Direct estimate of active bacteria: CTC use and limitations

Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, have become increasingly prevalent across all human generations. Despite advances in diagnosis, effective long-term therapeutic options remain limited, with many patients experiencing recurrent symptoms after treatment. The multifactorial origins of ulcerative colitis are widely recognized, but the intestinal microbiome, particularly bacteria from the Desulfovibrionaceae family, is thought to play a central role in the pathogenesis of the disease. These bacteria contribute significantly to gut microbial functions, yet their cytotoxic and viability characteristics under disease conditions remain poorly understood. Our review provides insights on recent advancements in methodologies for assessing the cytotoxicity and viability of anaerobic intestinal bacteria, with a specific focus on their relevance to gut health and disease. We introduce overview from current literature on modern techniques including flow cytometry, high-throughput screening, and molecular-based assays, highlighting their applications in understanding the role of Desulfovibrionaceae and other gut microbes in IBD pathogenesis. By bridging methodological advancements with functional implications, this review aims to enhance our understanding of gut microbiota-host interactions, which are crucial for maintaining health and preventing disease through immune modulation, where microbiota help regulate immune responses and prevent excessive inflammation; nutrient metabolism, including the breakdown of dietary fibers into short-chain fatty acids that support gut health; and colonization resistance, where beneficial microbes outcompete harmful pathogens to maintain microbial balance.

Distinct transcriptome and traits of freshly dispersed Pseudomonas aeruginosa cells

Bacteria assume two distinct lifestyles: the planktonic and biofilm modes of growth. Additionally, dispersion has emerged as a third phenotype, accompanied by the distinct phenotypes and the unique expression of >600 genes. Here, we asked whether the distinct phenotype of dispersed cells is already apparent within minutes of egressing from the biofilm. We used RNA-seq to show that the physiology of freshly dispersed cells from Pseudomonas aeruginosa biofilms is highly different from those of planktonic and biofilm cells, apparent by dispersed cells uniquely expressing 194 genes. Unique and differentially expressed genes relative to planktonic or biofilm cells include genes associated with type IV pili, pyoverdine, type III and type VI secretion systems, and antibiotic resistance that are downregulated in dispersed cells, whereas the transcript abundance of genes involved in swimming motility, Hxc type II secretion system and various other virulence factors, and metabolic and energy-generating pathways are increased, indicative of dispersion coinciding with an awakening and re-energizing of dispersed cells, and a switch in virulence, further apparent by freshly dispersed cells significantly subverting engulfment by macrophages. The findings suggest that dispersed cells display a distinct phenotype within minutes of egressing from the biofilm, with freshly dispersed cells already capable of efficiently evading phagocytosis.

IMPORTANCE

Dispersion is considered a transitionary phenotype, enabling bacteria to switch between the communal, biofilm lifestyle, where cells share resources and are protected from harmful conditions to the planktonic state. Here, we demonstrate that within minutes of leaving the biofilm, dispersed cells express genes and display phenotypic traits that are distinct from biofilms and planktonic cells. Our findings suggest that dispersed cells quickly adapt to a less structured and protected but more nutrient-rich environment, with this trade-off in environment coinciding with an awakening and a switch in virulence, specifically a switch from directly intoxicating host cells and potential competitors toward more broadly active virulence factors and strategies of evasion. To our knowledge, this is the first report of dispersed cells' distinct (trade-off) phenotype and their enhanced resilience so soon after egressing from the biofilm.

Engineering Cyborg Pathogens through Intracellular Hydrogelation

Synthetic biology primarily focuses on two kinds of cell chassis: living cells and nonliving systems. Living cells are autoreplicating systems that have active metabolism. Nonliving systems, including artificial cells and nanoparticles, are nonreplicating systems typically lacking active metabolism. In recent work, Cyborg bacteria that are nonreplicating-but-metabolically active have been engineered through intracellular hydrogelation. Intracellular hydrogelation is conducted by infusing gel monomers and photoactivators into cells, followed by the activation of polymerization of the gel monomers inside the cells. However, the previous work investigated only Escherichia coli cells. Extending the Cyborg-Cell method to pathogenic bacteria could enable the exploitation of their pathogenic properties in biomedical applications. Here, we focus on different strains of Pseudomonas aeruginosa, Staphylococcus aureus, and Klebsiella pneumoniae. To synthesize the Cyborg pathogens, we first reveal the impact of different hydrogel concentrations on the metabolism, replication, and intracellular gelation of Cyborg pathogens. Next, we demonstrate that the Cyborg pathogens are taken up by macrophages in a similar magnitude as wild-type pathogens through confocal microscopy and real-time PCR. Finally, we show that the macrophage that takes up the Cyborg pathogen exhibits a similar phenotypic response to the wild-type pathogen. Our work generalizes the intracellular hydrogelation approach from lab strains of E. coli to bacterial pathogens. The new Cyborg pathogens could be applied in biomedical applications ranging from drug delivery to immunotherapy.

Rapid detection of viable microbes with 5-cyano-2,3-di-(p-tolyl)tetrazolium chloride and 5(6)-carboxyfluorescein diacetate using a fibre fluorescence spectroscopy system

AIMS

To assess the efficacy of two commercially available viability dyes, 5-cyano-2,3-di-(p-tolyl)tetrazolium chloride (CTC) and 5(6)-carboxyfluorescein diacetate (CFDA), in reporting on viable cell concentration and species using an all-fibre fluorometer.

METHODS AND RESULTS

Four bacterial species (two Gram-positive and two Gram-negative) commonly associated with food poisoning or food spoilage (Escherichia coli, Salmonella enterica, Staphylococcus aureus, and Bacillus cereus) were stained with CTC or CFDA and the fibre fluorometer was used to collect full fluorescence emission spectra. A good correlation between concentration and fluorescence intensity was found for Gram-negative bacteria between 107 and 108 colony-forming units (CFU) ml-1. There was no correlation with concentration for Gram-positive bacteria; however, the information in the CTC and CFDA spectra shows the potential to distinguish Gram-negative cells from Gram-positive cells, although it may simply reflect the overall bacterial metabolic activity under staining conditions from this study.

CONCLUSIONS

The limit of detection (LoD) is too high in the dip-probe approach for analysis; however, the development of an approach measuring the fluorescence of single cells may improve this limitation. The development of new bacteria-specific fluorogenic dyes may also address this limitation. The ability to differentiate bacteria using these dyes may add value to measurements made to enumerate bacteria using CTC and CFDA.

Application of flow cytometry for rapid, high-throughput, multiparametric analysis of environmental microbiomes

Quantification of the abundance and understanding of the dynamics of the microbial communities is essential to establish a basis for microbiome characterization. The conventional techniques used for the quantification of microbes are complicated and time-consuming. With scientific advancement, many techniques evolved and came into account. Among them, flow cytometry is a robust, high-throughput technique through which microbial dynamics, morphology, microbial distribution, physiological characteristics, and many more attributes can be studied in a high-throughput manner with comparatively less time and resources. Flow cytometry, when combined with other omics-based methods, offers a rapid and efficient platform to analyze and understand the composition of microbiome at the cellular level. The microbial diversity observed through flow cytometry will not be equivalent to that obtained by sequencing methods, but this integrated approach holds great potential for high throughput characterization of microbiomes. Flow cytometry is regarded as an established characterization tool in haematology, oncology, immunology, and medical microbiology research; however, its application in environmental microbiology is yet to be explored. This comprehensive review aims to delve into the diverse environmental applications of flow cytometry across various domains, including but not limited to bioremediation, landfills, anaerobic digestion, industrial bioprocesses, water quality regulation, and soil quality regulation. By conducting an in-depth analysis, this article seeks to shed light on the potential benefits and challenges associated with the utilization of flow cytometry in addressing environmental concerns.

Self-repair and resuscitation of viable injured bacteria in chlorinated drinking water: Achromobacter as an example

Chlorine disinfection for the treatment of drinking water can cause injury to the membrane and DNA of bacterial cells and may induce the surviving injured bacteria into a viable but non-culturable (VBNC) state. It is difficult to monitor viable injured bacteria by heterotrophic plate counting (HPC), and their presence is also easily miscalculated in flow cytometry intact cell counting (FCM-ICC). Viable injured bacteria have a potential risk of resuscitation in drinking water distribution systems (DWDSs) and pose a threat to public health when drinking from faucets. In this study, bacteria with injured membranes were isolated from chlorinated drinking water by FCM cell sorting. The culture rate of injured bacteria varied from 0.08% to 2.6% on agar plates and 0.39% to 6.5% in 96-well plates. As the dominant genus among the five identified genera, as well as an opportunistic pathogen with multiple antibiotic resistance, Achromobacter was selected and further studied. After treatment with chlorine at a concentration of 1.2 mg/L, Achromobacter entered into the intermediate injured state on the FCM plot, and the injury on the bacterial surface was observed by electron microscopy. However, the CTC respiratory activity assay showed that 75.0% of the bacteria were still physiologically active, and they entered into a VBNC state. The injured VBNC Achromobacter in sterile drinking water were resuscitated after approximately 25 h. The cellular repair behavior of injured bacteria was studied by Fourier transform infrared attenuated total reflectance (FTIR-ATR) and comet assays. It was found that DNA injury rather than membrane injury was repaired first. The expression of Ku and ligD increased significantly during the DNA repair period, indicating that non-homologous end-joining (NHEJ) played an important role in repairing DNA double-strand breaks. This study deepened the understanding of the effect of chlorine disinfection on bacterial viability in drinking water and will provide support for the improvement of the chlorine disinfection process for the treatment of drinking water.

Current Perspectives on Viable but Non-Culturable Foodborne Pathogenic Bacteria: A Review

Foodborne diseases caused by foodborne pathogens pose risks to food safety. Effective detection and efficient inactivation of pathogenic bacteria has always been a research hotspot in the field of food safety. Complicating these goals, bacteria can be induced to adopt a viable but non-culturable (VBNC) state under adverse external environmental stresses. When in the VBNC state, pathogens cannot form visible colonies during traditional culture but remain metabolically active and toxic. The resulting false negative results in growth-related assays can jeopardize food safety. This review summarizes the latest research on VBNC foodborne pathogens, including induction conditions, detection methods, mechanism of VBNC formation, and possible control strategies. It is hoped that this review can provide ideas and methods for future research on VBNC foodborne pathogenic bacteria.

Copper-Based Compounds against Erwinia amylovora: Response Parameter Analysis and Suppression of Fire Blight in Apple

Fire blight, caused by Erwinia amylovora, is one of the major bacterial disease of apple and pear, causing enormous economic losses worldwide. Several control measures against E. amylovora have been reported till date, however, none of them have proved to be effective significantly against the pathogen. In this study, mechanisms of the copper-based control agents (CBCAs): copper oxychloride (COCHL), copper oxide (COX), copper hydroxide (CHY), copper sulfate basic (CSB), and tribasic copper sulfate (TCS) and their disease severity reduction efficacy against E. amylovora were analyzed. Bis-1,3-dibutylbarbituric acid trimethine oxonol, carboxyl fluorescein diacetate succinimidyl ester, and 5-cyano-2,3-ditolyl tetrazolium chloride staining were used to check the damage of membrane potential, cytoplasmic pHin, and respiration of CBCAs-treated E. amylovora, respectively. High disturbance in the membrane potential of E. amylovora was found under COX and COCHL treatments. Similarly, higher significant changes in the inner cytoplasmic pHin were observed under COX, COCHL, and TCS treatment. CHY and COCHL-treated E. amylovora showed a significant reduction in respiration. In vitro bioassay results revealed that CHY, CSB, and TCS at 2,000 ppm reduced the severity of fire blight both in pre- and post-treatment of CBCAs in immature apple fruits and seedlings. Overall, the most effective CBCAs against E. amylovora could be CHY at 2,000 ppm as its showed inhibition mechanisms and disease severity reduction.

Efficacy of Acidified Oils against Salmonella in Low-Moisture Environments

When processing low-moisture, high-fat foods such as peanut butter and nuts, water-based sanitization is unsuitable due to the immiscible nature of water and fats. Dry sanitization mainly uses flammable compounds such as isopropanol, requiring equipment cooling before application. The use of oils to deliver antimicrobials against foodborne pathogens enables the use of elevated temperatures, thus eliminating processing downtimes associated with dry sanitization. This study delivered organic acids and medium-chain fatty acids (100, 250, and 500 mM) in peanut oil against Salmonella enterica serovar Enteritidis desiccated at 75% relative humidity (RH). Acetic acid in peanut oil (AO) at 45°C was the most effective food-grade acid, causing a 4.4-log reduction in S. Enteritidis at 500 mM. AO caused cellular injury and was effective against a variety of S. Enteritidis strains. Confocal microscopy demonstrated that cells treated with 50 mM and 250 mM AO had significant membrane damage and reduced cellular respiration compared to untreated controls. Treatment efficacy increased with the increase in acid concentration, treatment duration, and treatment temperature from 20 to 45°C. Transmission electron microscopy after treatment with 100 and 250 mM AO revealed membrane ruffling and leakage in cell membranes, especially at 45°C. Reduction of the RH to 33% during desiccation of S. Enteritidis caused a decrease in AO efficacy compared to that at 75% RH, while at a higher RH of 90%, there was an increase in the efficacy of AO. Acidified oils can serve as robust, cost-effective replacements for dry-sanitation methods and improve safety of low moisture foods. IMPORTANCE Currently, dry sanitization products used during food processing often contain flammable compounds which require processing to stop and equipment to cool before application. This leads to processing downtimes and consequently, economic losses. This challenge is compounded by exposure to dryness which frequently renders Salmonella resistant to heat and different antimicrobials. Thus, the development of heat-tolerant oil-based antimicrobial compounds is a novel approach for sanitizing in low-moisture (dry) environments such as those found in peanut butter, tree nuts, and chocolate manufacturing. This study shows that acidified oils, especially acetic acid in peanut oil at elevated temperatures (45°C), was highly effective against desiccated Salmonella. Acidified oils have the potential to replace dry sanitizers, increasing the frequency of sanitization, leading to an improvement in food safety.

Metabolism differences of biofilm and planktonic Pseudomonas aeruginosa in viable but nonculturable state induced by chlorine stress

More than 95% of the bacteria in environment are viable but nonculturable (VBNC). However, it is difficult to elucidate directly the metabolic characteristics of these VBNC bacteria and the differences between biofilm-VBNC bacteria and planktonic-VBNC bacteria. In this study, VBNC P. aeruginosa induced by chlorine was used to clarify the metabolism characteristics and mechanism of differential metabolism between biofilm-VBNC bacteria and planktonic-VBNC bacteria. Results showed that P. aeruginosa in biofilm state was more likely to enter VBNC state. The mechanisms of differential metabolism were involved in the difference of reactive oxygen species production owing to the protection of extracellular polymers. ¹⁵N and ²H labeled single-cell Raman spectra directly proved that VBNC state bacteria still maintained low material and energy metabolism, and the metabolic activity of biofilm-VBNC P. aeruginosa was lower than that of planktonic-VBNC P. aeruginosa. GC-MS/MS analysis showed 51 metabolites with significant differences. KEGG analysis showed that the types and contents of extracellular metabolites from P. aeruginosa in VBNC states were significantly lower than those in the culturable state (p < 0.05), mainly involving in citrate cycle, glutathione metabolism, phenylalanine metabolism, tyrosine metabolism and fatty acid degradation. Also, the contents of most extracellular metabolites from P. aeruginosa in biofilm-VBNC state were lower than those in VBNC planktonic state. The significant differences (p < 0.05) were mainly involved in alanine, aspartate and glutamate metabolism, glycolysis/gluconeogenesis, D-Alanine metabolism and glycerophospholipid metabolism. The result of this research was favorable to the accurate identification of VBNC bacteria, the health risk assessment and scientific control of harmful VBNC bacteria.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

A simple colorimetric method for viable bacteria detection based on cell counting Kit-8

In this study, Cell Counting Kit-8 (CCK-8) was introduced to detect the concentration of live bacteria for the first time depending on the redox reaction between CCK-8 solution and dehydrogenase. CCK-8 solution can be reduced to form water soluble orange-yellow formazan by the dehydrogenase present in bacterial cells, and the concentration of live bacteria is proportional to the absorbance value of formazan at 450 nm. Based on this principle, Staphylococcus aureus and Escherichia coli were chosen as the model bacteria. The optimal detection conditions were investigated and a good linear relationship was obtained in the concentration range from 2.600 × 10² to 1.160 × 10⁹ CFU mL^-1 with a linear equation of Y = 0.06305 log₁₀ X-0.1153 (X in CFU mL^-1, R² = 0.9747) for S. aureus and 9.750 × 10² to 6.000 × 10⁸ CFU mL^-1 with a linear equation of Y = 0.06122 log₁₀ X-0.1358 (X in CFU mL^-1, R² = 0.9958) for E. coli. The CCK-8 based viable bacteria detection method can be completed within 2 h with a wide bacterial detection concentration range. Satisfactory results were obtained when applied to an actual sample analysis and there is a good consistency between the proposed CCK-8 based method and the traditional plate counting method. More importantly, this method can realize the one-time detection of a large number of samples with high sensitivity, which suggests its great potential in high-throughput bacterial detection.

Phenolic-rich extracts from acerola, cashew apple and mango by-products cause diverse inhibitory effects and cell damages on enterotoxigenic Escherichia coli

This study aimed to evaluate the inhibitory effects of phenolic-rich extracts from acerola (Malpighia emarginata D.C., PEA), cashew apple (Anacardium occidentale L., PEC) and mango (Mangifera indica L., PEM) by-products on distinct enterotoxigenic Escherichia coli (ETEC) strains. The capability of PEA and PEC of impairing various physiological functions of ETEC strains was investigated with multiparametric flow cytometry. Procyanidin B₂ , myricetin and p-coumaric acid were the major phenolic compounds in PEA, PEC and PEM, respectively. PEA and PEC had lower minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) (MIC: 31·25 mg ml^-1 ; MBC: 62·5 mg ml^-1 ) on ETEC strains than PEM (MIC and MIC: >1000 mg ml^-1 ). PEA and PEC (15·6, 31·2, 62·5 mg ml^-1 ) caused viable count reductions (P < 0·05) on ETEC strains after 24 h of exposure, notably the ≥3 log reductions caused by 62·5 mg ml^-1 . The 24 h exposure of ETEC strains to PEA and PEC (31·2, 62·5 mg ml^-1 ) led to high sizes of cell subpopulations with concomitant impairments in cell membrane polarization and permeability, as well as in enzymatic, respiratory and efflux activities. PEA and PEC are effective in inhibiting ETEC through a multi-target action mode with disturbance in different physiological functions.

Systematic variation in the temperature dependence of bacterial carbon use efficiency

Carbon use efficiency (CUE) is a key characteristic of microbial physiology and underlies community-level responses to changing environments. Yet, we currently lack general empirical insights into variation in microbial CUE at the level of individual taxa. Here, through experiments with 29 strains of environmentally isolated bacteria, we find that bacterial CUE typically responds either positively to temperature, or has no discernible response, within biologically meaningful temperature ranges. Using a global data synthesis, we show that these results are generalisable across most culturable groups of bacteria. This variation in the thermal responses of bacterial CUE is taxonomically structured, and stems from the fact that relative to respiration rates, bacterial population growth rates typically respond more strongly to temperature, and are also subject to weaker evolutionary constraints. Our results provide new insights into microbial physiology, and a basis for more accurately modelling the effects of thermal fluctuations on complex microbial communities.

Anaerobic condition induces a viable but nonculturable state of the PCB-degrading Bacteria Rhodococcus biphenylivorans TG9

Significant microbial removal of highly chlorinated polychlorinated biphenyls (PCBs) requires the cooperation of anaerobic and aerobic bacteria. During the sequencing process of anaerobic dechlorination and aerobic degradation of PCBs, aerobic degrading bacteria have to undergo anaerobic stress. However, the survival strategy of aerobic degrading bacteria under anaerobic condition is not well-understood. In this study, the culturable cells of Rhodococcus biphenylivorans TG9 decreased from 10⁸ CFU/mL to values below the detection limit after 60 days of anaerobic stress while the viable cells remained 10⁵-10⁶ cells/mL, indicating that anaerobic condition induced TG9 entering into the viable but nonculturable (VBNC) state. Cell resuscitation was observed when oxygen was supplied further confirming the VBNC state of TG9. The results of single-cell Raman spectroscopy combined with heavy water indicated the significant decrease of metabolic activity after TG9 entering into the VBNC state. Additionally, the degradation ability of TG9 in the VBNC state was also significantly reduced, while it recovered after resuscitation. Our research proved that entering into the VBNC state is a survival strategy of TG9 under anaerobic conditions, and the limited culturability and degrading capacity could be overcome by resuscitation. The present study provides new insights for improving the remediation efficiency of PCBs contamination.

The diagnostic tools for viable but nonculturable pathogens in the food industry: Current status and future prospects

Viable but nonculturable (VBNC) microorganisms have been recognized as pathogenic contaminants in foods and environments. The failure of VBNC cells to form the visible colonies hinders the ability to use conventional media for their detection. Efficient and rapid detection of pathogens in the VBNC state is a prerequisite to ensure the food safety and public health. Despite their nonculturability, VBNC cells have distinct characteristics, such as morphology, metabolism, chemical composition, and gene and protein expression, that have been used as the basis for the development of abundant diagnostic tools. This review covers the current status and advances in various approaches for examining microorganisms in the VBNC state, including but not limited to the methodological aspects, advantages, and drawbacks of each technique. Existing methods, such as direct viable count, SYTO/PI dual staining, and propidium monoazide quantitative polymerase chain reaction (PCR), as well as some techniques with potential to be applied in the future, such as digital PCR, enhanced-surface Raman spectroscopy, and impedance-based techniques, are summarized in depth. Finally, future prospects for the one-step detection of VBNC bacteria are proposed and discussed. We believe that this review can provide more optional methods for researchers and promote the development of rapid, accurate detecting methods, and for inspectors, the diagnostic tools can provide data to undertake risk analysis of VBNC cells.

Polymer Electrochromism Driven by Metabolic Activity Facilitates Rapid and Facile Bacterial Detection and Susceptibility Evaluation

The electrochromism of a water-soluble naturally oxidized electrochromic polymer, ox-PPE, is harnessed for rapid and facile bacterial detection, discrimination, and susceptibility testing. The ox-PPE solution shows distinct colorimetric and spectroscopic changes within 30 min when mixed with live bacteria. For the underlying mechanism, it is found that ox-PPE responds to the reducing species (e.g. cysteine and glutathione) released by metabolically active bacteria. This reduction reaction is ubiquitous among various bacterial strains, with a noticeable difference that enables discrimination of Gram-negative and Gram-positive bacterial strains. Combining ox-PPE with antibiotics, methicillin-susceptible and -resistant S. aureus can be differentiated within 2.5 h. Proof-of-concept demonstration of ox-PPE for antimicrobial susceptibility testing is carried out by incubating E. coli with various antibiotics. The obtained minimum inhibition concentrations are consistent with the conventional culture-based methods, but with the procedure time significantly shortened to 3 h.

A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology

Viability and metabolic assays are commonly used as proxies to assess the overall metabolism of microorganisms. The variety of these assays combined with little information provided by some assay kits or online protocols often leads to mistakes or poor interpretation of the results. In addition, the use of some of these assays is restricted to simple systems (mostly pure cultures), and care must be taken in their application to environmental samples. In this review, the necessary data are compiled to understand the reactions or measurements performed in many of the assays commonly used in various aspects of microbiology. Also, their relationships to each other, as metabolism links many of these assays, resulting in correlations between measured values and parameters, are discussed. Finally, the limitations of these assays are discussed.

Bacterial-like nitric oxide synthase in the haloalkaliphilic archaeon Natronomonas pharaonis

Bacterial nitric oxide (NO) synthases (bNOS) play diverse and important roles in microbial physiology, stress resistance, and virulence. Although bacterial and mammalian NOS enzymes have been well-characterized, comparatively little is known about the prevalence and function of NOS enzymes in Archaea. Analysis of archaeal genomes revealed that highly conserved bNOS homologs were restricted to members of the Halobacteria. Of these, Natronomonas pharaonis NOS (npNOS) was chosen for further characterization. NO production was confirmed in heterologously expressed His-tagged npNOS by coupling nitrite production from N-hydroxy-L-arginine in an H2O2-supported reaction. Additionally, the nos gene was successfully targeted and disrupted to create a Nmn. pharaonis nos mutant by adapting an established Natrialba magadii transformation protocol. Genome re-sequencing of this mutant revealed an additional frameshift in a putative cation-acetate symporter gene, which could contribute to altered acetate metabolism in the nos mutant. Inactivation of Nmn. pharaonis nos was also associated with several phenotypes congruent with bacterial nos mutants (altered growth, increased oxygen consumption, increased pigment, increased UV susceptibility), suggesting that NOS function may be conserved between bacteria and archaea. These studies are the first to describe genetic inactivation and characterization of a Nmn. pharaonis gene and provides enhanced tools for probing its physiology.

Synergistic bactericidal effect and mechanism of X-ray irradiation and citric acid combination against food-borne pathogens on spinach leaves

In this study, we investigated the antimicrobial activity of the X-ray irradiation and citric acid (CA) combination against Escherichia coli O157:H7 and Listeria monocytogenes on the surface of spinach leaves and elucidated the mechanisms underlying their synergistic interaction. Upon treatment with 0.3 kGy X-ray irradiation and 1% CA combination, the cell counts of E. coli O157:H7 and L. monocytogenes reduced by 4.23 and 3.69 log CFU/mL on spinach leaves, respectively. The synergistic reduction in the cell counts of E. coli O157:H7 and L. monocytogenes by the combination treatment was 0.95 and 1.14 log units, respectively. The X-ray and CA combination exerts its antimicrobial effect by damaging the bacterial cell membrane and enhancing the generation of intracellular reactive oxygen species in the pathogens. The enhanced bactericidal effect of the combination treatment may not be due to the loss of intracellular enzyme activity. We also evaluated the effect of the combination treatment on the quality attributes of spinach leaves. The combination treatment did not result in adverse changes in color and texture of spinach leaves. These results demonstrate the potential of citric acid and X-ray irradiation combination for decontaminating foodborne pathogens on fresh produce.

Modified semi-continuous fermentation for resuscitating nongrowing cells during high-temperature gluconic acid production by Acetobacter senegalensis

AIMS

The formation of metabolically inactive and nongrowing cells is an inevitable by-product of intensive fermentation. This study investigated whether co-feeding can be used to resuscitate nongrowing Acetobacter senegalensis cells to enable them to produce gluconic acid in successive fermentation runs at 38°C.

METHODS AND RESULTS

In the first fermentation cycle, 75 g l^-1 of glucose were converted to gluconic acid. Subsequently, however, stationary-phase cells were unable to initiate a new fermentation cycle. The majority of stationary-phase cells (97%) were nonculturable on glucose at 38°C. In addition, 54 and 41% of cells contained non-active cellular dehydrogenases and a compromised cell envelope respectively. Co-feeding stationary-phase cells with a mixture of ethanol, glucose and acetic acid for 7 h enabled these cells to grow on 75 g l^-1 of glucose and produce gluconic acid. Additionally, 74% of cells contained active forms of cellular dehydrogenases after 7 h of co-feeding. However, co-feeding did not improve cell envelope integrity. Quantification of cellular NAD content showed that stationary-phase cells contained moderately reduced levels of total NAD (NADt) as compared with exponential-phase cells. Interestingly, the analysis of stationary-phase cells showed that co-feeding resulted in higher levels of NADt and NADH, suggesting that the regeneration of NADH is one of the limiting factors of glucose consumption. Expression of catalase and superoxide dismutase was increased in stationary-phase cells, but analysis of protein carbonylation and lipid peroxidation did not confirm an extensive oxidative stress.

CONCLUSIONS

Co-feeding with favourable nutrients may enable resuscitation of cells and utilization of less-favourable carbon sources in successive cycles.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study proposed a unique method for resuscitation of nongrowing cells during high-temperature fermentation. By applying this method, cells can be used for consecutive fermentation cycles.

Detection of active pathogenic bacteria under stress conditions using lytic and specific phage

In this study, we have monitored the potential activity of a foodborne and waterborne pathogenic bacterium, Salmonella typhi, under starvation conditions. The interaction between lytic phage and starved-VBNC pathogenic bacteria was studied to establish reliable methods for the detection of active cells before resuscitation. The analysis of phage kinetic parameters has demonstrated the flexibility of lytic with the quantity and mainly the quality of host cells. After 2 h of phage-starved-VBNC bacteria interaction, the reduction of phage amplification rate can reveal the ability of specific-lytic phage to recognize and to attach to their host cells with a probability of burst and release of infectious phages by active bacteria. After an extension of the latent period, the boost of the phage amplification rate was directly related to the positive interaction between potential intracellular 'engaged' phages and potential active bacteria. Furthermore, the modeling of the Salmonella-specific phage growth cycle in relationship with starved host cells can highlight the impact of the viability and the activity state of the host cells on the phage's growth cycle.

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

Although the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for estimating microbial activity in plant-associated soil and found that they were largely in agreement in the overarching patterns. Our results suggest that 16S ratios and active cell staining provide complementary information for measuring and interpreting microbial activity-dormancy dynamics in soils. They also support the idea that 16S rRNA/rRNA gene ratios have comparative value and offer a high-throughput, sequencing-based option for understanding relative changes in microbiome activity, as long as this method is coupled with quantification of community size.

At any given time, only a subset of microbial community members are active in their environment. The others are in a state of dormancy, with strongly reduced metabolic rates. It is of interest to distinguish active and inactive microbial cells and taxa to understand their functional contributions to ecosystem processes and to understand shifts in microbial activity in response to change. Of the methods used to assess microbial activity-dormancy dynamics, 16S rRNA/rRNA gene amplicons (16S ratios) and active cell staining with 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) are two of the most common, yet each method has limitations. Given that in situ activity-dormancy dynamics are proxied only by laboratory methods, further study is needed to assess the level of agreement and potential complementarity of these methods. We conducted two experiments investigating microbial activity in plant-associated soils. First, we treated corn field soil with phytohormones to simulate plant soil stress signaling, and second, we used rhizosphere soil from common bean plants exposed to drought or nutrient enrichment. Overall, the 16S ratio and CTC methods exhibited similar patterns of relative activity across treatments when treatment effects were large, and the instances in which they differed could be attributed to changes in community size (e.g., cell death or growth). Therefore, regardless of the method used to assess activity, we recommend quantifying community size to inform ecological interpretation. Our results suggest that the 16S ratio and CTC methods report comparable patterns of activity that can be applied to observe ecological dynamics over time, space, or experimental treatment.

IMPORTANCE Although the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for estimating microbial activity in plant-associated soil and found that they were largely in agreement in the overarching patterns. Our results suggest that 16S ratios and active cell staining provide complementary information for measuring and interpreting microbial activity-dormancy dynamics in soils. They also support the idea that 16S rRNA/rRNA gene ratios have comparative value and offer a high-throughput, sequencing-based option for understanding relative changes in microbiome activity, as long as this method is coupled with quantification of community size.

The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures

Acetate as the major by-product in industrial-scale bioprocesses with Escherichia coli is found to decrease process efficiency as well as to be toxic to cells, which has several effects like a significant induction of cellular stress responses. However, the underlying phenomena are poorly explored. Therefore, we studied time-resolved population heterogeneity of the E. coli growth reporter strain MG1655/pGS20PrrnBGFPAAV expressing destabilized green fluorescent protein during batch growth on acetate and glucose as sole carbon sources. Additionally, we applied five fluorescent stains targeting different cellular properties (viability as well as metabolic and respiratory activity). Quantitative analysis of flow cytometry data verified that bacterial populations in the bioreactor are more heterogeneous in growth as well as stronger metabolically challenged during growth on acetate as sole carbon source, compared to growth on glucose or acetate after diauxic shift. Interestingly, with acetate as sole carbon source, significant subpopulations were found with some cells that seem to be more robust than the rest of the population. In conclusion, following batch cultures population heterogeneity was evident in all measured parameters. Our approach enabled a deeper study of heterogeneity during growth on the favored substrate glucose as well as on the toxic by-product acetate. Using a combination of activity fluorescent dyes proved to be an accurate and fast alternative as well as a supplement to the use of a reporter strain. However, the choice of combination of stains should be well considered depending on which population traits to aim for.

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

Crystalline bedrock has been chosen for deep geologic long-term storage of used nuclear fuel in Finland. The risks generated by the deep subsurface microbial communities in these disposal sites need to be well characterised in advance to ensure safety. Deep subsurface microbial communities in a steady state are unlikely to contribute to known risk factors, such as corrosion or gas production. However, the construction of the geological final-disposal facility, bedrock disturbances, and hydraulic gradients cause changes that affect the microbial steady-state. To study the induced metabolism of deep microbial communities in changing environmental conditions, the activating effect of different electron donors and acceptors were measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG). Fluids originating from two different fracture zones of the Finnish disposal site in Olkiluoto were studied. These fracture fluids were very dissimilar both chemically and in terms of bacterial and archaeal diversity. However, the microbial communities of both fracture fluids were activated, especially with acetate, which indicates the important role of acetate as a preferred electron donor for Olkiluoto deep subsurface communities.

Searching for Activity Markers that Approximate (VBNC) Legionella pneumophila Infectivity in Amoeba after Ultraviolet (UV) Irradiation

Legionella pneumophila is an increasingly recognized threat to public health via aerosol exposures; with a variety of control measures including: water temperature/flow management and free chlorine used to reduce the risk of infection within healthcare centers. Despite these efforts, L. pneumophila often recolonizes plumbing systems after specific treatments, which prompted us to examine ultraviolet (UV) irradiation for a point-of-use, secondary control measure. Currently, there is no data on the efficacy of high (>254 nm) wavelength UV-C (100–280 nm) light inactivation of L. pneumophila with resuscitation of viable but non-culturable (VBNC) cells. We report for the first time L. pneumophila dose-responses for 268.6 nm and 288.6 nm UV-C, as compared to 256 nm, and demonstrate UV induced VBNC L. pneumophila remaining infectious to Acanthamoeba polyphaga during co-culture experiments. Findings were correlated to molecular-based activity assays to identify additional measures of L. pneumophila viability following UV disinfection compared to culture. A collection of viability markers may provide a more representative measure of risk compared to current culture-based detection, since UV-C irradiated L. pneumophila lose culturability, yet retain activity, increased ATP production, and the ability to be resuscitated by amoeba co-culture. This finding is significant as it identifies potential concern from VBNC cells following UV-C disinfection and the need for further research into the efficacy of UV inactivation as a point-of-use application for L. pneumophila control and management.

Cellular Injuries in Cronobacter sakazakii CIP 103183T and Salmonella enterica Exposed to Drying and Subsequent Heat Treatment in Milk Powder

Because of the ability of foodborne pathogens to survive in low-moisture foods, their decontamination is an important issue in food protection. This study aimed to clarify some of the cellular mechanisms involved in inactivation of foodborne pathogens after drying and subsequent heating. Individual strains of Salmonella Typhimurium, Salmonella Senftenberg, and Cronobacter sakazakii were mixed into whole milk powder and dried to different water activity levels (0.25 and 0.58); the number of surviving cells was determined after drying and subsequent thermal treatments in closed vessels at 90 and 100°C, for 30 and 120 s. For each condition, the percentage of unculturable cells was estimated and, in parallel, membrane permeability and respiratory activity were estimated by flow cytometry using fluorescent probes. After drying, it was clearly observable that the percentage of unculturable cells was correlated with the percentage of permeabilized cells (responsible for 20–40% of the total inactivated bacteria after drying), and to a lesser degree with the percentage of cells presenting with loss of respiratory activity. In contrast, the percentages of unculturable cells observed after heat treatment were strongly correlated with the loss of respiratory activity and weakly with membrane permeability (for 70–80% of the total inactivated bacteria after heat treatment). We conclude that cell inactivation during drying is closely linked to membrane permeabilization and that heat treatment of dried cells affects principally their respiratory activity. These results legitimize the use of time–temperature scales and allow better understanding of the cellular mechanisms of bacterial death during drying and subsequent heat treatment. These results may also allow better optimization of the decontamination process to ensure food safety by targeting the most deleterious conditions for bacterial cells without denaturing the food product.

CO2 and carbonate as substrate for the activation of the microbial community in 180 m deep bedrock fracture fluid of Outokumpu Deep Drill Hole, Finland

Microbial communities in deep subsurface environments comprise a large portion of Earth's biomass, but the metabolic activities in these habitats are largely unknown. Here the effect of CO₂ and carbonate on the microbial community of an isolated groundwater fracture zone at 180 m depth of the Outokumpu Deep Scientific Drill Hole (Finland) was tested. Outokumpu groundwater at 180 m depth contains approximately 0.45 L L⁻¹ dissolved gas of which methane contributes 76%. CO₂, on the other hand, is scarce. The number of microbial cells with intracellular activity in the groundwater was low when examined with redox staining. Fluorescence Assisted Cell Sorting (FACS) analyses indicated that only 1% of the microbial community stained active with the redox sensing dye in the untreated groundwater after 4 weeks of starvation. However, carbon substrate and sulfate addition increased the abundance of fluorescent cells up to 7%. CO₂ and CO₂ + sulfate activated the greatest number of microbes, especially increasing the abundance of Pseudomonas sp., which otherwise was present at only low abundance in Outokumpu. Over longer exposure time (2 months) up to 50% of the bacterial cells in the groundwater were shown to incorporate inorganic carbon from carbonate into biomass. Carbon recapture is an important feature in this ecosystem since it may decrease the rate of carbon loss in form of CO₂ released from cellular processes.

Selection of DNA aptamers specific for live Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen that causes significant morbidity and mortality in immunocompromised patients, particular cystic fibrosis sufferers, burns victims, diabetics and neonates. It thrives in moist places where it forms biofilms that are exceedingly difficult to eradicate on hospital surfaces, in water supplies and implanted biomaterials. Using a live cell SELEX approach we selected DNA aptamers to P. aeruginosa grown as biofilms in microfluidic cells. From a pool of aptamer candidates showing tight binding a stem-loop structure was identified as being important for binding. Enhanced binding and increased specificity was achieved by truncating structures and generating chimeric aptamers from the pool of top candidates. The top candidates have low nanomolar binding constants and high discrimination for P. aeruginosa over other Gram-negative bacteria. The aptamers bind both planktonic grown and biofilm grown cells. They do not have intrinsic bacteriostatic or bactericidal activity, but are ideal candidates for modification for use as aptamer-drug conjugates and in biosensors.

Physiological Responses of Salinity-Stressed Vibrio sp. and the Effect on the Biofilm Formation on a Nanofiltration Membrane

This study evaluated the effects of salinity on the physiological characteristics of Vibrio sp. B2 and biofilm formation on nanofiltration (NF) membrane coupons used in the high recovery seawater desalination process. The test conditions were at 0.6, 1.2, and 2.4 M sodium chloride (NaCl), equivalent to salinity of seawater, brine at 50% and 75% water recovery, respectively. High salinity inhibited the cell growth rate but increased the viability and bacterial membrane integrity. In addition, protein and eDNA concentrations of salinity-stressed bacteria were increased at 1.2 and 2.4 M NaCl. In particular, protein concentration was linearly correlated with the NaCl concentration. Similarly, less biofilm formation on the NF membrane coupon (without permeation flux) was observed by the salinity-stressed bacteria; however, the production of extracellular polymeric substances (EPS) was significantly increased as compared to control, and protein was an influential factor for biofilm formation. This study shows that salinity-stressed bacteria have a high potential to cause biofouling on membrane surface as the bacteria still maintain the cell activity and overproduce EPS. The potential of biofilm formation by the salinity-stressed bacteria has not been reported. Therefore, the findings are important to understand the mechanisms of membrane biofouling in a high salinity environment.

Determination of viable legionellae in engineered water systems: Do we find what we are looking for?

In developed countries, legionellae are one of the most important water-based bacterial pathogens caused by management failure of engineered water systems. For routine surveillance of legionellae in engineered water systems and outbreak investigations, cultivation-based standard techniques are currently applied. However, in many cases culture-negative results are obtained despite the presence of viable legionellae, and clinical cases of legionellosis cannot be traced back to their respective contaminated water source. Among the various explanations for these discrepancies, the presence of viable but non-culturable (VBNC) Legionella cells has received increased attention in recent discussions and scientific literature. Alternative culture-independent methods to detect and quantify legionellae have been proposed in order to complement or even substitute the culture method in the future. Such methods should detect VBNC Legionella cells and provide a more comprehensive picture of the presence of legionellae in engineered water systems. However, it is still unclear whether and to what extent these VBNC legionellae are hazardous to human health. Current risk assessment models to predict the risk of legionellosis from Legionella concentrations in the investigated water systems contain many uncertainties and are mainly based on culture-based enumeration. If VBNC legionellae should be considered in future standard analysis, quantitative risk assessment models including VBNC legionellae must be proven to result in better estimates of human health risk than models based on cultivation alone. This review critically evaluates current methods to determine legionellae in the VBNC state, their potential to complement the standard culture-based method in the near future, and summarizes current knowledge on the threat that VBNC legionellae may pose to human health.

New Technologies for Studying Biofilms

Bacteria have traditionally been studied as single-cell organisms. In laboratory settings, aerobic bacteria are usually cultured in aerated flasks, where the cells are considered essentially homogenous. However, in many natural environments, bacteria and other microorganisms grow in mixed communities, often associated with surfaces. Biofilms are comprised of surface-associated microorganisms, their extracellular matrix material, and environmental chemicals that have adsorbed to the bacteria or their matrix material. While this definition of a biofilm is fairly simple, biofilms are complex and dynamic. Our understanding of the activities of individual biofilm cells and whole biofilm systems has developed rapidly, due in part to advances in molecular, analytical, and imaging tools and the miniaturization of tools designed to characterize biofilms at the enzyme level, cellular level, and systems level.

Near-zero growth kinetics of Pseudomonas putida deduced from proteomic analysis

Intensive microbial growth typically observed in laboratory rarely occurs in nature. Because of severe nutrient deficiency, natural populations exhibit near-zero growth (NZG). There is a long-standing controversy about sustained NZG, specifically whether there is a minimum growth rate below which cells die or whether cells enter a non-growing maintenance state. Using chemostat with cell retention (CCR) of Pseudomonas putida, we resolve this controversy and show that under NZG conditions, bacteria differentiate into growing and VBNC (viable but not non-culturable) forms, the latter preserving measurable catabolic activity. The proliferating cells attained a steady state, their slow growth balanced by VBNC production. Proteomic analysis revealed upregulated (transporters, stress response, self-degrading enzymes and extracellular polymers) and downregulated (ribosomal, chemotactic and primary biosynthetic enzymes) proteins in the CCR versus batch culture. Based on these profiles, we identified intracellular processes associated with NZG and generated a mathematical model that simulated the observations. We conclude that NZG requires controlled partial self-digestion and deep reconfiguration of the metabolic machinery that results in the biosynthesis of new products and development of broad stress resistance. CCR allows efficient on-line control of NZG including VBNC production. A well-nuanced understanding of NZG is important to understand microbial processes in situ and for optimal design of environmental technologies.

Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities

Chlamydiae are a group of obligate intracellular bacteria comprising important human and animal pathogens as well as symbionts of ubiquitous protists. They are characterized by a developmental cycle including two main morphologically and physiologically distinct stages, the replicating reticulate body and the infectious nondividing elementary body. In this review, we reconstruct the history of studies that have led to our current perception of chlamydial physiology, focusing on their energy and central carbon metabolism. We then compare the metabolic capabilities of pathogenic and environmental chlamydiae highlighting interspecies variability among the metabolically more flexible environmental strains. We discuss recent findings suggesting that chlamydiae may not live as energy parasites throughout the developmental cycle and that elementary bodies are not metabolically inert but exhibit metabolic activity under appropriate axenic conditions. The observed host-free metabolic activity of elementary bodies may reflect adequate recapitulation of the intracellular environment, but there is evidence that this activity is biologically relevant and required for extracellular survival and maintenance of infectivity. The recent discoveries call for a reconsideration of chlamydial metabolism and future in-depth analyses to better understand how species- and stage-specific differences in chlamydial physiology may affect virulence, tissue tropism, and host adaptation.

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.

Viability of calcifying bacterial formulations in fly ash for applications in building materials

Evidence of bacterial involvement in precipitation of calcium carbonates has brought a revolution in the field of applied microbiology, geotechnical sciences, environmental and civil engineering with its marked success in restoration of various building materials. For applications of these calcite binder-producing bacterial cultures, different expensive carrier materials have been used but their high costs have come in the way of their successful commercialization. In the present study, we have explored the potential of cheap industrial by-product fly ash as a carrier material for bacterial cells and investigated the viability of calcifying bacterial isolates: Bacillus megaterium, Bacillus cereus, and Lysinibacillus fusiformis in fly ash carrier at varying temperatures and moisture conditions along with biomineralization efficacy of these formulations. We used laser scanning confocal microscopy to analyze the viability of bacteria by florescent dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) along with the plate count method. Results revealed that fly ash successfully served as an effective carrier material and bacterial formulations stored at 4 °C provided longer shelf life than those stored at higher temperatures. Up to 106 cfu/g was found to sustain in all formulations at 4 °C compared to 104-105 cfu/g in case of higher temperatures up to 1 year. For 4 °C, higher moistures (50 %) were found to provide better survivability while for higher temperatures, lower moistures (30 %) favored higher viability. The biomineralization capability of fresh and formulated bacterial cells was compared on the basis of precipitation of carbonates and it was found that carbonate precipitation efficacy of formulated bacterial cells was comparable to fresh bacterial cells.

Metabolic features of Protochlamydia amoebophila elementary bodies--a link between activity and infectivity in Chlamydiae

The Chlamydiae are a highly successful group of obligate intracellular bacteria, whose members are remarkably diverse, ranging from major pathogens of humans and animals to symbionts of ubiquitous protozoa. While their infective developmental stage, the elementary body (EB), has long been accepted to be completely metabolically inert, it has recently been shown to sustain some activities, including uptake of amino acids and protein biosynthesis. In the current study, we performed an in-depth characterization of the metabolic capabilities of EBs of the amoeba symbiont Protochlamydia amoebophila. A combined metabolomics approach, including fluorescence microscopy-based assays, isotope-ratio mass spectrometry (IRMS), ion cyclotron resonance Fourier transform mass spectrometry (ICR/FT-MS), and ultra-performance liquid chromatography mass spectrometry (UPLC-MS) was conducted, with a particular focus on the central carbon metabolism. In addition, the effect of nutrient deprivation on chlamydial infectivity was analyzed. Our investigations revealed that host-free P. amoebophila EBs maintain respiratory activity and metabolize D-glucose, including substrate uptake as well as host-free synthesis of labeled metabolites and release of labeled CO₂ from ¹³C-labeled D-glucose. The pentose phosphate pathway was identified as major route of D-glucose catabolism and host-independent activity of the tricarboxylic acid (TCA) cycle was observed. Our data strongly suggest anabolic reactions in P. amoebophila EBs and demonstrate that under the applied conditions D-glucose availability is essential to sustain metabolic activity. Replacement of this substrate by L-glucose, a non-metabolizable sugar, led to a rapid decline in the number of infectious particles. Likewise, infectivity of Chlamydia trachomatis, a major human pathogen, also declined more rapidly in the absence of nutrients. Collectively, these findings demonstrate that D-glucose is utilized by P. amoebophila EBs and provide evidence that metabolic activity in the extracellular stage of chlamydiae is of major biological relevance as it is a critical factor affecting maintenance of infectivity.

The Chlamydiae are a group of bacteria that strictly rely on eukaryotic host cells as a niche for intracellular growth. This group includes major pathogens of humans and animals as well as symbionts of protists. Unlike most other bacteria, chlamydiae alternate between two distinct developmental stages. Here we provide novel insights into the infective stage, the elementary body (EB), which has been described almost a century ago and is commonly referred to as an inert spore-like particle. Our analyses of EBs of the amoeba symbiont Protochlamydia amoebophila provide a detailed overview of their metabolism outside of, and independent from, their natural host cells. We demonstrated that these EBs are capable of respiration and are active in the major routes of central carbon metabolism, including glucose import, biosynthetic reactions, and catabolism for energy generation. Glucose starvation resulted in a rapid decline of metabolic activity in P. amoebophila EBs and a concomitant decrease in their potential to infect new host cells. The human pathogen Chlamydia trachomatis was also dependent on nutrient availability for extracellular survival. The extent of metabolic activity in chlamydial EBs and its consequences for infectivity challenge long-standing textbook knowledge and demonstrate that the infective stage is far more dependent on its environment than previously recognized.

Exposure to the proton scavenger glycine under alkaline conditions induces Escherichia coli viability loss

Our previous work described a clear loss of Escherichia coli (E. coli) membrane integrity after incubation with glycine or its N-methylated derivatives N-methylglycine (sarcosine) and N,N-dimethylglycine (DMG), but not N,N,N-trimethylglycine (betaine), under alkaline stress conditions. The current study offers a thorough viability analysis, based on a combination of real-time physiological techniques, of E. coli exposed to glycine and its N-methylated derivatives at alkaline pH. Flow cytometry was applied to assess various physiological parameters such as membrane permeability, esterase activity, respiratory activity and membrane potential. ATP and inorganic phosphate concentrations were also determined. Membrane damage was confirmed through the measurement of nucleic acid leakage. Results further showed no loss of esterase or respiratory activity, while an instant and significant decrease in the ATP concentration occurred upon exposure to either glycine, sarcosine or DMG, but not betaine. There was a clear membrane hyperpolarization as well as a significant increase in cellular inorganic phosphate concentration. Based on these results, we suggest that the inability to sustain an adequate level of ATP combined with a decrease in membrane functionality leads to the loss of bacterial viability when exposed to the proton scavengers glycine, sarcosine and DMG at alkaline pH.

Viscosity dictates metabolic activity of Vibrio ruber

Little is known about metabolic activity of bacteria, when viscosity of their environment changes. In this work, bacterial metabolic activity in media with viscosity ranging from 0.8 to 29.4 mPas was studied. Viscosities up to 2.4 mPas did not affect metabolic activity of Vibrio ruber. On the other hand, at 29.4 mPas respiration rate and total dehydrogenase activity increased 8 and 4-fold, respectively. The activity of glucose-6-phosphate dehydrogenase (GPD) increased up to 13-fold at higher viscosities. However, intensified metabolic activity did not result in faster growth rate. Increased viscosity delayed the onset as well as the duration of biosynthesis of prodigiosin. As an adaptation to viscous environment V. ruber increased metabolic flux through the pentose phosphate pathway and reduced synthesis of a secondary metabolite. In addition, V. ruber was able to modify the viscosity of its environment.

Use of 5-cyano-2,3-ditolyl-tetrazolium chloride staining as an indicator of biocidal activity in a rapid assay for anti-Acanthamoeba agents

The usefulness of 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) staining to determine the respiratory activity of Acanthamoeba was evaluated in this study. Acanthamoeba trophozoites and cysts have a red fluorescence after staining with CTC. To determine the effectiveness of CTC staining as a CTC biocidal assay for Acanthamoeba, the trophozoites and cysts of Acanthamoeba castellanii (ATCC 5037) were treated with serial concentrations of disinfectant solutions, namely, polyhexamethylene biguanide (PHMB) and commercial soft contact lens (SCL) disinfectant solutions. The treated Acanthamoeba organisms were stained with CTC, and their respiratory activity was determined by the intensity of fluorescence in a fluorescence microplate reader. The survival rates of the same samples were determined by a culture-dependent biocidal assay using the Spearman-Karber method. Our results showed that the respiratory activities determined by the CTC biocidal assay and the survival rates determined by the culture-dependent biocidal assay for Acanthamoeba trophozoites and cysts decreased in a dose-dependent way after PHMB treatments, and the results were significantly correlated (r = 0.83 and P < 0.01 for trophozoites; r = 0.60 and P < 0.01 for cysts; Spearman rank correlation test). The respiratory activities in the trophozoites and cysts treated with SCL disinfectant solutions were significantly correlated with the survival rate (r = 0.70 and P < 0.01 for trophozoites; r = 0.64 and P < 0.01 for cysts; Spearman rank correlation test). The significant correlation of the results indicated that the CTC biocidal assay can be used as an alternative method to a culture-dependent biocidal assay. The CTC biocidal assay is a rapid and simple method to test the effectiveness of disinfectant solutions against Acanthamoeba trophozoites and cysts.

Persistence of bacterial proteolytic enzymes in lake ecosystems

This study analyzes proteolytic enzyme persistence and the role of dead (or metabolically inactive) aquatic bacteria in organic matter cycling. Samples from four lakes of different trophic status were used. Irrespective of the trophic status of the examined lakes, bacterial aminopeptidases remained active even 72 h after the death of the bacteria that produced them. The total pool of proteolytic enzymes in natural lake water samples was also stable. We found that the rates of amino acid enzymatic release from proteinaceous matter added to preserved lake water sample were constant for at least 96 h (r(2)  = 0.99, n = 17, P ≤ 0.0001, V(max)  = 84.6 nM h(-1) ). We also observed that proteases built into bacterial cell debris fragments remained active for a long time, even after the total destruction of cells. Moreover, during 24 h of incubation time, about 20% of these enzymatically active fragments adsorbed onto natural seston particles, becoming a part of the 'attached enzymes system' that is regarded as the 'hot-spot' of protein degradation in aquatic ecosystems.