Differentiation of Methanosaeta concilii and Methanosarcina barkeri in Anaerobic Mesophilic Granular Sludge by Fluorescent In Situ Hybridization and Confocal Scanning Laser Microscopy

Oligonucleotide probes, designed from genes coding for 16S rRNA, were developed to differentiate Methanosaeta concilii, Methanosarcina barkeri, and mesophilic methanogens. All M. concilii oligonucleotide probes (designated MS1, MS2, and MS5) hybridized specifically with the target DNA, but MS5 was the most specific M. concilii oligonucleotide probe. Methanosarcina barkeri oligonucleotide probes (designated MB1, MB3, and MB4) hybridized with different Methanosarcina species. The MB4 probe specifically detected Methanosarcina barkeri, and the MB3 probe detected the presence of all mesophilic Methanosarcina species. These new oligonucleotide probes facilitated the identification, localization, and quantification of the specific relative abundance of M. concilii and Methanosarcina barkeri, which play important roles in methanogenesis. The combined use of fluorescent in situ hybridization with confocal scanning laser microscopy demonstrated that anaerobic granule topography depends on granule origin and feeding. Protein-fed granules showed no layered structure with a random distribution of M. concilii. In contrast, a layered structure developed in methanol-enriched granules, where M. barkeri growth was induced in an outer layer. This outer layer was followed by a layer composed of M. concilii, with an inner core of M. concilii and other bacteria.     

Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms

The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.     

活细胞钙动态的共聚焦扫描显微镜检测技术

共聚焦激光扫描显微镜（Confocal Laser Scarming Microscope,CLSM）广泛应用于活细胞内钙敏感探针标记的钙水平的动态测量。较之传统的显微镜CLSM在钙成像分析上有着不可比拟的优越性,但也存在一些缺陷,近些年陆续出现了一些针对这些缺陷的改善措施,如比率法、葡聚糖探针及其他一些新技术与共聚焦显微镜的联合应用等,并且出现了诸如双光子显微镜等新型激光共聚焦显微镜。随着共聚焦钙成像技术的不断发展进步,其今后的应用前景将会越越广阔。     

激光扫描共聚焦显微镜荧光探针的选择和应用

激光扫描共聚焦显微镜是检测生物荧光信号的最新技术手段。不仅广泛用于荧光定性、定量测量,还可用于活细胞动态荧光监测、组织细胞断层扫描、三维图象重建、共聚焦图象分析、荧光光漂白恢复、激光显微切割手术等。本文拟就激光扫描共聚焦显微镜常用的检测内容及其相关荧光探针的选择和应用做一简单的介绍。     

Oral Biofilm Analysis of Palatal Expanders by Fluorescence In-Situ Hybridization and Confocal Laser Scanning Microscopy

Confocal laser scanning microscopy (CLSM) of natural heterogeneous biofilm is today facilitated by a comprehensive range of staining techniques, one of them being fluorescence in situ hybridization (FISH).^1,2 We performed a pilot study in which oral biofilm samples collected from fixed orthodontic appliances (palatal expanders) were stained by FISH, the objective being to assess the three-dimensional organization of natural biofilm and plaque accumulation.^3,4 FISH creates an opportunity to stain cells in their native biofilm environment by the use of fluorescently labeled 16S rRNA-targeting probes.^4-7,19 Compared to alternative techniques like immunofluorescent labeling, this is an inexpensive, precise and straightforward labeling technique to investigate different bacterial groups in mixed biofilm consortia.^18,20 General probes were used that bind to Eubacteria (EUB338 + EUB338II + EUB338III; hereafter EUBmix),^8-10 Firmicutes (LGC354 A-C; hereafter LGCmix),^9,10 and Bacteroidetes (Bac303).¹¹ In addition, specific probes binding to Streptococcus mutans (MUT590)^12,13 and Porphyromonas gingivalis (POGI)^13,14 were used. The extreme hardness of the surface materials involved (stainless steel and acrylic resin) compelled us to find new ways of preparing the biofilm. As these surface materials could not be readily cut with a cryotome, various sampling methods were explored to obtain intact oral biofilm. The most workable of these approaches is presented in this communication. Small flakes of the biofilm-carrying acrylic resin were scraped off with a sterile scalpel, taking care not to damage the biofilm structure. Forceps were used to collect biofilm from the steel surfaces. Once collected, the samples were fixed and placed directly on polysine coated glass slides. FISH was performed directly on these slides with the probes mentioned above. Various FISH protocols were combined and modified to create a new protocol that was easy to handle.^5,10,14,15 Subsequently the samples were analyzed by confocal laser scanning microscopy. Well-known configurations^3,4,16,17 could be visualized, including mushroom-style formations and clusters of coccoid bacteria pervaded by channels. In addition, the bacterial composition of these typical biofilm structures were analyzed and 2D and 3D images created.     

Apoptosis and Morphology in Mouse Embryos by Confocal Laser Scanning Microscopy

Confocal laser scanning microscopy combined with a vital stain was used to study apoptosis in organogenesis-stage mouse embryos. Apoptosis has previously been visualized in whole embryos using the vital dyes acridine orange, Nile blue sulfate, and neutral red. In the present study, mouse embryos were harvested on Gestation Day 9 and stained with the vital lysosomal dye LysoTracker Red. Following incubation in the stain, embryos were fixed overnight in 4% paraformaldehyde, dehydrated in a graded methanol series, and cleared in benzyl alcohol/benzyl benzoate. The resulting embryo is almost transparent and retains specific LysoTracker Red staining. To achieve optical sectioning through embryos, it was necessary to use low-power objectives. With this procedure, the entire embryo can be optically sectioned and reconstructed in three dimensions to reveal areas of dye staining. Our results demonstrate specific regions undergoing programmed cell death in normal development and increased LysoTracker staining in embryos exposed to hydroxyurea. This procedure allows for the optical imaging of whole Day 9 ( approximately 22 somites) embryos that were greater than 700 microm thick in the z axis and can be applied to studies involving neural tube formation or other aspects of organogenesis.     

Determination of Spatial Distributions of Zinc and Active Biomass in Microbial Biofilms by Two-Photon Laser Scanning Microscopy

The spatial distributions of zinc, a representative transition metal, and active biomass in bacterial biofilms were determined using two-photon laser scanning microscopy (2P-LSM). Application of 2P-LSM permits analysis of thicker biofilms than are amenable to observation with confocal laser scanning microscopy and also provides selective excitation of a smaller focal volume with greater depth localization. Thin Escherichia coli PHL628 biofilms were grown in a minimal mineral salts medium using pyruvate as the carbon and energy source under batch conditions, and thick biofilms were grown in Luria-Bertani medium using a continuous-flow drip system. The biofilms were visualized by 2P-LSM and shown to have heterogeneous structures with dispersed dense cell clusters, rough surfaces, and void spaces. Contrary to homogeneous biofilm model predictions that active biomass would be located predominantly in the outer regions of the biofilm and inactive or dead biomass (biomass debris) in the inner regions, significant active biomass fractions were observed at all depths in biofilms (up to 350 μm) using live/dead fluorescent stains. The active fractions were dependent on biofilm thickness and are attributed to the heterogeneous characteristics of biofilm structures. A zinc-binding fluorochrome (8-hydroxy-5-dimethylsulfoamidoquinoline) was synthesized and used to visualize the spatial location of added Zn within biofilms. Zn was distributed evenly in a thin (12 μm) biofilm but was located only at the surface of thick biofilms, penetrating less than 20 μm after 1 h of exposure. The relatively slow movement of Zn into deeper biofilm layers provides direct evidence in support of the concept that thick biofilms may confer resistance to toxic metal species by binding metals at the biofilm-bulk liquid interface, thereby retarding metal diffusion into the biofilm (G. M. Teitzel and M. R. Park, Appl. Environ. Microbiol. 69:2313-2320, 2003).     

Structure and Composition of Aggregates in Two Large European Rivers,Based on Confocal Laser Scanning Microscopy and Image and Statistical Analyses

Floating riverine aggregates are composed of a complex mixture of inorganic and organic components from their respective aquatic habitats. Their architecture and integrity are supplemented by the presence of extracellular polymeric substances of microbial origin. They are also a habitat for virus-like particles, bacteria, archaea, fungi, algae, and protozoa. In this study we present different confocal laser scanning microscopy strategies to examine aggregates collected from the Danube and Elbe Rivers. In order to collect multiple types of information, various approaches were necessary. Small aggregates were examined directly. To analyze large and dense aggregates, limitations of the technique were overcome by cryo-sectioning and poststaining of the samples. The staining procedure included positive staining (specific glycoconjugates and cellular nucleic acid signals) as well as negative staining (aggregate volume) and multichannel recording. Data sets of cellular nucleic acid signals (CNAS) and the structure of aggregates were visualized and quantified using digital image analysis. The Danube and Elbe Rivers differed in their aggregate composition and in the relative contribution of specific glycoconjugate and CNAS volume to the aggregate volume; these contributions also changed over time. We report different spatial patterns of CNAS inside riverine aggregates, depending on aggregate size and season. The spatial structure of CNAS inside riverine aggregates was more complex in the Elbe River than in the Danube River. Based on our samples, we discuss the strengths and challenges involved in scanning and quantifying riverine aggregates.In rivers, primary particles are frequently and perhaps characteristically transported as larger flocculated aggregates. They are structurally very stable because they are exposed to a constant shear force, resulting in relatively small aggregates compared to aggregates in lakes and marine systems (41, 49). Abiotic mechanisms such as physical coagulation, collision frequency, and stickiness are involved in particle aggregation (12). These aggregates, which may be regarded as mobile biofilms (e.g., 8, 9), can be very heterogeneous in their composition. Up to 97% of the biofilm matrix is actually water (46). Apart from water, biofilms may consist of dissolved, colloidal, and particulate materials varying in size and composition (12). They are composed of a complex mixture of components including inorganic (minerals), living organic (bacteria, archaea, fungi, algae, protozoa, and viruses), and nonliving organic (extracellular polymeric substances [EPS], allochthonous and autochthonous detritus, lignins, tannins, etc.) material from the respective aquatic habitat and its terrestrial environment (41). Cellular material within a biofilm can vary greatly. Measurements of organic carbon content suggest that cellular material represents 2 to 15% of the biofilm (46). Up to 95% of the biofilm is composed of EPS (13, 23, 42). The actual structure of the biofilm matrix varies greatly depending on the microbial cells present, their physiological status, the nutrients available, and the prevailing physical conditions (46).Knowledge about the structure and the function of aggregates, both in environmental and engineered systems, is very important (12). In engineered systems such as wastewater treatment plants, understanding flocculation can help in the management of that process. In environmental systems, such structure-function relationships can provide ecologically relevant information about material transfers between particulate and dissolved matter or about spatial distribution of microorganisms, with the related impacts on the aquatic food web. Numerous methods are available to help characterize aggregate properties. Microscopic as well as photographic techniques have been used to analyze aggregate structure. In recent years, confocal laser scanning microscopy (CLSM) data sets have allowed the visualization and quantification of three-dimensional (3-D) structures (18, 31).In this study, we analyzed aggregates from the Danube and Elbe Rivers by collecting reflection, nucleic acid, glycoconjugate, and negative stain signals using CLSM. In order to receive multifarious information about the aggregates, various approaches were necessary: small aggregates were examined directly, and large and dense aggregates were physically sectioned and poststained. Although most of the detected nucleic acid signals derive from bacteria, we refer to them as cellular nucleic acid signals (CNAS) including potential archaea and virus signals. Nucleic acid signals can potentially also be obtained from fungi, algae, and protozoa. But the detection of extracellular DNA can be excluded due to its type of appearance (7). Data sets of specific glycoconjugates, CNAS, and aggregate structure were visualized and quantified by using digital image analysis. The distribution of CNAS within riverine aggregates was determined by autocorrelation. Based on our samples, we describe the strengths and challenges in scanning and quantifying riverine aggregates using CLSM. Additionally, we discuss structure, function, and potentially important differences in aquatic aggregates from these two large European rivers.     

An Aufwuchs Chamber Slide for High-Resolution Confocal Laser Scanning Microscopy and Stereo Imaging of Microbial Communities in Natural Biofilms

Aufwuchs chamber slides were constructed by attaching a silicone rubber gasket to a glass slide with epoxy cement. For biofilm growth, the slides were suspended in Cayuga Lake near Ithaca, NY, for 27 days. Biofilms in the chamber were stained with 0.05% acridine orange. After rinsing, the chamber was filled with molten 1% agarose to stabilize filaments and delicate polymer structures at the biofilm surface. Areas of biofilm ~0.5 mm thick on the inner face of the wall of the chamber were selected for side-on optical sectioning in a confocal laser scanning microscope (CLSM). Stacks of high-resolution optical images captured by the CLSM z-sectioning software, were used to create left-right stereo image pairs. At low magnification the stereo pairs showed 3-D details of the microbial landscape in the mature biofilms. Channels, pores, and other structural features of the biofilm matrix were observed in peripheral regions. Higher magnification images revealed the 3-D distribution of specific biofilm components such as filaments of sheathed bacteria projecting outward into the liquid milieu, and organic coatings, including bacterial cells on the surfaces of mineral particles.     

激光扫描共聚焦显微镜术中活细胞标本的制备

激光扫描共聚焦显微镜是以单个的、活性的、贴壁的细胞标本为主要的研究对象。为了获得适合共聚焦显微镜分析的组织细胞标本,本文讨论了标本制备存在的一些问题并提出了改进的方法。结果显示：组织细胞外环境中盐溶液、ｐＨ值、温度、氧气等均为影响细胞活性的重要因素;而且细胞的贴壁效果也是观测分析的关键条件之一。本文对激光扫描共聚焦显微镜术中的组织细胞学方法进行了探讨,并为此提供一些有实效的实验方法。     

应用激光扫描共聚焦显微镜研究卵母细胞和早期胚胎的细胞骨架

介绍了应用激光扫描共聚焦显微镜, 结合免疫荧光技术研究卵母细胞和早期胚胎细胞骨架的方法.观察了β-微管蛋白、γ-微管蛋白、微丝以及染色体在小鼠卵母细胞和早期胚胎中的分布和形态, 讨论了实验过程中的注意事项以及实验结果的分析和处理方法.     

激光扫描共聚焦显微镜对人类染色体三维结构的观察

为了获得染色体内部结构的多种信息,以及对染色体形态构建提供有益的尝试,本试验利用荧光染料的特异性标记及激光扫描共聚焦显微镜的连续断层扫描和三维重建的特点,对人类染色体的形态结构进行观测,结果显示：本方法不仅能显示染色体的荧光带纹的分布状况,而且能作染色体内部的一系列光学切片和染色体三维结构的观测。     

Mapping of Heavy Metal Ion Sorption to Cell-Extracellular Polymeric Substance-Mineral Aggregates by Using Metal-Selective Fluorescent Probes and Confocal Laser Scanning Microscopy

Biofilms, organic matter, iron/aluminum oxides, and clay minerals bind toxic heavy metal ions and control their fate and bioavailability in the environment. The spatial relationship of metal ions to biomacromolecules such as extracellular polymeric substances (EPS) in biofilms with microbial cells and biogenic minerals is complex and occurs at the micro- and submicrometer scale. Here, we review the application of highly selective and sensitive metal fluorescent probes for confocal laser scanning microscopy (CLSM) that were originally developed for use in life sciences and propose their suitability as a powerful tool for mapping heavy metals in environmental biofilms and cell-EPS-mineral aggregates (CEMAs). The benefit of using metal fluorescent dyes in combination with CLSM imaging over other techniques such as electron microscopy is that environmental samples can be analyzed in their natural hydrated state, avoiding artifacts such as aggregation from drying that is necessary for analytical electron microscopy. In this minireview, we present data for a group of sensitive fluorescent probes highly specific for Fe³⁺, Cu²⁺, Zn²⁺, and Hg²⁺, illustrating the potential of their application in environmental science. We evaluate their application in combination with other fluorescent probes that label constituents of CEMAs such as DNA or polysaccharides and provide selection guidelines for potential combinations of fluorescent probes. Correlation analysis of spatially resolved heavy metal distributions with EPS and biogenic minerals in their natural, hydrated state will further our understanding of the behavior of metals in environmental systems since it allows for identifying bonding sites in complex, heterogeneous systems.     

Scanning Transmission X-Ray, Laser Scanning, and Transmission Electron Microscopy Mapping of the Exopolymeric Matrix of Microbial Biofilms

Confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and soft X-ray scanning transmission X-ray microscopy (STXM) were used to map the distribution of macromolecular subcomponents (e.g., polysaccharides, proteins, lipids, and nucleic acids) of biofilm cells and matrix. The biofilms were developed from river water supplemented with methanol, and although they comprised a complex microbial community, the biofilms were dominated by heterotrophic bacteria. TEM provided the highest-resolution structural imaging, CLSM provided detailed compositional information when used in conjunction with molecular probes, and STXM provided compositional mapping of macromolecule distributions without the addition of probes. By examining exactly the same region of a sample with combinations of these techniques (STXM with CLSM and STXM with TEM), we demonstrate that this combination of multimicroscopy analysis can be used to create a detailed correlative map of biofilm structure and composition. We are using these correlative techniques to improve our understanding of the biochemical basis for biofilm organization and to assist studies intended to investigate and optimize biofilms for environmental remediation applications.     

中国对虾卵子活化及卵裂的激光扫描共聚焦显微镜研究(英文)

有报导,与其它动物不同,对虾的卵子一接触海水、不经过受精,就可以被活化。但是,只有受精卵才能卵裂发育。而且,各种对虾卵子内皮质棒及皮层颗粒的形态结构、活化过程各有不同。本文就中国对虾卵子的活化及卵裂过程进行了激光扫描共聚焦显微镜（ＬＳＣＭ）研究。该技术可以清晰地显示细胞的立体图像。采集中国对虾,人工诱导产卵,未受精卵取自产卵虾体内,受精卵分期分批取样,固定。供试样品经ＰＢＳ漂洗,ＡＯ、ＦＩＴＣ和ＰＩ染色,ＬＳＣＭ观察、图像处理。刚产出的、未活化卵子形态不规则,皮层内富含皮质棒和皮层颗粒（Ｆｉｇ１）。不论受精与否,产入海水的卵子都能被激活并恢复减数分裂。活化后的卵子释放出皮层囊泡内的皮质棒（Ｆｉｇｓ２＆３）。释放出的皮质棒转变为均质的胶质层（Ｆｉｇｓ４＆５）。随后,皮层颗粒释放并在卵子表面转化为均质化的孵化膜。卵子开始举起,与孵化膜之间形成卵周隙。卵周隙内具有絮状物质（Ｆｉｇｓ６,７＆８）。卵子产出后笫８～１０ｍｉｎ,经过减数分裂,第一极体排放,并随着孵化膜的举起而被推向卵外（Ｆｉｇ５）。笫２０ｍｉｎ,第二极体排放,并由卵子表面到达孵化膜的内缘（Ｆｉｇ６）。在２０℃水温条件下,受精卵产入海水中６０     

Estimation of the State of the Bacterial Cell Wall by Fluorescent In Situ Hybridization

Fluorescent in situ hybridization (FISH) is now a widely used method for identification of bacteria at the single-cell level. With gram-positive bacteria, the thick peptidoglycan layer of a cell wall presents a barrier for entry of horseradish peroxidase (HRP)-labeled probes. Therefore, such probes do not give any signal in FISH unless cells are first treated with enzymes which hydrolyze the peptidoglycan. We explored this feature of FISH to detect cells which have undergone permeabilization due to expression of autolytic enzymes. Our results indicate that FISH performed with HRP-labeled probes provides a sensitive method to estimate the states of cell walls of individual gram-positive bacteria.     

In Situ Localization of Azospirillum brasilense in the Rhizosphere of Wheat with Fluorescently Labeled, rRNA-Targeted Oligonucleotide Probes and Scanning Confocal Laser Microscopy

The colonization of wheat roots by Azospirillum brasilense was used as a model system to evaluate the utility of whole-cell hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes for the in situ monitoring of rhizosphere microbial communities. Root samples of agar- or soil-grown 10- and 30-day-old wheat seedlings inoculated with different strains of A. brasilense were hybridized with a species-specific probe for A. brasilense, a probe hybridizing to alpha subclass proteobacteria, and a probe specific for the domain Bacteria to identify and localize the target bacteria. After hybridization, about 10 to 25% of the rhizosphere bacteria as visualized with 4(prm1),6-diamidino-2-phenylindole (DAPI) gave sufficient fluorescence signals to be detected with rRNA-targeted probes. Scanning confocal laser microscopy was used to overcome disturbing effects arising from autofluorescence of the object or narrow depth of focus in thick specimens. This technique also allowed high-resolution analysis of the spatial distribution of bacteria in the rhizosphere. Occurrence of cells of A. brasilense Sp7 and Wa3 was restricted to the rhizosphere soil, mainly to the root hair zone. C-forms of A. brasilense were demonstrated to be physiologically active forms in the rhizosphere. Strain Sp245 also was found repeatedly at high density in the interior of root hair cells. In general, the combination of fluorescently labeled oligonucleotide probes and scanning confocal laser microscopy provided a very suitable strategy for detailed studies of rhizosphere microbial ecology.     

Rotifer Nervous System Visualized by FMRFamide and 5-HT Immunocytochemistry and Confocal Laser Scanning Microscopy

The characteristic ecology of floodplain lakes is in part due to their relatively strong water-level fluctuations. We analyzed the factors determining water-level fluctuations in 100 floodplain lakes (during non-flooded conditions) in the active floodplains of the Lower Rhine in the Netherlands. Furthermore, we explored the relationship between water-level fluctuations and macrophyte species richness, and analyzed the suitability of artificially created lakes for macrophyte vegetation. During non-flooded conditions along the Rhine, lake water-level fluctuations are largely driven by groundwater connection to the river. Hence, water-level fluctuations are largest in lakes close to the main channel in strongly fluctuating sectors of the river and smallest in isolated lakes. Additionally, water-level fluctuations are usually small in old lakes, mainly due to reduced groundwater hydraulic conductivity resulting from accumulated clay and silt on the bottom. Species richness of floating-leaved and emergent macrophytes was reduced at both small and large water-level fluctuations, whereas species richness of submerged macrophytes was reduced at small water-level fluctuations only. In addition, species richness of submerged macrophytes was higher in lakes that experienced drawdown, whereas no similar pattern was detected for floating-leaved and emergent macrophytes. The decline in amplitude of lake water-level with lake age implies that the number of hydrologically dynamic lakes will decrease over time. Therefore, we suggest that excavation of new lakes is essential to conserve the successional sequence of floodplain water bodies including conditions of high biodiversity. Shallow, moderately isolated, lakes with occasional bottom exposure have the highest potential for creating macrophyte-rich floodplain lakes along large lowland rivers. The water-level regime of such lakes can in part be designed, through choice of the location along the river, the distance away from the river and the depth profile of the lake.     

共聚焦激光扫描显微镜在发育生物学中的应用

共聚焦激光扫描显微镜以高空间分辨率、非介入无损伤性连续光学切片、实时动态观察等优越性,应用于生物医学众多领域中。本文主要论述共聚焦激光扫描显微镜在发育生物学中的应用。     

Direct In Situ Viability Assessment of Bacteria in Probiotic Dairy Products Using Viability Staining in Conjunction with Confocal Scanning Laser Microscopy

The viability of the human probiotic strains Lactobacillus paracasei NFBC 338 and Bifidobacterium sp. strain UCC 35612 in reconstituted skim milk was assessed by confocal scanning laser microscopy using the LIVE/DEAD BacLight viability stain. The technique was rapid (<30 min) and clearly differentiated live from heat-killed bacteria. The microscopic enumeration of various proportions of viable to heat-killed bacteria was then compared with conventional plating on nutrient agar. Direct microscopic enumeration of bacteria indicated that plate counting led to an underestimation of bacterial numbers, which was most likely related to clumping. Similarly, LIVE/DEAD BacLight staining yielded bacterial counts that were higher than cell numbers obtained by plate counting (CFU) in milk and fermented milk. These results indicate the value of the microscopic approach for rapid viability testing of such probiotic products. In contrast, the numbers obtained by direct microscopic counting for Cheddar cheese and spray-dried probiotic milk powder were lower than those obtained by plate counting. These results highlight the limitations of LIVE/DEAD BacLight staining and the need to optimize the technique for different strain-product combinations. The minimum detection limit for in situ viability staining in conjunction with confocal scanning laser microscopy enumeration was ~10⁸ bacteria/ml (equivalent to ~10⁷ CFU/ml), based on Bifidobacterium sp. strain UCC 35612 counts in maximum-recovery diluent.