Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “MICROORGANISMS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 901 records · Page 50Linked to original sources
PubMed2004

Perchlorate-reducing microorganisms isolated from contaminated sites.

An extensive microcosm survey of perchlorate-contaminated sites was undertaken to assess the ability of indigenous microorganisms to degrade perchlorate. Samples from 12 contaminated sites and from one pristine location were analysed. Perchlorate was degraded to below detection limit in all electron donor-amended microcosms. Perchlorate-reducing microorganisms (PRMs) were numerous at most of these sites. Sixteen distinct PRMs were isolated that were phylogenetically related to either Dechloromonas in the Beta Proteobacteria (9/16 isolates) or to Azospirillum in the Alpha Proteobacteria (7/16 isolates). The majority of previously isolated PRMs are in the Beta Proteobacteria related to Dechloromonas or Dechlorosoma. This study indicates that PRMs of the genus Azospirillum may be more prevalent at contaminated sites than the current record of isolates suggests. Cell yields, electron donor to perchlorate ratios and maximum specific growth rates were similar among the isolates and similar to the few previously published values. However, the Monod half-saturation constants for perchlorate for the two Azospirillum isolates characterized were lower than those measured for other genera, suggesting that they may be more effective at low concentrations of perchlorate. These results extend the current understanding of PRMs from diverse environments and provide added confidence that microbial perchlorate reduction is ubiquitous, even at highly contaminated sites, and can be harnessed effectively for bioremediation.

Azospirillum↗
PubMed2004

The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms.

Summary In the post-genomic era, the focus of numerous researchers has moved to studying the functional products of gene expression. In microbiology, these "omic" approaches have largely been limited to pure cultures of microorganisms. Consequently, they do not provide information on gene expression in a complex mixture of microorganisms as found in the environment. Our method enabled the successful extraction and purification of the entire proteome from a laboratory-scale activated sludge system optimized for enhanced biological phosphorus removal, its separation by two-dimensional polyacrylamide gel electrophoresis and the mapping of this metaproteome. Highly expressed protein spots were excised and identified using quadrupole time-of-flight mass spectrometry with de novo peptide sequencing. The proteins isolated were putatively identified as an outer membrane protein (porin), an acetyl coenzyme A acetyltransferase and a protein component of an ABC-type branched-chain amino acid transport system. These proteins possibly stem from the dominant and uncultured Rhodocyclus-type polyphosphate-accumulating organism in the activated sludge. We propose the term "metaproteomics" for the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time.

Acetyl-CoA C-Acyltransferase↗
PubMed2006

Perception and modification of plant flavonoid signals by rhizosphere microorganisms.

Flavonoids are a diverse class of polyphenolic compounds that are produced as a result of plant secondary metabolism. They are known to play a multifunctional role in rhizospheric plant-microbe and plant-plant communication. Most familiar is their function as a signal in initiation of the legume-rhizobia symbiosis, but, flavonoids may also be signals in the establishment of arbuscular mycorrhizal symbiosis and are known agents in plant defence and in allelopathic interactions. Flavonoid perception by, and impact on, their microbial targets (e.g. rhizobia, plant pathogens) is relatively well characterized. However, potential impacts on 'non-target' rhizosphere inhabitants ('non-target' is used to distinguish those microorganisms not conventionally known as targets) have not been thoroughly investigated. Thus, this review first summarizes the conventional roles of flavonoids as nod gene inducers, phytoalexins and allelochemicals before exploring questions concerning 'non-target' impacts. We hypothesize that flavonoids act to shape rhizosphere microbial community structure because they represent a potential source of carbon and toxicity and that they impact on rhizosphere function, for example, by accelerating the biodegradation of xenobiotics. We also examine the reverse question, 'how do rhizosphere microbial communities impact on flavonoid signals?' The presence of microorganisms undoubtedly influences the quality and quantity of flavonoids present in the rhizosphere, both through modification of root exudation patterns and microbial catabolism of exudates. Microbial alteration and attenuation of flavonoid signals may have ecological consequences for below-ground plant-microbe and plant-plant interaction. We have a lack of knowledge concerning the composition, concentration and bioavailability of flavonoids actually experienced by microbes in an intact rhizosphere, but this may be addressed through advances in microspectroscopic and biosensor techniques. Through the use of plant mutants defective in flavonoid biosynthesis, we may also start to address the question of the significance of flavonoids in shaping rhizosphere community structure and function.

Biosensing Techniques↗
PubMed2006

Growth kinetics of microorganisms isolated from Alaskan soil and permafrost in solid media frozen down to -35 degrees C.

We developed a procedure to culture microorganisms below freezing point on solid media (cellulose powder or plastic film) with ethanol as the sole carbon source without using artificial antifreezes. Enrichment from soil and permafrost obtained on such frozen solid media contained mainly fungi, and further purification resulted in isolation of basidiomycetous yeasts of the genera Mrakia and Leucosporidium as well as ascomycetous fungi of the genus Geomyces. Contrary to solid frozen media, the enrichment of liquid nutrient solutions at 0 degrees C or supercooled solutions stabilized by glycerol at -1 to -5 degrees C led to the isolation of bacteria representing the genera Polaromonas, Pseudomonas and Arthrobacter. The growth of fungi on ethanol-microcrystalline cellulose media at -8 degrees C was exponential with generation times of 4.6-34 days, while bacteria displayed a linear or progressively declining curvilinear dynamic. At -17 to -0 degrees C the growth of isolates and entire soil community on 14C-ethanol was continuous and characterized by yields of 0.27-0.52 g cell C (g of C-substrate)(-1), similar to growth above the freezing point. The 'state of maintenance,' implying measurable catabolic activity of non-growing cells, was not confirmed. Below -18 to -35 degrees C, the isolated organisms were able to grow only transiently for 3 weeks after cooling with measurable respiratory and biosynthetic (14CO2 uptake) activity. Then metabolic activity declined to zero, and microorganisms entered a state of reversible dormancy.

Alaska↗
PubMed1995

Evidence that the novel microorganism 'Z' may belong to a new genus in the family Chlamydiaceae.

The purpose of this study was to investigate possible phylogenetic relationships of a new microorganism called 'Z'. The organism was previously shown to be similar to chlamydia in its growth cycle and some of its metabolic requirements, but different in others and in its major outer membrane protein. In this study we report the sequencing of 'Z"s 16S ribosomal DNA and comparison of the sequence with that of other microorganisms, including chlamydia and rickettsiae. While chlamydial species have 95.5% sequence identity among themselves, 'Z' had 83% identity with them, and 73% identity with certain rickettsia-like organisms. Based on the sequence analyses and taking into account physiologic considerations, we believe that 'Z' may belong to a novel genus in the family Chlamydiaceae.

Base Sequence↗
PubMed1993

Ribonucleotide reductases and their occurrence in microorganisms: a link to the RNA/DNA transition.

The evolution of a deoxyribonucleotide synthesizing ribonucleotide reductase might have initiated the transition from the ancient RNA world into the prevailing DNA world. At least five classes of ribonucleotide reductases have evolved. The ancient enzyme has not been identified. A reconstruction of the first ribonucleotide reductase requires knowledge of contemporary enzymes and of microbial evolution. Experimental work on the former focuses on few organisms, whereas the latter is now well understood on the basis of ribosomal RNA sequences. Deoxyribonucleotide formation has not been investigated in many evolutionary important microorganisms. This review covers our knowledge on deoxyribonucleotide synthesis in microorganisms and the distribution of ribonucleotide reductases in nature. Ecological constraints on enzyme evolution and knowledge deficiencies emerge from complete coverage of the phylogenetic groups.

Animals↗
PubMed1997

Microorganisms as tracers in groundwater injection and recovery experiments: a review.

Modern day injection and recovery techniques designed to examine the transport behavior of microorganisms in groundwater have evolved from experiments conducted in the late 1800s, in which bacteria that form red or yellow pigments were used to trace flow paths through karst and fractured-rock aquifers. A number of subsequent groundwater hydrology studies employed bacteriophage that can be injected into aquifers at very high concentrations (e.g., 10(13) phage ml-1) and monitored through many log units of dilution to follow groundwater flow paths for great distances, particularly in karst terrain. Starting in the 1930s, microbial indicators of fecal contamination (particularly coliform bacteria and their coliphages) were employed as tracers to determine potential migration of pathogens in groundwater. Several injection and recovery experiments performed in the 1990s employed indigenous groundwater microorganisms (both cultured and uncultured) that are better able to survive under in situ conditions. Better methods for labeling native bacteria (e.g. by stable isotope labeling or inserting genetic markers, such as the ability to cause ice nucleation) are being developed that will not compromise the organisms' viability during the experimental time course.

Enterobacteriaceae↗
PubMed2001

Interactions of chromium with microorganisms and plants.

Chromium is a highly toxic non-essential metal for microorganisms and plants. Due to its widespread industrial use, chromium (Cr) has become a serious pollutant in diverse environmental settings. The hexavalent form of the metal, Cr(VI), is considered a more toxic species than the relatively innocuous and less mobile Cr(III) form. The presence of Cr in the environment has selected microbial and plant variants able to tolerate high levels of Cr compounds. The diverse Cr-resistance mechanisms displayed by microorganisms, and probably by plants, include biosorption, diminished accumulation, precipitation, reduction of Cr(VI) to Cr(III), and chromate efflux. Some of these systems have been proposed as potential biotechnological tools for the bioremediation of Cr pollution. In this review we summarize the interactions of bacteria, algae, fungi and plants with Cr and its compounds.

Amino Acid Sequence↗
PubMed1994

Microorganisms in polytetrafluoroethylene barrier membranes for guided tissue regeneration.

This study examined the microflora in 11 barrier membranes around teeth with furcation involvement or 2 to 3 wall intrabony defects and in 16 membranes around implants with various types of bony defects. Total viable counts and the occurrence of selected microbial species were determined by non-selective and selective culture and by DNA probes. Study sites were examined for probing pocket depth and attachment level. All tooth-associated membranes yielded high levels of microorganisms. 4 of 5 teeth with membranes harboring less than 10(8) organisms gained 3 mm or more in probing attachment, whereas 6 teeth with membranes with more than 10(8) organisms exhibited loss or only small gains in attachment. 3 membranes with high levels of black-pigmented anaerobic rods lost 1 to 2 mm of attachment. Ten implant-associated membranes with no cultivable microorganisms demonstrated a mean probing gain of 4.9 mm. 6 implants with infected membranes only gained an average of 2.0 mm of supportive bone. The present findings underscore the importance of controlling or eliminating periodontal pathogens on barrier membranes in order to gain new attachment.

Adult↗
PubMed1985

Host responses to bacteria and bacterial products in periodontal disease: immunosuppressive effects of periodontitis-related microorganisms?

Several recent investigations indicate that some patients with adult periodontitis have lowered serum antibody levels or reduced lymphoproliferative responses to certain periodontitis-related microorganisms. Many such patients tend to show increased responses after therapy. Some suggested mechanisms of such responses are reviewed and the possible significance of immunosuppressive effects of periodontitis-related microorganisms are briefly discussed.

Adult↗
PubMed1990

Salivary conditions and cariogenic microorganisms in 55, 65, and 75-year-old Swedish individuals.

Secretion rate, buffer capacity, and cariogenic microorganisms of resting and stimulated whole saliva were examined in 208 55-, 65-, and 75-yr-old Swedes. The secretion rate for both resting and stimulated saliva decreased with age. When the use of drugs was taken into account the difference in terms of age group was significant for resting saliva alone (P less than 0.01). In 22% the resting saliva was less than 0.1 ml/min, and in 5% the stimulated saliva was less than 0.7 ml/min. Persons with subjective dryness in the mouth had a lower salivary flow. Men had higher secretion rates than women irrespective of medication (P less than 0.05). The buffer capacity was strongly correlated to the secretion rate of both resting and stimulated saliva (r = 0.39 and r = 0.44, respectively). The number of mutans streptococci and lactobacilli increased with age, although significant in terms of age group for lactobacilli alone (P less than 0.05). The number of these microorganisms was lower in resting saliva than in stimulated saliva (P less than 0.0001). Individuals harboring both Streptococcus mutans and Streptococcus sobrinus had higher values of mutans streptococci in resting and stimulated saliva than those harboring only S. mutans (P less than 0.001). Actinomyces viscosus and Actinomyces naeslundii comprised greater than or equal to 1% of the total CFU in 89% of the plaque samples. The corresponding figures for lactobacilli and mutans streptococci were 6% and 38%, respectively.

Actinomyces↗
PubMedDate not supplied

Electrophoresis of whole-cell soluble proteins of microorganisms isolated from bacteremias in endodontic therapy.

We have previously demonstrated that anaerobic bacteria are the microorganisms most frequently isolated from blood following endodontic therapy of teeth with apical periodontitis. Phenotypic characterisation of the isolates suggested that the bacteria in the blood originated from the root canal. The present experiment using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was carried out in an effort to verify these findings, and to further study the microorganisms involved in endodontic bacteremias. Soluble cellular proteins were extracted from 11 reference strains and 26 bacterial isolates recovered from the root canal and blood. These included Propionibacterium acnes, Peptostreptococcus prevotii, Fusobacterium nucleatum, Prevotella intermedia. Actinomyces israelii, Streptococcus intermedius, Streptococcus sanguis. The electrophoretic patterns mostly confirmed the identity of the isolates as determined by the biochemical and antimicrobial resistance tests. Furthermore, with this typing method the species Prevotella intermedia and Prevotella nigrescens could be differentiated. These species had been recovered from both root canal and blood. Also, differences between subspecies of Fusobacterium nucleatum became evident with SDS-PAGE, and the results indicated that the organism recovered from the root canal and blood was Fusobacterium nucleatum subsp. vincentii. The electrophoretic patterns of the different organisms isolated from the root canal and the blood were similar, providing further evidence that the bacteria found in the blood originated from the root canal.

Bacteremia↗
PubMed1997

Vital microorganisms in early supragingival dental plaque and in stimulated human saliva.

The aim of this study was to compare the percentage of vital microorganisms (= microbial vitality) of saliva with that of supragingival plaque both collected at various times during the early phases of de novo plaque formation. Between intervals of optimal oral hygiene, 14 healthy participants refrained from all oral hygiene measures for periods of 1, 4, 8 and 72 h. Stimulated whole saliva was collected at the beginning (= baseline) and the end of each period. Vestibular plaque was removed from teeth 13-16, and 23-26. Analysis of the pooled plaque (p) and saliva (s) samples comprised the total number of bacterial counts and colony-forming units to estimate the percentage of viable microorganisms (PEp; PEs). The microbial vitality (VFp; VFs) was determined by using a fluorescence staining to differentiate vital from dead bacterial cells. The bulk of the PEs values reached 5-30%. At baseline VFs ranged between 70% and 90%. The VFs values recorded at baseline or in the presence of 1 h and 4 h-old plaque, were significantly (alpha = 0.05) higher than the corresponding VFp values ranging from 5% to 30%. It was concluded that there is a considerable discrepancy between the microbial vitality of a very early dental plaque and that of whole surrounding saliva sampled at the same time. Unfavourable local environmental conditions prevailing at cervical tooth surfaces are suggested to restrain the survival of the majority of the first bacteria adhering to a particular tooth area during the early phases of supragingival plaque formation.

Adult↗
PubMed1997

Evidence for genetic control of changes in f-actin polymerization caused by pathogenic microorganisms: in vitro assessment using gingival fibroblasts from human twins.

Attachment to and migration upon a substratum, as well as other functions of connective tissue cells, are regulated mainly by cytoplasmic structural proteins, particularly filamentous actin (f-actin). Pathogenic microorganisms exert negative effects on cytoskeletal proteins. In the present study, normal gingival fibroblasts from 10 sets of human twins (6 fraternal, DZ; 4 identical, MZ) were exposed to soluble extracts from Porphyromonas gingivalis or Fusobacterium nucleatum, then f-actin was stained using FITC-labeled phalloidin. Cells were examined under fluorescence, and a computer-assisted image analyzer quantitated f-actin polymerization as fluorescence intensity on a per-cell basis. Intraclass correlation coefficients for f-actin in MZ/MZ vis-a-vis DZ/DZ paired cell cultures were determined to assess the possible heritability of responses to the microorganism preparations. F-actin labeling was significantly different between control cultures and those exposed to the extracts. Both F. nucleatum and P. gingivalis effected f-actin and fibroblast morphology. When the data were adjusted for gender and age effects, and for differences in control f-actin levels, fibroblasts from MZ twin pairs were moderately similar in both absolute and relative responses to bacterial challenges; cells from DZ twins showed little similarity when response was measured on the absolute scale, and moderate similarity using the relative scale.

Actins↗
PubMed1999

Antigen activation of THP-1 human monocytic cells after stimulation with lipopolysaccharide from oral microorganisms and granulocyte-macrophage colony-stimulating factor.

A human THP-1 monocyte cell line culture system has been utilized to evaluate the morphological changes in THP-1 cells and to measure expression of activation antigens (CD-11b, CD-11c, CD-14, CD-35, CD-68, CD-71 and HLA-DR) as evidence of maturation of THP-1 cells in response to stimulation by lipopolysaccharide (LPS) from the oral microorganisms, Fusobacterium nucleatum and Porphyromonas gingivalis, and granulocyte-macrophage colony-stimulating factor. THP-1 cells were stimulated with LPS (1 microgram/ml) of P. gingivalis or F. nucleatum for different time periods (1, 2, 4 and 7 d). Detection of different activation antigens on THP-1 cells was performed by indirect immunohistochemical staining followed by light microscopy. Confirmational studies were performed in parallel using indirect immunofluorescence and immunogold electron microscopy for detection of the corresponding activation antigens. Expression of different activation antigens by resting THP-1 cells revealed HLA-DR to be on 3% of the cells; CD-11b, 9%; CD-11c, 8%; CD-14, 22%; CD-35, 9% and CD-68, 7%. The CD-71 activation antigen was not expressed in untreated THP-1 cells. LPS stimulation increased expression of all activation antigens. A significant (p < 0.05) increase in expression of CD-11b, CD-11c, CD-14, CD-35, CD-68 and CD-71 was observed when GM-CSF (50 IU/ml) was supplemented during the treatment of THP-1 cells with LPS of F. nucleatum or P. gingivalis. Activation and differentiation of THP-1 cells by LPS from oral microorganisms in the presence of GM-CSF supports a role for human macrophages in acute and chronic periodontal diseases and may explain the clinically observable periodontal exacerbations in some patients after GM-CSF therapy.

Antigens, CD↗
PubMed2002

Electrode-reducing microorganisms that harvest energy from marine sediments.

Energy in the form of electricity can be harvested from marine sediments by placing a graphite electrode (the anode) in the anoxic zone and connecting it to a graphite cathode in the overlying aerobic water. We report a specific enrichment of microorganisms of the family Geobacteraceae on energy-harvesting anodes, and we show that these microorganisms can conserve energy to support their growth by oxidizing organic compounds with an electrode serving as the sole electron acceptor. This finding not only provides a method for extracting energy from organic matter, but also suggests a strategy for promoting the bioremediation of organic contaminants in subsurface environments.

Aerobiosis↗
PubMed1961

Effect of ultrahigh vacuum on viability of microorganisms.

Three species of resistant microorganisms were exposed for 5 days to an ultrahigh vacuum approaching that of interplanetary space. Since no lethal effect was observed, there is no indication that the vacuum of outer space would prevent transport of viable microorganisms on unsterilized space vehicles.

Atmospheric Pressure↗
PubMed1967

Stereoscan electron microscopy of soil microorganisms.

Details of the surface structure of microorganisms growing in soil and the complex topography of individual soil particles were observed with the Stereoscan electron microscope. Because it was not necessary to remove the microorganisms from the soil particles, it was possible to establish their occurrence in different microhabitats. This technique can provide useful ecological information about the soil microflora.

Ecology↗