Nucleic acid-based fluorescent probes in microbial ecology: application of flow cytometry

The Challenges and Advances in Diagnosis of Vector-Borne Diseases: Where Do We Stand?

Vector-borne diseases (VBD) are of major importance to human and animal health. In recent years, VBD have been emerging or re-emerging in many geographical areas, alarming new disease threats and economic losses. The precise diagnosis of many of these diseases still remains a major challenge because of the lack of comprehensive data available on accurate and reliable diagnostic methods. Here, we conducted a systematic and in-depth review of the former, current, and upcoming techniques employed for the diagnosis of VBD.

Effect of dissolved oxygen changes on activated sludge fungal bulking during lab-scale treatment of acidic industrial wastewater

The cloning and sequencing of fungal 18S rRNA genes followed by the identification of filamentous fungal species by fluorescent in situ hybridization (FISH) and the enumeration of filamentous fungal cells by flow cytometry-FISH (FC-FISH) were used to investigate the effect of dissolved oxygen (DO) changes on activated sludge (AS) fungal bulking during a lab-scale treatment of acidic industrial wastewater. By increasing DO levels from < .5 to > 2 mg L⁻¹, bulking started to occur due to the outbreak of fungal filaments, whereas the chemical oxygen demand (COD) removals sharply increased from < 40 to > 70%. Clone library analyses revealed that all clonal fungal sequences were of yeast origin, and that only one and four yeast species were individually detected in AS at two DO levels. Subsequent FISH identification of filamentous yeast species within bulking sludge using self-designed oligonucleotide probes suggested that all probe-reactive cells of Trichosporon asahii had a filamentous morphology and were the dominating filamentous microorganism in the AS. The FC-FISH analyses of bacteria and two main yeast species showed that the DO shift resulted in a sharp increase of T. asahii, by a factor of 48-60, which caused filamentous yeast bulking. Subsequently, the restoration of DO levels to <0.5 mg L⁻¹ effectively restored the sludge settlement and yeast community, as well as unacceptable COD removals.

Comparative study of a new quantitative real-time PCR targeting the xylulose-5-phosphate/fructose-6-phosphate phosphoketolase bifidobacterial gene (xfp) in faecal samples with two fluorescence in situ hybridization methods

AIMS

To detect and enumerate bifidobacteria in faeces with a new quantitative multiplex real-time PCR (qPCR) method and to compare the results obtained with fluorescence in situ hybridization (FISH) methods.

METHODS AND RESULTS

A multiplex qPCR assay was developed, which enabled the enumeration of Bifidobacterium spp. by targeting the bifidobacterial xylulose-5-phosphate/fructose-6-phosphate phosphoketolase gene (xfp) and total bacteria using universal Eub-primers targeting 16S rRNA gene from the domain bacteria. The qPCR assay showed high sensitivity and specificity and a low detection limit of about 2.5 x 10(3) bifidobacterial cells per gram of faeces. The qPCR results were compared with FISH combined with microscopy or flow cytometry (FCM). No statistical differences among bifidobacterial counts averages measured in adult faeces with the three methods were observed. Total bacterial count averages were higher with the FISH method coupled with microscopic analyses compared to FISH with FCM, whereas total cell numbers estimated by qPCR were intermediate between the two FISH methods.

CONCLUSIONS

The new qPCR assay was shown to be sensitive, rapid and accurate for enumerating bifidobacteria in faeces.

SIGNIFICANCE AND IMPACT OF THE STUDY

This method is a valuable alternative for other molecular methods for detecting faecal bifidobacteria, especially when their counts are below the detection limit of the FISH methods.

Microbial communities in acid mine drainage and their interaction with pyrite surface

Microbes such as Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans have been investigated a lot, because of their important role in acid mine drainage (AMD) generation. In this article, the composition of microbial communities in two AMD samples was studied. A culture-independent 16S rDNA-based cloning approach, restriction fragment length polymorphism has been used. The interaction between microbes and natural pyrite specimen surface was researched by scanning electrode microscopy (SEM) and fluorescence in situ hybridization (FISH). The phylogenetic analysis revealed bacteria in these two samples fell into three major groups: Proteobacteria, Nitrospira, and Firmicutes. Archaea was also detected in these two samples. Thermoplasma and Ferroplasma lineages were abundant. From SEM and FISH, a number of A. ferrooxidans, a few cells of Archaea and Acidiphilium were detected adsorbed on the pyrite specimen surface. Leptospirillum sp. (hybridize with the probe LF655) has not been detected to be present on the pyrite specimen surface.

State transitions of Vibrio parahaemolyticus VBNC cells evaluated by flow cytometry

BACKGROUND

Vibrio parahaemolyticus, in response to environmental conditions, may be present in a viable but nonculturable state (VBNC), which can still be responsible for cases of infectious diseases in humans.

METHODS

The characterization of the cellular states of V. parahaemolyticus during entry into, persistence in, and resuscitation from the VBNC state, was assessed through plate culture method and epifluorescence microscope evaluation of actively respiring cells. Flow cytometry (FCM) in combination with SYBR Green I (SG) and propidium iodide allowed us to distinguish between viable, dead, and damaged-cells. Immunofluorescence labeling detected by FCM was used to study changes in antibody affinity.

RESULTS

Two groups of bacteria, one with High Nucleic Acid (HNA) and one having Low Nucleic Acid (LNA) content, were differentiated using SG and FCM and each was correlated with cell viability. With the aging of the microcosm, the LNA bacteria population increased while the HNA population gradually disappeared. Cytofluorimetric immunofluorescence analyses showed that the bacterial cell levels dropped from 95% at day 0 to 40% at day 26 and by day 29, antibody affinity was virtually lost. FCM analyses of light scatter signals expressed by cell population highlighted morphological changes indicating a reduction in cell size, as also shown by scanning electron microscopy images and variations in cell structure.

CONCLUSIONS

The methodology used has provided useful data in relation to the state transitions of V. parahaemolyticus regarding cell viability, antigenic surface components, and the quantification of morphological variations during its entry into the VBNC state.

A comparative study of the cytometric characteristics of high and low nucleic-acid bacterioplankton cells from different aquatic ecosystems

Flow cytometry has revealed the existence of two distinct fractions of bacterioplankton cells, characterized by high and low nucleic acid contents (HNA and LNA cells). Although these fractions seem ubiquitous in aquatic systems, little is known concerning the variation in the cytometric parameters used to characterize them. We have performed cytometric analyses of samples from a wide range of aquatic systems to determine the magnitude and variability in the cytometric characteristics of HNA/LNA. We show that neither group is associated to a fixed level of fluorescence and of light scatter. Rather, the relative position of HNA and LNA in the fluorescence versus side scatter cytograms varies greatly, both within and among ecosystems. Although the cytometric parameters of both groups tend to covary, there is often uncoupling between the two, particularly in light scatter. Our results show that, although the basic HNA/LNA configuration is present in most samples, its cytometric expression changes greatly in different ecosystems and along productivity gradients. The patterns in cytometric parameters do not support the simple, dichotomous view of HNA and LNA as active and inactive cells, or the notion of two distinct and independent communities, but rather suggest that there may be cells that are intrinsic to each fraction, as well as others that may exchange between fractions.

New method for assimilable organic carbon determination using flow-cytometric enumeration and a natural microbial consortium as inoculum

The concentration of easily assimilable organic carbon (AOC) largely determines the microbiological stability of drinking water. However, AOC determination is often neglected in practice due to the complex and tedious nature of the conventional bioassay. The three major drawbacks of the conventional method are (1) a long assay time of 9-12 days, (2) the use of a labor-intensive enumeration technique (plating on growth media), and (3) limited information supplied by the use of selected pure cultures (Pseudomonas fluorescens P-17 and Spirillum NOX) for measuring a complex pool of natural bioavailable carbon compounds. A new method is proposed here, in which plating was replaced with fluorescence staining of total nucleic acids combined with flow cytometry as a rapid and straightforward growth enumeration method. This approach also allowed for the detection of inactive and/or unculturable microorganisms. Hence, the conventionally used pure cultures were replaced in the new AOC assay with a natural microbial consortium. It was shown that the flow-cytometric enumeration method could be used to establish complete growth curves for a natural microbial consortium growing on AOC. Compared to the end-point measurements of the conventional method, such kinetic data provide much clearer insight into the actual growth potential of a water.

Detection of Salmonella in environmental water and sediment by a nested-multiplex polymerase chain reaction assay

From 1995 to 2002, 53 serovars of Salmonella were isolated in the Seine estuary (France). The 3 serovars most frequently found were S. enterica serovar Typhimurium, S. enterica serovar Infantis and S. enterica serovar Virchow. A nested multiplex PCR (nm-PCR) assay was developed to detect the presence of Salmonella in estuarine water and sediment samples. The target gene used was the phase 1 flagellin fliC chromosomal gene, present in all Salmonella serovars. A set of 4 primers was first used to amplify an 890-bp sequence of the fliC gene, and then a second set of 3 primers was used for the nested PCR. The nmPCR method has been successfully tested for 28 serovars, 13 of which are of epidemiological significance. The detection limit of the assay, without any pre-enrichment step, was estimated at 1 CFU in deionized water, and at 4-5 CFU in the reaction mixture when tested on estuarine water seeded with a Salmonella strain. When the nmPCR was used together with the classical culture method in environmental samples, it gave additional positive results for 11.3% of the sediment samples and 20% of the water samples despite a high background of other bacteria. Overall, the results demonstrated that this molecular approach informed us about the contamination by Salmonella of estuarine water and sediment samples. Positive amplifications suggested the presence of Salmonella DNA and could thus provide information about a recent (culturable) or past (non-culturable, released DNA) contamination of environmental samples by this pathogenic bacteria.

Effect of trophic status on the culturability and activity of bacteria from a range of lakes in the English Lake District

The bacterioplankton from a number of lakes that differed in nutrient status in the English Lake District was examined with a number of techniques for enumeration and activity assessment. Natural water samples showed a clear correlation between total counts and trophic status. Esterase activity measurements with Chemchrome B were able to distinguish high- and low-nutrient-status lakes, whereas tetrazolium salt (5-cyano-2,3-ditoyltetrazolium chloride) reduction, the direct viable count-cell elongation assay, and culturability measurements could not. Tetrazolium salt reduction and esterase activity measurements labeled a significant number of cells from water of all nutrient levels, whereas the direct viable count-cell elongation method was of use only in oligotrophic waters. Size fractionation of samples showed that the culturable cells were retained by the larger filters, especially in nutrient-rich waters. Esterase activity measurements also favored the larger cells. The differences observed between assays using water that differed in trophic status raise questions about the use of these tests as a definitive measure of viability.

Intestinal microecology and quality of life in irritable bowel syndrome patients

AIM: It has been noticed that gastroenteritis or dysentery plays a role in pathogenesis of irritable bowel syndrome (IBS), and antibiotics can increase functional abdominal symptoms, both of which may be partly due to intestinal flora disorders. This study was to determine the change of gut flora of IBS, a cluster of abdominal symptoms. Because of the chronic course and frequent occurrence of the disease, IBS patients suffered much from it. So the quality of life (Qol) of IBS patients was also evaluated in this study.

METHODS: Twenty-five Rome II criteria-positive IBS patients were recruited, and 25 age and gender-matched healthy volunteers were accepted as control. The fecal flora, including Lactobacillus, Bifidobacterium, Bacteroides , C. perfringens Enterobacteriacea and Enterococus, were analyzed quantitatively and qualitatively. We also calculated the ratio of Bifidobacterium to Enterobacteriaceae (B/E ratio) in both IBS patients and controls. In both groups, the data were further analyzed based on age difference, and comparisons were made between the younger and elder subgroups. We also evaluated the quality of life (QoL) of IBS patients and the control group using the Chinese version of SF-36 health questionnaire.

RESULTS: In IBS patients, the number of fecal Bifidobacterium was significantly decreased and that of Enterobacteriaceae was significantly increased compared with that in healthy controls (both P < 0.05).The mean microbial colonization resistance (CR) of the bowel in IBS patients was smaller than 1, making a significant difference compared with that in control which was more than 1 (P < 0.01). There was no significant difference in gut flora between two subgroups. While in control, the elder subgroup presented more Enterobacteriacea than the younger one (P < 0.05). Compared with the control group, IBS patients had significantly lower scores on all SF-36 scales, with the exception of physical functioning. However, there was no significant correlation between quality of life and enteric symptoms in IBS patients.

CONCLUSION: There are intestinal flora disorders in IBS patients, which may be involved in triggering the IBS-like symptoms. IBS patients experience significant impairment in QoL, however, the impairment is not caused directly by enteric symptoms.

Quenched auto-ligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution

We describe the synthesis and study of multicolor quenched autoligating (QUAL) probes for identification and discrimination of closely related RNA and DNA sequences in solution and in bacteria. In these probes, a dabsyl quencher doubles as an activator in the oligonucleotide-joining reaction. The oligonucleotides remain dark until they bind at adjacent sites, and "light up" on nucleophilic displacement of the dabsyl probe by the phosphorothioate probe. Four fluorescent dye conjugates were prepared and tested with probes and targets that differ by one nucleotide. Experiments on polymer beads show clear color-based discrimination of DNAs added in solution. Two-color quenched probe pairs were then tested in the discrimination of 16S rRNA sequences in Escherichia coli. Single nucleotide resolution was achieved in the cells with green/red QUAL probes, allowing identification of a one-base sequencing error in the 16S rRNA database. Finally, QUAL probes were successfully applied in live bacterial cells. The method requires only incubation followed by fluorescence imaging, and requires no enzymes, added reagents, cross-linking, fixing, or washes. Because probes must bind side-by-side to generate signal, there is little or no interference from unintended protein binding, which can occur with other probe types. The results suggest that QUAL probes may be of general use in the detection and identification of sequences in solution, on microarrays, and in microorganisms.

Growth of mixed cultures on mixtures of substitutable substrates: the operating diagram for a structured model

The growth of mixed microbial cultures on mixtures of substrates is a problem of fundamental biological interest. In the last two decades, several unstructured models of mixed-substrate growth have been studied. It is well known, however, that the growth patterns in mixed-substrate environments are dictated by the enzymes that catalyse the transport of substrates into the cell. We have shown previously that a model taking due account of transport enzymes captures and explains all the observed patterns of growth of a single species on two substitutable substrates (J. Theor. Biol. 190 (1998) 241). Here, we extend the model to study the steady states of growth of two species on two substitutable substrates. The model is analysed to determine the conditions for existence and stability of the various steady states. Simulations are performed to determine the flow rates and feed concentrations at which both species coexist. We show that if the interaction between the two species is purely competitive, then at any given flow rate, coexistence is possible only if the ratio of the two feed concentrations lies within a certain interval; excessive supply of either one of the two substrates leads to annihilation of one of the species. This result simplifies the construction of the operating diagram for purely competing species. This is because the two-dimensional surface that bounds the flow rates and feed concentrations at which both species coexist has a particularly simple geometry: It is completely determined by only two coordinates, the flow rate and the ratio of the two feed concentrations. We also study commensalistic interactions between the two species by assuming that one of the species excretes a product that can support the growth of the other species. We show that such interactions enhance the coexistence region.

Use of a similarity index based on microbial fatty acid (MFA) analysis to monitor biological wastewater treatment systems

Estimating the stability of microbial community structures may be useful in advanced biological wastewater treatment system design and operation. In this research, a monitoring method using fatty acid profiles was evaluated for detecting changes in microbial community structures. For the evaluation, the operating parameters such as pH, organic loading, and chlorine addition were varied in two identical laboratory scale conventional activated sludge systems. A similarity index based on microbial fatty acid analysis was used to express the stability of microbial community structures in the systems. Experiments using a model microbial community showed that microbial compositions changed daily even under constant operating conditions and that the rate of change increased under dynamic operating conditions. Substrate changes brought about a relatively large change in a microbial community structure, eventually resulting in a very different microbial community. After only 7 days following a substrate change in a lab-scale bioreactor, the biomass exhibited only 45% similarity to the original structure. The analysis of microbial fatty acids conveys additional information, in that it could be used for the calculation of biomass concentrations in a wastewater treatment system if microbial fatty acid analyses are executed on a routine basis as a monitoring tool for biological wastewater treatment systems. The total fatty acid concentrations were about 0.61% of the biomass concentration as mixed liquor volatile suspended solid concentrations in this research.

The identification of microorganisms by fluorescence in situ hybridisation

Fluorescence in situ hybridisation (FISH) with rRNA-targeted oligonucleotide probes facilitates the rapid and specific identification of individual microbial cells in their natural environments. Over the past year there have been a number of methodological developments in this area and new applications of FISH in microbial ecology and biotechnology have been reported.

Microbial analysis at the single-cell level: tasks and techniques

The heterogeneity of microorganisms themselves is orders of magnitude greater than the heterogeneity of perspectives from which they are contemplated by human observers. Even closely related species may exhibit marked differences in biochemistry and behavior, and, under many conditions, similar, striking heterogeneity may exist within a clonal population of organisms which, in the aggregate, occupy too small a region of space to be visible to the unaided human eye. Using methods of microscopy, microspectrophotometry, and cytometry developed and refined since the 1960s, it is now possible to characterize the physiology and pharmacology of individual microorganisms, and, in many cases, to isolate organisms with selected characteristics for culture and/or further analysis. These methods include fluorescent and confocal microscopy, scanning and image cytometry, and flow cytometry. Fluorescence measurements are particularly important in single-cell analysis; they allow demonstration and quantification of cells' nucleic acid content and sequence, of the presence of specific antigens, and of physiologic characteristics such as enzyme activity and membrane potential. Multiparameter cytometry, combined with cell sorting, provides insight into population heterogeneity and allows selected cells to be separated for further analysis and culture. The technology is applicable to a wide range of problems in contemporary microbiology, including strain selection and the development of antimicrobial agents.