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PubMedDate not supplied

[Morpho-physiological research on Schizomycetes. Morphogenesis and cytoarchitecture of the microbial colony. I: B. anthracis].

The cytoarchitecture of B. anthracis can be easily studied in serial sections both at the light and at the electron microscope. The morphogenesis of the colony makes clear the peculiar structure of B. anthracis which seems essentially due to the chemical and physical characteristics of the cell envelopes and to the incomplete division of daughter cells. Other factors such as surface tension, humidity, mechanical obstacles and regressive phenomena, seem to be active, in B. anthracis, only since the third day.

Bacillus anthracis↗
PubMed2006

Effects of the antibiotic ciprofloxacin on stream microbial communities and detritivorous macroinvertebrates.

Microbial communities play an important role in stream ecosystem processes, such as breakdown of senescent leaf litter, and as a primary nutritional source for detritivorous macroinvertebrates. Antibiotics may affect stream microbial communities and associated ecosystem processes, especially because recent stream and river monitoring programs have indicated the presence of antibiotics downstream of wastewater treatment plants. In the current study, effects of chronic exposure to the fluoroquinolone antibiotic ciprofloxacin (Cipro) were examined on stream microbial community-level physiological profiles and growth indices of detritivorous amphipods (Gammarus spp.) and caddisflies (Lepidostoma liba). Microcosm experiments were conducted using stream sediments and water, senesced leaf material (Acer saccharum), and macroinvertebrates. A shift in function of leaf-associated microbial communities (based on carbon source utilization) was observed for samples exposed to 100 microg/L of Cipro for 12 d compared to control and treatments exposed to 1 and 10 microg/L of Cipro. This was attributable to carbohydrate substrates, which had 2.7- to 3.5-fold lower microbial respiration than the lower concentrations and control (p < 0.001). For detritivores, Gammarus spp. condition index did not differ among control, 0.1, and 1.0 microg/L treatments after 30-d exposures (p > 0.05). Similarly, L. liba growth rate did not vary among control, 10, and 100 microg/L treatments after 45-d exposures (p > 0.05). These results suggest that Cipro may affect leaf-associated microbial communities, but at concentrations four orders of magnitude above those detected in streams. However, effects of the antibiotic on growth and condition of detritivores were not observed. Future work should focus on identifying specific changes in stream microbial communities as a result of Cipro exposure and impacts on other aquatic species.

Animals↗
PubMedDate not supplied

Comparative genomics and understanding of microbial biology.

The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.

Bacteria↗
PubMed2003

Marker and reporter genes: illuminating tools for environmental microbiologists.

Fluorescent and luminescent marker and reporter genes provide easily detectable phenotypes to microbial cells and are therefore valuable tools for the study of microorganisms in the environment. Although these tools are becoming widely adopted, there are still issues that remain to be solved, such as the dependence of the reporter output on the physiological status of the cell. Eventually it might be the use of marker and reporter genes themselves that will contribute towards better understanding of the physiological status of specific microbial populations in nature.

Bacteria↗
PubMed2006

Application of cell-based biosensors for the detection of bacterial elicitor flagellin.

Cell-based biosensors, bioelectronic portable devices containing plant living cells have been used for monitoring some physiological changes induced by pathogen-derived signal molecules called flagellin. The screen-printed electrodes have been adapted for preparation of biosensors. The proton-sensitive thick films have been printed using composite bulk modified with edition of RuO(2). Obtained disposable electrodes were made possible to measure the pH change with well sensitivity and reproducibility. Tobacco cells attached to the electrode surface, cell-based biosensor, can be used for the detection of flagellin, the virulence factor of bacterial pathogen. We culture tobacco cells on the surface of such electrotransducer for several weeks and monitor of potential of cells under flagellin stimulation. The detection of the electrochemical proton gradient across the plasma membrane serves as the analytical signal. The electrode response depended upon H(+) concentration in extracellular solution. It can be conveniently observed on the surfaces of biosensors. Suitable stability and the good response time of constructed biosensors were observed. Future development of these cell-based biosensors could draw advances in selective monitoring of microbial pathogens and other physiologically active components. Moreover, this new method is much faster compared with the traditional microbial testing.

Agrobacterium tumefaciens↗
PubMed1999

Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles.

The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.

Bacteria↗
PubMed2006

Characterization of methods for determining sterilization efficacy and reuse efficiency of oxygen biosensor multiwell plates.

High-throughput screening (HTS) assays based upon fluorometric detection of oxygen consumption in microtiter plates were primarily developed for applications in drug discovery and ecotoxicology but have recently been adopted for use in microbial community-level physiological profiling assays (CLPP). The widespread use of oxygen biosensor systems for CLPP applications has, however, been hindered by the relatively high cost of oxygen biosensor reagent systems and limited access to microplate fluorometer instrumentation platforms. The ability to recycle and reuse oxygen biosensor system plates would expand their utilization for CLPP assays and other research applications in microbial ecology. Here, the efficacy and cost effectiveness of multiple procedures for sterilization of Oxygen Biosensor System (OBS; BD Biosciences) plates for reuse was evaluated. OBS plates were sterilized using ethylene oxide, ultraviolet radiation, and bleach treatments, then evaluated for biosensor response and plate life-cycle performance. Of the sterilization methods tested, ethylene oxide sterilization was most effective based on its low cost, high sterilization efficacy, and minimal impact upon OBS plate response.

Biosensing Techniques↗
PubMed2026

[Intestinal microbiota alterations after digestive tract reconstruction surgery and their impacts on host physiology].

The gut microbiota, acknowledged as the human body's 'second genome', plays a pivotal role in maintaining health. Digestive tract reconstruction surgery profoundly alters the anatomical structure and physiological environment of the gastrointestinal tract, thereby inducing significant shifts in the intestinal microbiota. These microbial changes subsequently influence host physiological functions through metabolic, immune, neuroendocrine, and other pathways. For instance, Roux-en-Y gastric bypass surgery enriches short-chain fatty acid(SCFA)-producing Bacteroides, improving systemic insulin sensitivity. Conversely, pancreaticoduodenectomy leads to a marked enrichment of potential pathobionts such as Klebsiella and Clostridium, which may elevate the risk of infections and tumor recurrence. This review comprehensively summarizes the characteristic changes in the gut microbiota following various digestive tract reconstruction procedures and discusses their multifaceted impacts on host physiology, aiming to provide insights for future experimental research and clinical practice.

Humans↗
PubMed1997

Microbial biodegradation of organic wastes containing surfactants in a continuous-flow reactor.

In a continuous flow bioreactor seeded with microbes from municipal activated sludge, complete organic carbon oxidation of simulated graywater (wastewater produced in human residences, excluding toilet wastes) was achieved at dilution rates up to 0.36 h-1 in the presence of 64.1 microM linear alkylbenzenesulfonate (LAS) L-1. At LAS concentrations of 187 microM, the system functioned only at dilution rates up to 0.23 h-1, and the biomass yield was two-fold lower. There were physiological changes in the microbial communities under different operating conditions, as measured by specific contents of ATP and extracellular hydrolases as well as the respiratory potential of the biomass. LAS inhibited the activity of LAS-degrading microbes at >150 microM LAS, and the activity of other microbes at >75 microM LAS. Chemical analysis of graywater indicated that samples consisted primarily of biological polymers (proteins and polysaccharides) and lower concentrations of surfactants. Biological remediation of graywater is possible, although treatment efficiency is influenced by the operating conditions and wastestream composition.

Alkanesulfonates↗
PubMed2003

Radioisotopic, culture-based, and oligonucleotide microchip analyses of thermophilic microbial communities in a continental high-temperature petroleum reservoir.

Activity measurements by radioisotopic methods and cultural and molecular approaches were used in parallel to investigate the microbial biodiversity and its physiological potential in formation waters of the Samotlor high-temperature oil reservoir (Western Siberia, Russia). Sulfate reduction with rates not exceeding 20 nmol of H(2)S liter(-1) day(-1) occurred at 60 and 80 degrees C. In upper horizons (AB, A, and B), methanogenesis (lithotrophic and/or acetoclastic) was detected only in wells in which sulfate reduction did not occur. In some of the wells from deeper (J) horizons, high-temperature sulfate reduction and methanogenesis occurred simultaneously, the rate of lithotrophic methanogenesis exceeding 80 nmol of CH(4) liter(-1) day(-1). Enrichment cultures indicated the presence of diverse physiological groups representing aerobic and anaerobic thermophiles and hyperthermophiles; fermentative organotrophs were predominant. Phylogenetic analyses of 15 isolates identified representatives of the genera Thermotoga, Thermoanaerobacter, Geobacillus, Petrotoga, Thermosipho, and Thermococcus, the latter four being represented by new species. Except for Thermosipho, the isolates were members of genera recovered earlier from similar habitats. DNA obtained from three samples was hybridized with a set of oligonucleotide probes targeting selected microbial groups encompassing key genera of thermophilic bacteria and archaea. Oligonucleotide microchip analyses confirmed the cultural data but also revealed the presence of several groups of microorganisms that escaped cultivation, among them representatives of the Aquificales/Desulfurobacterium-Thermovibrio cluster and of the genera Desulfurococcus and Thermus, up to now unknown in this habitat. The unexpected presence of these organisms suggests that their distribution may be much wider than suspected.

Archaea↗
PubMed2003

Rhizosphere microflora of plants used for the phytoremediation of bitumen-contaminated soil.

The microbial communities and their degradative potential in rhizospheres of alfalfa (Medicago sativa) and reed (Phragmites australis) and in unplanted soil in response to bitumen contamination of soil were studied in pot experiments. According to the results of fluorescence microscopy, over a period of 27 months, bitumen contamination of soil reduced the total number of microorganisms more significantly (by 75%) in unplanted than in rhizosphere soil (by 42% and 7% for reed and alfalfa, respectively) and had various effects on some important physiological groups of microorganisms such as actinomycetes as well as nitrogen-fixing, nitrifying, denitrifying, ammonifying, phosphate-solubilizing, sulphur-oxidizing, cellulolytic and hydrocarbon-degrading microorganisms. The changes in the physiological structure of the microbial community under bitumen contamination were found to hinge on not merely the presence of plants but also their type. It was noted that the rhizosphere microflora of alfalfa was less inhibited by hydrocarbon pollution and had a higher degradative potential than the rhizosphere microflora of reed.

Actinobacteria↗
PubMed2003

Modification in the ppk gene of Helicobacter pylori during single and multiple experimental murine infections.

The bacterial pathogen Helicobacter pylori is highly adapted to the human stomach, and a high level of polymorphism is observed among clinical isolates. This polymorphism may be the consequence of adaptive changes during colonization, making a strain better able to survive, to evade the immune system, and to provoke a chronic infection. To investigate the mechanisms involved in the acquisition of diversity in H. pylori, mouse models of single infections, coinfections, and superinfections were developed. These experimental infections were conducted with strain SS1, well known to be mouse adapted, and with two strains freshly isolated from infected patients: Hp141 and Hp145. Genetic modifications occurring in these strains were studied over time by comparing randomly selected colonies of the emerging strains to those of the infecting strains by using randomly amplified polymorphic DNA fingerprinting with six different primers and by using PCR to amplify the vacA and cagA genes. We showed that, regardless of the number of infecting strains, only one emerged from the animals and that the establishment of a first strain thwarted the implantation of a second strain. During both a single infection and a coinfection with SS1, Hp141 was replaced by a genetic variant (Hp141v) that overcame SS1 in coinfection experiments. Hp141v exhibited a deletion of a 102-bp repeated sequence within the ppk gene, which encodes polyphosphate kinase (PPK), an enzyme involved in the physiological adaptation of the microbial cell to nutritional and environmental stresses. The deletion led to higher enzymatic activity of PPK, and the variant exhibited a better capacity to colonize mice. Considering that the modified gene is known to be involved in adaptation to a new environment, our results are consistent with an adaptive change in strain Hp141 and suggest that PPK is an important virulence factor in H. pylori.

Adaptation, Physiological↗
PubMed1996

Biodegradation of organic wastes containing surfactants in a biomass recycle reactor.

The microbial biodegradation of simulated graywater, containing 21.5 mg of linear alkylbenzene sulfonate liter-1, was investigated with a continuous-flow bioreactor with 100% biomass recycle. Low concentrations of organic matter in the ultrafiltration eluate were achieved by hydraulic residence times as short as 1.6 h and for periods of up to 74 days at a hydraulic residence time of 6 h. Upon a shift from the chemostat to the biomass recycle mode, the increase in biomass with time approximated a linear rather than an exponential function. Biomass densities as high as 6.8 g of cell protein liter-1 were reached; this was 50-fold higher than the steady-state biomass level in chemostats fed the same medium. We assessed physiological changes in the microbial community after a switch from the chemostat to the biomass recycle mode. Over 150 h, there was a two- to fourfold decrease in the respiratory potential of the microbes. After this decrease, respiratory potentials were relatively constant up to 74 days of operation. A decline in reactivity was also indicated by increasing lag periods before growth in response to organic nutrient inputs and by a decrease in the proportion of cells able to reduce tetrazolium dye. However, the bioreactor system was still capable of rapidly metabolizing inputs of organic matter, because of the very high biomass concentrations. It appears that < 10% of the organic carbon inputs accumulate as biomass.

Bacteria↗
PubMed2002

Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communities.

We used geochemical analyses of groundwater and laboratory-incubated microcosms to investigate the physiological responses of naturally occurring microorganisms to coal-tar-waste constituents in a contaminated aquifer. Waters were sampled from wells along a natural hydrologic gradient extending from uncontaminated (1 well) into contaminated (3 wells) zones. Groundwater analyses determined the concentrations of carbon and energy sources (pollutants or total organic carbon), final electron acceptors (oxygen, nitrate, sulfate), and metabolic byproducts (dissolved inorganic carbon [DIC], alkalinity, methane, ferrous iron, sulfide, Mn2+). In the contaminated zone of the study site, concentrations of methane, hydrogen, alkalinity, and DIC were enhanced, while dissolved oxygen and nitrate were depleted. Field-initiated biodegradation assays using headspace-free serum bottle microcosms filled with groundwater examined metabolism of the ambient organic contaminants (naphthalene, 2-methylnaphthalene, benzothiophene, and indene) by the native microbial communities. Unamended microcosms from the contaminated zone demonstrated the simultaneous degradation of several coal-tar-waste constituents at the in situ temperature (10 degrees C). Lag phases prior to the onset of biodegradation indicated the prevalence of both aerobic and anaerobic conditions in situ. Electron acceptor-amended microcosms from the most contaminated well waters demonstrated only aerobic naphthalene degradation. Collectively, the geochemical and microbial evidence show that biodegradation of coal-tar-waste constituents occurs via both aerobic and anaerobic terminal electron accepting processes at this site.

Bacteria, Aerobic↗
PubMed2005

Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes.

The rhizosphere differs from the bulk soil in a range of biochemical, chemical and physical processes that occur as a consequence of root growth, water and nutrient uptake, respiration and rhizodeposition. These processes also affect microbial ecology and plant physiology to a considerable extent. This review concentrates on two features of this unique environment: rhizosphere geometry and heterogeneity in both space and time. Although it is often depicted as a soil cylinder of a given radius around the root, drawing a boundary between the rhizosphere and bulk soil is an impossible task because rhizosphere processes result in gradients of different sizes. For instance, because of diffusional constraints, root uptake can result in a depletion zone extending <1 mm for phosphate to several centimetres for nitrate, while respiration may affect the bulk of the soil. Rhizosphere processes are responsible for spatial and temporal heterogeneities in the soil, although these are sometimes difficult to distinguish from intrinsic soil heterogeneity. A further complexity is that these processes are regulated by plants, microbial communities and soil constituents, and their many interactions. Novel in situ techniques and modelling will help in providing a holistic view of rhizosphere functioning, which is a prerequisite for its management and manipulation.

Ecosystem↗
PubMed2003

Probiotics: what are they? What are their effects on gut physiology?

Probiotics can be defined as microbial cells that have a beneficial effect on the health and well-being of the host. Since the gastrointestinal mucosa is the surface of contact with probiotics, it seems evident that the first effects of probiotics relate to digestive function. A brief review of the literature indicates that probiotics have very few effects on the main physiological functions of the gastrointestinal tract, which are digestion, absorption and propulsion. The main action of probiotics can be summarised as a reinforcement of the intestinal mucosal barrier against deleterious agents. Experimental data indicate that some probiotics reduce pathological alterations in paracellular permeability to large molecules or bacteria, stimulate mucosal immunity, display a trophic action on the mucosa, reduce mucus degradation and interact with mediators of inflammation. Yoghurt may help lactose digestion, and some data needing confirmation indicate a stimulation of water absorption and an acceleration of intestinal transit by some bacteria.

Animals↗
PubMed2005

Flow-cytometric detection of changes in the physiological state of E. coli expressing a heterologous membrane protein during carbon-limited fedbatch cultivation.

The key to optimizing productivity during industrial fermentations is the ability to rapidly monitor and interpret the physiological state of single microbial cells in a population and to recognize and characterize different sub-populations. Here, a flow cytometry-based method for the reproducible detection of changes in membrane function and/or structure of recombinant E. coli JM101 (pSPZ3) expressing xylene monooxygenase (XMO), was developed. XMO expression led to compromised but not permeabilized cell membranes. This was deduced from the fact that recombinant cells only stained with ethidium bromide (EB) and not with propidium iodide (PI). During the glucose-limited fedbatch cultivation, an increase from 25% to 95% of EB-stained cells was observed, occurring between 2 and 5 h after induction. Control experiments confirmed that this increase was due to the recombinant protein production and not caused by any possible effects of varying substrate availability, high cell density, plasmid replication or the presence of the inducing agent. We hypothesize that the integration of the recombinant protein into the cell membrane physically disrupted the functionality of the efflux pumps, thus resulting in EB-staining of the recombinant cells. This method enabled us to detect changes in the physiological state of single cells 2-4 h before other indications of partial cell damage, such as unbalanced growth, acetate accumulation and an increased CO(2) production rate, were observed. This method therefore shows promise with respect to the further development of an early-warning system to prevent sudden productivity decreases in processes with recombinant E. coli expressing heterologous membrane proteins.

Acetates↗