Enumeration and biomass estimation of bacteria in aquifer microcosm studies by flow cytometry

Flow cytometry and environmental microbiology

This survey unit discusses many of the issues involved for flow cytometry in the field of microbiology, particularly the preparative procedures, which are far more stringent than many other procedures using larger cells. For instance, it is often necessary to filter laboratory agents multiple times to obtain the true particle-free solutions needed for flow cytometry of microbes. It is difficult enough to recognize bacteria in cell extracts from soil, sediment, or sludge given the background of same-size particles. This unit provides an excellent overview of a potentially large application area in flow cytometry and is written by one of the most respected scientists in the field.

Fluorochrome and flow cytometry to monitor microorganisms in treated hospital wastewater

Flow cytometry with a fluorescent technique (FCM/FL), epifluorescence microscopy with a fluorescent technique (EFM/FL), and a culture method were used and compared to study the microorganism population profiles in wastewater treatment. In the two non-culture methods (FCM/FL and EFM/FL), four fluorescent dyes [acridine orange (AO), 4',6-diamino-2-phenylindole dihydrochloride (DAPI), propidium iodide (PI), and YOPRO-1] were used to determine the total concentration and viability of microorganisms in the wastewater samples. Results showed that the total cell concentrations (both the bacteria and fungi) determined by using the non-culture-based methods were 18 to 67 times higher than those by the culture method (p = 0.036): the total cell concentration ranged from 1.10 x 10(7) to 2.44 x 10(8) cells/mL determined by both FCM and EFM with AO-staining method, and from 1.02 x 10(7) to 2.00 x 10(8) cells/mL by EFM with DAPI-staining method, whereas the culturable concentration of bacteria and fungi ranged from 0 to 3.22 x 10(6) CFU/mL and from 0 to 4.13 x 10(5) CFU/mL, respectively. No difference in total concentrations between dyes (AO and DAPI) and methods (FCM and EFM) were observed. By using EFM method, the microorganism viability ranged from 0.24 to 0.86 with PI staining and from 0.09 to 0.74 with YOPRO-1 staining. In the FCM analysis, the microorganism viability ranged from 0.23 to 0.87 with PI staining and from 0.18 to 0.73 with YOPRO-1 staining. In addition, the cultivability of microorganism ranged from 0 to 0.105 by the culture method. The total concentrations and viabilities of microorganisms were highly underestimated by the culture method. Results also showed that the viabilities determined by using either EFM/FL or FCM/FL were significantly higher than the cultivabilities. In addition, significant difference in viability between PI and YOPRO-1 for both EFM and FCM analysis was observed. However, the difference in viability between EFM and FCM depended on dyes. In regard to the difference between bacteria and fungi, significant difference in total concentration, viability, and cultivability was observed. In conclusion, the EFM/FL and FCM/FL methods can effectively assess total concentration and viability of microorganisms in environmental samples.

Comparison between direct microscopy and flow cytometry for rRNA-based quantification of Candidatus Accumulibacter phosphatis in activated sludge

A comparison of the quantification of a specific microbial group in activated sludge by fluorescent in-situ hybridization, coupled with either direct microscopic counting or flow cytometry, was performed using an enhanced-biological-phosphorus-removal, sequencing-batch reactor. The population dynamics of Candidatus Accumulibacter phosphatis (Cand. A. phosphatis) was evaluated during two separate runs of the reactor. With the operational conditions used, Cand. A. phosphatis was enriched until a failure in the pH controller eliminated its ecological advantage. As a result, the comparison of quantification techniques included Cand. A. phosphatis concentrations as low as 11% and as high as 96% of the total cells in the samples. The analysis demonstrated that, regardless of the particular limitations of each technique, both provided similar results when the activated-sludge flocs were easily dispersed. However, when the activated-sludge samples contained flocs that were difficult to disperse, flow cytometry failed to provide quantitative results.

Measurement of the viability of Lawsonia intracellularis

The objective of this study was to develop and test both a flow cytometry method (FCM) and a direct count method (DCM) that both use fluorescent stains to determine the viability of Lawsonia intracellularis (LI), an obligate intracellular bacterium and the cause of proliferative enteropathy (PE) in pigs and other animal species. Live LI were passaged in cell culture and harvested from infected McCoy cells. Dead LI were prepared by exposing live LI to 70% isopropyl alcohol for 30 min. Seven samples with dead:live ratios of 0:100 (live control), 10:90, 30:70, 50:50, 70:30, 90:10, and 100:0 (dead control) were prepared for testing by both the FCM and the DCM. For the FCM, TO-PRO-3 iodine was applied to the samples, and viable LI were counted. For the DCM, the samples were stained with LIVE/DEAD BacLight, which contains SYTO 9 and propidium iodine, then filtered through 0.2-microm Nuclepore black polycarbonate filters, viewed, and counted with the use of an epifluorescence microscope. Data were evaluated by estimating 95% limits of agreement and the concordance correlation coefficient (CCC). The limits of agreement between the FCM and the DCM versus the standard ratio of added LI showed mean differences not equal to zero, suggesting that systematic bias was introduced. The CCC showed almost perfect agreement (r = 0.9898). With a specific fluorescent probe, the FCM is useful and as good as the DCM for determining LI viability.

Bioaerosol characterization by flow cytometry with fluorochrome

Traditional culture and microscopy methods for evaluation of bioaerosols are slow, tedious, and rather imprecise. In this study, the application of flow cytometry that was combined with a fluorescent technique (FCM/FL) was evaluated as a technique to quickly and accurately determine and quantify the total concentration and viability of bioaerosols. The optimal conditions of five fluorescent dyes [acridine orange (AO), SYTO-13, propidium iodide (PI), YOPRO-1, and 5-cyano-2,3-ditolytetrazolium chloride (CTC)] used in FCM/FL were determined for laboratory samples of bacterial aerosols (Escherichia coli, and endospores of Bacillus subtilis) and fungal aerosols (Candida famata and Penicillium citrinum spores). Based on the measured cell concentration, fluorescence intensity, and staining efficiency as indicators for dye performance evaluation, SYTO-13 was found to be the most suitable fluorescent dye for determining the total concentration of the bioaerosols, as well as YOPRO-1 was the most suitable for determining viability. Moreover, the established optimal FCM/FL with dyes was validated for characterizing microorganism profiles from both air and water samples from the aeration tank of hospital wastewater treatment plant. In conclusion, the FCM/FL successfully assessed the total concentration and viability for bacterial and fungal microorganisms in environmental field samples.

Real-time quantitative PCR with gene probe, fluorochrome and flow cytometry for microorganism analysis

Microorganism concentrations and viability can be better understood and clarified by using both culture and non-culture methods. Here, using pure suspensions of E. coli, three non-culture methods, namely, flow cytometry (FCM), epifluorescence microscopy (EFM), and real-time quantitative polymerase chain reaction (real-time qPCR), were compared with a traditional culture-based method. Using fluorocome-labeling methods with FCM and EFM applications, acridine orange (AO) and propidium iodide (PI) dyes were used to determine the total cell concentration and microorganism viability, respectively. The results indicated that total cell concentrations determined using FCM were statistically higher (2.62-4.94 times) than those determined using EFM. The difference might be due to cell losses induced by extensive preparations needed for EFM. In addition, EFM and FCM were highly associated for both the total cell concentration and viability. FCM-measured viability was the highest, whereas the culture-measured viability was the lowest. Furthermore, DNA concentrations measured by real-time qPCR with gene probe were highly associated with the total number concentrations measured by either the EFM or FCM. In summary, the three non-culture methods compared here could provide rapid and accurate information about microorganism concentrations and viabilities.

Development and use of flow cytometry for detection of airborne fungi

Traditional methods for the enumeration of airborne fungi are slow, tedious, and rather imprecise. In this study, the possibility of using flow cytometry (FCM) for the assessment of exposure to the fungus aerosol was evaluated. Epifluorescence microscopy direct counting was adopted as the standard for comparison. Setting up of the method was achieved with pure suspensions of Aspergillus fumigatus and Penicillium brevicompactum conidia at different concentrations, and then analyses were extended to field samples collected by an impinger device. Detection and quantification of airborne fungi by FCM was obtained combining light scatter and propidium iodide red fluorescence parameters. Since inorganic debris are unstainable with propidium iodide, the biotic component could be recognized, whereas the preanalysis of pure conidia suspensions of some species allowed us to select the area corresponding to the expected fungal population. A close agreement between FCM and epifluorescence microscopy counts was found. Moreover, data processing showed that FCM can be considered more precise and reliable at any of the tested concentrations.

Using light scatter signal to estimate bacterial biovolume by flow cytometry

BACKGROUND

In the past decade, flow cytometry has become a useful and precise alternative to microscopic bacterial cell counts in aquatic samples. However, little evidence of its usefulness for the evaluation of bacterial biovolumes has emerged in from the literature.

METHODS

The light scattering and cell volume of starved bacterial strains and natural bacterial communities from the Black Sea were measured by flow cytometry and epifluorescence microscopy, respectively, in order to establish a relationship between light scattering and cell volume.

RESULTS

With the arc-lamp flow cytometer, forward angle light scatter (FALS) was related to cell size in both the starved strains and natural communities, although regression parameters differed. We tested the predictive capacity of the FALS verous cell size relationship in a bacterial community from the North Sea. That analysis showed that a reliable bacterial biovolume prediction of a natural bacterial community can be obtained from FALS using a model generated from natural bacterial community data.

CONCLUSIONS

Bacterial biovolume is likely to be related to FALS measurements. It is possible to establish a generally applicable model derived from natural bacterial assemblages for flow cytometric estimation of bacterial biovolumes by light scatter.

Determination of total protein content of bacterial cells by SYPRO staining and flow cytometry

An assay has been developed for measuring protein biomass of marine planktonic bacteria by flow cytometry. The method was calibrated by using five species of Bacteria (an Arcobacter sp., a Cytophaga sp., an Oceanospirillum sp., a Pseudoalteromonas sp., and a Vibrio sp.) recently isolated from seawater samples and grown in culture at different temperatures. The intensity of SYPRO-protein fluorescence of these bacteria strongly correlated with their total protein content, measured by the bicinchoninic acid method to be in the range of 60 to 330 fg of protein cell-1 (r2 = 0.93, n = 34). According to the calibration, the mean biomass of planktonic bacteria from the North Sea in August 1998 was 24 fg of protein cell-1.

Response to high-pressure, low-temperature treatment in vegetables: determination of survival rates of microbial populations using flow cytometry and detection of peroxidase activity using confocal microscopy

Application of high hydrostatic pressure (200, 300, 350 and 400 MPa) at 5 degrees C for 30 min to different micro-organisms, including Gram-positive and Gram-negative bacteria, moulds and yeasts, proved to be more effective in inactivating these organisms than treatments at 20 degrees C for 10 min and at 10 degrees C for 20 min. Moulds, yeasts, Gram-negative bacteria and Listeria monocytogenes were most sensitive, and their populations were completely inactivated at pressures between 300 and 350 MPa. The same conditions of pressure, temperature, and time were applied to different vegetables (lettuce, tomato, asparagus, spinach, cauliflower and onion), achieving reductions of from 2-4 log units in both viable mesophiles and moulds and yeasts at pressures of between 300 and 400 MPa. Sensory characteristics were unaltered, especially in asparagus, onion, tomato and cauliflower, though slight browning was observed in cauliflower at 350 MPa. Flow cytometry was applied to certain of the microbial populations used in the above experiment before and after the pressurization treatment. The results were indicative of differing percentage survival rates depending on micro-organism type, with higher survival rates for Gram-positive bacteria, except L. monocytogenes, than in the other test micro-organisms. Growth of survivors was undetectable using the plate count method, suggesting that micro-organisms suffering from pressure stress were metabolically inactive though alive. The pressurization treatments did not inactivate the peroxidase responsible for browning in vegetables. Confocal microscopic examination of epidermal tissue from onion showed that the enzyme had been displaced to the cell interior. Use of low temperatures and moderately long pressurization times yielded improved inactivation of micro-organisms and better sensorial characteristics of the vegetables, and should lower industrial costs.

Determination of the biomasses of small bacteria at low concentrations in a mixture of species with forward light scatter measurements by flow cytometry

The forward light scatter intensity of bacteria analyzed by flow cytometry varied with their dry mass, in accordance with theory. A standard curve was formulated with Rayleigh-Gans theory to accommodate cell shape and alignment. It was calibrated with an extinction-culture isolate of the small marine organism Cycloclasticus oligotrophus, for which dry weight was determined by CHN analysis and 14C-acetate incorporation. Increased light scatter intensity due to formaldehyde accumulation in preserved cells was included in the standard curve. When differences in the refractive indices of culture media and interspecies differences in the effects of preservation were taken into account, there was agreement between cell mass obtained by flow cytometry for various bacterial species and cell mass computed from Coulter Counter volume and buoyant density. This agreement validated the standard curve and supported the assumption that cells were aligned in the flow stream. Several subpopulations were resolved in a mixture of three species analyzed according to forward light scatter and DNA-bound DAPI (4', 6-diamidino-2-phenylindole) fluorescence intensity. The total biomass of the mixture was 340 &mgr;g/liter. The lowest value for mean dry mass, 0.027 +/- 0.008 pg/cell, was for the subpopulation of C. oligotrophus containing cells with a single chromosome. Calculations from measurements of dry mass, Coulter Counter volume, and buoyant density revealed that the dry weight of the isolate was 14 to 18% of its wet weight, compared to 30% for Escherichia coli. The method is suitable for cells with 0.005 to about 1.2 pg of dry weight at concentrations of as low as 10(3) cells/ml and offers a unique capability for determining biomass distributions in mixed bacterial populations.