Evaluation of a Rapid, Quantitative Real-Time PCR Method for Enumeration of Pathogenic Candida Cells in Water

Quantitative PCR (QPCR) technology, incorporating fluorigenic 5′ nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C. lusitaniae) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.     

Long-term survival of and plasmid stability inPseudomonas andKlebsiella species and appearance of nonculturable cells in agricultural drainage water

One year after introduction into agricultural drainage waterPseudomonas fluorescens R2f (RP4),Pseudomonas putida CYM318 (pRK2501), andKlebsiella aerogenes NCTC418 (pBR322) could be recovered on agar media. Survival of the introduced strains depended on competition with the indigenous microflora, the presence of nutrients, and the availability of air.In contrast toK. aerogenes NCTC418 (pBR322), bothPseudomonas species lost their plasmids, as indicated by the consistently lower colony counts on selective medium compared with the counts on nonselective medium. The plasmid loss did not depend on nutrient status and oxygen supply. P. fluorescens R2f cells could be detected with the immunofluorescence (IF) technique. Total cell counts determined by IF were consistently higher than corresponding colony counts. Even in samples where no colonies were recovered, R2f cells could be detected by IF. This indicated the occurrence of nonculturable R2f cells in drainage water. Homology with³²P-labelled plasmid RP4 DNA was found in several drainage water samples that originally receivedP. fluorescens R2f (RP4), by using the cell suspension filter hybridization technique. P. putida CYM318 andK. aerogenes NCTC418 cells could also be detected in sterile drainage water samples, after nonspecific staining with fluorescein isothiocyanate. Cell counts of both strains were consistently higher than corresponding plate counts.     

Effect of CO2 on Colony Development by Bifidobacterium Species

This report investigates the requirement for CO₂ for colony formation by Bifidobacterium species in both anoxic and oxic environments. All tested Bifidobacterium species exhibited difficulty in developing colonies in an atmosphere of 100% N₂ but developed well when 1% CO₂ was present. In the presence of CO₂, the oxygen tolerance of the tested species was not improved. In the absence of CO₂, only B. boum, a microaerophilic species, could develop colonies under an N₂-based 5% O₂ atmosphere, indicating that while CO₂ is not an essential factor for colony development, both CO₂ and O₂ have stimulatory effects on B. boum colony development.     

Infecciones urinarias nosocomiales por levaduras. Estudio multicéntrico de 14 hospitales de la red de micología de la Ciudad Autónoma de Buenos Aires

BackgroundUrinary tract infections are a frequent ailment in patients in intensive care units. Candida and other yeasts cause 5-12% of these infections. The value of the finding of any yeast is controversial, and there is no consensus about which parameters are adequate for differentiating urinary infections from colonization or contamination.AimsTo analyse the epidemiological characteristics of patients with funguria, to determine potential cut-off points in cultures (to distinguish an infection from other conditions), to identify the prevalent yeast species, and to determine the value of a second urine sample.MethodsA multicentre study was conducted in intensive care units of 14 hospitals in the Buenos Aires City Mycology Network. The first and second samples of urine from every patient were cultured. The presence of white cells and yeasts in direct examination, colony counts, and the identification of the isolated species, were evaluated.ResultsYeasts grew in 12.2% of the samples. There was no statistical correlation between the number of white cells and the fungal colony-forming units. Eighty five percent of the patients had indwelling catheters. Funguria was not prevalent in women or in patients over the age of 65. Candida albicans, followed by Candida tropicalis, were the most frequently isolated yeasts. Candida parapsilosis and Candida glabrata appeared less frequently. The same species were isolated in 70% of second samples, and in 23% of the cases the second culture was negative.ConclusionsIt was not possible to determine a useful cut-off point for colony counts to help in the diagnosis of urinary infections. As in other publications, C. albicans, followed by C. tropicalis, were the most prevalent species.     

Bioluminescent Most-Probable-Number Method To Enumerate lux-Marked Pseudomonas aeruginosa UG2Lr in Soil

Bioluminescence measured with a luminometer and charge-coupled device was an effective marker in most-probable-number assays for luxAB-marked Pseudomonas aeruginosa UG2Lr in soil. Most-probable-number assays with microtiter plate wells and luminometer tubes gave estimates for UG2Lr that were similar to viable colony counts. Both methods detected five cells per g of soil.     

Comparison of Gelman and Millipore Membrane Filters for Enumerating Fecal Coliform Bacteria

Tests of two leading brands of membrane filters used for enumerating fecal coliform bacteria showed that Gelman GN-6 filters recovered statistically more colonies of bacteria than did Millipore HAWG 047SO filters from pure cultures incubated at either 35 C (the optimal growth temperature) or 44.5 C (the standard temperature for the fecal coliform test). Standard membrane filter procedures with M-FC broth base were used to enumerate the organisms. Densities of colonies incubated on Gelman filters at 44.5 C averaged 2.3 times greater than those on Millipore filters. Plate counts of the bacteria at both temperatures indicated that incubation at 44.5 C did not inhibit propagation of fecal coliform bacteria. For the pour plates, M-FC broth base plus 1.5% agar was used. This modified medium compared favorably to plate count agar for enumerating Escherichia coli. At 35 and 44.5 C, colony counts on Gelman filters agreed closely with plate counts prepared concurrently, but Millipore counts were consistently lower than plate counts, especially at 44.5 C. Comparative analyses of river water for fecal coliform bacteria by the membrane filter technique gave results comparable to those for the pure cultures.     

Oxygen Concentration Inside a Functioning Photosynthetic Cell

The excess oxygen concentration in the photosynthetic membranes of functioning oxygenic photosynthetic cells was estimated using classical diffusion theory combined with experimental data on oxygen production rates of cyanobacterial cells. The excess oxygen concentration within the plesiomorphic cyanobacterium Gloeobactor violaceus is only 0.025 μM, or four orders of magnitude lower than the oxygen concentration in air-saturated water. Such a low concentration suggests that the first oxygenic photosynthetic bacteria in solitary form could have evolved ∼2.8 billion years ago without special mechanisms to protect them against reactive oxygen species. These mechanisms instead could have been developed during the following ∼500 million years while the oxygen level in the Earth’s atmosphere was slowly rising. Excess oxygen concentrations within individual cells of the apomorphic cyanobacteria Synechocystis and Synechococcus are 0.064 and 0.25 μM, respectively. These numbers suggest that intramembrane and intracellular proteins in isolated oxygenic photosynthetic cells are not subjected to excessively high oxygen levels. The situation is different for closely packed colonies of photosynthetic cells. Calculations show that the excess concentration within colonies that are ∼40 μm or larger in diameter can be comparable to the oxygen concentration in air-saturated water, suggesting that species forming colonies require protection against reactive oxygen species even in the absence of oxygen in the surrounding atmosphere.     

Oxygen Concentration Inside a Functioning Photosynthetic Cell

The excess oxygen concentration in the photosynthetic membranes of functioning oxygenic photosynthetic cells was estimated using classical diffusion theory combined with experimental data on oxygen production rates of cyanobacterial cells. The excess oxygen concentration within the plesiomorphic cyanobacterium Gloeobactor violaceus is only 0.025 μM, or four orders of magnitude lower than the oxygen concentration in air-saturated water. Such a low concentration suggests that the first oxygenic photosynthetic bacteria in solitary form could have evolved ∼2.8 billion years ago without special mechanisms to protect them against reactive oxygen species. These mechanisms instead could have been developed during the following ∼500 million years while the oxygen level in the Earth’s atmosphere was slowly rising. Excess oxygen concentrations within individual cells of the apomorphic cyanobacteria Synechocystis and Synechococcus are 0.064 and 0.25 μM, respectively. These numbers suggest that intramembrane and intracellular proteins in isolated oxygenic photosynthetic cells are not subjected to excessively high oxygen levels. The situation is different for closely packed colonies of photosynthetic cells. Calculations show that the excess concentration within colonies that are ∼40 μm or larger in diameter can be comparable to the oxygen concentration in air-saturated water, suggesting that species forming colonies require protection against reactive oxygen species even in the absence of oxygen in the surrounding atmosphere.     

A microculture hybridization technique for the detection of specific DNA sequences in filamentous fungi

A procedure that permits the successful application of the technique of colony hybridization to the filamentous fungi is described. The method involves the growth of microcultures in the wells of a microtiter tray using spore inocula. These microcultures are protoplastedin situ and transferred to a nylon filter through a device made by drilling out the wells of a second microtiter tray. The transferred protoplasts are confined to defined areas of the membrane, where they may be lysed and subjected to hybridization with a radioactive probe. The technique gives highly reproducible results and is of sufficient sensitivity to detect the integration of a single copy of a transforming plasmid into the genome ofAspergillus nidulans.     

Recovery of Clostridia on Catalase-Treated Plating Media

Four plating media commonly used for culturing clostridia were tested for their ability to support growth of several Clostridium species after storage of the plates for 1 to 10 days at 4 and 25°C with and without subsequent addition of catalase. Liver-veal (LV) agar and brain heart infusion (BHI) agar rapidly became incapable of supporting growth after storage without added catalase, whereas Shahidi Ferguson perfringens agar base and Brewer anaerobic agar were less affected. Plate counts of vegetative cells of nine of the less fastidious Clostridium species on untreated LV and BHI agars, stored for 3 days at 4°C, were 60 to 90% lower than counts on catalase-treated media. Counts on Shahidi Ferguson perfringens agar base were only 1 to 24% lower on untreated medium with the same species. Addition of 500 U of purified beef liver catalase to the surface of the 3-day-old agars before inoculation resulted in substantial restoration of the ability of the media to support colony formation from vegetative cells except with the most strictly anaerobic species (nonproteolytic C. botulinum types B, E, and F, and C. novyii types A and B). A similar response was obtained with spores of the less fastidious species on catalase-treated media. Our results suggest that inhibition of most Clostridium species on LV and BHI agars may be due to accumulation of peroxide during preparation, storage, and incubation of the media, and also suggest that the presence of glucose in these media is a major factor contributing to their inability to support growth. It is believed that the addition of exogenous catalase prevents the accumulation of peroxide(s), thus allowing colony formation from vegetative cells of the clostridia under what would otherwise be unsuitable cultural conditions.     

GELRITE as an Agar Substitute for the Cultivation of Mesophilic Methanobacterium and Methanobrevibacter Species

GELRITE was evaluated as a gelling agent for the growth of mesophilic Methanobacterium and Methanobrevibacter species. GELRITE was shown to be superior to agar in its gel strength and clarity. Viable cell counts and colony sizes of Methanobacterium species were greater on GELRITE-based medium compared with agar-based medium.     

A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability

Microbiologists have been using agar growth medium for over 120 years. It revolutionized microbiology in the 1890s when microbiologists were seeking effective methods to isolate microorganisms, which led to the successful cultivation of microorganisms as single clones. But there has been a disparity between total cell counts and cultivable cell counts on plates, often referred to as the “great plate count anomaly,” that has long been a phenomenon that still remains unsolved. Here, we report that a common practice microbiologists have employed to prepare agar medium has a hidden pitfall: when phosphate was autoclaved together with agar to prepare solid growth media (PT medium), total colony counts were remarkably lower than those grown on agar plates in which phosphate and agar were separately autoclaved and mixed right before solidification (PS medium). We used a pure culture of Gemmatimonas aurantiaca T-27^T and three representative sources of environmental samples, soil, sediment, and water, as inocula and compared colony counts between PT and PS agar plates. There were higher numbers of CFU on PS medium than on PT medium using G. aurantiaca or any of the environmental samples. Chemical analysis of PT agar plates suggested that hydrogen peroxide was contributing to growth inhibition. Comparison of 454 pyrosequences of the environmental samples to the isolates revealed that taxa grown on PS medium were more reflective of the original community structure than those grown on PT medium. Moreover, more hitherto-uncultivated microbes grew on PS than on PT medium.     

Quantification of Different Eubacterium spp. in Human Fecal Samples with Species-Specific 16S rRNA-Targeted Oligonucleotide Probes

Species-specific 16S rRNA-targeted, Cy3 (indocarbocyanine)-labeled oligonucleotide probes were designed and validated to quantify different Eubacterium species in human fecal samples. Probes were directed at Eubacterium barkeri, E. biforme, E. contortum, E. cylindroides (two probes), E. dolichum, E. hadrum, E. lentum, E. limosum, E. moniliforme, and E. ventriosum. The specificity of the probes was tested with the type strains and a range of common intestinal bacteria. With one exception, none of the probes showed cross-hybridization under stringent conditions. The species-specific probes were applied to fecal samples obtained from 12 healthy volunteers. E. biforme, E. cylindroides, E. hadrum, E. lentum, and E. ventriosum could be determined. All other Eubacterium species for which probes had been designed were under the detection limit of 10⁷ cells g (dry weight) of feces⁻¹. The cell counts obtained are essentially in accordance with the literature data, which are based on colony counts. This shows that whole-cell in situ hybridization with species-specific probes is a valuable tool for the enumeration of Eubacterium species in feces.     

Diversity of Aquatic Pseudomonas Species and Their Activity against the Fish Pathogenic Oomycete Saprolegnia

Emerging fungal and oomycete pathogens are increasingly threatening animals and plants globally. Amongst oomycetes, Saprolegnia species adversely affect wild and cultivated populations of amphibians and fish, leading to substantial reductions in biodiversity and food productivity. With the ban of several chemical control measures, new sustainable methods are needed to mitigate Saprolegnia infections in aquaculture. Here, PhyloChip-based community analyses showed that the Pseudomonadales, particularly Pseudomonas species, represent one of the largest bacterial orders associated with salmon eggs from a commercial hatchery. Among the Pseudomonas species isolated from salmon eggs, significantly more biosurfactant producers were retrieved from healthy salmon eggs than from Saprolegnia-infected eggs. Subsequent in vivo activity bioassays showed that Pseudomonas isolate H6 significantly reduced salmon egg mortality caused by Saprolegnia diclina. Live colony mass spectrometry showed that strain H6 produces a viscosin-like lipopeptide surfactant. This biosurfactant inhibited growth of Saprolegnia in vitro, but no significant protection of salmon eggs against Saprolegniosis was observed. These results indicate that live inocula of aquatic Pseudomonas strains, instead of their bioactive compound, can provide new (micro)biological and sustainable means to mitigate oomycete diseases in aquaculture.     

Cytochrome Oxidase: Subcellular Distribution and Relationship to Nitrogenase Expression in the Nonheterocystous Marine Cyanobacterium Trichodesmium thiebautii

Immunochemical labeling was used to study the subcellular distribution of cytochrome oxidase, a respiratory protein, in Trichodesmium thiebautii. The protein was found associated with both cytoplasmic and thylakoid membranes. About a sixfold variation in the protein content (gold particle count) was found among Trichodesmium cells within a single colony. Double labeling was performed with cytochrome oxidase and nitrogenase antisera. Regression analysis of gold particle counts per unit of cell area of cytochrome oxidase and nitrogenase showed a positive correlation (r² = 0.911); cells with higher nitrogenase levels also had higher levels of cytochrome oxidase. The parallel expression of two proteins suggests that respiratory oxygen uptake may be involved in nitrogenase protection (respiratory protection) in Trichodesmium spp.     

Ethanol production from d-xylose in batch fermentations with Candida shehatae: process variables

Summary These studies examined several process variables important in scaling up the fermentation of xylose by Candida shehatae. Inoculum age and cell density were particularly influential. Young (24-h) inocula fermented xylose to ethanol two to three times as fast as older (48- or 72-h) inocula. With all three inocula ages, the initial fermentation rates were essentially linear with cell density, up to 4 g dry wt cells L^-1. Above that cell density, the ethanol production rate appeared to be oxygen limited, particularly with 24-h old cells. Aeration also played a role in xylose utilization. The fermentation proceeded under both aerobic and anaerobic conditions, but xylose was not completely utilized anaerobically. With aeration, 25% more ethanol was formed in about one third the time than without aeration. Ethanol yields were similar under the two conditions. Cell growth on xylose was observed in the absence of oxygen. Cells went through essentially one doubling in 24 h. Based on the sugar consumed, a Y _ATP of 9.9 was obtained. Slow continuous feeding of glucose significantly increased the xylose utilization rate.Maintained in cooperation with the University of Wisconsin, Madison, Wisconsin, USA     

Improved 18-Hour Methyl Red Test

Standard methods for the methyl red (MR) test are not practical for routine use in clinical laboratories because of the necessarily prolonged incubation period. When read after overnight incubation, the usual MR test is often equivocal or falsely positive. The present study demonstrates the importance of standardizing the total volume of broth, the size of the vessel in which the cultures are incubated, and the density of the inoculum. In very small volumes of broth, cultures are better exposed to atmospheric oxygen, and thus MR-negative organisms tend to revert the initial acidic pH much more quickly than in deeper, large-volume broth cultures. In the proposed technique, a single colony was inoculated into a 0.5-ml amount of MR-Voges Proskauer (VP) broth (13- by 100-mm tube), and, after 18 to 24 hr at 37 C, one drop of MR was added. With this technique, the broth cultures produced either a definite red (positive) or yellow (negative) color, whereas various shades of orange were frequently observed when larger volumes of broth were tested after only 1 to 2 days of incubation. With 6.0-ml broth cultures, 18-hr MR tests were totally unreliable, but 18-hr tests in 0.5 ml of broth were comparable to the standard MR test performed after 5 days of incubation and superior to those performed after 48 hr in 6.0-ml broth cultures. With the proposed technique, the MR test can be incorporated readily into the routine scheme for identification of Enterobacteriaceae.     

The efficacy of Scenedesmus morphology as a defense mechanism against grazing by selected species of rotifers and cladocerans

Phytoplankton often develop various defense mechanisms in response to zooplankton grazing, such as spines and colonies. While it is now known that increased spine length and cells in a colony of members of the genus Scenedesmus, when zooplankton grazing is intense, helps in reducing zooplankton filtering rates, the effect of these defense mechanisms at the population level has been observed in few studies. Here we present data on the growth rates of four zooplankton species, Brachionus calyciflorus, B. patulus, Ceriodaphnia dubia and Daphnia pulex at two food levels using two species of colony-forming Scenedesmus spp.: S. acutus (cell length = 18.2 ± 0.4 µm; width = 4.2 ± 0.1 µm; average colony length = 90 µm; width: 21 µm) and S. quadricauda (cell length: 21 ± 0.5 width 7.5 ± 0.3 µm; average colony length: 84 µm; width: 30 µm). Whereas S. acutus had no spines, S. quadricauda had spines of 6–10 µm. Population growth experiments of the test rotifers and cladocerans were conducted in 100 ml containers with 50 ml of the medium with test algae. Algae concentrations used were: 13 and 52 mg dw l^–1 of each of the two algal species offered in colonial forms. We used an initial inoculation zooplankter density of 1 ind. ml^–1 for either of the rotifer species and 0.2 ind. ml^–1 for either of the cladoceran species. In all, we had 64 test containers (4 test species of zooplankton × 2 test species of algae × 2 algal densities × 4 replicates). We found a significant effect of algal size on the growth rates of all the four tested species of zooplankton. The population growth rates of zooplankton ranged from ?0.58 to 0.66 and were significantly higher on diet of S. acutus than of S. quadricauda. Thus, our study confirms that the larger colony size and the formation of spines in S. quadricauda were effective defenses against grazing by both rotifers and smaller sized cladoceran Ceriodaphnia dubia but that larger-bodied Daphnia pulex could exploit both the algal populations equally.     

Assessing penguin colony size and distribution using digital mapping and satellite remote sensing

Changes in penguin abundance and distribution can be used to understand the response of species to climate change and fisheries pressures, and as a gauge of ecosystem health. Traditionally, population estimates have involved direct counts, but remote sensing and digital mapping methodologies can provide us with alternative techniques for assessing the size and distribution of penguin populations. Here, we demonstrate the use of a field-based digital mapping system (DMS), combining a handheld geographic information system with integrated geographical positioning system as a method for: (a) assessing penguin colony area and (b) ground-truthing colony area as derived from satellite imagery. Work took place at Signy Island, South Orkneys, where colonies of the three congeneric pygoscelid penguins: Adélie Pygoscelis adeliae, chinstrap P. antarctica and gentoo P. papua were surveyed. Colony areas were derived by mapping colony boundaries using the DMS with visual counts of the number of nesting birds made concurrently. Area was found to be a good predictor for number of nests for all three species of penguin. Using a maximum likelihood multivariate classification of remotely sensed satellite imagery (QuickBird2, 18 January 2010; Digital Globe ID: 01001000B90AD00), we were able to identify penguin colonies from the spectral signature of guano and differentiate between colonies of Adélie and chinstrap penguins. The area classified (all species combined) from satellite imagery versus area from DMS data was closely related (R ² = 0.88). Combining these techniques gives a simple and transferrable methodology for examining penguin distribution and abundance at local and regional scales.     

Protoplast culture in high molecular oxygen atmospheres

The effect of a molecular oxygen atmosphere on protoplast culture, compared with normal cultural procedures, was investigated for tomato, rice and jute protoplast systems. Protoplasts, in unsealed Petri dishes were cultured in a sealed 250 ml volume container in which the atmosphere was replaced with sterile molecular oxygen (O₂ 100% v/v) achieved by a one minute oxygen flow (10 mBar). Controls were cultured in a similar way but with a normal atmosphere (20.5% v/v oxygen). For all three species a major improvement in plating efficiency and colony formation was observed in the oxygen-enriched atmospheres. In the case of rice, cultivar Taipei 309, a significant increase in plant regeneration capacity, from protoplast-derived colonies, was observed for the high oxygen cultures.Abbreviations MES 2-N-morpholinoethane sulfonic acid - PE plating efficiency