Evaluation of detachment methods for the enumeration of Bacteroides fragilis in sediments via propidium monoazide quantitative PCR, in comparison with Enterococcus faecalis and Escherichia coli

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet-microbiome interactions. Here, we used a click chemistry-based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine [sphinganine alkyne (SAA)] into the murine gut microbial community (bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet-microbiome interactions.

Scratching and transplanting of electro-active biofilm in fruit peeling leachate by ultrasound: re-inoculation in new microbial fuel cell for enhancement of bio-energy production and organic matter detection

OBJECTIVE

An electro-active biofilm of Fruit Peeling (FP) leachate was formed onto the Carbon Felt (CF) bio-anode in a Microbial Fuel Cell (MFC), after functioning for a long time. The electro active-biofilm thus formed was then scratched by ultrasound and re-inoculated in a new leachate to be transplanted onto the bio-anode. This procedure allowed the microbial electron charge transfer and therefore the enhancement of the bio-energy production of the fuel cell.

RESULTS

By using the repetitive mechanical biofilm removal, re-suspension and electrochemically facilitated biofilm formation, the voltage was substantially increased. In effect, the voltage of the 1st G of biofilm, rose gradually and reached its maximum value of 65 mV after 10 days. Whilst the 2nd generation allowed to obtain the maximum voltage 276 mV and without any lag time. The DCO abatement using the 1st G biofilm was 68% greater than the 3rd G 26%. Besides, the electrochemical impedance spectroscopy characterization and cyclic voltammetry of bio-anode with 2nd G biofilm confirmed the ability of electro-active biofilm formation on a new support. The biofilm transplanted showed thus greater kinetic performance, with reduced lag time demonstrating the interest of the selection that took place during the formation of successive biofilms.

CONCLUSIONS

Despite the transplantation of the electro-active biofilm onto the bio-anode, the MFC still produced relatively lower power output. Nevertheless, it has been tested successfully for monitoring and detecting the oxidation of sodium acetate substrate in the very wide concentration range 0.0025-35 g/l.

Sediments quality must be considered when evaluating freshwater aquatic environments used for recreational activities

Although water quality from freshwater recreational aquatic environments (RAEs) has been long analyzed worldwide, little information is available about their sediments. The aim of this work was to study the physicochemical and bacteriological quality of water and sediment under different seasonal events. For that, Wierna River (WR) and General Belgrano reservoir (GB) were used as freshwater RAEs models. A total of 33 water and 33 sediment samples (15 from WR and 18 from GB from each phase) were collected and analyzed. Physicochemical variables in water (pH, turbidity, dissolved oxygen, temperature, conductivity, alkalinity, hardness) and sediments (organic matter, humidity, ash, and conductivity) were measured. For the bacteriological characterization, total aerobic mesophiles, total and thermotolerant coliforms, E. coli, enteroccocci, Salmonella spp., and Pseudomonas aeruginosa were evaluated using culture-based methods. Universal and human Bacteroides were also quantified by real-time PCR. Univariate (Kruskall-Wallis), bivariate (Spearman correlation), and multivariate (cluster analysis, principal component analysis) statistical techniques were applied for data analysis. All bacterial indicators were almost two-logs higher in sediments than in water, for both RAEs. Also, due to rainfall events and recreational activities, sediments were resuspended in surface water exceeding in most cases the limit values established by international regulation for bacteria. Significant correlation was observed between culturable bacteria and turbidity (p < 0.05) supporting this. We found that while physicochemical variables clustered samples by geographical location in water and sediments, microbiological aggrupation in water was mostly driven by seasonal events. No aggrupation was observed when using microbiological variables in sediments. Thus, geographical location, type of water and sediments, and seasonal events influenced on RAEs quality. Including sediment analysis during RAEs monitoring campaigns is essential as it will allow knowing the real health risk to which bathers are exposed and proposing solutions to mitigate it.

Controlling the Distribution of Microbially Precipitated Calcium Carbonate in Radial Flow Environments

Bacterially driven reactions such as ureolysis can induce calcium carbonate precipitation, a well-studied process called microbially induced calcium carbonate precipitation (MICP). MICP is of interest in subsurface applications such as sealing leaks around wells. For effective field deployment, it is important to study MICP under radial flow conditions, which are relevant to near-well environments. In this study, a laboratory-scale radial flow reactor of 23 cm diameter, with a 1 mm glass bead monolayer serving as a porous medium, was used to investigate the effects of fluid flow rates and calcium concentrations on the mass and distribution of MICP by the ureolytic bacterium Sporosarcina pasteurii. Experiments were performed at hydraulic residence times of 14, 7, and 3.5 min and calcium to urea molar ratios of 0.5:1, 1:1, and 2:1. The total amount of CaCO₃ precipitated in the reactor increased with increasing residence time and with decreasing Ca²⁺ to urea molar ratios. Increased bacterial attachment and increased CaCO₃ precipitation were observed with distance from the center inlet of the reactor in all experiments. More uniform calcium distribution was achieved at lower flow rates. The relationship between reaction and transport rate (i.e., the Damköhler number) is identified as a useful parameter for the prediction of MICP in radial flow environments.

Viability-based quantification of antibiotic resistance genes and human fecal markers in wastewater effluent and receiving waters

Antibiotic resistance is a public health issue with links to environmental sources of antibiotic resistance genes (ARGs). ARGs from nonviable sources may pose a hazard given the potential for transformation whereas ARGs in viable sources may proliferate during host growth or conjugation. In this study, ARGs in the effluent from three municipal wastewater treatment plants (WWTPs) and the receiving surface waters were investigated using a viability-based qPCR technique (vPCR) with propidium monoazide (PMA). ARGs sul1, tet(G), and bla_TEM, fecal indicator marker BacHum, and 16S rRNA gene copies/mL were found to be significantly lower in viable-cells than in total concentrations for WWTP effluent. Viable-cell and total gene copy concentrations were similar in downstream samples except for tet(G). Differences with respect to season in the prevalence of nonviable ARGs in surface water or WWTP effluent were not observed. The results of this study indicate that qPCR may overestimate viable-cell ARGs and fecal indicator genes in WWTP effluent but not necessarily in the surface water >1.8 km downstream.

Propidium monoazide real-time PCR amplification for viable Salmonella species and Salmonella Heidelberg in pork

Salmonella enterica serovar Heidelberg causes foodborne infections and is a major threat to the food chain and public health. In this study, we aimed to develop a rapid molecular typing approach to identify Salmonella enterica serovar Heidelberg. Using comparative genomics, four serovar-specific gene fragments were identified, and a real-time polymerase chain reaction (PCR) combined with a propidium monoazide (PMA) pretreatment method was developed for simultaneous detection of viable Salmonella sp. (invA) and Salmonella Heidelberg (SeHA_C3258). The assay showed 100% specificity for all strains tested. The assay was able to distinguish effectively viable or dead cells with the PMA. The detection limit was 2.4 CFU/mL following 6 h of incubation in enrichment Luria-Bertani medium, and the assay could detect 1.7 × 10² CFU/mL in the presence of pork background flora. In artificially contaminated pork, real-time PCR detected inoculum levels of 1.15 CFU/25 g of pork after a 6 h enrichment. Thus, our findings indicated that this comparative genomics approach could be used to screen for serovar-specific fragments and that real-time PCR with PMA was a simple and reliable method for detecting viability of Salmonella species and Salmonella Heidelberg.

Evaluation of Molecular Methods for the Detection and Quantification of Pathogen-Derived Nucleic Acids in Sediment

The accurate detection of pathogens in environmental matrices, such as sediment, is critical in understanding pathogen fate and behavior in the environment. In this study, we assessed the usefulness of methods for the detection and quantification of Vibrio spp. and norovirus (NoV) nucleic acids in sediment. For bacteria, a commonly used direct method using hexadecyltrimethylammonium bromide (CTAB) and phenol-chloroform-isoamyl alcohol (PCI) extraction was optimized, whereas for NoV, direct and indirect (virus elution-concentration) methods were evaluated. For quantification, commercially available quantitative PCR (qPCR) and reverse transcription qPCR (RT-qPCR) kits were tested alongside a digital PCR (dPCR) approach. CTAB-based extraction combined with 16 h polyethylene glycol 6000 (PEG6000) precipitation was found to be suitable for the direct extraction of high abundance bacterial and viral nucleic acids. For the indirect extraction of viral RNA, beef extract-based elution followed by PEG6000 precipitation and extraction using the NucliSENS® MiniMag® Nucleic Acid Purification System and the PowerViral® Environmental RNA/DNA Isolation Kit and qRT-PCR resulted in 83-112 and 63-69% recoveries of NoV, respectively. dPCR resulted in lower viral recoveries (47 and 9%) and ~4 orders of magnitude lower Vibrio concentrations (3.6-4.6 log10 gc/100 g sediment) than was observed using qPCR. The use of internal controls during viral quantification revealed that the RT step was more affected by inhibitors than the amplification. The methods described here are suitable for the enumeration of viral and/or bacterial pathogens in sediment, however the use of internal controls to assess efficiency is recommended.

Survival and persistence of host-associated Bacteroidales cells and DNA in comparison with Escherichia coli and Enterococcus in freshwater sediments as quantified by PMA-qPCR and qPCR

Decay of the fecal source identifier Bacteroidales in sediments has not been studied until now. Two types of microcosms inoculated with human, cow and dog feces were constructed to investigate the survival and persistence of host-associated Bacteroidales cells and their DNA, respectively, in freshwater sediments: (i) a completely anaerobic microcosm where feces were entirely mixed with sediments for estimating decay of Bacteroidales in oxygen-free sediments at two temperatures (6 °C and 20 °C) and (ii) a core microcosm where feces in the overlying water column settled on top of undisturbed core sediments. Quantitative PCR (qPCR) along with propidium monoazide (PMA) was used to differentiate between genetic markers present in intact cells and total intracellular as well as extracellular marker DNA. Regulated fecal indicator bacteria were measured by cultivation (Escherichia coli and Enterococcus) and qPCR (Enterococcus) in relation to Bacteroidales-associated host markers. In anaerobic microcosms, the survival and persistence of Bacteroidales cells and DNA in sediments were considerably extended, especially at the lower temperature of 6 °C, with two-log reduction times (T99) >56 d (cells) and >169 d (DNA). Bacteroidales DNA persisted up to five times longer than cells in anaerobic microcosms at 6 °C, whereas decay rates of cells and DNA were not significantly different at 20 °C in anaerobic microcosms. In core microcosms, the levels of Bacteroidales cells and DNA decreased approximately six times more slowly in sediments than in overlying water; T99 values of Bacteroidales cells and DNA were 6-9 d (water) and 29-82 d (sediment). The survival of universal, human-, ruminant- and dog-associated Bacteroidales cells in sediments was similar in both microcosms under each given condition, as was the persistence of DNA. Decay rate constants of Bacteroidales cells and DNA were comparable with those of cultivable Enterococcus and E. coli cells in core sediments while Enterococcus DNA levels fluctuated without noticeable decay. The prolonged persistence of host-associated Bacteroidales suggests that sediments should be considered in practical applications of microbial source tracking, because they can act as non-point sources of fecal markers.

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples

In clinical trials investigating human health and in the analysis of microbial communities in cultures and natural environments, it is a substantial challenge to differentiate between living, potentially active communities and dead cells. The DNA-intercalating dye propidium monoazide (PMA) enables the selective masking of DNA from dead, membrane-compromised cells immediately before DNA extraction. In the present study, we evaluated for the first time a PMA treatment for methanogenic archaea in cultures and particle-rich environmental samples. Using microscopic analyses, we confirmed the applicability of the LIVE/DEAD(®) BacLight™ kit to methanogenic archaea and demonstrated the maintenance of intact cell membranes of methanogens in the presence of PMA. Although strain-specific differences in the efficiency of PMA treatment to methanogenic archaea were observed, we developed an optimal procedure using 130 μM PMA and 5min of photo-activation with blue LED light. The results showed that the effectiveness of the PMA treatment strongly depends on the texture of the sediment/soil: silt and clay-rich sediments represent a challenge at all concentrations, whereas successful suppression of DNA from dead cells with compromised membranes was possible for low particle loads of sandy soil (total suspended solids (TSS)≤200 mg mL(-1)). Conclusively, we present two strategies to overcome the problem of insufficient light activation of PMA caused by the turbidity effect (shielding) in particle-rich environmental samples by (i) dilution of the particle-rich sample and (ii) detachment of the cells and the free DNA from the sediment prior to a PMA treatment. Both strategies promise to be usable options for distinguishing living cells and free DNA in complex environmental samples.