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Attempted isolation of Nanobacterium sp. microorganisms from upper urinary tract stones.

A single team has reported isolation of nanobacteria in human and bovine blood products, as well as, more recently, kidney stones. This has raised controversy. To confirm the data, we searched for nanobacteria from 10 aseptically removed upper urinary tract (UUT) stones. We used scanning electronic microscopy (SEM) with four stones and culture of stones on either 3T6 fibroblast monolayers or liquid RPMI medium. Detection of nanobacteria was made with a commercially available monoclonal antibody, 16S ribosomal DNA amplification with specific primers, and transmission electronic microscopy (TEM) of inoculated cells. SEM showed nanoparticles in four of four UUT stones similar to those recently described. TEM of inoculated 3T6 cell monolayers has shown transient intracytoplasmic vacuolar formations containing 200- to 500-nm particles in 3 of 10 cell cultures. Gimenez staining, Hoechst staining, and specific monoclonal immunofluorescence failed to reveal nanobacteria. Finally, we could not grow Nanobacterium sp. microorganisms by the techniques described. Although with SEM, we observed nanoparticles morphologically similar to nanobacteria, we failed to isolate Nanobacterium sp. microorganisms in culture and to prove the bacterial nature of these nanoparticles in stones.

Bacteria↗

Use of 16S rRNA, 23S rRNA, and gyrB gene sequence analysis to determine phylogenetic relationships of Bacillus cereus group microorganisms.

In order to determine if variations in rRNA sequence could be used for discrimination of the members of the Bacillus cereus group, we analyzed 183 16S rRNA and 74 23S rRNA sequences for all species in the B. cereus group. We also analyzed 30 gyrB sequences for B. cereus group strains with published 16S rRNA sequences. Our findings indicated that the three most common species of the B. cereus group, B. cereus, Bacillus thuringiensis, and Bacillus mycoides, were each heterogeneous in all three gene sequences, while all analyzed strains of Bacillus anthracis were found to be homogeneous. Based on analysis of 16S and 23S rRNA sequence variations, the microorganisms within the B. cereus group were divided into seven subgroups, Anthracis, Cereus A and B, Thuringiensis A and B, and Mycoides A and B, and these seven subgroups were further organized into two distinct clusters. This classification of the B. cereus group conflicts with current taxonomic groupings, which are based on phenotypic traits. The presence of B. cereus strains in six of the seven subgroups and the presence of B. thuringiensis strains in three of the subgroups do not support the proposed unification of B. cereus and B. thuringiensis into one species. Analysis of the available phenotypic data for the strains included in this study revealed phenotypic traits that may be characteristic of several of the subgroups. Finally, our results demonstrated that rRNA and gyrB sequences may be used for discriminating B. anthracis from other microorganisms in the B. cereus group.

Bacillus cereus↗

Comparative recovery of microorganisms from BacT/ALERT plastic and glass FA and FN blood culture bottles.

bioMerieux, Inc., has recently introduced plastic bottles to replace glass bottles for use in the BacT/ALERT blood culture system. We compared the performance of the plastic to the glass bottles in a large clinical evaluation. Two blood cultures were collected from each patient, one using glass FA (aerobic) and FN (anaerobic) bottles and one using plastic FA and FN bottles. Of the 4,040 sets of four bottles collected, 3,110 contained the recommended 8 to 12 ml of blood, yielding 524 microorganisms with 359 judged to be clinically significant. Of the 359 significant organisms, 255 were recovered in either one or two bottles from both pairs of bottles in a set while 56 organisms were recovered only from the glass bottles and 48 were recovered only from the plastic bottles (P, not significant [NS]). Of the 286 significant organisms recovered only in the FA bottles (glass and plastic), 180 were recovered in both bottles, 57 in the plastic bottles only, and 49 in the glass bottles only (P, NS). Of the 303 significant organisms recovered in the FN bottles only (glass and plastic), 212 were recovered in both bottles, 46 in the plastic bottles only, and 45 in the glass bottles only (P, NS). For individual organisms, the only significant difference in recovery was obtained for Escherichia coli, with more isolates recovered in the FN plastic than in the FN glass bottles (P = 0.02). These data suggest that recovery of microorganisms with plastic FA/FN bottles is at least equal to that with glass FA/FN bottles while offering greater safety for users.

Aerobiosis↗

Participation of proteolytic enzymes in the interaction of plants with phytopathogenic microorganisms.

Different forms of participation of proteolytic enzymes in pathogenesis and plant defense are reviewed. Together with extracellular proteinases, phytopathogenic microorganisms produce specific effectors with proteolytic activity and are able to act on proteins inside the plant cell. In turn, plants use both extracellular and intracellular proteinases for defense against phytopathogenic microorganisms. Among the latter, a special role belongs to vacuolar processing enzymes (legumains), which perform the function of caspases in the plant cell.

Bacteria↗

Microorganisms in the aetiology of atherosclerosis.

Recent publications have suggested that infective pathogens might play an important role in the pathogenesis of atherosclerosis. This review focuses on these microorganisms in the process of atherosclerosis. The results of in vitro studies, animal studies, tissue studies, and serological studies will be summarised, followed by an overall conclusion concerning the strength of the association of the microorganism with the pathogenesis of atherosclerosis. The role of the bacteria Chlamydia pneumoniae and Helicobacter pylori, and the viruses human immunodeficiency virus, coxsackie B virus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus, and measles virus will be discussed.

Arteriosclerosis↗

A method for the detection and analysis of growth patterns of microorganisms in soil.

A fluorescence-staining technique using the magnesium salt of 8-anilino-1-naphthalene sulfonic acid is described and used to follow the changes in the distribution patterns of microorganisms in soils. A statistical procedure was used to determine the occurrence of significant differences in clumping of bacteria (i.e., production of colonies) in different regions of artificial soil-aggregate systems treated with nutrient solutions and also with a herbicide, Linuron. The response of soil microorganisms to glucose amendment was most marked in the aerobic, outer zone of aggregates. Linuron inhibited colony formation in aggregates treated with the herbicide. The method allows continued observations to be made on the same soil sample at intervals during incubation and os can be used to determine growth rates, inhibitory effects of chemicals, distribution patterns in soils, effects of added nutrients, and other effects where growth in situ is important.

Anilino Naphthalenesulfonates↗

Use of fluorochromes for direct observation of microorganisms associated with wheat roots.

The use of several fluorochromes and staining methods was tried out for observation of microorganisms on the surface of wheat roots sampled from soil. Good contrast between fluorescence of microorganisms and fluorescence of root and soil structures was obtained after successive staining of roots with coriphosphine (1:2000, 15 min), congo red (1:10 000, 10 min), and acridine-orange (1:10 000, 2 min).

Bacteria↗

Degradation of parathion in culture by microorganisms found in cranberry bogs.

Oxygen concentration and different carbon sources drastically altered parathion degradation in culture media inoculated with microorganisms from Wisconsin cranberry (Vaccinium macrocarpon Ait.) growing soils. These microorganisms also grew in basal salts media utilizing parathion as the sole carbon source. 14CO2 was produced only from [phenyl-14C]parathion, whereas [ethyl-14C]parathion-derived radiocarbon remained in the stale media of the soil-free cultures. Addition of 0.05% glucose to basal salts medium inhibited [phenyl-14C]parathion degradation, whereas the addition of 0.05% yeast extract to basal salts medium also inhibited microbiological degradation of the insecticide to 14CO2, but to a lesser extent. Aminoparathion and aminoparaoxon were formed only in basal salts medium with 0.05% yeast extract. Aerobic cultures produced more 14CO2 and less aminoparathion from [phenyl-14C]parathion than did anaerobic cultures. Aminoparathion was more abundant in cultures with inocula obtained from the 18- to 23-cm soil layer than with culture inocula obtained from the 0- to 5-cm soil layer under both aerobic and anaerobic conditions.

Aerobiosis↗

Physical and chemical control of released microorganisms at field sites.

An important consideration in the environmental release of a genetically engineered microorganism is the capability for reduction or elimination of microorganism populations once their function is completed or if adverse environmental effects are observed. In this study the decontamination treatments of burning and biocide application, alone and in combination with tilling, were evaluated for their ability to reduce populations of bacteria released on the phylloplane. Field plots of bush beans (Phaseolus vulgaris), sprayed with the bacterium Erwinia herbicola, received the following treatments: control; control + till; burn; burn + till; Kocide (cupric hydroxide); Kocide + till; Agri-Strep (streptomycin sulfate); and Agri-Strep + till. Leaves and soil from the plots were sampled -1, 1, 5, 8, 12, 15, 19, and 27 days after application of the decontamination treatments. Burning produced a significant reduction in the number of E. herbicola, whereas tilling, alone or in combination with the biocide treatments, stimulated a significant increase in E. herbicola populations, which persisted for several weeks. The individual treatments of the biocides, Kocide and Agri-Strep, produced a rate of decline in E. herbicola populations that did not significantly differ from that of the control treatment.

Copper↗

The second messenger cyclic 3',5'-adenosine monophosphate in pathogenic microorganisms with special reference to protozoa.

There is a growing body of information on signal transduction components in microorganisms. Elements of the cyclic 3',5'-adenosine monophosphate signaling system and molecules similar to hormones and receptors have been identified in the majority of prokaryotes and unicellular eukaryotes that have been studied. The presence of ligand- and receptor-like molecules in parasitic microorganisms raises the possibility that these molecules may interact with host communication systems. Adrenergic control of proliferation, differentiation, and infectivity has been described in the flagellate protozoan Trypanosoma cruzi, the etiological agent of Chagas' disease. Interactions between host and parasitic systems could also be antibody mediated, with antigenic cross-reactivity between components of their cAMP-dependent systems. In this review, we discuss these possibilities and summarize the existing data in this area.

Animals↗

Use of continuous culture to screen for lipase-producing microorganisms and interesterification of butter fat by lipase isolates.

The continuous cultivation technique was used to investigate the screening for lipase-producing microorganisms from four commercial starters suitable for the degradation of domestic wastes. Using this technique, three strains of lipase-producing bacteria were isolated and identified: Pantoea agglomerans (BB96CC1, BB168CC2) and Pseudomonas fluorescens (BW96CC1). In addition, butter fat induced more lipase production when present in the growth medium. Interesterification of butter fat triacylglycerols by enzymatic extracts of the isolated strains of microorganisms resulted in an appreciable interesterification yield, implying that hydrolysis was suppressed and interesterification of butter fat triacylglycerols was maximized in a microemulsion free-cosurfactant system.

Biodegradation, Environmental↗

Occurrence and identification of microorganisms in compacted clay-based buffer material designed for use in a nuclear fuel waste disposal vault.

A full-scale nuclear fuel waste disposal container experiment was carried out 240 m below ground in an underground granitic rock research laboratory in Canada. An electric heater was surrounded by buffer material composed of sand and bentonite clay and provided heat equivalent to what is anticipated in a Canadian nuclear fuel waste repository. During the experiment, the heat caused a mass transport of water and moisture content gradients developed in the buffer ranging from 13% closest to the heater to 23% at the rock wall of the deposition hole. Upon decommissioning after 2.5 years, microorganisms could be cultured from all samples having a moisture content above 15% but not from samples with a moisture content below 15%. Heterotrophic aerobic and anaerobic bacteria were found in numbers ranging from 10(1) to 10(6) cells/g dry weight buffer. Approximately 10(2), or less, sulphate-reducing bacteria and methanogens per gram of dry weight buffer were also found. Identification of buffer population members was performed using Analytical Profile Index (API) strips for isolated bacteria and 16S rRNA gene sequencing for in situ samples. A total of 79 isolates from five buffer layers were identified with API strips as representing the beta, gamma and delta groups of Proteobacteria and Gram-positive bacteria. Sixty-seven 16S rRNA clones that were obtained from three buffer layers were classified into 21 clone groups representing alpha and gamma groups of Proteobacteria, Gram-positive bacteria, and a yeast. Approximately 20% of the population comprised Gram-positive bacteria. Members of the genera Amycolatopsis, Bacillus, and Nocardia predominated. Among Gram-negative bacteria, the genera Acinetobacter and Pseudomonas predominated. Analysis of lipid biomarker signatures and in situ leucine uptake demonstrated that the buffer population was viable. The results suggest that a nuclear fuel waste buffer will be populated by active microorganisms only if the moisture content is above a value where free water is available for active life.

Aluminum Silicates↗

Designing microorganisms for the treatment of toxic wastes.

The genetic design of novel metabolic routes offers exciting possibilities for biological research and biotechnology, both in the exploration of the metabolic/evolutionary potential of cells and in the development of innovative applications. In this chapter, we review recent advances in the development of genetic tools and strategies for the design of new microorganisms for elimination of environmental pollutants. These include the design of regulated gene expression circuits that provide high levels of catalytic activity, even under environmental conditions that ordinarily repress expression of catabolic genes; the rational alteration of relevant properties of proteins that qualitatively or quantitatively restrict catabolic activities; the judicious assembly of gene blocks encoding selected metabolic modules to create novel metabolic routes and combinations of routes; and the design of microorganisms exhibiting properties that contribute to better process development.

Bacteria↗

Towards a unified evolutionary genetics of microorganisms.

I propose here that evolutionary genetics, apart from improving our basic knowledge of the taxonomy and evolution of microbes (either eukaryotes or prokaryotes), can also greatly contribute to applied research in microbiology. Evolutionary genetics provides convenient guidelines for better interpreting genetic and molecular data dealing with microorganisms. The three main potential applications of evolutionary genetics in microbiology are (a) epidemiological follow-up (with the necessity of evaluating the stability of microbial genotypes over space and time); (b) taxonomy in the broad sense (better definition and sharper delimitation of presently described taxa, research of hidden genetic subdivisions); and (c) evaluation of the impact of the genetic diversity of microbes on their relevant properties (pathogenicity, resistance to drugs, etc). At present, two main kinds of population structure can be distinguished in natural microbial populations: (a) species that are not subdivided into discrete phylogenetic lineages (panmictic species or basically sexual species with occasional bouts of short-term clonality fall into this category); (b) species that are strongly subdivided by either cryptic speciation or clonal evolution. Improvements in available statistical methods are required to refine these distinctions and to better quantify the actual impact of gene exchange in natural microbial populations. Moreover, a codified selection of markers with appropriate molecular clocks (in other words: adapted levels of resolution) is sorely needed to answer distinct questions that address different scales of time and space: experimental, epidemic, and evolutionary. The problems raised by natural genetic diversity are very similar for all microbial species, in terms of both basic and applied science. Despite this fact, a regrettable compartmentalization among specialists has hampered progress in this field. I propose a synthetic approach, relying on the statistical improvements and technical standardizations called for above, to settle a unified evolutionary genetics of microorganisms, valid whatever the species studied, whether eukaryotic (parasitic protozoa and fungi) or prokaryotic (bacteria). Apart from benefits for basic evolutionary research, the anticipated payoff from this synthetic approach is to render routine and common-place the use of microbial evolutionary genetics in the fields of epidemiology, medicine, and agronomy.

Animals↗

The Ecology and Biogeography of Microorganisms on Plant Surfaces.

The vast surface of the plant axis, stretching from root tips occasionally buried deeply in anoxic sediment, to apical meristems held far aloft, provides an extraordinarily diverse habitat for microorganisms. Each zone has to a greater or lesser extent its own cohort of microorganisms, in aggregate comprising representatives from all three primary domains of life-Bacteria, Archaea, and Eucarya. While the plant sets the stage for its microbial inhabitants, they, in turn, have established varied relationships with their large partner. These associations range from relatively inconsequential (transient epiphytic saprophytes) to substantial (epiphytic commensals, mutualistic symbionts, endophytes, or pathogens). Through recent technological breakthroughs, a much better perspective is beginning to emerge on the nature of these relationships, but still relatively little is known about the role of epiphytic microbial associations in the life of the plant.

ecophysiology↗

Netilmicin: in vitro activity, time-kill evaluation and postantibiotic effect on microorganisms isolated from ocular infections.

The in vitro activity of netilmicin and other antibiotics against ocular gram-positive and gram-negative microorganisms was evaluated. Netilmicin showed excellent activity against all the tested microorganisms, with more than 90% susceptibility. Many gentamicin- and tobramycin-resistant strains were still susceptible to netilmicin, although the minimum inhibitory concentration values of netilmicin were higher than those for the fully susceptible strains. In time-kill studies, netilmicin showed bactericidal activity within 1 h against Pseudomonas aeruginosa and Staphylococcus aureus. Moreover, netilmicin showed a postantibiotic effect of 2.4 h against P. aeruginosa and 1.5 h against S. aureus. These values were longer than those showed by ofloxacin, i.e. 2.1 and 1.4 h, respectively.

Eye Infections, Bacterial↗

Suppression of caries-related microorganisms in dentine lesions after short-term chlorhexidine or antibiotic treatment.

This study investigated the efficiency of a chlorhexidine varnish and an antibiotic paste in suppressing the cultivable microflora of deep dentine cavities in a stepwise excavation procedure. Subsequent to enamel preparation and removal of the central biomass, infected dentine was sampled from the cavity floor. Ten cavities each were either covered with the 1% chlorhexidine- and 1% thymol-containing varnish Cervitec (CE), the demeclocycline hydrocortisone-containing ointment Ledermix (LE) or received no treatment as control (CO). A compomer composite was used as intermediate restorative. Cavities were reassessed after 6 weeks and again dentine samples were microbiologically investigated for total viable counts, mutans streptococci and lactobacilli. After 6 weeks a significant reduction of the total viable counts was observed in the LE group (p = 0.011) compared to the control, whereas no differences were found in the CE group (p > 0.05). Mutans streptococci were rarely recovered at baseline and after 6 weeks. Compared to the CO group counts of lactobacilli were significantly reduced in the CE and LE groups (p < 0.05). Lactobacillus species were frequently recovered at baseline and after 6 weeks of observation. Lactobacillus rhamnosus was the predominant species in all samples investigated. Application of CE or LE resulted in reduced counts of lactobacilli after a period of 6 weeks. Although none of the materials completely eliminated the viable microorganisms, the use of LE was more effective than CE in reducing the total anaerobic microorganisms associated with carious dentine.

Actinomyces↗

Molecular effects of povidone-iodine on relevant microorganisms: an electron-microscopic and biochemical study.

The aim of this study was to elucidate the effects of povidone-iodine (PVP-I) on cell ultrastructure by electron microscopy and to monitor changes in enzyme activity and nucleotide efflux. Staphylococcus aureus, Escherichia coli and Candida albicans, medically relevant gram-positive, gram-negative and yeast microorganisms, served as models. In the presence of PVP-I, rapid partitioning of the cytoplasm and pronounced coagulation of nuclear material was noted. E. coli and S. aureus showed no major structural wall damage. C. albicans exhibited a rapid, dose-dependent 'loosening' of the cell wall; cells remained intact without lysis, rupture or wall breakage. Changes in beta-galactosidase and nucleotide concentrations were measured in E. coli. A rapid and dose-dependent loss of cellular beta-galactosidase activity was found, with no increase in the supernatant; loss of cellular nucleotides corresponded with an increase in the supernatant. Electron-microscopic and biochemical observations support the conclusion that PVP-I interacts with cell walls of microorganisms causing pore formation or generating solid-liquid interfaces at the lipid membrane level which lead to loss of cytosol material, in addition to enzyme denaturation.

Anti-Infective Agents, Local↗