorganisms.

We examined the degradation of biphenyl and the commercial polychlorinated biphenyl (PCB) mixture Aroclor 1221 by indigenous Arctic soil microorganisms to assess both the response of the soil microflora to PCB pollution and the potential of the microflora for bioremediation. In soil slurries, Arctic soil microflora and temperate-soil microflora had similar potentials to mineralize [14C]biphenyl. Mineralization began sooner and was more extensive in slurries of PCB-contaminated Arctic soils than in slurries of uncontaminated Arctic soils. The maximum mineralization rates at 30 and 7 degrees C were typically 1.2 to 1.4 and 0.52 to 1.0 mg of biphenyl g of dry soil-1 day-1, respectively. Slurries of PCB-contaminated Arctic soils degraded Aroclor 1221 more extensively at 30 degrees C (71 to 76% removal) than at 7 degrees C (14 to 40% removal). We isolated from Arctic soils organisms that were capable of psychrotolerant (growing at 7 to 30 degrees C) or psychrophilic (growing at 7 to 15 degrees C) growth on biphenyl. Two psychrotolerant isolates extensively degraded Aroclor 1221 at 7 degrees C (54 to 60% removal). The soil microflora and psychrotolerant isolates degraded all mono-, most di-, and some trichlorobiphenyl congeners. The results suggest that PCB pollution selected for biphenyl-mineralizing microorganisms in Arctic soils. While low temperatures severely limited Aroclor 1221 removal in slurries of Arctic soils, results with pure cultures suggest that more effective PCB biodegradation is possible under appropriate conditions.

Aerobiosis↗
PubMed1999

Culture-independent identification of microorganisms that respond to specified stimuli.

A new approach that permits culture-independent identification of microorganisms that respond to specified stimuli was developed. This approach was illustrated by examination of microorganisms that grew in response to various nutrient supplements added to soil. A thymidine nucleotide analog, bromodeoxyuridine (BrdU), and supplements were added to soil and incubated for 3 days. DNA was extracted from the soil, and the newly synthesized DNA was isolated by immunocapture of the BrdU-labeled DNA. The unique perspective this approach offers was demonstrated by comparing the microbial community structures obtained from total soil DNA and the BrdU-labeled fraction in an rRNA gene (rDNA) analysis. The traditional total DNA analysis revealed no notable differences between the treatments, whereas the BrdU-labeled DNA showed significantly different banding patterns between the nutrient supplement treatments and compared with total DNA banding patterns. PCR primers were developed to specifically amplify the intergenic region of an rDNA sequence unique to the BrdU analysis of a phosphate supplement treatment. Amplification of DNA from all treatments using these primers showed that it was unique to the phosphate treatment and that it was present in both the total DNA and BrdU-labeled DNA fractions. This result demonstrates the promise of this new strategy, because it was able to permit identification of a sequence from a phosphate-responsive organism that was not discernable in the traditional total DNA community structure analysis.

Base Sequence↗
PubMed2000

Heavy metal coprecipitation with hydrozincite [Zn(5)(CO(3))(2)(OH)(6)] from mine waters caused by photosynthetic microorganisms.

An iron-poor stream of nearly neutral pH polluted by mine tailings has been investigated for a natural phenomenon responsible for the polishing of heavy metals in mine wastewaters. A white mineralized mat, which was determined to be hydrozincite [Zn(5)(CO(3))(2)(OH)(6)] by X-ray diffraction analysis, was observed in the stream sediments mainly in spring. The precipitate shows a total organic matter residue of 10% dry weight and contains high concentrations of Pb, Cd, Ni, Cu, and other metals. Scanning electron microscopy analysis suggests that hydrozincite is mainly of biological origin. Dormant photosynthetic microorganisms have been retrieved from 1-year-old dry hydrozincite. The autofluorescent microorganisms were imaged by a scanning confocal laser microscope. A photosynthetic filamentous bacterium, classified as Scytonema sp. strain ING-1, was found associated with microalga Chlorella sp. strain SA1. This microbial community is responsible for the natural polishing of heavy metals in the water stream by coprecipitation with hydrozincite.

Carbonates↗
PubMed2000

A new system for three-dimensional tracking of motile microorganisms.

A new three-dimensional (3D)-tracking system with optimized dark-field illumination is presented. It allows simultaneous 3D tracking of several free-swimming microorganisms with diameters of >10 microm. Resolution limits and illumination efficiencies for different size classes of microorganisms are treated analytically. First applications for 3D tracking of protists are demonstrated.

Animals↗
PubMed2000

Distribution of aldoxime dehydratase in microorganisms.

The distribution of phenylacetaldoxime-degrading and pyridine-3-aldoxime-degrading ability was examined with intact cells of 975 microorganisms, including 45 genera of bacteria, 11 genera of actinomyces, 22 genera of yeasts, and 37 genera of fungi, by monitoring the decrease of the aldoximes by high-pressure liquid chromatography. The abilities were found to be widely distributed in bacteria, actinomyces, fungi, and some yeasts: 98 and 107 strains degraded phenylacetaldoxime and pyridine-3-aldoxime, respectively. All of the active strains exhibited not only the aldoxime-dehydration activity to form nitrile but also nitrile-hydrolyzing activity. On the other hand, all of 19 nitrile-degrading microorganisms (13 species, 7 genera) were found to exhibit aldoxime dehydration activity. It is shown that aldoxime dehydratase and nitrile-hydrolyzing activities are widely distributed among 188 aldoxime and 19 nitrile degraders and that the enzymes were induced by aldoximes or nitriles.

Bacteria↗
PubMed2001

Rapid evolution of novel traits in microorganisms.

The use of natural microorganisms in biotransformations is frequently constrained by their limited tolerance to the high concentrations of metabolites and solvents required for effective industrial production. In many cases, more robust strains have to be generated by random mutagenesis and selection. This process of directed evolution can be accelerated in mutator strains, which carry defects in one or more of their DNA repair genes. However, in order to use mutator strains, it is essential to restore the normal low mutation rate of the selected organisms immediately after selection to prevent the accumulation of undesirable spontaneous mutations. To enable this process, we constructed temperature-sensitive plasmids that temporarily increase the mutation frequency of their hosts by 20- to 4,000-fold. Under appropriate selection pressure, microorganisms transformed with mutator plasmids can be quickly evolved to exhibit new, complex traits. By using this approach, we were able to increase the tolerance of three bacterial strains to dimethylformamide by 10 to 20 g/liter during only two subsequent transfers. Subsequently, the evolved strains were returned to their normal low mutation rate by curing the cells of the mutator plasmids. Our results demonstrate a new and efficient method for rapid strain improvement based on in vivo mutagenesis.

Dimethylformamide↗
PubMed2003

Enumeration and characterization of acidophilic microorganisms isolated from a pilot plant stirred-tank bioleaching operation.

Microorganisms were enumerated and isolated on selective solid media from a pilot-scale stirred-tank bioleaching operation in which a polymetallic sulfide concentrate was subjected to biologically accelerated oxidation at 45 degrees C. Four distinct prokaryotes were isolated: three bacteria (an Acidithiobacillus caldus-like organism, a thermophilic Leptospirillum sp., and a Sulfobacillus sp.) and one archaeon (a Ferroplasma-like isolate). The relative numbers of these prokaryotes changed in the three reactors sampled, and the Ferroplasma isolate became increasingly dominant as mineral oxidation progressed, eventually accounting for >99% of plate isolates in the third of three in-line reactors. The identities of the isolates were confirmed by analyses of their 16S rRNA genes, and some key physiological traits (e.g., oxidation of iron and/or sulfur and autotrophy or heterotrophy) were examined. More detailed studies were carried out with the Leptospirillum and Ferroplasma isolates. The data presented here represent the first quantitative study of the microorganisms in a metal leaching situation and confirm that mixed cultures of iron- and sulfur-oxidizing prokaryotic acidophiles catalyze the accelerated dissolution of sulfidic minerals in industrial tank bioleaching operations. The results show that indigenous acidophilic microbial populations change as mineral dissolution becomes more extensive.

Bacteria↗
PubMed2003

Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney.

A large, intact sulfide chimney, designated Finn, was recovered from the Mothra Vent Field on the Juan de Fuca Ridge in 1998. Finn was venting 302 degrees C fluids on the seafloor and contained complex mineralogical zones surrounding a large open central conduit. Examination of microorganisms within these zones, followed by community analysis with oligonucleotide probes, showed that there were variations in the abundance and diversity of eubacteria and archaea from the exterior to the interior of the chimney. The microbial abundance based upon epifluorescence microscopy and quantitative fatty acid analyses varied from >10(8) cells/g of sulfide 2 to 10 cm within the chimney wall to <10(5) cells/g in interior zones. Direct microscopic observation indicated that microorganisms were attached to mineral surfaces throughout the structure. Whole-cell hybridization results revealed that there was a transition from a mixed community of eubacteria and archaea near the cool exterior of the chimney to primarily archaea near the warm interior. Archaeal diversity was examined in three zones of Finn by cloning and sequencing of the 16S rRNA gene. The majority of sequences from the exterior of the chimney were related to marine group I of the Crenarchaeota and uncultured Euryarchaeota from benthic marine environments. In contrast, clone libraries from interior regions of the chimney contained sequences closely related to methanogens, Thermococcales, and Archaeoglobales, in addition to uncultured crenarchaeal phylotypes obtained from deep subsurface sites. These observations of microbial communities within an active hydrothermal chimney provide insight into the microbial ecology within such structures and may facilitate follow-up exploration into expanding the known upper temperature limits of life.

Archaea↗
PubMed2004

Enzyme production-based approach for determining the functions of microorganisms within a community.

The functions of specific microorganisms in a microbial community were investigated during the composting process. Cerasibacillus quisquiliarum strain BLx(T) and Bacillus thermoamylovorans strain BTa were isolated and characterized in our previous studies based on their dominance in the composting system. Strain BLx(T) degrades gelatin, while strain BTa degrades starch. We hypothesized that these strains play roles in gelatinase and amylase production, respectively. The relationship between changes in the abundance ratios of each strain and those of each enzyme activity during the composting process was examined to address this hypothesis. The increase in gelatinase activity in the compost followed a dramatic increase in the abundance ratio of strain BLx(T). Zymograph analysis demonstrated that the pattern of active gelatinase bands from strain BLx(T) was similar to that from the compost. Gelatinases from both BLx(T) and compost were partially purified and compared. Homologous N-terminal amino acid sequences were found in one of the gelatinases from strain BLx(T) and that of compost. These results indicate strain BLx(T) produces gelatinases during the composting process. Meanwhile, the increase in the abundance ratio of strain BTa was not concurrent with that of amylase activity in the compost. Moreover, the amylase activity pattern of strain BTa on the zymogram was different from that of the compost sample. These results imply that strain BTa may not produce amylases during the composting process. To our knowledge, this is the first report demonstrating that the function of a specific microorganism is directly linked to a function in the community, as determined by culture-independent and enzyme-level approaches.

Amino Acid Sequence↗
PubMed1962

Fate of staphylococci and enteric microorganisms introduced into slurry of frozen pot pies.

A slurry was prepared from six frozen pot pies diluted 1:5 with distilled water, two chicken, two turkey, and two beef pies of different brands. This slurry formed a reference sample and was placed in sterilized jars, frozen, and used as needed throughout the experiments. A second slurry was prepared in a similar manner from a frozen beef pot pie and a chicken pot pie, and was used as a control in only one experiment. The total count of microorganisms and the number of coliforms, Escherichia coli, salmonellae, and coagulase-positive staphylococci per gram were determined. Samples of slurry were inoculated in decimal dilutions with one or more of the following: Salmonella typhimurium, E. coli, and a strain of staphylococcus that causes food poisoning. The natural flora was found to exert an inhibitory effect upon the growth of the added microorganisms after incubation at 35 C for 18 hr. The inhibitory effect on growth was in part due to pH. The predominating organism isolated from the natural flora after incubation was a lactobacillus, which, when added in mixture with the test organisms in sterilized slurry, did not exert the profound inhibitory effect observed in the case of the natural flora. Some factors which may be concerned with the inhibition were investigated.

Animals↗
PubMed1963

Soil microorganisms of the McMurdo Sound area, Antarctica.

A study of soil microorganisms of Ross Island and the adjacent mainland was carried out during the brief austral summer of 1961-1962. In some cases, seasonal changes in microbial numbers were observed, although microorganisms could not be detected in some soils. Bacterial species common to temperate regions were isolated from a number of different samples. Thermophilic bacteria were present in some of the soils, and a significant portion of the bacterial population was capable of growth at 2 C. The soil microflora were capable of carrying out certain reactions of the nitrogen cycle at a very slow rate. In addition to temperature, other environmental factors which might influence growth and metabolic activity were discussed.

Antarctic Regions↗
PubMed1965

FERMENTATION CAPACITY AS A MEASURE OF NET GROWTH OF RUMEN MICROORGANISMS.

A simple technique for measuring the rate of fermentation of rumen microorganisms is described. It allows quick preparation and handling of the rumen sample immediately after collection. The average rate of fermentation of rumen samples collected from a lactating cow fed on alfalfa hay and concentrate in the ratio of 2:1 was very similar to the rate obtained by other methods. On the assumption that when substrate is in excess, the fermentation rate is proportional to the total microbial cells, the method was used to estimate the net growth of rumen microorganisms. The maximal fermentation rate of subsamples, taken at the beginning and after 1 hr of incubation of a sample, was measured. The results indicate a net average growth of 8% per hr, or 192% per day, in approximate agreement with rumen turnover time. The highest net growth does not necessarily coincide with the highest gas-production rate in the rumen, in part because the bicarbonate concentration in the rumen contents varies. In a cow fed on hay and concentrate, the net growth was lowest before feeding and immediately after feeding.

Animals↗
PubMed1965

ABUNDANT MICROORGANISM IN SOIL.

The presence in soil of large numbers of a catalase-negative, microaerophilic, coccoid microorganism was demonstrated. Use of media of high nutrient value, without incorporation of inhibitors, and growth in the absence of antagonistic microorganisms were utilized to isolate this organism from soil dilutions greater than those providing growth by other means. The organism described does not grow on soil extract agars and is missed by conventional counting techniques for soil organisms. On the basis of morphological and growth characteristics, this organism appears to have at least some taxonomic relationships to the families Actinomycetaceae and Mycobacteriaceae. It is proposed that this organism makes up much of the coccoid microflora of soil as observed by light and ultraviolet fluorescence microscopy.

Actinomyces↗
PubMed1967

Lipid patterns of selected microorganisms as determined by gas-liquid chromatography.

The cellular lipid patterns of seven strains of microorganisms were examined by gas-liquid chromatography in this preliminary study. The chloroform methanol-soluble lipids were extracted by the Soxhlet method from dried cultures which had been grown at 25 +/- 2 C for 18 hr with mechanical shaking. The cellular extract was methylated by use of a low temperature sulfuric acid method, and the resulting methyl esters were chromatographed. Considerable differences in the lipid patterns among the seven microorganisms tested indicated that this method might be useful for the identification of closely related microbial genera, and possibly for species differentiation.

Alcaligenes↗
PubMed1967

Inactivation of microorganisms by electrohydraulic shock.

The electrohydraulic shock treatment of microorganisms was accomplished by discharging high-voltage electricity (8 to 15 kv) across an electrode gap below the surface of aqueous suspensions of the microorganisms. This treatment was effective in destroying Escherichia coli, Streptococcus faecalis, vegetative cells and spores of Bacillus subtilis, and bacteriophage specific for S. cremoris ML1. The presence of added protein in bacterial suspensions resulted in reduced bactericidal action. Water subjected to electrohydraulic treatment retained a certain amount of toxicity when copper-core electrodes were used to apply the treatment. This was caused by copper liberated from the electrode during electrohydraulic discharge.

Aluminum↗
PubMed1968

Roles of microorganisms in the deterioration of rockfish.

Seven species of microorganisms indigenous to fish were inoculated into sterile fish muscle, obtained from Sebastodes alutus and Sebastalobus alascanus, and the production of total volatile acids (TVA) and total volatile bases (TVB) was determined during storage at 1 C. No production of TVA and TVB was noted in sterile fish, fish inoculated with Pseudomonas type III species (PIII-985), or fish inoculated with Flavobacterium (F-1070). The inactivity of PIII-985 was due to its low maximal growth level, whereas the inactivity of F-1070 was due to its slow growth rate. Pseudomonas type I species (PI-950), Pseudomonas type II species (PII-952), and two Achromobacter (Acinetobacter) species (A-981 and A-70) grew and actively produced TVA and TVB. TVB levels increased steadily even after the microbial number reached a maximum, whereas TVA levels declined toward the end of the storage period. It appeared that a minimal microbial growth level of 10(8) cells/g was needed before detectable levels of TVA or TVB could be produced. Regardless of genera, microorganisms which grew well in fish were able to produce TVA and TVB.

Alcaligenes↗