Evaluating the flow-cytometric nucleic acid double-staining protocol in realistic situations of planktonic bacterial death

Enhancing microbiologically influenced corrosion protection of carbon steels with silanized epoxy-biocide hybrid coatings

Microbial biofilms and microbiologically influenced corrosion (MIC) pose serious problems in pipelines transporting freshwater from the reservoir to service water systems and fire water systems of power reactors. The present work aims to design a silane-based epoxy-biocide hybrid coating along with antibacterial compounds on carbon steels (CS) for controlling the MIC of pipeline materials. The optimal inhibitory concentrations of biocides are identified and a robust protocol has been developed to prepare epoxy-based coatings impregnated with three biocides (25 ppm each of benzalkonium chloride, bronopol, and isothiazoline). Microbiological and accelerated corrosion studies were carried out by exposing the coated CS specimens to the enriched freshwater bacterial culture (FWC). As compared to the impedance value of 102 Ohms for the polished CS, the values were 106 and 105 Ohms, respectively, for epoxy-coated specimens (CSE) and epoxy-coated specimens impregnated with biocides (CSEB). The corrosion protection efficiency of CSE and CSEB coated specimens exposed to FWC was 99.9% and 98.1%, respectively. Confocal microscopic analysis showed the average biomass thickness was 51.3 ± 0.6 µm and 24.4 ± 0.5 µm, respectively, for CSE and CSEB specimens in comparison to 94.1 ± 0.2 µm on CS specimens. The improved anticorrosion and antifouling behaviors observed in the CSEB specimens suggest that the new coating strategy has the potential for the development of multifunctional hybrid epoxy coatings for pipeline materials to mitigate MIC-related issues in water-transporting pipeline systems.

Cytokine Profile Response of Human Peripheral Blood Mononuclear Cells Stimulated by Bartonella bacilliformis

Carrion's disease is a neglected endemic disease found in remote Andean areas. As an overlooked disease, knowledge of innate immune responses to Bartonella bacilliformis, the etiological agent, is scarce. This study aimed to evaluate the cytokine response to B. bacilliformis using in vitro human peripheral blood mononuclear cells (PBMCs) stimulations. PBMCs from naive adults were isolated by gradient centrifugation and cocultured with heat-inactivated (HI) B. bacilliformis at different incubation times (3, 6, 12, 24, and 36 h). Cytokines, chemokines, and growth factors were determined in culture supernatants by multiplex fluorescent bead-based quantitative suspension array technology. During the first 36 h, a proinflammatory response was observed, including tumor necrosis factor-α, interleukin (IL)-1α, IL-1β, interferon-α2, and IL-6, followed by an anti-inflammatory response mainly related to IL-1RA. Moreover, high expression levels of chemokines IL-8, monocyte chemoattractant protein-1α, and macrophage inflammatory protein (MIP)-1β were detected from 3 h poststimulation and MIP-1α was detected at 24 h. Some growth factors, mainly granulocyte macrophage colony-stimulating factor and granulocyte colony-stimulating factor, and in minor concentrations vascular endothelial growth factor, epidermal growth factor, and eotaxin, were also detected. Innate response to HI B. bacilliformis stimulation consists of a rapid and strong proinflammatory response characterized by a wide range of cytokines and chemokines followed by an anti-inflammatory response and increased specific growth factors.

Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Opportunities in optical and electrical single-cell technologies to study microbial ecosystems

New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica

As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.

Responses of Coastal Marine Microbiomes Exposed to Anthropogenic Dissolved Organic Carbon

Coastal seawaters receive thousands of organic pollutants. However, we have little understanding of the response of microbiomes to this pool of anthropogenic dissolved organic carbon (ADOC). In this study, coastal microbial communities were challenged with ADOC at environmentally relevant concentrations. Experiments were performed at two Mediterranean sites with different impact by pollutants and nutrients: off the Barcelona harbor ("BCN"), and at the Blanes Bay ("BL"). ADOC additions stimulated prokaryotic leucine incorporation rates at both sites, indicating the use of ADOC as growth substrate. The percentage of "membrane-compromised" cells increased with increasing ADOC, indicating concurrent toxic effects of ADOC. Metagenomic analysis of the BCN community challenged with ADOC showed a significant growth of Methylophaga and other gammaproteobacterial taxa belonging to the rare biosphere. Gene expression profiles showed a taxon-dependent response, with significantly enrichments of transcripts from SAR11 and Glaciecola spp. in BCN and BL, respectively. Further, the relative abundance of transposon-related genes (in BCN) and transcripts (in BL) correlated with the number of differentially abundant genes (in BCN) and transcripts (in BLA), suggesting that microbial responses to pollution may be related to pre-exposure to pollutants, with transposons playing a role in adaptation to ADOC. Our results point to a taxon-specific response to low concentrations of ADOC that impact the functionality, structure and plasticity of the communities in coastal seawaters. This work contributes to address the influence of pollutants on microbiomes and their perturbation to ecosystem services and ocean health.

Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean

Thousands of man-made synthetic chemicals are released to oceans and compose the anthropogenic dissolved organic carbon (ADOC). Little is known about the effects of this chronic pollution on marine microbiome activities. In this study, we measured the pollution level at three sites in the Northeast Subarctic Pacific Ocean (NESAP) and investigated how mixtures of three model families of ADOC at different environmentally relevant concentrations affected naturally occurring marine bacterioplankton communities' structure and metabolic functioning. The offshore northernmost site (North) had the lowest concentrations of hydrocarbons, as well as organophosphate ester plasticizers, contrasting with the two other continental shelf sites, the southern coastal site (South) being the most contaminated. At North, ADOC stimulated bacterial growth and promoted an increase in the contribution of some Gammaproteobacteria groups (e.g. Alteromonadales) to the 16 rRNA pool. These groups are described as fast responders after oil spills. In contrast, minor changes in South microbiome activities were observed. Gene expression profiles at Central showed the coexistence of ADOC degradation and stress-response strategies to cope with ADOC toxicities. These results show that marine microbial communities at three distinct domains in NESAP are influenced by background concentrations of ADOC, expanding previous assessments for polar and temperate waters.

Ohmic heating increases inactivation and morphological changes of Salmonella sp. and the formation of bioactive compounds in infant formula

The effect of ohmic heating (OH) (50, 55, and 60 °C, 6 V/cm) on the inactivation kinetics (Weibull model) and morphological changes (scanning electron microscopy and flow cytometry) of Salmonella spp. in infant formula (IF) was evaluated. In addition, thermal load indicators (hydroxymethylfurfural and whey protein nitrogen index, HMF, and WPNI) and bioactive compounds (DPPH, total phenolics, ACE, α-amylase, and α-glucosidase inhibitory activities) were also studied. OH presented a more intense inactivation rate than conventional heating, resulting in a reduction of about 5 log CFU per mL at 60 °C in only 2.91 min, being also noted a greater cell membrane deformation, higher formation of bioactive compounds, and lower values for the thermal load parameters. Overall, OH contributed to retaining the nutritional value and improve food safety in IF processing.

Ozonation enhancement of low cost double-stranded DNA binding dye based fluorescence measurement of total bacterial load in water

We demonstrated the feasibility of using ozonation to enhance the performance of dsDNA binding dye SYBR Green I in the fluorescence measurement of total bacterial load in water. Unlike its membrane permeable but expensive equivalent such as SYTO82 dye, SYBR Green I is many times cheaper but membrane impermeable. Ozonation allowed SYBR Green I dye to permeate the membrane and bind with the dsDNA within by first breaching it. Using E. coli K12 bacteria at serial dilution ratios from 1/1 (980 CFU mL⁻¹) to 1/200, we achieved corresponding quantification from 618.7 ± 9.4 to 68.0 ± 1.9 RFU (100 to 11.00% normalized RFU). In comparison, plate counting and optical density measurement were only able to quantify up till a serial dilution ratio of 1/50 (40 CFU mL⁻¹ and 0.0421, respectively). Most importantly with ozonation, the sensitivity of SYBR Green I dye based fluorescence measurement was improved by ∼140 to 210% as compared to that without ozonation. Given its low electrical power consumption, lab-on-chip compatibility and reagent-less nature, ozonation is highly compatible with portable fluorimeters to realize low-cost monitoring of total bacterial load in water.

Principle of ozonation enhanced dsDNA binding dye based fluorescence measurement of total bacterial load in water.

Chlorination effects on DNA based characterization of water microbiomes and implications for the interpretation of data from disinfected systems

Quantitative PCR (qPCR) and next generation sequencing (NGS) are nucleic acid based microbiology techniques that provide new insights into drinking water quality, but considerable uncertainty remains around their correct interpretation. We noticed the presence of bacterial DNA from various putative pathogens, including from faecal indicator bacteria (FIB), in disinfected water, when culturable FIB were absent. To understand these observations better we studied the effect of chlorination on conventional and DNA based microbial water quality assessments. Surface water chlorination reduced plate counts for various FIB by up to >6 log units, intact cell counts by flow cytometry by 3.3 log units, and 16S rRNA gene copies by qPCR by 1.5 and 1.6 log units for total bacteria and total coliforms, respectively. Nanopore sequencing of 16S rRNA amplicons with the portable MinION device revealed the DNA from several families containing putative pathogens appeared to be more resistant than that of other bacteria to degradation by chlorine disinfection. For instance, 16S rRNA genes assigned to the Enterobacteriaceae family, members of which are mostly the target of coliform tests, increased in relative abundance from 0.001 ± 0.0002% to 0.0036 ± 0.003% after chlorine treatment. Hence, metagenomic drinking water data needs to be interpreted with caution. Plate counts and flow cytometry in combination with DNA based analysis provide more robust insight than NGS or qPCR alone.

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin

The use of additives in food products has become an important public health concern. In recent reports, dietary emulsifiers have been shown to affect the gut microbiota, contributing to a pro-inflammatory phenotype and metabolic syndrome. So far, it is not yet known whether similar microbiome shifts are observable for a more diverse set of emulsifier types and to what extent these effects vary with the unique features of an individual's microbiome. To bridge this gap, we investigated the effect of five dietary emulsifiers on the fecal microbiota from 10 human individuals upon a 48 h exposure. Community structure was assessed with quantitative microbial profiling, functionality was evaluated by measuring fermentation metabolites, and pro-inflammatory properties were assessed with the phylogenetic prediction algorithm PICRUSt, together with a TLR5 reporter cell assay for flagellin. A comparison was made between two mainstream chemical emulsifiers (carboxymethylcellulose and P80), a natural extract (soy lecithin), and biotechnological emulsifiers (sophorolipids and rhamnolipids). While fecal microbiota responded in a donor-dependent manner to the different emulsifiers, profound differences between emulsifiers were observed. Rhamnolipids, sophorolipids, and soy lecithin eliminated 91 ± 0, 89 ± 1, and 87 ± 1% of the viable bacterial population after 48 h, yet they all selectively increased the proportional abundance of putative pathogens. Moreover, profound shifts in butyrate (-96 ± 6, -73 ± 24, and -34 ± 25%) and propionate (+13 ± 24, +88 ± 50, and +29 ± 16%) production were observed for these emulsifiers. Phylogenetic prediction indicated higher motility, which was, however, not confirmed by increased flagellin levels using the TLR5 reporter cell assay. We conclude that dietary emulsifiers can severely impact the gut microbiota, and this seems to be proportional to their emulsifying strength, rather than emulsifier type or origin. As biotechnological emulsifiers were especially more impactful than chemical emulsifiers, caution is warranted when considering them as more natural alternatives for clean label strategies.

INT Toxicity over Natural Bacterial Assemblages from Surface Oligotrophic Waters: Implications for the Assessment of Respiratory Activity

Plankton community respiration (R) is a major component of the carbon flux in aquatic ecosystems. However, current methods to measure actual respiration from oxygen consumption at relevant spatial scales are not sensitive enough in oligotrophic environments where respiration rates are very low. To overcome this drawback, more sensitive indirect enzymatic approaches are commonly used as R proxies. The in vivo electron transport system (ETSvivo) assay, which measures the reduction of (2-(4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl tetrazolium chloride salt, INT) to INT-formazan in the presence of natural substrate levels, was recently proposed as an indirect reliable estimation of R for natural plankton communities. However, under in vivo conditions, formazan salts could be toxic to the cells. Here, we test the toxicity of 0.2 mM of final INT concentration, widely used for ETSvivo assays, on natural bacterial assemblages collected in coastal and oceanic waters off Gran Canaria (Canary Islands, subtropical North Atlantic), in eight independent experiments. After 0.5 h of incubation, a significant but variable decline in cell viability (14-49%) was observed in all samples inoculated with INT. Moreover, INT also inhibited leucine uptake in less than 90 min of incubation. In the light of these results, we argue that enzymatic respiratory rates obtained with the ETSvivo method need to be interpreted with caution to derive R in oceanic regions where bacteria largely contribute to community respiration. Moreover, the variable toxicity on bacterial assemblages observed in our experiments questions the use of a single R/ETSvivo relationship as a universal proxy for regional studies.

Responses of physiological groups of tropical heterotrophic bacteria to temperature and dissolved organic matter additions: food matters more than warming

Compared to higher latitudes, tropical heterotrophic bacteria may be less responsive to warming because of strong bottom‐up control. In order to separate both drivers, we determined the growth responses of bacterial physiological groups to temperature after adding dissolved organic matter (DOM) from mangroves, seagrasses and glucose to natural seawater from the Great Barrier Reef. Low (LNA) and high (HNA) nucleic acid content, membrane‐intact (Live) and membrane‐damaged (Dead) plus actively respiring (CTC+) cells were monitored for 4 days. Specific growth rates of the whole community were significantly higher (1.9 day^‐1) in the mangrove treatment relative to the rest (0.2–0.4 day^‐1) at in situ temperature and their temperature dependence, estimated as activation energy, was also consistently higher. Strong bottom‐up control was suggested in the other treatments. Cell size depended more on DOM than temperature. Mangrove DOM resulted in significantly higher contributions of Live, HNA and CTC+ cells to total abundance, while the seagrass leachate reduced Live cells below 50%. Warming significantly decreased Live and CTC+ cells contributions in most treatments. Our results suggest that only in the presence of highly labile compounds, such as mangroves DOM, can we anticipate increases in heterotrophic bacteria biomass in response to warming in tropical regions.

Impact of sterilization methods on dissolved trace metals concentrations in complex natural samples: Optimization of UV irradiation

Sterilization is essential for discriminating biotic responses from abiotic reactions in laboratory experiments investigating biogeochemical processes of complex natural samples. However, the conventional methods used to effectively sterilize materials or culture media do not allow sterilizing complex natural samples while maintaining biogeochemical balances. The aim of this study was to develop a low-cost and easy-to-use method to obtain geochemically unmodified and sterilized samples from complex lacustrine or coastal marine ecosystems. In preliminary assays, the impact of several sterilization methods (autoclaving, chemical poisoning, microwave, UV irradiation) on the trace metals balances was studied using borosilicate glass (BG), fluorinated ethylene-propylene (FEP) or polyethylene terephthalate (PET) bottles. Unlike other methods, UV sterilization had minor effects on the distribution of dissolved trace metals. Additional tests using complex lacustrine and coastal marine samples under 10 g/L sediments were performed using a homemade UV sterilization chamber designed to simultaneously irradiate a large number samples. Results showed: •very reproducible UV tests in BG and FEP bottles•faster sterilization using FEP bottles than using BG bottles•low variations of dissolved trace metals concentrations, except for Al, Cu, Fe and Zn.

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

Thousands of semi-volatile hydrophobic organic pollutants (OPs) reach open oceans through atmospheric deposition, causing a chronic and ubiquitous pollution by anthropogenic dissolved organic carbon (ADOC). Hydrophobic ADOC accumulates in cellular lipids, inducing harmful effects on marine biota, and can be partially prone to microbial degradation. Unfortunately, their possible effects on microorganisms, key drivers of global biogeochemical cycles, remain unknown. We challenged coastal microbial communities from Ny-Ålesund (Arctic) and Livingston Island (Antarctica) with ADOC concentrations within the range of oceanic concentrations in 24 h. ADOC addition elicited clear transcriptional responses in multiple microbial heterotrophic metabolisms in ubiquitous groups such as Flavobacteriia, Gammaproteobacteria and SAR11. Importantly, a suite of cellular adaptations and detoxifying mechanisms, including remodelling of membrane lipids and transporters, was detected. ADOC exposure also changed the composition of microbial communities, through stimulation of rare biosphere taxa. Many of these taxa belong to recognized OPs degraders. This work shows that ADOC at environmentally relevant concentrations substantially influences marine microbial communities. Given that emissions of organic pollutants are growing during the Anthropocene, the results shown here suggest an increasing influence of ADOC on the structure of microbial communities and the biogeochemical cycles regulated by marine microbes.

Flow cytometry, a powerful novel tool to rapidly assess bacterial viability in metal working fluids: Proof-of-principle

Metalworking fluids (MWF) are water- or oil-based liquids to cool and lubricate tools, work pieces and machines, inhibit corrosion and remove swarf. One of the major problems in the MWF industry is bacterial growth as bacterial enzymes can cause MWF degradation. In addition, bacteria can form biofilms which hamper the functioning of machines. Last but not least, some bacterial by-products are toxic (e.g. endotoxins) and present potential health risks for metalworking machine operators via the formation of aerosols. Therefore, a novel fast yet accurate analytical method to evaluate and predict the antibacterial capacity of MWF would be an important asset. As such a tool is currently lacking, the present study aimed to develop a protocol based on flow cytometry (FCM) to assess the antibacterial potential of newly developed MWF independent of bacterial growth. Results of this novel method were compared to a biochallenge test currently used in MWF industry and also to traditional plate counts. Our results represent a proof-of-principle that FCM can reliably predict the antibacterial capacity of MWF already within one day of incubation with Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Proteus mirabilis, being substantially faster than the current growth-based methods.

Microbial consumption of organophosphate esters in seawater under phosphorus limited conditions

The anthropogenic perturbation of the phosphorus (P) marine biogeochemical cycle due to synthetic organophosphorus compounds remains unexplored. The objective of this work was to investigate the microbial degradation of organophosphate triesters (OPEs), widely used as plasticizers and flame retardants, in seawater and their effects on the physiology and composition of microbial communities. Experiments were performed in July 2014 using surface seawater from the Blanes Bay Microbial Observatory (NW Mediterranean) to which OPEs were added at environmentally relevant concentrations. The concentrations of OPEs in the dissolved-phase generally decreased after 24 hours of incubation at in situ conditions. The fitted first order reaction constants were significantly different than zero for the trihaloalkyl phosphate, tris(2-chloroethyl) phosphate and trialyl phosphate tricresyl phosphate. In general, OPEs triggered an increase of the percentage of actively respiring bacteria, total bacterial activity, and the number of low-nucleic acid bacteria, and a decrease in the percentage of membrane-compromised bacteria. Members of some bacterial groups, in particular Flavobacteria, increased their specific activity, indicating that seawater contains bacteria with the potential to degrade OPEs. In aged seawater that was presumably depleted of labile dissolved organic carbon and inorganic P, alkaline phosphatase activities significantly decreased when OPEs were added, indicating a relief on P stress, consistent with the role of OPEs as potential P sources.

Resolution of Viable and Membrane-Compromised Free Bacteria in Aquatic Environments by Flow Cytometry

In aquatic environments, free heterotrophic bacteria play an extremely important role due to their high biomass, wide panel of metabolisms, and ubiquity, as well as the toxicity of certain species. This unit presents a nucleic-acid double-staining protocol (NADS) for flow cytometry that can distinguish fractions of viable, damaged, or membrane-compromised cells within the free-bacterial community. The NADS protocol is based on the simultaneous utilization of two nucleic acid stains-membrane-permeant SYBR Green and membrane-impermeant propidium iodide (PI). The efficiency of the double staining on fresh samples is magnified by the FRET from SYBR Green to PI when both are bound to the nucleic acids. Full quenching of SYBR Green fluorescence by PI identifies cells with a compromised membrane, partial quenching indicates cells with a slightly damaged membrane, and lack of quenching characterizes cells with an intact membrane. Samples do not require any pretreatment and this protocol can be performed almost anywhere. © 2018 by John Wiley & Sons, Inc.

Phenalen-1-one-Mediated Antimicrobial Photodynamic Therapy: Antimicrobial Efficacy in a Periodontal Biofilm Model and Flow Cytometric Evaluation of Cytoplasmic Membrane Damage

In light of increasing resistance toward conventional antibiotics and antiseptics, antimicrobial photodynamic therapy (aPDT) may be a valuable alternative, especially for use in dentistry. In this regard, photosensitizers (PS) based on a phenalen-1-one structure seem to be especially favorable due to their high singlet oxygen quantum yield. However, the actual target structures of phenalen-1-one-mediated aPDT are still unclear. The aim of the present study was to investigate the antimicrobial efficacy of aPDT mediated by phenalen-1-one derivatives SAPYR and SAGUA for inactivation of a polymicrobial biofilm consisting of three putative periodontal pathogens in vitro and to get first insights in the mechanism of action of phenalen-1-one-mediated aPDT by assessing damage of cytoplasmic membranes. aPDT with SAPYR exhibited identical antimicrobial efficacy as compared to chlorhexidine (CHX) [4.4-6.1 log₁₀ reduction of colony forming units (CFUs) depending on bacterial species] while aPDT with SAGUA was less effective (2.0-2.8 log₁₀). Flow cytometric analysis combined with propidium iodide (PI) staining revealed no damage of cytoplasmic membranes after aPDT with both phenalen-1-one derivatives, which was confirmed by spectroscopic measurements for release of nucleic acids after treatment. Spectrophotometric PS-uptake measurements showed no uptake of SAPYR by bacterial cells. Despite the inability to pinpoint the actual target of phenalen-1-one-mediated aPDT, this study shows the high antimicrobial potential of phenalen-1-on mediated aPDT (especially when using SAPYR) and represents a first step for getting insights in the mechanism and damage patterns of aPDT with this class of PS.

Analysis of Staphylococcus aureus cell viability, sublethal injury and death induced by synergistic combination of ultrasound and mild heat

This study was designed to investigate the combined effects of ultrasound and mild heat on the viability of S. aureus in association with the cell membrane integrity and intracellular enzyme activity. Cells were treated by ultrasound under 55°C for 3, 5, 7, 10, and 15min. The dynamic changes of S. aureus cell viability, sublethal injury and death were evaluated using flow cytometric assay. Microscopies were applied to identify the morphological appearance, ultrastructure and topography of S. aureus. The results showed the membrane damage was synchronous with esterase inhibition during the exposure to sonication, leading to the immediate lethal effect. On the other hand, bacteria under the mild heat at 55°C were inactivated via a sublethal injury process. The different lethal modes were observed between sonication and mild heat treatments, which could synergistically inactivate S. aureus. The antibacterial value of thermo-sonication was greater than the sum of the individual treatments. The thermo-sonication combination synergistically reduced the number of sublethal cells and also resulted in severe cell damage.

Synergetic effects of ultrasound and slightly acidic electrolyzed water against Staphylococcus aureus evaluated by flow cytometry and electron microscopy

This study evaluated the synergetic effects of ultrasound and slightly acidic electrolyzed water (SAEW) on the inactivation of Staphylococcus aureus using flow cytometry and electron microscopy. The individual ultrasound treatment for 10min only resulted in 0.36logCFU/mL reductions of S. aureus, while the SAEW treatment alone for 10min resulted in 3.06logCFU/mL reductions. The log reductions caused by combined treatment were enhanced to 3.68logCFU/mL, which were greater than the sum of individual treatments. This phenomenon was referred to as synergistic effects. FCM analysis distinguished live and dead cells as well as revealed dynamic changes in the physiological states of S. aureus after different treatments. The combined treatment greatly reduced the number of viable but nonculturable (VBNC) bacteria to 0.07%; in contrast, a single ultrasound treatment for 10min induced the formation of VBNC cells to 45.75%. Scanning and transmission electron microscopy analysis revealed that greater damage to the appearance and ultrastructure of S. aureus were achieved after combined ultrasound-SAEW treatment compared to either treatment alone. These results indicated that combining ultrasound with SAEW is a promising sterilization technology with potential uses for environmental remediation and food preservation.

Effective methods for extracting extracellular polymeric substances from Shewanella oneidensis MR-1

Extracellular polymeric substances (EPS) play crucial roles in bio-aggregate formation and survival of bacterial cells. To develop an effective but harmless method for EPS extraction from Shewanella oneidensis MR-1, five extraction methods, i.e. centrifugation (control), heating (40, 45, 50, and 60 °C), and treatments with H₂SO₄, ethylenediaminetetraacetic acid (EDTA) and NaOH, were examined, respectively. Results from scanning electron microscope and flow cytometric analyses indicate that MR-1 cells were severely broken by H₂SO₄, NaOH and heating temperature ≥45 °C. Proteins and polysaccharides in EPS extracted by heating at 40 °C were 7.12 and 1.60 mg g^-1 dry cell, respectively. Although EDTA treatment had a relatively lower yield of EPS (proteins and polysaccharides yields of 5.15 and 1.30 mg g^-1 dry cell, respectively), cell lysis was barely found after EPS extraction. Three peaks were identified from the three-dimensional excitation-emission matrix spectrum of each EPS sample, suggesting the presence of protein-like substances. Furthermore, the peak intensity was in good accordance with protein concentration measured by the chemical analysis. In short, heating (40 °C) and EDTA treatments were found the most suitable methods for EPS extraction considering the cell lysis and EPS content, composition and functional groups together.

Reevaluating multicolor flow cytometry to assess microbial viability

Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.

TiO2 nanoparticles in the marine environment: Physical effects responsible for the toxicity on algae Phaeodactylum tricornutum

Nanoscale titanium dioxide (nTiO2) has been widely used in cosmetics, catalysts, varnishes, etc., which is raising concerns about its potential hazards to the ecosystem, including the marine environment. In this study, the toxicological effect of nTiO2 on the marine phytoplankton Phaeodactylum tricornutum was carefully investigated. The results showed that nTiO2 at concentrations ≥20mg/L could significantly inhibit P. tricornutum growth. The 5-day EC50 of nTiO2 to P. tricornutum growth is 167.71mg/L. Interestingly, nTiO2 was found to exert its most severe inhibition effects on the first day of exposure, at a lower EC50 of 12.65mg/L. During the experiment, nTiO2 aggregates were found to entrap algae cells, which is likely responsible for the observed toxic effects. Direct physical effects such as cell wall damage from the algae entrapment were confirmed by flow cytometry and TEM imaging. Moreover, low indirect effects such as shading and oxidative stress were observed, which supported the idea that direct physical effects could be the dominant factor that causes nTiO2 toxicity in P. tricornutum. Our research provides direct evidence for the toxicological impact of nTiO2 on marine microalgae, which will help us to build a good understanding of the ecological risks of nanoparticles in the marine environment.

Temperature dependences of growth rates and carrying capacities of marine bacteria depart from metabolic theoretical predictions

Using the metabolic theory of ecology (MTE) framework, we evaluated over a whole annual cycle the monthly responses to temperature of the growth rates (μ) and carrying capacities (K) of heterotrophic bacterioplankton at a temperate coastal site. We used experimental incubations spanning 6ºC with bacterial physiological groups identified by flow cytometry according to membrane integrity (live), nucleic acid content (HNA and LNA) and respiratory activity (CTC+). The temperature dependence of μ at the exponential phase of growth was summarized by the activation energy (E), which was variable (-0.52 to 0.72 eV) but followed a seasonal pattern, only reaching the hypothesized value for aerobic heterotrophs of 0.65 eV during the spring bloom for the most active bacterial groups (live, HNA, CTC+). K (i.e. maximum experimental abundance) peaked at 4 × 10(6) cells mL(-1) and generally covaried with μ but, contrary to MTE predictions, it did not decrease consistently with temperature. In the case of live cells, the responses of μ and K to temperature were positively correlated and related to seasonal changes in substrate availability, indicating that the responses of bacteria to warming are far from homogeneous and poorly explained by MTE at our site.

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions

To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 × 10(6) cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 × 10(4) cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (∼3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 × 10(6) bacteria per ml per day) and bacterial production (from 3 to 379 μg per C l per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.

Microbial food web components, bulk metabolism, and single-cell physiology of piconeuston in surface microlayers of high-altitude lakes

Sharp boundaries in the physical environment are usually associated with abrupt shifts in organism abundance, activity, and diversity. Aquatic surface microlayers (SML) form a steep gradient between two contrasted environments, the atmosphere and surface waters, where they regulate the gas exchange between both environments. They usually harbor an abundant and active microbial life: the neuston. Few ecosystems are subjected to such a high UVR regime as high altitude lakes during summer. Here, we measured bulk estimates of heterotrophic activity, community structure and single-cell physiological properties by flow cytometry in 19 high-altitude remote Pyrenean lakes and compared the biological processes in the SML with those in the underlying surface waters. Phototrophic picoplankton (PPP) populations, were generally present in high abundances and in those lakes containing PPP populations with phycoerythrin (PE), total PPP abundance was higher at the SML. Heterotrophic nanoflagellates (HNF) were also more abundant in the SML. Bacteria in the SML had lower leucine incorporation rates, lower percentages of “live” cells, and higher numbers of highly-respiring cells, likely resulting in a lower growth efficiency. No simple and direct linear relationships could be found between microbial abundances or activities and environmental variables, but factor analysis revealed that, despite their physical proximity, microbial life in SML and underlying waters was governed by different and independent processes. Overall, we demonstrate that piconeuston in high altitude lakes has specific features different from those of the picoplankton, and that they are highly affected by potential stressful environmental factors, such as high UVR radiation.

Combining flow cytometry and 16S rRNA gene pyrosequencing: a promising approach for drinking water monitoring and characterization

The combination of flow cytometry (FCM) and 16S rRNA gene pyrosequencing data was investigated for the purpose of monitoring and characterizing microbial changes in drinking water distribution systems. High frequency sampling (5 min intervals for 1 h) was performed at the outlet of a treatment plant and at one location in the full-scale distribution network. In total, 52 bulk water samples were analysed with FCM, pyrosequencing and conventional methods (adenosine-triphosphate, ATP; heterotrophic plate count, HPC). FCM and pyrosequencing results individually showed that changes in the microbial community occurred in the water distribution system, which was not detected with conventional monitoring. FCM data showed an increase in the total bacterial cell concentrations (from 345 ± 15 × 10(3) to 425 ± 35 × 10(3) cells mL(-1)) and in the percentage of intact bacterial cells (from 39 ± 3.5% to 53 ± 4.4%) during water distribution. This shift was also observed in the FCM fluorescence fingerprints, which are characteristic of each water sample. A similar shift was detected in the microbial community composition as characterized with pyrosequencing, showing that FCM and genetic fingerprints are congruent. FCM and pyrosequencing data were subsequently combined for the calculation of cell concentration changes for each bacterial phylum. The results revealed an increase in cell concentrations of specific bacterial phyla (e.g., Proteobacteria), along with a decrease in other phyla (e.g., Actinobacteria), which could not be concluded from the two methods individually. The combination of FCM and pyrosequencing methods is a promising approach for future drinking water quality monitoring and for advanced studies on drinking water distribution pipeline ecology.

Species-specific viability analysis of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus in mixed culture by flow cytometry

BACKGROUND

Bacterial species coexist commonly in mixed communities, for instance those occurring in microbial infections of humans. Interspecies effects contribute to alterations in composition of communities with respect to species and thus, to the course and severity of infection. Therefore, knowledge concerning growth and viability of single species in medically-relevant mixed communities is of high interest to resolve complexity of interspecies dynamics and to support development of treatment strategies. In this study, a flow cytometric method was established to assess the species-specific viability in defined three-species mixed cultures. The method enables the characterization of viability of Pseudomonas aeruginosa, Burkholderia cepacia and Staphylococcus aureus, which are relevant to lung infections of Cystic Fibrosis (CF) patients. The method combines fluorescence detection by antibody and lectin labeling with viability fluorescence staining using SYBRGreen I and propidium iodide. In addition, species-specific cell enumeration analysis using quantitative terminal restriction fragment length polymorphisms (qT-RFLP) was used to monitor the growth dynamics. Finally, to investigate the impact of substrate availability on growth and viability, concentrations of main substrates and metabolites released were determined.

RESULTS

For each species, the time course of growth and viability during mixed culture cultivations was obtained by using qT-RFLP analysis in combination with flow cytometry. Comparison between mixed and pure cultures revealed for every species differences in growth properties, e.g. enhanced growth of P. aeruginosa in mixed culture. Differences were also observed for B. cepacia and S. aureus in the time course of viability, e.g. an early and drastic reduction of viability of S. aureus in mixed culture. Overall, P. aeruginosa clearly dominated the mixed culture with regard to obtained cell concentrations.

CONCLUSIONS

In combination with qT-RFLP analysis, the methods enabled monitoring of species-specific cell concentrations and viability during co-cultivation of theses strains. Experimental findings suggest that the predominance of P. aeruginosa over B. cepacia and S. aureus in mixed culture under the chosen cultivation conditions is promoted by more efficient substrate consumption of P. aeruginosa, and antagonistic interspecies effects induced by P. aeruginosa.

Contrasting responses of marine bacterial strains exposed to carboxylated single-walled carbon nanotubes

The potential toxic effects of carboxylated (COOH) single-walled carbon nanotubes (SWNTs) were investigated on the cell growth and viability of two reference (Silicibacter pomeroyi, Oceanospirillum beijerinckii) and two environmental (Vibrio splendidus, Vibrio gigantis) Gram-negative marine bacterial strains. Bacterial cells were exposed to six concentrations of SWNT-COOH, during different incubation times. Our results revealed different sensitivity levels of marine bacterial strains toward SWNT-COOH exposure. A bactericidal effect of SWNT-COOH has been observed only for Vibrio species, with cell loss viability estimated to 86% for V. gigantis and 98% for V. splendidus exposed to 100 μg mL(-1) of SWNT-COOH during 2h. For both Vibrio strains, dead cells were well individualized and no aggregate formation was observed after SWNT-COOH treatment. The toxic effect of SWNT-COOH on O. beijerinckii cells displayed time dependence, with a longer exposure time reducing their specific growth rate by a factor of 1.2. No significant effect of SWNT-COOH concentration or incubation time had been demonstrated on both growth ability and viability of S. pomeroyi, suggesting a stronger resistance capacity of this strain to carbon nanotubes. The analysis of the relative expression of some functional genes involved in stress responses, using the real-time reverse transcriptase PCR, suggests that the cell membrane damage is not the main toxicity mechanism by which SWNT-COOH interacts with marine bacterial strains. Overall, our results show that SWNT-COOH present a strain dependent toxic effect to marine bacteria and that membrane damage is not the main toxicity mechanism of SWNT in these bacteria.

A flow cytometric method for viability assessment of Staphylococcus aureus and Burkholderia cepacia in mixed culture

Mixed bacterial communities are commonly encountered in microbial infections of humans. Knowledge on the composition of species and viability of each species in these communities allows for a detailed description of the complexity of interspecies dynamics and contributes to the assessment of the severity of infections. Several assays exist for quantification of specific species in mixed communities, including analysis of quantitative terminal restriction fragment length polymorphisms. While this method allows for species-specific cell enumeration, it cannot provide viability data. In this study, flow cytometry was applied to assess the viability of Staphylococcus aureus and Burkholderia cepacia in mixed culture by membrane integrity analysis using SYBR® Green I and propidium iodide staining. Both bacteria are relevant to pulmonary infections of cystic fibrosis patients. Fluorescence staining was optimized separately for each species in pure culture due to differences between species in cell wall structure and metabolic capabilities. To determine viability of species in mixed culture, a protocol was established as a compromise between optimum conditions determined before for pure cultures. This protocol allowed the detection of viable and dead cells of both species, exhibiting an intact and a permeabilized membrane, respectively. To discriminate between S. aureus and B. cepacia, the protocol was combined with Gram-specific fluorescent staining using wheat germ agglutinin. The established three-color staining method was successfully tested for viability determination of S. aureus and B. cepacia in mixed culture cultivations. In addition, growth of both species was monitored by quantitative terminal restriction fragment length polymorphisms. The obtained data revealed alterations in viability during cultivations for different growth phases and suggest interspecies effects in mixed culture. Overall, this method allows for rapid simultaneous Gram-differentiation and viability assessment of bacterial mixed cultures and is therefore suitable for the analysis of dynamics of mixed communities of medical, environmental, and biotechnological relevance.

Development and laboratory-scale testing of a fully automated online flow cytometer for drinking water analysis

Accurate and sensitive online detection tools would benefit both fundamental research and practical applications in aquatic microbiology. Here, we describe the development and testing of an online flow cytometer (FCM), with a specific use foreseen in the field of drinking water microbiology. The system incorporated fully automated sampling and fluorescent labeling of bacterial nucleic acids with analysis at 5-min intervals for periods in excess of 24 h. The laboratory scale testing showed sensitive detection (< 5% error) of bacteria over a broad concentration range (1 × 10(3) -1 × 10(6) cells mL(-1) ) and particularly the ability to track both gradual changes and dramatic events in water samples. The system was tested with bacterial pure cultures as well as indigenous microbial communities from natural water samples. Moreover, we demonstrated the possibility of using either a single fluorescent dye (e.g., SYBR Green I) or a combination of two dyes (SYBR Green I and Propidium Iodide), thus broadening the application possibilities of the system. The online FCM approach described herein has considerable potential for routine and continuous monitoring of drinking water, optimization of specific drinking water processes such as biofiltration or disinfection, as well as aquatic microbiology research in general.

Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical northeast atlantic ocean

We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 to 200 m) and mesopelagic (200 to 1,000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean NE Atlantic Subtropical Gyre, and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected, accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryote-to-nanoflagellate abundance ratio) than within the epipelagic (i.e., bulk activity, nucleic acid content, and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the Northeast Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations.

Assessing the viability of bacterial species in drinking water by combined cellular and molecular analyses

The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining ("live/dead staining" indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the DNA- and RNA-based overall community structure differed substantially, (2) the community retrieved from RNA and DNA reflected different bacterial species, classified as 53 phylotypes (with only two common phylotypes), (3) the percentage of phylotypes with intact membranes or damaged cells were comparable for RNA- and DNA-based analyses, and (4) the retrieved species were primarily of aquatic origin. The pronounced difference between phylotypes obtained from DNA extracts (dominated by Betaproteobacteria, Bacteroidetes, and Actinobacteria) and from RNA extracts (dominated by Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria) demonstrate the relevance of concomitant RNA and DNA analyses for drinking water studies. Unexpected was that a comparable fraction (about 21%) of phylotypes with membrane-injured cells was observed for DNA- and RNA-based analyses, contradicting the current understanding that RNA-based analyses represent the actively growing fraction of the bacterial community. Overall, we think that this combined approach provides an interesting tool for a concomitant phylogenetic and viability analysis of bacterial species of drinking water.

Seasonal patterns in the sunlight sensitivity of bacterioplankton from Mediterranean surface coastal waters

The sensitivity of coastal marine bacterioplankton to natural photosynthetically active radiation (PAR, 400-700 nm) and ultraviolet radiation (UVR, 280-400 nm) was evaluated in five experiments over a seasonal cycle in the Blanes Bay, NW Mediterranean Sea. Exposure to natural solar radiation generally inhibited bulk bacterial activities or damaged membrane integrity when irradiances were high (i.e. spring and summer experiments) and, in general, UVB (280-320 nm) accounted for most of the inhibition. When assessing activity ((3) H-leucine uptake) at the single-cell level by microautoradiography and rRNA gene probing, seasonally varying responses and sensitivities were found among bacterial groups. While autumn and winter irradiances seemed too low to cause changes in activity, variable effects were found in spring and summer. SAR11 was consistently inhibited by UVR and PAR exposure, whereas Gammaproteobacteria and Bacteroidetes showed higher resistance. Roseobacter, Synechococcus and the NOR5 clade were occasionally photostimulated in their activity, mainly because of PAR. Our results indicate that a component of seasonality exists in the bacterial responses to solar radiation, which vary not only depending on the irradiance and the spectral characteristics, but also on the previous light history and the taxonomic composition of the community.

Use of flow cytometry to measure biogeochemical rates and processes in the ocean

An important goal of marine biogeochemists is to quantify the rates at which elements cycle through the ocean's diverse microbial assemblage, as well as to determine how these rates vary in time and space. The traditional view that phytoplankton are producers and bacteria are consumers has been found to be overly simplistic, and environmental metagenomics is discovering new and important microbial metabolisms at an accelerating rate. Many nutritional strategies previously attributed to one microorganism or functional group are also or instead carried out by other groups. To tease apart which organism is doing what will require new analytical approaches. Flow cytometry, when combined with other techniques, has great potential for expanding our understanding of microbial interactions because groups can be distinguished optically, sorted, and then collected for subsequent analyses. Herein, we review the advances in our understanding of marine biogeochemistry that have arisen from the use of flow cytometry.

Improved method for bacterial cell capture after flow cytometry cell sorting

Fixed cells with different nucleic acid contents and scatter properties (low nucleic acid [LNA], high nucleic acid 1 [HNA1], and HNA2) were sorted by flow cytometry (FCM). For each sort, 10,000 cells were efficiently captured on poly-l-lysine-coated microplates, resulting in efficient and reproducible PCR amplification.

A 96-well-plate-based optical method for the quantitative and qualitative evaluation of Pseudomonas aeruginosa biofilm formation and its application to susceptibility testing

A major reason for bacterial persistence during chronic infections is the survival of bacteria within biofilm structures, which protect cells from environmental stresses, host immune responses and antimicrobial therapy. Thus, there is concern that laboratory methods developed to measure the antibiotic susceptibility of planktonic bacteria may not be relevant to chronic biofilm infections, and it has been suggested that alternative methods should test antibiotic susceptibility within a biofilm. In this paper, we describe a fast and reliable protocol for using 96-well microtiter plates for the formation of Pseudomonas aeruginosa biofilms; the method is easily adaptable for antimicrobial susceptibility testing. This method is based on bacterial viability staining in combination with automated confocal laser scanning microscopy. The procedure simplifies qualitative and quantitative evaluation of biofilms and has proven to be effective for standardized determination of antibiotic efficiency on P. aeruginosa biofilms. The protocol can be performed within approximately 60 h.

Selected fluorescent techniques for identification of the physiological state of individual water and soil bacterial cells - review

Stimulated by demands of the natural environment conservation, the need for thorough structural and functional identification of microorganisms colonizing different ecosystems has contributed to an intensive advance in research techniques. The article shows that some of these techniques are also a convenient tool for determination of the physiological state of single cells in a community of microorganisms. The paper presents selected fluorescent techniques, which are used in research on soil, water and sediment microorganisms. It covers the usability of determination of the dehydrogenase activity of an individual bacterial cell (CTC+) and of bacteria with intact, functioning cytoplasmic membranes, bacteria with an integrated nucleiod (NuCC+) as well as fluorescent in situ hybridization (FISH).

Mesoscale eddies: hotspots of prokaryotic activity and differential community structure in the ocean

To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0-200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200-1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic 'hotspots' of prokaryotic activity (in the epi- and mesopelagic realms).