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PubMed2004

Construction of bacterial artificial chromosome library from electrochemical microorganisms.

A microbial fuel cell is a device that directly converts metabolic energy into electricity, using electrochemical technology. The analysis of large genome fragments recovered directly from microbial communities represents one promising approach to characterizing uncultivated electrochemical microorganisms. To further assess the utility of this approach, we constructed large-insert (140 kb) bacterial artificial chromosome (BAC) libraries from the genomic DNA of a microbial fuel cell, which had been operated for three weeks using acetate media. We screened the expression of several ferric reductase activities in the Escherichia coli host, in order to determine the extent of heterologous expression of metal-ion-reducing enzymes in the library. Phylogenetic analysis of 16S rRNA gene sequences recovered from the BAC libraries indicates that they contain DNA from a wide diversity of microbial organisms. The constructed bacterial library proved a powerful tool for exploring metal-ion reductase activities, providing information on the electron transport pathway of electrochemical microbial (ECM) organisms.

Bacteria↗
PubMed2005

Polymerase chain reaction for identification of aldoxime dehydratase in aldoxime- or nitrile-degrading microorganisms.

We developed a molecular screening procedure using Southern hybridization and polymerase chain reaction (PCR) to identify aldoxime dehydratase (Oxd) encoding genes (oxds) among 14 aldoxime- or nitrile-degrading microorganisms. When an oxd gene of Rhodococcus erythropolis N-771 was used as a probe, positive hybridization signals were seen with the chromosomal DNA of eight strains, suggesting that these strains have similar oxd genes to R. erythoropolis N-771. By analyzing the PCR-amplified fragments with degenerate consensus primers, the occurrence of homologous Oxd coexisting with Fe-containing NHase in the active eight strains was demonstrated coinciding with the results of Southern hybridization. Whole length of oxd gene was cloned as an example from one of the positive strains, Pseudomonas sp. K-9, sequenced, and expressed in E. coli. Analysis of the primary structure of the protein (OxdK) encoded by the oxd gene of Pseudomonas sp. K-9 led to identify an Oxd having a new primary structure. Thus, the PCR-based analysis of oxd gene is a useful tool to detect and analyze the "aldoxime-nitrile pathway" in nature, since Oxd is the key enzyme for the pathway.

Amino Acid Sequence↗
PubMed2004

A quasi-chemical model for the growth and death of microorganisms in foods by non-thermal and high-pressure processing.

Predictive microbial models generally rely on the growth of bacteria in laboratory broth to approximate the microbial growth kinetics expected to take place in actual foods under identical environmental conditions. Sigmoidal functions such as the Gompertz or logistics equation accurately model the typical microbial growth curve from the lag to the stationary phase and provide the mathematical basis for estimating parameters such as the maximum growth rate (MGR). Stationary phase data can begin to show a decline and make it difficult to discern which data to include in the analysis of the growth curve, a factor that influences the calculated values of the growth parameters. In contradistinction, the quasi-chemical kinetics model provides additional capabilities in microbial modelling and fits growth-death kinetics (all four phases of the microbial lifecycle continuously) for a general set of microorganisms in a variety of actual food substrates. The quasi-chemical model is differential equations (ODEs) that derives from a hypothetical four-step chemical mechanism involving an antagonistic metabolite (quorum sensing) and successfully fits the kinetics of pathogens (Staphylococcus aureus, Escherichia coli and Listeria monocytogenes) in various foods (bread, turkey meat, ham and cheese) as functions of different hurdles (a(w), pH, temperature and anti-microbial lactate). The calculated value of the MGR depends on whether growth-death data or only growth data are used in the fitting procedure. The quasi-chemical kinetics model is also exploited for use with the novel food processing technology of high-pressure processing. The high-pressure inactivation kinetics of E. coli are explored in a model food system over the pressure (P) range of 207-345 MPa (30,000-50,000 psi) and the temperature (T) range of 30-50 degrees C. In relatively low combinations of P and T, the inactivation curves are non-linear and exhibit a shoulder prior to a more rapid rate of microbial destruction. In the higher P, T regime, the inactivation plots tend to be linear. In all cases, the quasi-chemical model successfully fit the linear and curvi-linear inactivation plots for E. coli in model food systems. The experimental data and the quasi-chemical mathematical model described herein are candidates for inclusion in ComBase, the developing database that combines data and models from the USDA Pathogen Modeling Program and the UK Food MicroModel.

Bacteria↗
PubMed2006

The efficacy of electrolysed oxidising water for inactivating spoilage microorganisms in process water and on minimally processed vegetables.

The efficacy of Electrolysed Oxidising Water (EOW) for inactivating spoilage microorganisms in process water and on minimally processed vegetables was investigated. The direct effect of EOW on three important spoilage bacteria namely; Pseudomonas fluorescens, Pantoea agglomerans or Rahnella aquatilis was determined by inoculating tap water or "artificial process water" with approximately 8 log CFU/ml pure culture and electrolysing the resultant solutions. The three bacteria were each reduced to undetectable levels at low (0.5 A) and relatively higher levels (1.0 A) of current in tap water and "artificial process water", respectively. The residual effect of EOW on P. fluorescens, P. agglomerans or R. aquatilis was determined by incubating at room temperature 1 ml (approximately 9 log CFU/ml) pure culture suspensions in 9 ml of EOW-T (EOW produced from tap water), EOW-A (EOW produced from "artificial process water" supplemented with approximately 60.7 mg Cl(-)/l and 39.3 mg Na(+)/l) or deionised water (control) for 0, 15, 45 or 90 min. The bactericidal activity of both EOW-T and EOW-A increased with the concentration of free oxidants and incubation period and the three bacteria were completely reduced at free oxidants-incubation period combinations of 3.88 mg/l-45 min and 5.1 mg/l-90 min in EOW-T and EOW-A, respectively. Two types of industrial vegetable process water; salad-mix and soup process water, which had each a total psychrotrophic count of approximately 8 log CFU/ml were then electrolysed. Without any NaCl addition, only 1.2 and 2.1 log reductions of the psychrotrophs in soup and salad-mix process water was attained respectively. Supplementation of the process water with approximately 60.7 mg Cl(-)/l and 39.3 mg Na(+)/l afterwards resulted in complete reduction of the psychrotrophic count in both process waters, but soup process water required relatively higher levels of current compared to salad-mix water. Finally, fresh-cut lettuce was washed in EOW-T containing 3.62 mg free oxidants/l, EOW-IP (EOW produced from industrial process water) containing 2.8 mg free oxidants/l or tap water (control) for 1 or 5 min. Washing the vegetables for 1 min in EOW-T resulted in 1.9, 1.2, and 1.3 log reductions of psychrotrophs, lactic acid bacteria and Enterobacteriacae, respectively, which increased to 3.3, 2.6, and 1.9 log reductions after washing for 5 min instead. EOW-IP tested in this work had no bactericidal effect on the microflora of fresh-cut lettuce. Electrolysis could therefore be used to decontaminate process water for vegetable pre-washing and to sanitise tap water for final rinsing of vegetables, respectively.

Colony Count, Microbial↗
PubMed2004

ATPS applied to extraction of small molecules - polycetides - and simultaneous clarification of culture media with filamentous microorganisms.

Aqueous two-phase systems (ATPS) were applied for extraction of small molecules (polycetides) - retamycin, an anthracyclin, and two red pigments, rubropunctamin and monascorubramin - from the whole culture media of Streptomyces olindensis and Monascus purpureus. ATPS allows, in one step, the separation of the small hydrophobic molecules in the PEG rich phase, from the filamentous microorganisms, which remains in the salt phase. Through experimental designs, the main variables and their levels were defined, as follows: for retamycin extraction, PEG 6000 (10%, w/w), phosphate at 20% (w/w) and pH 6.0 led to the higher partition coefficient, K(r) = 8.2, and yield = 91.3%; for red pigments, the statistical analysis indicate PEG 6000 (20%, w/w) and phosphate at 15% (w/w), for a high partition coefficient, (K(pig) = 113 and 150).

Anthracyclines↗
PubMed2006

Evaluation of the in-situ aerobic cometabolism of chlorinated ethenes by toluene-utilizing microorganisms using push-pull tests.

A series of transport, biostimulation, and activity push-pull tests were performed under induced and natural gradient conditions in a trichloroethene (TCE) and cis-dichloroethene (c-DCE) contaminated aquifer. Transport tests demonstrated the feasibility of injecting and recovering complex solute mixtures from the aquifer. During the biostimulation tests, decreases in toluene concentration and the production of o-cresol as an intermediate oxidation product indicated the presence of toluene-utilizing microorganisms. Activity tests demonstrated that the stimulated microbial community had the ability to transform injected c-DCE and trans-dichloroethene (t-DCE) at similar zero-order rates. Injected isobutene was oxidized to isobutene oxide, which indicated that a toluene ortho-monooxygenase enzyme system was likely responsible for the observed c-DCE and t-DCE transformations. c-DCE zero-order transformation rates in drift push-pull tests were similar to those obtained from traditional push-pull tests (about 0.1 microM/h). Analysis of drift test data using first-order kinetic analysis resulted in similar conclusions as those obtained using zero-order kinetic analyses. When 1-butyne, an inhibitor of toluene ortho-monooxygenase, was added to injected test solutions, the oxidation of toluene, and the transformation of isobutene, c-DCE, and t-DCE were inhibited. The results illustrate how a series of push-pull tests can be used in combination to detect, quantify and confirm in-situ cometabolic microbial transformations.

Aerobiosis↗
PubMed2006

Effect of acclimatization of microorganisms to heavy metals on the performance of activated sludge process.

Although selected heavy metals (HMs) stimulate biological reactions at low concentrations, all HMs are toxic to microorganisms (MOs) at moderate concentrations and can cause inhibitory effects on the biological processes. Therefore, MOs must be acclimated to HMs or other toxic substances present in wastewaters (WWs) before they are used in an activated sludge process (ASP). In this study, combined effect of Cu(2+) and Zn(2+) ions in a synthetic WW on the efficiency of a laboratory-scale ASP without recycle was investigated using acclimated MOs at different extents.A synthetic feed solution of 1222 mg L(-1) proteose-peptone (corresponding to 1300 mg COD L(-1)) served as a source of carbon. Cu(2+) and Zn(2+) ions at different concentrations (1.5, 4.5 and 9, 27 mg L(-1), respectively) were introduced in the feed to a continuously stirred activated sludge reactor at different hydraulic residence times (2-40 h) keeping pH, temperature and stock feed composition constant. The combined effects of copper and zinc ions were determined by mixing these metallic ions at the specified combinations of concentrations such as "1.5 mg L(-1) of Cu(2+)+9 mg L(-1) of Zn(2+)" and "4.5 mg L(-1) of Cu(2+)+27 mg L(-1) of Zn(2+)". It was observed that using seed MOs acclimatized to two times of the combined threshold concentration of these HMs for an unduly long period of time (1-4 months) caused adverse effects on the ASP performance. Besides, it was found that usual inhibition effects of these HMs were enhanced with increasing period of acclimation. Substantially lower substrate removal efficiencies were obtained with acclimatized MOs than those obtained with non-acclimatized MOs. At the higher initial substrate concentration of 2500 mg COD L(-1), substrate-inhibition occurred causing a decrease in the specific growth rate constant (k); however, HM inhibition was suppressed, resulting to about 20% increase in treatment efficiency of the ASP. It can be concluded that the time period necessary for acclimatization of seed MOs must be adjusted carefully with concentrations of HMs lower than their threshold concentrations to achieve an optimal operation of an aerobic biological process.

Adaptation, Physiological↗
PubMed2004

A Malthusian curb on spatial structure in microorganism populations.

That all organisms are born in the company of a parent but die alone is a fundamental biological asymmetry. It has been suggested that this provides a deep-rooted source of spatial pattern formation for microorganisms even at the scale of the population. Such a theory, however, neglects the strong influence in nature of the limited and spatially variable availability of food. The tendency, first recognized by Thomas Malthus in the 18th century, of a population to out-strip its food resources will eventually lead, through local starvation, to the suppression of a heterogeneity growing within a population. Using a generic model it is demonstrated that including local food limitation of breeding strongly dampens spatial structure otherwise resulting from birth and death. The extent of this damping is shown to be a function of the strength of the coupling between organisms and their food and of the total abundance of organic material. Moreover, this work provides an example of a density-dependent process acting to diminish spatial structure rather than to create it and highlights the rich variety of behaviour that is missed by continuum models which fail to represent such local dynamics.

Animals↗
PubMed2026

Research on the genome of microorganisms: ethical considerations and recommendations regarding the incidental bystander sequencing of human genetic material.

In genomic research primarily targeting microorganisms (or pathogens), a substantial risk exists that the presence of human genetic bycatch is not sufficiently recognised, and that the potential harm of unwarranted analysis, access, or sharing of human genetic bystander data is also insufficiently acknowledged or mitigated. In this Personal View, we contend that mandatory risk mitigation measures are necessary, more so in view of the likely increase of sharing of materials and pathogen sequence information under the WHO Pandemic Agreement and the related Pathogen Access and Benefit Sharing framework. Based on a joint reflection of the Institutional Review Board and individual researchers at the Institute of Tropical Medicine in Antwerp, Belgium, we propose a four-step approach to mitigate such risks: prevention or early removal of human genetic sequences, secure storage of samples and data, adaptation of informed consent, and targeted ethics review. This approach should contribute to maintaining ethical integrity, protect the rights of individuals and communities, and bolster public trust in the expanding use of untargeted sequencing in global health research.

Humans↗
PubMed2004

[Retrospective study of bacteremia diagnosed in an emergency department: frequency, susceptibility of microorganisms, and impact on therapeutic management].

OBJECTIVE: The authors had for aim to determine the prevalence of bacteremia diagnosed in an emergency department (ED), the susceptibility of microorganisms to antibiotics, and the impact on therapeutic management. DESIGN: A retrospective analysis was made on patient features, microbiological ecology, susceptibility to antibiotics, and modalities of antimicrobial therapy in the Georges Pompidou European hospital ED of Hôpital, between 1 November 2001 and 30 June 2002. RESULTS: One thousand four hundred and thirty two blood cultures were obtained from 1069 patients. The rate of positive cultures was 12%, but only 8.7% (n = 125) were proved as true bacteremia. The most frequently identified organisms were: Enterobacteriaceae (n = 63, 39.4%) with a predominance of Escherichia coli (n = 48, 30%), and Streptococcus pneumoniae (n = 16, 10%). Forty two cases of pyelonephritis and 34 of prostatitis both due to E. coli were diagnosed. 76.5% of these were resistant to amoxicillin, 64.7% to amoxicillin-clavulanic acid, 11.8% to ciprofloxacin, and 44% to cotrimoxazole. No resistance to third generation cephalosporin was detected in E. coli isolates. Fourteen S. pneumoniae pneumonia cases were diagnosed. 57.1% of isolates presented with a decreased susceptibility to penicillin (CMI > 0.1 mg/l). Susceptibility to amoxicillin and cefotaxim was 85.7% and 92.9% respectively. Blood culture was the only exam available for bacterial diagnosis in 51.5% of true bacteremia. 1.6% of blood cultures from ED samples had an impact on therapeutic management. CONCLUSIONS: Blood culture is a relevant exam for the diagnosis of infection in patients admitted to the ED.

Bacteremia↗
PubMed2004

Colloidal chitin stained with Remazol Brilliant Blue R, a useful substrate to select chitinolytic microorganisms and to evaluate chitinases.

A simple and sensitive method based on the use of colloidal chitin stained with Remazol Brilliant Blue R (RBB) is proposed to evaluate chitinase activity. If this colloidal-stained substrate is included as a carbon source in a liquid medium, this technique allows the selection or the comparison of chitinolytic microorganisms. The colloidal substrate is proportionally solubilized and the dye released is spectrophotometrically quantified at 595 nm. The procedures used for the staining and fixing of RBB in the colloidal chitin, and a comparison with the commercial substrate chitin-azure, are presented. The influence of several physicochemical and enzymatic parameters on the release of dyes is also shown. Both stained substrates were used for studying the effect of pH, substrate concentration, temperature and time on the chitinase reaction of Bacillus thuringiensis Bt-107.

Anthraquinones↗
PubMed2004

Identification and biodegradation potential of tropical aerobic hydrocarbon-degrading microorganisms.

Screening of aerobic culturable hydrocarbon (HC)-degrading microorganisms isolated from petroleum-polluted soils and cyanobacterial mats from Indonesia resulted in the collection of 33 distinct species. Eight bacteria, 21 fungi and 4 yeasts were identified to the specific level by molecular and phenotypic techniques. Bacterial strains belonged to the genera Gordonia, Brevibacterium, Aeromicrobium, Dietzia, Burkholderia and Mycobacterium. Four species are new and not yet described. Fungi belonged to Aspergillus, Penicillium, Fusarium, Amorphoteca, Neosartorya, Paecilomyces, Talaromyces and Graphium. Yeasts were Candida, Yarrowia and Pichia. All strains were cultivated axenically in synthetic liquid media with crude oil as sole carbon and energy source. After incubation, the detailed chemical composition of the residual oil was studied by gravimetric and gas-chromatographic techniques. Thirteen parameters for assessing the biodegradation potential were defined and computed for each strain. Maximum degradation was observed on the saturated HCs (n- and isoalkanes, isoprenoids), whereas aromatic HC degradation was lower and was related to the structural composition of the molecules. A principal components analysis (PCA) permitted grouping and classifying the strains as a function of their degradative capacities. It was shown that the most active strains produced polar metabolites which accumulated in the resins and asphaltene fractions. These fractions are highly resistant to microbial metabolism. No taxonomic trend could be defined between microbial phyla in terms of HC biodegradation activity.

Bacteria↗
PubMed2005

Biodegradation or metabolism of bisphenol A: from microorganisms to mammals.

Bisphenol A (BPA; 2,2-bis(4-hydroxyphenyl)propane; CAS Registry No. 80-05-7) is one of endocrine disruptors and is made by combining acetone and phenol. BPA can be metabolized by extensive organisms. In this review these BPA biodegradations or metabolisms by many organisms from microorganisms to mammals were referred. Though the metabolites of BPA can enhance estrogenicity or toxicity, generally, BPA metabolism by organisms leads to detoxication of BPA.

Animals↗
PubMed2005

The potential to reduce emissions of airborne microorganisms by means of biological waste gas treatment systems.

Investigations regarding the reduction of airborne germs in the waste gas of biowaste composting processes have been carried out at the Hamburg University of Science and Technology and the University of Leipzig. Numerous waste gas treatment plants, ranging from laboratory-scale to technical-scale, have been available at the institutes of these two project partners. All plants consisted of bioscrubber/biofilter combinations. The results showed that these biological systems designed for odour control are able to successfully reduce bioaerosol emissions, even though a reduction to background levels could not be achieved. The bioscrubber, if equipped with a droplet separator, proved to be mainly responsible for the reduction, whereas the biofilter acted as a source for microbial emissions originating from the filter material. It could be observed that the microbial population changed while passing the treatment system, indicating the ability of biological waste gas treatment systems to retain potentially pathogenic microorganisms from waste gases.

Air Microbiology↗
PubMed2005

Inactivation of enteric microorganisms with chemical disinfectants, UV irradiation and combined chemical/UV treatments.

The relative disinfection efficiencies of peracetic acid (PAA), hydrogen peroxide (H2O2) and sodium hypochlorite (NaOCl) against Escherichia coli, Enterococcus faecalis, Salmonella enteritidis and coliphage MS2 virus were studied in laboratory-scale experiments. This study also evaluated the efficiency of combined PAA/ultraviolet irradiation (UV) and H2O2/UV treatments to determine if the microbial inactivation was synergistic. Microbial cultures were added into a synthetic wastewater-like test medium and treated by chemical disinfectants with a 10 min contact time, UV irradiation or the combination of chemical and UV treatments. A peracetic acid dose of 3 mg/l resulted in approximately 2-3 log enteric bacterial reductions, whereas 7-15 mg/l PAA was needed to achieve 1-1.5 log coliphage MS2 reductions. Doses of 3-150 mg/l hydrogen peroxide achieved below 0.2 log microbial reductions. Sodium hypochlorite treatments caused 0.3-1 log microbial reductions at an 18 mg/l chlorine dose, while 2.6 log reductions of E. faecalis were achieved at a 12 mg/l chlorine dose. The results indicate that PAA could represent a good alternative to chlorine compounds in disinfection procedures, especially in wastewaters containing easily oxidizable organic matter. Hydrogen peroxide is not an efficient disinfectant against enteric microorganisms in wastewaters. The combined PAA/UV disinfection showed increased disinfection efficiency and synergistic benefits with all the enteric bacteria tested but lower synergies for the coliphage MS2. This suggests that this method could improve the efficiency and reliability of disinfection in wastewater treatment plants. The combined H2O2/UV disinfection only slightly influenced the microbial reductions compared to UV treatments and showed some antagonism and no synergies.

Disinfectants↗
PubMed1991

Phospholipase C activity in microorganisms associated with reproductive tract infection.

Phospholipase C (lecithinase or phosphatidylcholine phosphorylase) catalyzes the hydrolysis of lecithin into phosphorylcholine and 1,2-diglyceride. Bacterial production of phospholipase C may damage reproductive tract tissues by both direct and indirect mechanisms. Use of the synthetic substrate p-nitrophenylphosphorylcholine phospholipase C activity was determined in 204 isolates representative of those found in female genital tract. Multiple aerobic (28%) and anaerobic (28%) reproductive tract microorganisms showed phospholipase C activity. Phospholipase C-producing isolates included strains of Bacteroides fragilis, B. bivius, B. thetaiotaomicron, Gardnerella vaginalis, and group B streptococcus. Phospholipase C activity was heterogenous; not all isolates that belong to a particular species showed activity. Phospholipase C production may be a possible virulence factor produced by a number of microflora commonly implicated in various reproductive tract infections or conditions, as well as in some instances of preterm birth.

Bacteria, Aerobic↗
PubMed2001

Spatial distribution of vital and dead microorganisms in dental biofilms.

To examine the spatial structure of dental biofilms a vital fluorescence technique was combined with optical analysis of sections in a confocal laser scanning microscope (CLSM). Enamel slaps were worn in intraoral splints by three volunteers for five days to accumulate smooth-surface plaque. After vital staining with fluorescein diacetate and ethidium bromide the specimens were processed for CLSM examination. Optical sections 1 microm apart were analysed in the z-axis of these dental biofilms. One of the films was 15 microm high, sparse and showed low vitality, i.e. <16%, while the others were taller (25 and 31 microm) and more vital, i.e. up to 30 and 69%, respectively. In all instances the bacterial vitality increased from the enamel surface to the central part of the plaque and decreased again in the outer parts of the biofilm. The spatial arrangement of the microorganisms in the biofilm showed voids outlined by layers of vital bacteria, which themselves were packed in layers of dead material.

Biofilms↗
PubMed1997

CDP-diacylglycerol synthase of microorganisms.

The synthesis and utilization of CDP-diacylglycerol in mammalian cells was demonstrated over 35 years ago when initial studies were carried out. However, CDP-diacylglycerol synthases and the genes encoding these enzymes have been studied in the greatest detail in Escherichia coli and Saccharomyces cerevisiae. The involvement of CDP-diacylglycerol in regulation of phospholipid metabolism has recently been demonstrated in Saccharomyces cerevisiae, and evidence now exists from studies in Drosophila that this liponucleotide may be important in regulation of lipid-dependent signal transduction processes. The vast amount of biochemical and genetic information on the synthases from microorganisms has led to the cloning of genes that encode CDP-diacylglycerol synthases from somatic cells. The combination of information on these synthases from all organisms will lead to a clearer understanding of the role CDP-diacylglycerol plays in cellular processes.

Cloning, Molecular↗