Sensitive Determination of Microbial Growth by Nucleic Acid Staining in Aqueous Suspension

Tip extension and simultaneous multiple fission in a filamentous bacterium

Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.

Study of antibiotic resistance in freshwater ecosystems with low anthropogenic impact

This study aimed to investigate the bacterial diversity and the background level of antibiotic resistance in two freshwater ecosystems with low anthropogenic impact in order to evaluate the presence of natural antimicrobial resistance in these areas and its potential to spread downstream. Water samples from a pre-Alpine and an Apennine river (Variola and Tiber, respectively) were collected in three different sampling campaigns and bacterial diversity was assessed by 16S sequencing, while the presence of bacteria resistant to five antibiotics was screened using a culturable approach. Overall bacterial load was higher in the Tiber River compared with the Variola River. Furthermore, the study revealed the presence of resistant bacteria, especially the Tiber River showed, for each sampling, the presence of resistance to all antibiotics tested, while for the Variola River, the detected resistance was variable, comprising two or more antibiotics. Screening of two resistance genes on a total of one hundred eighteen bacterial isolates from the two rivers showed that bla_TEM, conferring resistance to β-lactam antibiotics, was dominant and present in ~58 % of isolates compared to only ~9 % for mefA/E conferring resistance to macrolides. Moreover, β-lactam resistance was detected in various isolates showing also resistance to additional antibiotics such as macrolides, aminoglycosides and tetracyclines. These observations would suggest the presence of co-resistant bacteria even in non-anthropogenic environments and this resistance may spread from the environment to humans and/or animals.

Holistic approach to chemical and microbiological quality of aquatic ecosystems impacted by wastewater effluent discharges

Wastewater treatment plants (WWTPs) collect wastewater from various sources and use different treatment processes to reduce the load of pollutants in the environment. Since the removal of many chemical pollutants and bacteria by WWTPs is incomplete, they constitute a potential source of contaminants. The continuous release of contaminants through WWTP effluents can compromise the health of the aquatic ecosystems, even if they occur at very low concentrations. The main objective of this work was to characterize, over a period of four months, the treatment steps starting from income to the effluent and 5 km downstream to the receiving river. In this context, the efficiency removal of chemical pollutants (e.g. hormones and pharmaceuticals, including antibiotics) and bacteria was assessed in a WWTP case study by using a holistic approach. It embraces different chemical and biological-based methods, such as pharmaceutical analysis by HPLC-MSMS, growth rate inhibition in algae, ligand binding estrogen receptor assay, microbial community study by 16S and shotgun sequencing along with relative quantification of resistance genes by quantitative polymerase chain reaction. Although both, chemical and biological-based methods showed a significant reduction of the pollutant burden in effluent and surface waters compared to the influent of the WWTP, no complete removal of pollutants, pathogens and antibiotic resistance genes was observed.

Flow cytometry-based viability staining: an at-line tool for bioprocess monitoring of Sulfolobus acidocaldarius

Determination of the viability, ratio of dead and live cell populations, of Sulfolobus acidocaldarius is still being done by tedious and material-intensive plating assays that can only provide time-lagged results. Although S. acidocaldarius, an extremophilic Archaeon thriving at 75 °C and pH 3.0, and related species harbor great potential for the exploitation as production hosts and biocatalysts in biotechnological applications, no industrial processes have been established yet. One hindrance is that during development and scaling of industrial bioprocesses timely monitoring of the impact of process parameters on the cultivated organism is crucial—a task that cannot be fulfilled by traditional plating assays. As alternative, flow cytometry (FCM) promises a fast and reliable method for viability assessment via the use of fluorescent dyes. In this study, commercially available fluorescent dyes applicable in S. acidocaldarius were identified. The dyes, fluorescein diacetate and concanavalin A conjugated with rhodamine, were discovered to be suitable for viability determination via FCM. For showing the applicability of the developed at-line tool for bioprocess monitoring, a chemostat cultivation on a defined growth medium at 75 °C, pH 3.0 was conducted. Over the timeframe of 800 h, this developed FCM method was compared to the plating assay by monitoring the change in viability upon controlled pH shifts. Both methods detected an impact on the viability at pH values of 2.0 and 1.5 when compared to pH 3.0. A logarithmic relationship between the viability observed via plating assay and via FCM was observed.

Development of a flow cytometry (FCM) method for viability determination of S. acidocaldarius using the fluorescent dyes fluorescein diacetate and concanavalin A conjugated with rhodamine.

Applicability of the developed method was shown via viability monitoring during a continuous cultivation with triggered pH shifts.

A logarithmic trend was observed between the developed FCM method and the state-of-the-art method, plating assay.

Analysis of Polyhydroxyalkanoates Granules in Haloferax mediterranei by Double-Fluorescence Staining with Nile Red and SYBR Green by Confocal Fluorescence Microscopy

Haloferaxmediterranei is a haloarchaeon of high interest in biotechnology because it produces and mobilizes intracellular polyhydroxyalkanoate (PHA) granules during growth under stress conditions (limitation of phosphorous in the culture media), among other interesting metabolites (enzymes, carotenoids, etc.). The capability of PHA production by microbes can be monitored with the use of staining-based methods. However, the staining of haloarchaea cells is a challenging task; firstly, due to the high ionic strength of the medium, which is inappropriate for most of dyes, and secondly, due to the low permeability of the haloarchaea S-layer to macromolecules. In this work, Haloferax mediterranei is used as a halophilic archaeon model to describe an optimized protocol for the visualization and analysis of intracellular PHA granules in living cells. The method is based on double-fluorescence staining using Nile red and SYBR Green by confocal fluorescence microscopy. Thanks to this method, the capability of PHA production by new haloarchaea isolates could be easily monitored.

Performance Evaluation of Biozentech Malaria Scanner in Plasmodium knowlesi and P. falciparum as a New Diagnostic Tool

The computer vision diagnostic approach currently generates several malaria diagnostic tools. It enhances the accessible and straightforward diagnostics that necessary for clinics and health centers in malaria-endemic areas. A new computer malaria diagnostics tool called the malaria scanner was used to investigate living malaria parasites with easy sample preparation, fast and user-friendly. The cultured Plasmodium parasites were used to confirm the sensitivity of this technique then compared to fluorescence-activated cell sorting (FACS) analysis and light microscopic examination. The measured percentage of parasitemia by the malaria scanner revealed higher precision than microscopy and was similar to FACS. The coefficients of variation of this technique were 1.2–6.7% for Plasmodium knowlesi and 0.3–4.8% for P. falciparum. It allowed determining parasitemia levels of 0.1% or higher, with coefficient of variation smaller than 10%. In terms of the precision range of parasitemia, both high and low ranges showed similar precision results. Pearson’s correlation test was used to evaluate the correlation data coming from all methods. A strong correlation of measured parasitemia (r²=0.99, P<0.05) was observed between each method. The parasitemia analysis using this new diagnostic tool needs technical improvement, particularly in the differentiation of malaria species.

Accurate identification and quantification of commensal microbiota bound by host immunoglobulins

BACKGROUND

Identifying which taxa are targeted by immunoglobulins can uncover important host-microbe interactions. Immunoglobulin binding of commensal taxa can be assayed by sorting bound bacteria from samples and using amplicon sequencing to determine their taxonomy, a technique most widely applied to study Immunoglobulin A (IgA-Seq). Previous experiments have scored taxon binding in IgA-Seq datasets by comparing abundances in the IgA bound and unbound sorted fractions. However, as these are relative abundances, such scores are influenced by the levels of the other taxa present and represent an abstract combination of these effects. Diversity in the practical approaches of prior studies also warrants benchmarking of the individual stages involved. Here, we provide a detailed description of the design strategy for an optimised IgA-Seq protocol. Combined with a novel scoring method for IgA-Seq datasets that accounts for the aforementioned effects, this platform enables accurate identification and quantification of commensal gut microbiota targeted by host immunoglobulins.

RESULTS

Using germ-free and Rag1^-/- mice as negative controls, and a strain-specific IgA antibody as a positive control, we determine optimal reagents and fluorescence-activated cell sorting (FACS) parameters for IgA-Seq. Using simulated IgA-Seq data, we show that existing IgA-Seq scoring methods are influenced by pre-sort relative abundances. This has consequences for the interpretation of case-control studies where there are inherent differences in microbiota composition between groups. We show that these effects can be addressed using a novel scoring approach based on posterior probabilities. Finally, we demonstrate the utility of both the IgA-Seq protocol and probability-based scores by examining both novel and published data from in vivo disease models.

CONCLUSIONS

We provide a detailed IgA-Seq protocol to accurately isolate IgA-bound taxa from intestinal samples. Using simulated and experimental data, we demonstrate novel probability-based scores that adjust for the compositional nature of relative abundance data to accurately quantify taxon-level IgA binding. All scoring approaches are made available in the IgAScores R package. These methods should improve the generation and interpretation of IgA-Seq datasets and could be applied to study other immunoglobulins and sample types. Video abstract.

A Reusable Column Method Using Glycopolymer-Functionalized Resins for Capture-Detection of Proteins and Escherichia coli

The use of glycopolymer-functionalized resins (Resin-Glc), as a solid support, in column mode for bacterial/protein capture and quantification is explored. The Resin-Glc is synthesized from commercially available chloromethylated polystyrene resin and glycopolymer, and is characterized by fourier transform infrared spectroscopy, thermogravimetry, and elemental analysis. The percentage of glycopolymer functionalized on Resin-Glc is accounted to be 5 wt%. The ability of Resin-Glc to selectively capture lectin, Concanavalin A, over Peanut Agglutinin, reversibly, is demonstrated for six cycles of experiments. The bacterial sequestration study using SYBR (Synergy Brands, Inc.) Green I tagged Escherichia coli/Staphylococcus aureus reveals the ability of Resin-Glc to selectively capture E. coli over S. aureus. The quantification of captured cells in the column is carried out by enzymatic colorimetric assay using methylumbelliferyl glucuronide as the substrate. The E. coli capture studies reveal a consistent capture efficiency of 10⁵  CFU (Colony Forming Units) g^-1 over six cycles. Studies with spiked tap water samples show satisfactory results for E. coli cell densities ranging from 10² to 10⁷  CFU mL^-1 . The method portrayed can serve as a basis for the development of a reusable solid support in capture and detection of proteins and bacteria.

Physiological Capabilities of Cryoconite Hole Microorganisms

Cryoconite holes are miniature freshwater aquatic ecosystems that harbor a relatively diverse microbial community. This microbial community can withstand the extreme conditions of the supraglacial environment, including fluctuating temperatures, extreme and varying geochemical conditions and limited nutrients. We analyzed the physiological capabilities of microbial isolates from cryoconite holes from Antarctica, Greenland, and Svalbard in selected environmental conditions: extreme pH, salinity, freeze-thaw and limited carbon sources, to identify their physiological limits. The results suggest that heterotrophic microorganisms in cryoconite holes are well adapted to fast-changing environmental conditions, by surviving multiple freeze-thaw cycles, a wide range of salinity and pH conditions and scavenging a variety of organic substrates. Under oxic and anoxic conditions, the communities grew well in temperatures up to 30°C, although in anoxic conditions the community was more successful at colder temperatures (0.2°C). The most abundant cultivable microorganisms were facultative anaerobic bacteria and yeasts. They grew in salinities up to 10% and in pH ranging from 4 to 10.5 (Antarctica), 2.5 to 10 (Svalbard), and 3 to 10 (Greenland). Their growth was sustained on at least 58 single carbon sources and there was no decrease in viability for some isolates after up to 100 consecutive freeze-thaw cycles. The elevated viability of the anaerobic community in the lowest temperatures indicates they might be key players in winter conditions or in early melt seasons, when the oxygen is potentially depleted due to limited flow of meltwater. Consequently, facultative anaerobic heterotrophs are likely important players in the reactivation of the community after the polar night. This detailed physiological investigation shows that despite inhabiting a freshwater environment, cryoconite microorganisms are able to withstand conditions not typically encountered in freshwater environments (namely high salinities or extreme pH), making them physiologically more similar to arid soil communities. The results also point to a possible resilience of the most abundant microorganisms of cryoconite holes in the face of rapid change regardless of the location.

A simple, fast and reliable scan-based technique as a novel approach to quantify intracellular bacteria

Background

Quantification of intracellular bacteria is fundamental in many areas of cellular and clinical microbiology to study acute and chronic infections. Therefore, rapid, accurate and low-cost methods represent valuable tools in determining bacterial ability to persist and proliferate within eukaryotic cells.

Results

Herein, we present the first application of the immunofluorescence In-Cell Western (ICW) assay aimed at quantifying intracellular bacteria in in vitro infection models. The performance of this new approach was evaluated in cell culture infection models using three microorganisms with different lifestyles. Two facultative intracellular bacteria, the fast-growing Shigella flexneri and a persistent strain of Escherichia coli, as well as the obligate intracellular bacterium Chlamydia trachomatis were chosen as bacterial models. The ICW assay was performed in parallel with conventional quantification methods, i.e. colony forming units (CFUs) and inclusion forming units (IFUs). The fluorescence signal intensity values from the ICW assay were highly correlated to CFU/IFUs counting and showed coefficients of determination (R²), ranging from 0,92 to 0,99.

Conclusions

The ICW assay offers several advantages including sensitivity, reproducibility, high speed, operator-independent data acquisition and overtime stability of fluorescence signals. All these features, together with the simplicity in performance, make this assay particularly suitable for high-throughput screening and diagnostic approaches.

Determination of live and dead Komagataeibacter xylinus cells and first attempt at precise control of inoculation in nanocellulose production

The timely enumeration of cells of nanocellulose-producing bacteria is challenging due to their unique growth properties. To better understand the metabolism of the bacteria and better control the concentration of living cells during cultivation, a prompt cell counting technology is crucial and urgently required. In this work, two fluorescent dyes, the asymmetrical anthocyanidin dye SYBR Green I (SG) and propidium iodide (PI), were first combined for Komagataeibacter xylinus species to determine live/dead bacterial cells quantitatively and promptly. The number of live and dead K. xylinus cells determined using an epifluorescence microscope corresponded well to the results obtained using a fluorescence microplate reader. The R² values were 0.9986 and 0.9920, respectively, and were similar to those obtained with the LIVE/DEAD^® BacLight^TM commercial kit. SG/PI double-staining showed proper efficiency in distinguishing live/dead cells for the K. xylinus strain (R²  = 0.9898). The technology was applied to standardize four different K. xylinus strains, and the initial cell concentration of the strains was precisely controlled (no significant difference among the strains, P> 0.05). The cellulose yield per live cell was calculated, and significant differences (P < 0.05) were found among the four strains in the following order: DHU-ATCC-1> DHU-ZCY-1> DHU-ZGD-1> ATCC 23770. The study shows (i) the application of the SG/PI staining to standardizing inocula for bacterial cellulose production so that a more accurate comparison can be made between different strains, and (ii) the lower cost of using SG rather than the SYTO 9 of the commercially available LIVE/DEAD^® BacLight^TM kit.

Flow cytometry applications in water treatment, distribution, and reuse: A review

Ensuring safe and effective water treatment, distribution, and reuse requires robust methods for characterizing and monitoring waterborne microbes. Methods widely used today can be limited by low sensitivity, high labor and time requirements, susceptibility to interference from inhibitory compounds, and difficulties in distinguishing between viable and non-viable cells. Flow cytometry (FCM) has recently gained attention as an alternative approach that can overcome many of these challenges. This article critically and systematically reviews for the first time recent literature on applications of FCM in water treatment, distribution, and reuse. In the review, we identify and examine nearly 300 studies published from 2000 to 2018 that illustrate the benefits and challenges of using FCM for assessing source-water quality and impacts of treatment-plant discharge on receiving waters, wastewater treatment, drinking water treatment, and drinking water distribution. We then discuss options for combining FCM with other indicators of water quality and address several topics that cut across nearly all applications reviewed. Finally, we identify priority areas in which more work is needed to realize the full potential of this approach. These include optimizing protocols for FCM-based analysis of waterborne viruses, optimizing protocols for specifically detecting target pathogens, automating sample handling and preparation to enable real-time FCM, developing computational tools to assist data analysis, and improving standards for instrumentation, methods, and reporting requirements. We conclude that while more work is needed to realize the full potential of FCM in water treatment, distribution, and reuse, substantial progress has been made over the past two decades. There is now a sufficiently large body of research documenting successful applications of FCM that the approach could reasonably and realistically see widespread adoption as a routine method for water quality assessment.

High-Throughput Quantification of Bacterial-Cell Interactions Using Virtual Colony Counts

The quantification of bacteria in cell culture infection models is of paramount importance for the characterization of host-pathogen interactions and pathogenicity factors involved. The standard to enumerate bacteria in these assays is plating of a dilution series on solid agar and counting of the resulting colony forming units (CFU). In contrast, the virtual colony count (VCC) method is a high-throughput compatible alternative with minimized manual input. Based on the recording of quantitative growth kinetics, VCC relates the time to reach a given absorbance threshold to the initial cell count using a series of calibration curves. Here, we adapted the VCC method using the model organism Salmonella enterica sv. Typhimurium (S. Typhimurium) in combination with established cell culture-based infection models. For HeLa infections, a direct side-by-side comparison showed a good correlation of VCC with CFU counting after plating. For MDCK cells and RAW macrophages we found that VCC reproduced the expected phenotypes of different S. Typhimurium mutants. Furthermore, we demonstrated the use of VCC to test the inhibition of Salmonella invasion by the probiotic E. coli strain Nissle 1917. Taken together, VCC provides a flexible, label-free, automation-compatible methodology to quantify bacteria in in vitro infection assays.

Clinical and molecular characteristics of infective β-hemolytic streptococcal endocarditis

Streptococcus pyogenes (S. pyogenes) and Streptococcus dysgalactiae subspecies equisimilis (SDSE) cause considerable morbidity and mortality, and show similarities in disease manifestations and pathogenic mechanisms. Their involvement in infective endocarditis, however, has not been well described. Invasive S. pyogenes and SDSE infections in Health Region Bergen, Norway, in the period 1999-2013 were reviewed, and sixteen cases of endocarditis were identified. The median duration of symptoms was 2.5days, the frequency of embolic events 50%, 38% received valve replacement and the 30-day mortality was 25%. In S. pyogenes, a significant correlation was observed between the repertoire of fibronectin-binding genes, phenotypic binding ability to fibronectin and disease manifestations. Conversely, no associations between phenotypic and genotypic characteristics were detected in SDSE. S. pyogenes and SDSE endocarditis is characterized by rapid and severe clinical manifestations. The pathogenesis is multifactorial, but our results infer a potential role of fibronectin binding in the development of S. pyogenes endocarditis.

Distinct compositions of free-living, particle-associated and benthic communities of the Roseobacter group in the North Sea

The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1 × 10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.

Rapid and accurate detection of Escherichia coli growth by fluorescent pH-sensitive organic nanoparticles for high-throughput screening applications

Rapid detection of bacterial growth is an important issue in the food industry and for medical research. Here we present a novel kind of pH-sensitive fluorescent nanoparticles (FANPs) that can be used for the rapid and accurate real-time detection of Escherichia coli growth. These organic particles are designed to be non-toxic and highly water-soluble. Here we show that the coupling of pH sensitive fluoresceinamine to the nanoparticles results in an increased sensitivity to changes in pH within a physiologically relevant range that can be used to monitor the presence of live bacteria. In addition, these FANPs do not influence bacterial growth and are stable over several hours in a complex medium and in the presence of bacteria. The use of these FANPs allows for continuous monitoring of bacterial growth via real-time detection over long time scales in small volumes and can thus be used for the screening of a large number of samples for high-throughput applications such as screening for the presence of antibiotic resistant strains.

Dual investigation of methanogenic processes by quantitative PCR and quantitative microscopic fingerprinting

Monitoring of methanogenic communities in anaerobic digesters using molecular-based methods is very attractive but can be cost-intensive. A new and fast quantification method by microscopic image analysis was developed to accompany molecular-based methods. This digitalized method, called quantitative microscopic fingerprinting (QMF), enables quantification of active methanogenic cells (N mL(-1)) by their characteristic auto-fluorescence based on coenzyme F420 . QMF was applied to analyze the methanogenic communities in three biogas plant samples, and the results were compared with the relative proportion of gene copy numbers obtained with the quantitative PCR (qPCR). Analysis of QMF demonstrated dominance of Methanomicrobiales and Methanobacteriales in relation to the total methanogenic community in digesters operating at high ammonia concentrations, which corresponded to the results established by qPCR. Absolute microbial counts by QMF and the numbers obtained by qPCR were not always comparable. On the other hand, the restricted morphological analysis by QMF was enhanced by the capability of qPCR to identify microbes. Consequently, dual investigations of both methods are proposed to improve monitoring of anaerobic digesters. For a rough estimation of the methanogenic composition in anaerobic digesters, the QMF method seems to be a promising approach for the rapid detection of microbial changes.

Investigation of microbial biofilm structure by laser scanning microscopy

Microbial bioaggregates and biofilms are hydrated three-dimensional structures of cells and extracellular polymeric substances (EPS). Microbial communities associated with interfaces and the samples thereof may come from natural, technical, and medical habitats. For imaging such complex microbial communities confocal laser scanning microscopy (CLSM) is the method of choice. CLSM allows flexible mounting and noninvasive three-dimensional sectioning of hydrated, living, as well as fixed samples. For this purpose a broad range of objective lenses is available having different working distance and resolution. By means of CLSM the signals detected may originate from reflection, autofluorescence, reporter genes/fluorescence proteins, fluorochromes binding to specific targets, or other probes conjugated with fluorochromes. Recorded datasets can be used not only for visualization but also for semiquantitative analysis. As a result CLSM represents a very useful tool for imaging of microbiological samples in combination with other analytical techniques.

Xenobiotics shape the physiology and gene expression of the active human gut microbiome

The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider interindividual variations in the active human gut microbiome.

Acridine orange as an alternative to optical density to study growth kinetics of Lactobacillus bulgaricus ATCC 7517

In this study we assessed the use of acridine orange as an alternative to optical density to quantify the growth of Lactobacillus bulgaricus ATCC 7517. The growth of bacteria in Lactobacillus de Man Rogosa Sharpe (MRS) medium was measured by both acridine orange (AO) and optical density (OD) measurements for 24 h. The relationship between both methods was compared via correlation analysis. The doubling time of bacteria based on the values of OD600 and AO obtained during 24 h growth were also calculated. The result shows strong correlation of cell growth between OD600 and AO during the first 10 hours of growth, but the correlation was less strong when analyzing the data from 0 to 24 hours. Growth rates, generation time and lag time were also similar. This study indicates that AO could be used in place of OD to prepare growth curves of Lactobacillus bulgaricus during the exponential phase of growth, and to compare growth rates, generation times or lag times.

Quantifying and identifying the active and damaged subsets of indigenous microbial communities

Flow cytometry and fluorescent dyes represent valuable experimental tools for studying complex microbial communities, enabling the quantification and sorting of cells with distinct levels of activity or damage, and providing information that can be difficult to infer from metagenomic sequencing alone. Despite this potential, these single-cell methods have seldom been applied to the study of host-associated microbial communities. Here, we present our recently developed protocols utilizing four distinct fluorescent dyes that label cells based on nucleic acid content, respiratory activity, and membrane damage. These methods have been successfully applied to study the trillions of microorganisms inhabiting the human gastrointestinal tract (the gut microbiota), in addition to a collection of isolates from five common gut-associated bacterial phyla. By merging these protocols with fluorescence-activated cell sorting and downstream multiplex 16S rRNA gene sequencing, it is possible to rapidly assess the taxonomic composition of each physiological category. These methods provide an initial step toward a robust toolkit allowing a rapid, culture-independent, and comprehensive assessment of the physiology and metabolic activity of host-associated microbial communities.

Enrichment and cultivation of prokaryotes associated with the sulphate-methane transition zone of diffusion-controlled sediments of Aarhus Bay, Denmark, under heterotrophic conditions

The prokaryotic activity, diversity and culturability of diffusion-controlled Aarhus Bay sediments, including the sulphate-methane transition zone (SMTZ), were determined using a combination of geochemical, molecular (16S rRNA and mcrA genes) and cultivation techniques. The SMTZ had elevated sulphate reduction and anaerobic oxidation of methane, and enhanced cell numbers, but no active methanogenesis. The prokaryotic population was similar to that in other SMTZs, with Deltaproteobacteria, Gammaproteobacteria, JS1, Planctomycetes, Chloroflexi, ANME-1, MBG-D and MCG. Many of these groups were maintained in a heterotrophic (10 mM glucose, acetate), sediment slurry with periodic low sulphate and acetate additions (~2 mM). Other prokaryotes were also enriched including methanogens, Firmicutes, Bacteroidetes, Synergistetes and TM6. This slurry was then inoculated into a matrix of substrate and sulphate concentrations for further selective enrichment. The results demonstrated that important SMTZ bacteria can be maintained in a long-term, anaerobic culture under specific conditions. For example, JS1 grew in a mixed culture with acetate or acetate/glucose plus sulphate. Chloroflexi occurred in a mixed culture, including in the presence of acetate, which had previously not been shown to be a Chloroflexi subphylum I substrate, and was more dominant in a medium with seawater salt concentrations. In contrast, archaeal diversity was reduced and limited to the orders Methanosarcinales and Methanomicrobiales. These results provide information about the physiology of a range of SMTZ prokaryotes and shows that many can be maintained and enriched under heterotrophic conditions, including those with few or no cultivated representatives.

High abundance of ammonia-oxidizing Archaea in coastal waters, determined using a modified DNA extraction method

Molecular characterizations of environmental microbial populations based on recovery and analysis of DNA generally assume efficient or unbiased extraction of DNA from different sample matrices and microbial groups. Appropriate controls to verify this basic assumption are rarely included. Here three different DNA extractions, performed with two commercial kits (FastDNA and UltraClean) and a standard phenol-chloroform method, and two alternative filtration methods (Sterivex and 25-mm-diameter polycarbonate filters) were evaluated, using the addition of Nitrosopumilus maritimus cells to track the recovery of DNA from marine Archaea. After the comparison, a simplified phenol-chloroform extraction method was developed and shown to be significantly superior, in terms of both the recovery and the purity of DNA, to other protocols now generally applied to environmental studies. The simplified and optimized method was used to quantify ammonia-oxidizing Archaea at different depth intervals in a fjord (Hood Canal) by quantitative PCR. The numbers of Archaea increased with depth, often constituting as much as 20% of the total bacterial community.

Tateyamaria pelophila sp. nov., a facultatively anaerobic alphaproteobacterium isolated from tidal-flat sediment, and emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii

A Gram-negative motile rod, strain SAM4T, was isolated from the highest positive dilution of a most probable number series inoculated with tidal-flat sediments from the German North Sea coast. The isolate grew at 4-35 degrees C and showed constant growth yields throughout almost the whole temperature range. Growth was observed between pH 6 and 9 and at salinities of 0.3-10.2%. Strain SAM4T required Na+ for growth, contained bacteriochlorophyll a and was catalase- and oxidase-positive. It was nutritionally versatile growing on a variety of carbon compounds including carbohydrates, amino acids and organic acids like lactate or succinate. It grew anaerobically on complex media such as marine broth, indicating fermentation, and by reducing trimethylammonium oxide. The dominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol, whereas only traces of phosphatidylcholine and an unidentified lipid were found. The major fatty acid was n-C18:1omega7c. The DNA G+C content was 56.4 mol%. The isolate was identified as a member of the Roseobacter clade within the class Alphaproteobacteria. However, based on phylogenetic, phenotypic and physiological data, it clearly differs from its closest relative Tateyamaria omphalii. Therefore, a novel species is proposed: Tateyamaria pelophila sp. nov., with strain SAM4T (=DSM 17270T=LMG 23018T) as the type strain. Emended descriptions of the genus Tateyamaria and of Tateyamaria omphalii are also presented.

Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307)

The Porcupine Seabight Challenger Mound is the first carbonate mound to be drilled (∼270 m) and analyzed in detail microbiologically and biogeochemically. Two mound sites and a non-mound Reference site were analyzed with a range of molecular techniques [catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative PCR (16S rRNA and functional genes, dsrA and mcrA), and 16S rRNA gene PCR-DGGE] to assess prokaryotic diversity, and this was compared with the distribution of total and culturable cell counts, radiotracer activity measurements and geochemistry. There was a significant and active prokaryotic community both within and beneath the carbonate mound. Although total cell numbers at certain depths were lower than the global average for other subseafloor sediments and prokaryotic activities were relatively low (iron and sulfate reduction, acetate oxidation, methanogenesis) they were significantly enhanced compared with the Reference site. In addition, there was some stimulation of prokaryotic activity in the deepest sediments (Miocene, > 10 Ma) including potential for anaerobic oxidation of methane activity below the mound base. Both Bacteria and Archaea were present, with neither dominant, and these were related to sequences commonly found in other subseafloor sediments. With an estimate of some 1600 mounds in the Porcupine Basin alone, carbonate mounds may represent a significant prokaryotic subseafloor habitat.

Burkholderia sediminicola sp. nov., isolated from freshwater sediment

A Gram-negative, motile and rod-shaped bacterium, designated HU2-65W(T), was isolated from freshwater sediment. The strain possessed ubiquinone 8 as the predominant isoprenoid quinone and contained major amounts of omega7-cis-octadecenoic acid and hexadecanoic acid in its cell envelope, which are properties shared by members of the genus Burkholderia. On the basis of 16S rRNA gene sequence similarity, strain HU2-65W(T) was most closely related to the type strain of Burkholderia xenovorans (98.4 %). The DNA G+C content of strain HU2-65W(T) was 61.2 mol%, and DNA-DNA relatedness values to type strains of closely related species were found to be much lower than 70 %, indicating that the strain represents a separate genomic species within the genus Burkholderia. Strain HU2-65W(T) was also differentiated from other species of the genus by physiological and biochemical characteristics. Consequently, strain HU2-65W(T) is considered to represent a single, novel species of the genus Burkholderia, for which the name Burkholderia sediminicola sp. nov. is proposed, with the type strain HU2-65W(T) (=KCTC 22086(T) =LMG 24238(T)).

Two distinct Photobacterium populations thrive in ancient Mediterranean sapropels

Eastern Mediterranean sediments are characterized by the periodic occurrence of conspicuous, organic matter-rich sapropel layers. Phylogenetic analysis of a large culture collection isolated from these sediments revealed that about one third of the isolates belonged to the genus Photobacterium. In the present study, 22 of these strains were examined with respect to their phylogenetic and metabolic diversity. The strains belonged to two distinct Photobacterium populations (Mediterranean cluster I and II). Strains of cluster I were isolated almost exclusively from organic-rich sapropel layers and were closely affiliated with P. aplysiae (based on their 16S rRNA gene sequences). They possessed almost identical Enterobacterial Repetitive Intergenic Consensus (ERIC) and substrate utilization patterns, even among strains from different sampling sites or from layers differing up to 100,000 years in age. Strains of cluster II originated from sapropels and from the surface and carbon-lean intermediate layers. They were related to Photobacterium frigidiphilum but differed significantly in their fingerprint patterns and substrate spectra, even when these strains were obtained from the same sampling site and layer. Temperature range for growth (4 to 33 degrees C), salinity tolerance (5 to 100 per thousand), pH requirements (5.5-9.3), and the composition of polar membrane lipids were similar for both clusters. All strains grew by fermentation (glucose, organic acids) and all but five by anaerobic respiration (nitrate, dimethyl sulfoxide, anthraquinone disulfonate, or humic acids). These results indicate that the genus Photobacterium forms subsurface populations well adapted to life in the deep biosphere.

Application of a microfluidic device for counting of bacteria

AIMS

To develop a miniaturized analytical system for counting of bacteria.

METHODS AND RESULTS

Escherichia coli cells were used throughout the experiments. The system consists of a microfluidic chamber, a fluorescence microscope with a charge-coupled device (CCD) camera and syringe pumps. The chamber was made of a silicone rubber (30 x 30 mm and 4 mm high). The E. coli cells were flowed from a micro-nozzle fabricated in the chamber and detected with the CCD camera. The individual cells were indicated as signal peaks on a computer. The cell counts showed a good correlation compared with that of a conventional plate counting method, and results of the simultaneous detection of live and dead cells were also presented.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

The system having a small disposable nozzle has the advantages for low cost and safe medical or environmental analysis, when compared with a conventional flow cytometer. This is the first step of the development of a one-chip microbe analyzer.

Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.