Detection, enumeration, and sizing of planktonic bacteria by image-analyzed epifluorescence microscopy

A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell

We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.

Metabolically active bacteria detected with click chemistry in low organic matter rainwater

Rain contains encapsulated bacteria that can be transported over vast distances during relatively short periods of time. However, the ecological significance of bacteria in "precontact" rainwater-rainwater prior to contact with non-atmospheric surfaces-remains relatively undefined given the methodological challenges of studying low-abundance microbes in a natural assemblage. Here, we implement single-cell "click" chemistry in a novel application to detect the protein synthesis of bacteria in precontact rainwater samples as a measure of metabolic activity. Using epifluorescence microscopy, we find approximately 103-104 bacteria cells mL-1 with up to 7.2% of the observed cells actively synthesizing protein. Additionally, our measurement of less than 30 μM total organic carbon in the samples show that some rainwater bacteria can metabolize substrates in very low organic matter conditions, comparable to extremophiles in the deep ocean. Overall, our results raise new questions for the field of rainwater microbiology and may help inform efforts to develop quantitative microbial risk assessments for the appropriate use of harvested rainwater.

Leaching material from Antarctic seaweeds and penguin guano affects cloud-relevant aerosol production

Within the Southern Ocean, the greatest warming is occurring on the Antarctic Peninsula (AP) where clear cryospheric and biological consequences are being observed. Antarctic coastal systems harbour a high diversity of marine and terrestrial ecosystems heavily influenced by Antarctic seaweeds (benthonic macroalgae) and bird colonies (mainly penguins). Primary sea spray aerosols (SSA) formed by the outburst of bubbles via the sea-surface microlayer depend on the organic composition of the sea water surface. In order to gain insight into the influence of ocean biology and biogeochemistry on atmospheric aerosol, we performed in situ laboratory aerosol bubble chamber experiments to study the effect of different leachates of biogenic material - obtained from common Antarctic seaweeds as well as penguin guano - on primary SSA. The addition of different leachate materials on a seawater sample showed a dichotomous effect depending on the leachate material added - either suppressing (up to 52%) or enhancing (22-88%) aerosol particle production. We found high ice nucleating particle number concentrations resulting from addition of guano leachate material. Given the evolution of upper marine polar coastal ecosystems in the AP, further studies on ocean-atmosphere coupling are needed in order to represent the currently poorly understood climate feedback processes.

A state-of-the-art survey of object detection techniques in microorganism image analysis: from classical methods to deep learning approaches

Microorganisms play a vital role in human life. Therefore, microorganism detection is of great significance to human beings. However, the traditional manual microscopic detection methods have the disadvantages of long detection cycle, low detection accuracy in large orders, and great difficulty in detecting uncommon microorganisms. Therefore, it is meaningful to apply computer image analysis technology to the field of microorganism detection. Computer image analysis can realize high-precision and high-efficiency detection of microorganisms. In this review, first,we analyse the existing microorganism detection methods in chronological order, from traditional image processing and traditional machine learning to deep learning methods. Then, we analyze and summarize these existing methods and introduce some potential methods, including visual transformers. In the end, the future development direction and challenges of microorganism detection are discussed. In general, we have summarized 142 related technical papers from 1985 to the present. This review will help researchers have a more comprehensive understanding of the development process, research status, and future trends in the field of microorganism detection and provide a reference for researchers in other fields.

Dominant marine heterotrophic flagellates are adapted to natural planktonic bacterial abundances

Grazing controls bacterial abundances and composition in many ecosystems. In marine systems, heterotrophic flagellates (HFs) are important predators. Assemblages of HFs are primarily formed by species still uncultured, therefore many aspects of their trophic behavior are poorly known. Here we assessed the functional response of the whole assemblage and of four taxa grown in an unamended seawater incubation. We used fluorescently labeled bacteria to create a prey gradient of two orders of magnitude in abundance, and estimated ingestion rates. Natural HFs had a half-saturation constant of 6.7x10⁵ prey ml^-1 , a value lower than that of cultured flagellates and within the range of marine planktonic bacterial abundances. Minorisa minuta was well adapted to low prey abundances and very efficient in ingesting bacteria. MAST-4 and MAST-7 were also well adapted to the typical marine abundances but less voracious. In contrast, Paraphysomonas imperforata, a typical cultured species, did not achieve ingestion rate saturation even at the highest prey concentration assayed. Our study, beside to set the basis for the fundamental differences between cultured and uncultured bacterial grazers, indicate that the examined predator taxa have different functional responses, suggesting that they occupy distinct ecological niches according to their grazing strategies and prey preferences. This article is protected by copyright. All rights reserved.

Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study

Metabarcoding in combination with high-throughput sequencing (HTS) allows simultaneous detection of multiple taxa by targeting single or several taxonomically informative gene regions from environmental DNA samples. In this study, a multiple-marker HTS approach was applied to investigate the plankton diversity and seasonal succession in the Baltic Sea from winter to autumn. Four different markers targeting the 16S, 18S, and 28S ribosomal RNA genes were employed, including a marker for more efficient dinoflagellate detection. Typical seasonal changes were observed in phyto- and bacterioplankton communities. In phytoplankton, the appearance patterns of selected common, dominant, or harmful species followed the patterns also confirmed based on 20 years of phytoplankton monitoring data. In the case of zooplankton, both macro- and microzooplankton species were detected. However, no seasonal patterns were detected in their appearance. In total, 15 and 2 new zoo- and phytoplankton species were detected from the Baltic Sea. HTS approach was especially useful for detecting microzooplankton species as well as for investigating the co-occurrence and potential interactions of different taxa. The results of this study further exemplify the efficiency of metabarcoding for biodiversity monitoring and the advantage of employing multiple markers through the detection of species not identifiable based on a single marker survey and/or by traditional morphology-based methods.

A comprehensive review of image analysis methods for microorganism counting: from classical image processing to deep learning approaches

Microorganisms such as bacteria and fungi play essential roles in many application fields, like biotechnique, medical technique and industrial domain. Microorganism counting techniques are crucial in microorganism analysis, helping biologists and related researchers quantitatively analyze the microorganisms and calculate their characteristics, such as biomass concentration and biological activity. However, traditional microorganism manual counting methods, such as plate counting method, hemocytometry and turbidimetry, are time-consuming, subjective and need complex operations, which are difficult to be applied in large-scale applications. In order to improve this situation, image analysis is applied for microorganism counting since the 1980s, which consists of digital image processing, image segmentation, image classification and suchlike. Image analysis-based microorganism counting methods are efficient comparing with traditional plate counting methods. In this article, we have studied the development of microorganism counting methods using digital image analysis. Firstly, the microorganisms are grouped as bacteria and other microorganisms. Then, the related articles are summarized based on image segmentation methods. Each part of the article is reviewed by methodologies. Moreover, commonly used image processing methods for microorganism counting are summarized and analyzed to find common technological points. More than 144 papers are outlined in this article. In conclusion, this paper provides new ideas for the future development trend of microorganism counting, and provides systematic suggestions for implementing integrated microorganism counting systems in the future. Researchers in other fields can refer to the techniques analyzed in this paper.

Water mass shapes the distribution patterns of planktonic ciliates (Alveolata, Ciliophora) in the subtropical Pearl River Estuary

Ciliates comprise essential components of microzooplankton in diverse marine environments. However, the extent to which environmental variables shape the distribution of planktonic ciliates in complex estuarine systems remains unclear. Here, 52 samples were collected from the Pearl River Estuary, China to reveal the influence of environmental variables on planktonic ciliate communities. Distinct community compositions of ciliates were found in three identified water masses: Pearl River diluted water mass, South China Sea surface water mass, and South China Sea bottom water mass. Significant differences in abundance, biomass, cell size, and oral diameter structure of ciliates were also detected among the three water masses. The partial Mantel test showed that water mass (as represented by water temperature and salinity) surpassed other environmental variables to be the primary factor driving the dynamics of the ciliate community. This study revealed the controlling mechanisms of planktonic ciliate communities in a subtropical, hydrographically complex estuarine ecosystem.

Seasonal Distribution of Cyanobacteria in Three Urban Eutrophic Lakes Results from an Epidemic-like Response to Environmental Conditions

Cyanobacterial communities of three co-located eutrophic sandpit lakes were surveyed during 2016 and 2017 over season and depth using high-throughput DNA sequencing of the 16S rRNA gene. All three lakes were stratified except during April 2017 when the lakes were recovering from a strong mixing event. 16S rRNA gene V4 sequences were parsed into operational taxonomic units (OTUs) at 99% sequence identity. After rarefaction of 139 samples to 25,000 sequences per sample, a combined total of 921,529 partial 16S rRNA gene sequences were identified as cyanobacteria. They were binned into 19,588 unique cyanobacterial OTUs. Of these OTUs, 11,303 were Cyanobium. Filamentous Planktothrix contributed 1537 and colonial Microcystis contributed 265. The remaining 6482 OTUs were considered unclassified. For Planktothrix and Microcystis one OTU accounted for greater than 95% of the total sequences for each genus. However, in both cases the non-dominant OTUs clustered with the dominant OTUs by date, lake, and depth. All Planktothrix OTUs and a single Cyanobium OTU were detected below the oxycline. All other Cyanobium and Microcystis OTUs were detected above the oxycline. The distribution of Cyanobium OTUs between lakes and seasons can be explained by an epidemic-like response where individual OTUs clonally rise from a diverse hypolimnion population when conditions are appropriate. The importance of using 99% identity over the more commonly used 97% is discussed with respect to cyanobacterial community structure. The approach described here can provide another valuable tool for assessing cyanobacterial populations and provide greater insight into the controls of cyanobacterial blooms.

Enhanced Viral Activity in the Surface Microlayer of the Arctic and Antarctic Oceans

The ocean surface microlayer (SML), with physicochemical characteristics different from those of subsurface waters (SSW), results in dense and active viral and microbial communities that may favor virus–host interactions. Conversely, wind speed and/or UV radiation could adversely affect virus infection. Furthermore, in polar regions, organic and inorganic nutrient inputs from melting ice may increase microbial activity in the SML. Since the role of viruses in the microbial food web of the SML is poorly understood in polar oceans, we aimed to study the impact of viruses on prokaryotic communities in the SML and in the SSW in Arctic and Antarctic waters. We hypothesized that a higher viral activity in the SML than in the SSW in both polar systems would be observed. We measured viral and prokaryote abundances, virus-mediated mortality on prokaryotes, heterotrophic and phototrophic nanoflagellate abundance, and environmental factors. In both polar zones, we found small differences in environmental factors between the SML and the SSW. In contrast, despite the adverse effect of wind, viral and prokaryote abundances and virus-mediated mortality on prokaryotes were higher in the SML than in the SSW. As a consequence, the higher carbon flux released by lysed cells in the SML than in the SSW would increase the pool of dissolved organic carbon (DOC) and be rapidly used by other prokaryotes to grow (the viral shunt). Thus, our results suggest that viral activity greatly contributes to the functioning of the microbial food web in the SML, which could influence the biogeochemical cycles of the water column.

Distinct capabilities of different Gammaproteobacterial strains on utilizing small peptides in seawater

Proteins and peptides account for 20–75% of marine biota biomass, of which a major fraction is metabolized by bacteria, thus deciphering interactions between bacteria and peptides is important in understanding marine carbon and nitrogen cycling. To better understand capabilities of different bacterial strains on peptide decomposition, four Gammaproteobacteria (Pseudoalteromonas atlantica, Alteromonas sp., Marinobacterium jannaschii, Amphritea japonica) were incubated in autoclaved seawater amended with tetrapeptide alanine-valine-phenylalanine-alanine (AVFA), a fragment of RuBisCO. While AVFA was decomposed greatly by Pseudoalteromonas atlantica and Alteromonas sp, it remained nearly intact in the Marinobacterium jannaschii and Amphritea japonica incubations. Pseudoalteromonas and Alteromonas decomposed AVFA mainly through extracellular hydrolysis pathway, releasing 71–85% of the AVFA as hydrolysis products to the surrounding seawater. Overall, this study showed that Gammaproteobacterial strains differ greatly in their capabilities of metabolizing peptides physiologically, providing insights into interactions of bacteria and labile organic matter in marine environments.

Warming and CO2 Enhance Arctic Heterotrophic Microbial Activity

Ocean acidification and warming are two main consequences of climate change that can directly affect biological and ecosystem processes in marine habitats. The Arctic Ocean is the region of the world experiencing climate change at the steepest rate compared with other latitudes. Since marine planktonic microorganisms play a key role in the biogeochemical cycles in the ocean it is crucial to simultaneously evaluate the effect of warming and increasing CO₂ on marine microbial communities. In 20 L experimental microcosms filled with water from a high-Arctic fjord (Svalbard), we examined changes in phototrophic and heterotrophic microbial abundances and processes [bacterial production (BP) and mortality], and viral activity (lytic and lysogenic) in relation to warming and elevated CO₂. The summer microbial plankton community living at 1.4°C in situ temperature, was exposed to increased CO₂ concentrations (135–2,318 μatm) in three controlled temperature treatments (1, 6, and 10°C) at the UNIS installations in Longyearbyen (Svalbard), in summer 2010. Results showed that chlorophyll a concentration decreased at increasing temperatures, while BP significantly increased with pCO₂ at 6 and 10°C. Lytic viral production was not affected by changes in pCO₂ and temperature, while lysogeny increased significantly at increasing levels of pCO₂, especially at 10°C (R² = 0.858, p = 0.02). Moreover, protistan grazing rates showed a positive interaction between pCO₂ and temperature. The averaged percentage of bacteria grazed per day was higher (19.56 ± 2.77% d^-1) than the averaged percentage of lysed bacteria by virus (7.18 ± 1.50% d^-1) for all treatments. Furthermore, the relationship among microbial abundances and processes showed that BP was significantly related to phototrophic pico/nanoflagellate abundance in the 1°C and the 6°C treatments, and BP triggered viral activity, mainly lysogeny at 6 and 10°C, while bacterial mortality rates was significantly related to bacterial abundances at 6°C. Consequently, our experimental results suggested that future increases in water temperature and pCO₂ in Arctic waters will produce a decrease of phytoplankton biomass, enhancement of BP and changes in the carbon fluxes within the microbial food web. All these heterotrophic processes will contribute to weakening the CO₂ sink capacity of the Arctic plankton community.

Viruses and Protists Induced-mortality of Prokaryotes around the Antarctic Peninsula during the Austral Summer

During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1-100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP). Viral lytic production, lysogeny, and mortality rates of prokaryotes due to viruses and protists were estimated at surface (0.1-1 m) and at the Deep Fluorescence Maximum (DFM, 12-55 m) at eight representative stations of the three areas. The average viral lytic production ranged from 1.0 ± 0.3 × 10⁷ viruses ml^-1 d^-1 in the Bellingshausen Sea to1.3 ± 0.7 × 10⁷ viruses ml^-1 d^-1 in the Bransfield Strait, while lysogeny, when detectable, recorded the lowest value in the Bellingshausen Sea (0.05 ± 0.05 × 10⁷ viruses ml^-1 d^-1) and the highest in the Weddell Sea (4.3 ± 3.5 × 10⁷ viruses ml^-1 d^-1). Average mortality rates due to viruses ranged from 9.7 ± 6.1 × 10⁴ cells ml^-1 d^-1 in the Weddell Sea to 14.3 ± 4.0 × 10⁴ cells ml^-1 d^-1 in the Bellingshausen Sea, and were higher than averaged grazing rates in the Weddell Sea (5.9 ± 1.1 × 10⁴ cells ml^-1 d^-1) and in the Bellingshausen Sea (6.8 ± 0.9 × 10⁴ cells ml^-1 d^-1). The highest impact on prokaryotes by viruses and main differences between viral and protists activities were observed in surface samples: 17.8 ± 6.8 × 10⁴ cells ml^-1 d^-1 and 6.5 ± 3.9 × 10⁴ cells ml^-1 d^-1 in the Weddell Sea; 22.1 ± 9.6 × 10⁴ cells ml^-1 d^-1 and 11.6 ± 1.4 × 10⁴ cells ml^-1 d^-1 in the Bransfield Strait; and 16.1 ± 5.7 × 10⁴ cells ml^-1 d^-1 and 7.9 ± 2.6 × 10⁴ cells ml^-1 d^-1 in the Bellingshausen Sea, respectively. Furthermore, the rate of lysed cells and PHP showed higher sensitivity to temperature than grazing rates by protists. We conclude that viruses were more important mortality agents than protists mainly in surface waters and that viral activity has a higher sensitivity to temperature than grazing rates. This suggests a reduction of the carbon transferred through the microbial food-web that could have implications in the biogeochemical cycles in a future warmer ocean scenario.

A Simple yet Accurate Method for the Estimation of the Biovolume of Planktonic Microorganisms

Determining the biomass of microbial plankton is central to the study of fluxes of energy and materials in aquatic ecosystems. This is typically accomplished by applying proper volume-to-carbon conversion factors to group-specific abundances and biovolumes. A critical step in this approach is the accurate estimation of biovolume from two-dimensional (2D) data such as those available through conventional microscopy techniques or flow-through imaging systems. This paper describes a simple yet accurate method for the assessment of the biovolume of planktonic microorganisms, which works with any image analysis system allowing for the measurement of linear distances and the estimation of the cross sectional area of an object from a 2D digital image. The proposed method is based on Archimedes' principle about the relationship between the volume of a sphere and that of a cylinder in which the sphere is inscribed, plus a coefficient of 'unellipticity' introduced here. Validation and careful evaluation of the method are provided using a variety of approaches. The new method proved to be highly precise with all convex shapes characterised by approximate rotational symmetry, and combining it with an existing method specific for highly concave or branched shapes allows covering the great majority of cases with good reliability. Thanks to its accuracy, consistency, and low resources demand, the new method can conveniently be used in substitution of any extant method designed for convex shapes, and can readily be coupled with automated cell imaging technologies, including state-of-the-art flow-through imaging devices.

Accuracy of biovolume formulas for CMEIAS computer-assisted microscopy and body size analysis of morphologically diverse microbial populations and communities

Cell biovolume is a commonly used metric of microbial abundance analyzed by computer-assisted microscopy, but the accuracies of most biovolume formulas have not been validated by ground truth data. We examined the accuracy of 17 biovolume formulas by comparing the computed volumes of 3D models representing 11 microbial morphotypes (cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, prosthecates, rudimentary branched rods, and branched filaments) to the volume displacement of the same objects as ground truth. As anticipated, formula accuracy was significantly influenced by the morphotype examined. A few formulas performed very accurately (> 95 %), especially those that adapted to the cell's shape, whereas others were consistently inaccurate or only accurate for one or two morphotypes. As an example of application, indices of morphological diversity in a freshwater biofilm assemblage were shown to be significantly different when microbial abundance among morphotype classes was measured as biovolume body mass rather than cell counts. Spatial analysis of biovolume body mass can also provide insights on the in situ ecophysiological attributes among individuals in microbial populations and communities, including their spatially autocorrelated allometric scaling interrelationships between body size, metabolic activity, resource apportionment and use, food web dynamics, and various cell-cell interactions affecting their growth and colonization behavior within spatially structured biofilm landscapes. This improved computing technology of biovolume algorithms with proven accuracy identifies which formula(s) should be used to compute microbial biovolumes in 2D images of morphologically diverse communities acquired by conventional phase-contrast light microscopy at single-cell resolution.

Optimization of an automatic counting system for the quantification of Staphylococcus epidermidis cells in biofilms

Biofilm formation is recognized as the main virulence factor in a variety of chronic infections. In vitro evaluation of biofilm formation is often achieved by quantification of viable or total cells. However, these methods depend on biofilm disruption, which is often achieved by vortexing or sonication. In this study, we investigated the effects of sonication on the elimination of Staphylococcus epidermidis cell clusters from biofilms grown over time, and quantification was performed by three distinct analytical techniques. Even when a higher number of sonication cycles was used, some stable cell clusters remained in the samples obtained from 48- and 72-h-old biofilms, interfering with the quantification of sessile bacteria by plate counting. On the other hand, the fluorescence microscopy automatic counting system allowed proper quantification of biofilm samples that had undergone any of the described sonication cycles, suggesting that this is a more accurate method for assessing the cell concentration in S. epidermidis biofilms, especially in mature biofilms.

The role of extracellular polymeric substances on the sorption of natural organic matter

In this study, the influence of extracellular polymeric substances (EPS) composition and quantity was explored for biosorption of natural organic matter (NOM), using variants of Pseudomonas aeruginosa and Pseudomonas putida. Model EPS (sodium alginate beads) were tested and sorption capacity for NOM was also elucidated. In the absence of divalent ions, minimal NOM biosorption was observed and differences among strains were negligible. Under presence of divalent ions, biosorption of NOM was proportional to the amount of EPS secreted by P. aeruginosa variants. For sorption tests with model EPS, divalent ions also promoted biosorption of tested NOM, and total biosorption was also proportional to alginate quantity. Carboxyl group content in both alginate EPS and NOM appeared to be linked to increased biosorption via bridging with divalent ions. The alginate overproducing strain possessed more potential NOM biosorption sites, while the wild-type and alginate deficient strains possessed fewer potential binding sites. In comparison, P. putida, secreting protein-based EPS, behaved differently for NOM biosorption, due to its hydrophobicity and the structural characteristics of proteins. Hydrophobic interactions appeared to enhance the biosorption of more hydrophobic Suwannee River humic acid by P. putida, whose biosorption of more hydrophilic NOM variants was similar to the alginate deficient strain. Mechanistically, the presence of a diffuse electrical double layer will present potential energy barriers limiting biosorption; however, divalent ion concentrations in the aquatic environment will promote biosorption processes, permitting functional group interactions between EPS and NOM. Bridging between hydrophilic carboxyl groups on alginate EPS and NOM appeared to be the dominant form of biosorption, while hydrophobic interactions enhanced biosorption for protein-based EPS.

Use of metabolic inhibitors to estimate protozooplankton grazing and bacterial production in a monomictic eutrophic lake with an anaerobic hypolimnion

Inhibitors of eucaryotes (cycloheximide and amphotericin B) and procaryotes (penicillin and chloramphenicol) were used to estimate bacterivory and bacterial production in a eutrophic lake. Bacterial production appeared to be slightly greater than protozoan grazing in the aerobic waters of Lake Oglethorpe. Use of penicillin and cycloheximide yielded inconsistent results in anaerobic water and in aerobic water when bacterial production was low. Production measured by inhibiting eucaryotes with cycloheximide did not always agree with [H]thymidine estimates or differential filtration methods. Laboratory experiments showed that several common freshwater protozoans continued to swim and ingest bacterium-size latex beads in the presence of the eucaryote inhibitor. Penicillin also affected grazing rates of some ciliates. We recommend that caution and a corroborating method be used when estimating ecologically important parameters with specific inhibitors.

Particle counter determination of bacterial biomass in seawater

The applicability of the Elzone particle counter to the determination of marine bacterial biomass was investigated. The biomass of bacterial pure cultures and a mixed natural population were followed by using the particle counter, a CHN analyzer, and an ATP analyzer. The particle counter showed the precise size distribution of number and volume of submicron-size particles in seawater. For the pure cultured bacterial strains, the conversion factor from volume to carbon is 0.209 mg of C per mm, and for natural bacterial cells of >0.6 mum in diameter, it is 0.184 mg of C per mm. It is recommended that 0.2 be used as the conversion factor for both pure cultured marine bacterial cells and natural bacteria from coastal and near-shore marine environments.

In situ classification and image cytometry of pelagic bacteria from a high mountain lake (gossenkollesee, austria)

We describe a procedure to measure the cell sizes of pelagic bacteria after determinative hybridization with rRNA-targeted fluorescently labeled oligonucleotide probes. Our approach is based on established image analysis techniques modified for objects simultaneously stained with two fluorescent dyes. It allows the estimation of biomass and cell size distribution and the morphological characterization of different bacterial taxa in plankton samples. The protocol was tested in a study of the bacterioplankton community of a high mountain lake during and after the ice break period. Cells that hybridized with a probe for the domain Bacteria accounted for 70% of the bacterial abundance (range, 49 to 83%) as determined by 4(prm1),6(prm1)-diamidino-2-phenylindole staining (K. G. Porter and Y. S. Feig, Limnol. Oceanogr. 25:943-948, 1980), but for >85% of the total biomass (range, 78 to 99%). The size distribution for members of the beta subclass of the Proteobacteria shifted toward larger cells and clearly distinguished this group from the total bacterial assemblage. In the surface water layer beneath the winter cover, bacteria belonging to the beta 1 subgroup constituted about one-half of the beta subclass abundance. The mean cell volume of the beta 1 subgroup bacteria was significantly less than that of the beta subclass proteobacteria, and the beta 1 subgroup accounted for less than 30% of the total beta subclass biovolume. Two weeks later, the biovolume of the beta Proteobacteria had decreased to the level of the beta 1 subgroup, and both the biovolume size distributions and cell morphologies of the beta Proteobacteria and the beta 1 subgroup were very similar. We could thus quantify the disappearance of large, morphologically distinct beta subclass proteobacteria which were not members of the beta 1 subgroup during the ice break period. Our results demonstrate that changes in biovolumes and cell size distributions of different bacterial taxa, and eventually of individual populations, reveal hitherto unknown processes within aquatic bacterial assemblages and may open new perspectives for the study of microbial food webs.

Automatic determination of bacterioplankton biomass by image analysis

Image analysis was applied to epifluorescense microscopy of acridine orange-stained plankton samples. A program was developed for discrimination and binary segmentation of digitized video images, taken by an ultrasensitive video camera mounted on the microscope. Cell volumes were estimated from area and perimeter of the objects in the binary image. The program was tested on fluorescent latex beads of known diameters. Biovolumes measured by image analysis were compared with directly determined carbon biomasses in batch cultures of estuarine and freshwater bacterioplankton. This calibration revealed an empirical conversion factor from biovolume to biomass of 0.35 pg of C mum (+/- 0.03 95% confidence limit). The deviation of this value from the normally used conversion factors of 0.086 to 0.121 pg of C mum is discussed. The described system was capable of measuring 250 cells within 10 min, providing estimates of cell number, mean cell volume, and biovolume with a precision of 5%.

Agreement, precision, and accuracy of epifluorescence microscopy methods for enumeration of total bacterial numbers

To assess interchangeability of estimates of bacterial abundance by different epifluorescence microscopy methods, total bacterial numbers (TBNs) determined by most widely accepted protocols were statistically compared. Bacteria in a set of distinctive samples were stained with acridine orange (AO), 4'-6-diamidino-2-phenylindole (DAPI), and BacLight and enumerated by visual counting (VC) and supervised image analysis (IA). Model II regression and Bland-Altman analysis proved general agreements between IA and VC methods, although IA counts tended to be lower than VC counts by 7% on a logarithmic scale. Distributions of cells and latex beads on polycarbonate filters were best fitted to negative binomial models rather than to Poisson or log-normal models. The fitted models revealed higher precisions of TBNs by the IA method than those by the VC method. In pairwise comparisons of the staining methods, TBNs by AO and BacLight staining showed good agreement with each other, but DAPI staining had tendencies of underestimation. Although precisions of the three staining methods were comparable to one another (intraclass correlation coefficients, 0.97 to 0.98), accuracy of the DAPI staining method was rebutted by disproportionateness of TBNs between pairs of samples that carried 2-fold different volumes of identical cell suspensions. It was concluded that the TBN values estimated by AO and BacLight staining are relatively accurate and interchangeable for quantitative interpretation and that IA provides better precision than does VC. As a prudent measure, it is suggested to avoid use of DAPI staining for comparative studies investigating accuracy of novel cell-counting methods.

High-resolution imaging of pelagic bacteria by Atomic Force Microscopy and implications for carbon cycling

In microbial oceanography, cell size, volume and carbon (C) content of pelagic bacteria and archaea ('bacteria') are critical parameters in addressing the in situ physiology and functions of bacteria, and their role in the food web and C cycle. However, because of the diminutive size of most pelagic bacteria and errors caused by sample fixation and processing, an accurate measurement of the size and volume has been challenging. We used atomic force microscopy (AFM) to obtain high-resolution images of pelagic bacteria and Synechococcus. We measured the length, width and height of live and formalin-fixed pelagic bacteria, and computed individual cell volumes. AFM-based measurements were compared with those by epifluorescence microscopy (EFM) using 4',6-diamidino-2-phenylindole (DAPI). The ability to measure cell height by AFM provides methodological advantage and ecophysiological insight. For the samples examined, EFM (DAPI)-based average cell volume was in good agreement (1.1-fold) with live sample AFM. However, the agreement may be a fortuitous balance between cell shrinkage due to fixation/drying (threefold) and Z-overestimation (as EFM does not account for cell flattening caused by sample processing and assumes that height=width). The two methods showed major differences in cell volume and cell C frequency distributions. This study refines the methodology for quantifying bacteria-mediated C fluxes and the role of bacteria in marine ecosystems, and suggests the potential of AFM for individual cell physiological interrogations in natural marine assemblages.

Particle size analysis of dispersed oil and oil-mineral aggregates with an automated ultraviolet epi-fluorescence microscopy system

This paper describes recent advances in microscopic analysis for quantitative measurement of oil droplets. Integration of a microscope with bright-field and ultraviolet epi-fluorescence illumination (excitation wavelengths 340-380 nm; emission wavelengths 400-430 nm) fitted with a computer-controlled motorized stage, a high resolution digital camera, and new image-analysis software, enables automatic acquisition of multiple images and facilitates efficient counting and sizing of oil droplets. Laboratory experiments were conducted with this system to investigate the size distribution of chemically dispersed oil droplets and oil-mineral aggregates in baffled flasks that have been developed for testing chemical dispersant effectiveness. Image acquisition and data processing methods were developed to illustrate the size distribution of chemically dispersed oil droplets, as a function of energy dissipation rate in the baffled flasks, and the time-dependent change of the morphology and size distribution of oil-mineral aggregates. As a quantitative analytical tool, epifluorescence microscopy shows promise for application in research on oil spill response technologies, such as evaluating the effectiveness of chemical dispersant and characterizing the natural interaction between oil and mineral fines and other suspended particulate matters.

Fate of heterotrophic microbes in pelagic habitats: focus on populations

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a"Gleasonian" perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.

Biomass production and assimilation of dissolved organic matter by SAR11 bacteria in the Northwest Atlantic Ocean

Members of the SAR11 clade often dominate the composition of marine microbial communities, yet their contribution to biomass production and the flux of dissolved organic matter (DOM) is unclear. In addition, little is known about the specific components of the DOM pool utilized by SAR11 bacteria. To better understand the role of SAR11 bacteria in the flux of DOM, we examined the assimilation of leucine (a measure of biomass production), as well as free amino acids, protein, and glucose, by SAR11 bacteria in the Northwest Atlantic Ocean. We found that when SAR11 bacteria were >25% of total prokaryotes, they accounted for about 30 to 50% of leucine incorporation, suggesting that SAR11 bacteria were major contributors to bacterial biomass production and the DOM flux. Specific growth rates of SAR11 bacteria either equaled or exceeded growth rates for the total prokaryotic community. In addition, SAR11 bacteria were typically responsible for a greater portion of amino acid assimilation (34 to 61%) and glucose assimilation (45 to 57%) than of protein assimilation (< or = 34%). These data suggest that SAR11 bacteria do not utilize various components of the DOM pool equally and may be more important to the flux of low-molecular-weight monomers than to that of high-molecular-weight polymers.

Direct estimation of biofilm density on different pipe material coupons using a specific DNA-probe

A variety of approaches to quantify biomass in biofilms without disruption due to detachment have been developed over the years. One basic approach is the combination of advanced microscopy with molecular staining. However, many stains (e.g. 4',6-diamino-2-phenylindole, acridine orange or live-dead stains) can be non-specific when corrosion products, precipitates, and pipe material are present. In addition, some pipe materials cause high background when using epifluorescent microscopy. The new refinement discussed in this presentation used fluorescence spectroscopy to obtain the spectra from four common distribution system pipe materials: PVC, 'concrete' lined cast iron, cast iron, and galvanized steel. The emission maximum for all four materials was between 500 and 550 nm, but emissions radically decreased around 575-600 nm. A molecular probe, BO-PRO-3 (Molecular Probes, Inc., Eugene, OR, USA) was identified which has an emission intensity maximum at 599 nm (red), with emission intensity 200 times greater when it is bound to DNA. The BO-PRO-3 has greatly reduced non-specific staining and background problems. In the preliminary experiment, using diluted waste water, a significant exponential relationship was found between stained surface area/total area ratio and fixed biofilm inventory measurements from scraping heterotrophic plate counts (SHPC) on R2A medium. In addition, the biofilm inventory on different pipe material coupons from pilot distribution systems was also correlated to the stained surface area fraction and SHPC.

Development of an adhesive sheet for direct counting of bacteria on solid surfaces

An adhesive sheet was developed for direct counting of microorganisms on solid surfaces. The sheet consists of a polyurethane film base and water insoluble adhesive. SYBR Green II (for total direct counting) or 6-carboxyfluorescein diacetate (6CFDA) (for fluorescent vital staining) was used for fluorescent microscopy of bacteria collected on the adhesive face of the sheet. Adhesive sheet sampling showed a higher recovery rate for microbial enumeration than conventional swab method or stamp agar. This method is simple, rapid, inexpensive and reproducible.

Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization

We describe here an automated system for the counting of multiple samples of double-stained microbial cells on sections of membrane filters. The application integrates an epifluorescence microscope equipped with motorized z-axis drive, shutters, and filter wheels with a scanning stage, a digital camera, and image analysis software. The relative abundances of specific microbial taxa are quantified in samples of marine picoplankton, as detected by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition. Pairs of microscopic images are automatically acquired from numerous positions at two wavelengths, and microbial cells with both general DNA and FISH staining are counted after object edge detection and signal-to-background ratio thresholding. Microscopic fields that are inappropriate for cell counting are automatically excluded prior to measurements. Two nested walk paths guide the device across a series of triangular preparations until a user-defined number of total cells has been analyzed per sample. A backup autofocusing routine at incident light allows automated refocusing between individual samples and can reestablish the focal plane after fatal focusing errors at epifluorescence illumination. The system was calibrated to produce relative abundances of FISH-stained cells in North Sea samples that were comparable to results obtained by manual evaluation. Up to 28 preparations could be analyzed within 4 h without operator interference. The device was subsequently applied for the counting of different microbial populations in incubation series of North Sea waters. Automated digital microscopy greatly facilitates the processing of numerous FISH-stained samples and might thus open new perspectives for bacterioplankton population ecology.

SAR11 clade dominates ocean surface bacterioplankton communities

The most abundant class of bacterial ribosomal RNA genes detected in seawater DNA by gene cloning belongs to SAR11-an alpha-proteobacterial clade. Other than indications of their prevalence in seawater, little is known about these organisms. Here we report quantitative measurements of the cellular abundance of the SAR11 clade in northwestern Sargasso Sea waters to 3,000 m and in Oregon coastal surface waters. On average, the SAR11 clade accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions, members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the subeuphotic microbial community. By extrapolation, we estimate that globally there are 2.4 x 10(28) SAR11 cells in the oceans, half of which are located in the euphotic zone. Although the biogeochemical role of the SAR11 clade remains uncertain, these data support the conclusion that this microbial group is among the most successful organisms on Earth.

A fully automated microscope bacterial enumeration system for studies of oral microbial ecology

A fast and fully automated image analysis technique for the enumeration of fluorescence-labeled bacteria in oral sampleswas developed. This paper describes the system configuration, application strategy, automated operation, and initial validation experiments using fluorescent microspheres, bacterial cultures, in vitro grown biofilms and human dental plaque. Following a series of brief operator-controlled calibration steps, the technique automatically performs all necessary microscope operations (stage translation, focus, sampling and analysis) on slides with up to 48 wells for as many different samples. It quantifies bacteria from differential interference contrast images, images showing cells that had been labeled by immunofluorescence with monoclonal antibodies, or images with cells labeled by a fluorescent DNA stain. With all evaluated samples, close agreement between the automated system and the assessor's visual counts was observed. This novel automated image grabbing and analysis procedure is applicable to the enumeration of specific taxa in clinical samples by both immunofluorescence and fluorescent in situ hybridization.

Automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of Lumbricus terrestris L

An image analysis procedure was developed for bacterial cells after staining with the DNA-intercalating dye 4'-6-diamidino-2-phenylindole (DAPI), and after in situ hybridization with Cy3-labeled, rRNA-targeted oligonucleotide probes. DAPI- and Cy3-images were captured separately from the same scenery with a cooled digital video camera with three CCD chips for the basic colors red (R), green (G) and blue (B). Using the appropriate filter sets, images of DAPI-stained cells were captured with the red channel shut down, while Cy3-stained cells were captured with the green and blue channels shut down. DAPI images and Cy3 images were subsequently merged to produce virtual color (RGB)-images. Processing of all color channels allowed to specifically enumerate DAPI-stained and hybridized bacteria, to measure their cell sizes, to subsequently calculate their biovolumes and to estimate their biomass. Using this procedure, significant differences were detected in bacterial populations in food resources, digestive tract and cast of the earthworm L. terrestris L. In leaves, bacteria were on average ten times more abundant and two times larger than in soil. In the digestive tract of L. terrestris, however, numbers and volumes of bacteria were comparable to those in soil indicating the disruption of cells originating from leaves before arriving in the foregut. Passage through the digestive tract of L. terrestris significantly reduced bacterial populations belonging to the alpha-, beta- and gamma-subdivisions of Proteobacteria. While these populations did not recover during incubation of cast, populations of the delta-subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster of the CFB phylum increased in cast. These results suggest a large impact of passage through the digestive tract of L. terrestris on bacterial community structure and demonstrate the usefulness of our image analysis procedure for the determination of cell sizes and biovolumes and thus biomass of specific bacterial populations in different terrestrial habitats.

Surfactant polymers designed to suppress bacterial (Staphylococcus epidermidis) adhesion on biomaterials

We describe a series of surfactant polymers designed as surface-modifying agents for the suppression of bacterial adhesion on biomaterials. The surfactant polymers consist of a poly(vinyl amine) backbone with hydrophilic poly(ethylene oxide) (PEO) and hydrophobic hexanal (Hex) side chains (PVAm/PEO:Hex). Surface modification is accomplished by simple dip coating from aqueous solution, from which surfactant polymers undergo spontaneous surface-induced assembly on hydrophobic biomaterials. The stability of PVAm/PEO:Hex on pyrolytic graphite (HOPG) and polyethylene (PE) was demonstrated by the absence of detectable desorption under flow conditions of pure water over a 24-h period. PEO surfactant polymers with four different PEO:Hex ratios (1:1.4, 1:2.5, 1:4.6, and 1:10.7) and a dextran surfactant polymer were compared with respect to S. epidermidis adhesion under dynamic flow conditions. Suppression of S. epidermidis adhesion was achieved for all modified surfaces over the shear range 0-15 dyn/cm(2). The effectiveness depended on the surfactant polymer composition such that S. epidermidis adhesion to modified surfaces decreased significantly with increasing PEO packing density. Modified HOPG was more effective in reducing bacterial adhesion compared with the corresponding modification on PE, which we attribute to the presence of defects in surfactant polymer assembly on PE. Our results are discussed from the perspective of critical factors, such as optimal PEO packing density and hydration thickness, that contribute to the effectiveness of surfactant polymers to shield a biomaterial from adhesive bacterial interactions.

Automatic enumeration of adherent streptococci or actinomyces on dental alloy by fluorescence image analysis

The aim of the present study was to develop an automated image analysis method to quantify adherence of Streptococcus sanguinis or Actinomyces viscosus on surfaces of a currently used dental alloy. Counting such bacterial strains was difficult because of their arrangement, thus S. sanguinis being a coccus arranged in chains or pairs, and A. viscosus a long complexly arranged polymorph rod. Direct counting of fluorescently stained adherent bacteria was done visually and with image analysis methods. To differentiate these two morphotypes, two programs were developed: (i) for streptococci, thresholding and selection of the object maxima, and (ii) for actinomyces, two step thresholding and processing of the characteristic points of the object skeletons. The triplicate enumerations for each bacterial strain were not significantly different (p > 0.005) and correlations between visual counting and automated counting were significant (r = 0.91 for S. sanguinis and r = 0.99 for A. viscosus, p <00.0001). These rapid and reproducible methods, allowed us to count either cocci or rods, adherent on an inert substratum, in high density conditions.

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.

Flow cytometric analysis of 5-cyano-2,3-ditolyl tetrazolium chloride activity of marine bacterioplankton in dilution cultures

The respiratory activity of marine bacteria is an important indication of the ecological functioning of these organisms in marine ecosystems. The redox dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) is reduced intracellularly in respiring cells to an insoluble, fluorescent precipitate. This product is detectable and quantifiable by flow cytometry in individual cells. We describe here an evaluation of flow cytometry for measuring CTC activity in natural assemblages of marine bacteria growing in dilution cultures. We found that more CTC-positive cells are detected by flow cytometry than by visual epifluorescence microscopy. Samples can be stored refrigerated or frozen in liquid nitrogen for at least 4 weeks without a significant loss of total cells, CTC-positive cells, or CTC fluorescence. Cytometry still may not detect all active cells, however, since the dimmest fluorescing cells are not clearly separated from background noise. Reduction of CTC is very fast in most active cells, and the number of active cells reaches 80% of the maximum number within 2 to 10 min. The proportion of active cells is correlated with the growth rate, while the amount of fluorescence per cell varies inversely with the growth rate. The CTC reduction kinetics in assemblages bubbled with nitrogen and in assemblages bubbled with air to vary the oxygen availability were the same, suggesting that CTC can effectively compete with oxygen for reducing power. A nonbubbled control, however, contained more CTC-positive cells, and the amount of fluorescence per cell was greater. Activity may have been reduced by bubble-induced turbulence. Addition of an artificial reducing agent, sodium dithionite, after CTC incubation and fixation resulted in a greater number of positive cells but did not "activate" a majority of the cells. This indicated that some of the negative cells actually transported CTC across their cell membranes but did not reduce it to a detectable level. Automated analysis by flow cytometry allows workers to study single-cell variability in marine bacterioplankton activity and changes in activity on a small temporal or spatial scale.