Determination of in situ bacterial growth rates in aquifers and aquifer sediments

Methods to monitor bacterial growth and replicative rates at the single-cell level

The heterogeneity of bacterial growth and replicative rates within a population was proposed a century ago notably to explain the presence of bacterial persisters. The term "growth rate" at the single-cell level corresponds to the increase in size or mass of an individual bacterium while the "replicative rate" refers to its division capacity within a defined temporality. After a decades long hiatus, recent technical innovative approaches allow population growth and replicative rates heterogeneity monitoring at the single-cell level resuming in earnest. Among these techniques, the oldest and widely used is time-lapse microscopy, most recently combined with microfluidics. We also discuss recent fluorescence dilution methods informing only on replicative rates and best suited. Some new elegant single cell methods so far only sporadically used such as buoyant mass measurement and stable isotope probing have emerged. Overall, such tools are widely used to investigate and compare the growth and replicative rates of bacteria displaying drug-persistent behaviors to that of bacteria growing in specific ecological niches or collected from patients. In this review, we describe the current methods available, discussing both the type of queries these have been used to answer and the specific strengths and limitations of each method.

Repeated centrifuging and washing concentrates bacterial samples in peritoneal dialysis for optimal culture: an original article

Background

Bacterial cultures allow the identification of infectious disease pathogens. However, obtaining the results of conventional culture methods is time-consuming, taking at least two days. A more efficient alternative is the use of concentrated bacterial samples to accelerate culture growth. Our study focuses on the development of a high-yield sample concentrating technique.

Results

A total of 71 paired samples were obtained from patients on peritoneal dialysis (PD). The peritoneal dialysates were repeat-centrifuged and then washed with saline, namely the centrifuging and washing method (C&W method). The concentrated samples were Gram-stained and inoculated into culture plates. The equivalent unprocessed dialysates were cultured as the reference method. The times until culture results for the two methods were compared. The reference method yielded no positive Gram stain results, but the C&W method immediately gave positive Gram stain results for 28 samples (p < 0.001). The culture-negative rate was lower in the C&W method (5/71) than in the reference method (13/71) (p = 0.044). The average time for bacterial identification achieved with the C&W method (22.0 h) was shorter compared to using the reference method (72.5 h) (p < 0.001).

Conclusions

The C&W method successfully concentrated bacterial samples and superseded blood culture bottles for developing adequate bacterial cultures. The C&W method may decrease the culture report time, thus improving the treatment of infectious diseases.

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

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

Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface

While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.

Lessons learned from bacterial transport research at the South Oyster Site

This paper provides a review of bacterial transport experiments conducted by a multiinvestigator, multiinstitution, multidisciplinary team of researchers under the auspices of the U.S. Department of Energy (DOE). The experiments were conducted during the time period 1999-2001 at a field site near the town of Oyster, Virginia known as the South Oyster Site, and included four major experimental campaigns aimed at understanding and quantifying bacterial transport in the subsurface environment. Several key elements of the research are discussed here: (1) quantification of bacterial transport in physically, chemically, and biologically heterogeneous aquifers, (2) evaluation of the efficacy of conventional colloid filtration theory, (3) scale effects in bacterial transport, (4) development of new methods for microbial enumeration and screening for low adhesion strains, (5) application of novel hydrogeophysical techniques for aquifer characterization, and (6) experiences regarding management of a large field research effort. Lessons learned are summarized in each of these areas. The body of literature resulting from South Oyster Site research has been widely cited and continues to influence research into the controls exerted by aquifer heterogeneity on reactive transport (including microbial transport). It also served as a model (and provided valuable experience) for subsequent and ongoing highly-instrumented field research efforts conducted by DOE-sponsored investigators.

Contrasting influence of geology on E. coli and arsenic in aquifers of Bangladesh

Arsenic in groundwater has been a concern in South and Southeast Asia for more than a decade. We explore here the possibility that hydrogeologic factors recently shown to influence the distribution of arsenic might also affect the level of contamination of shallow (<20 m) wells with microbial pathogens. A total of 96 shallow tube wells in two nearby villages of Bangladesh were surveyed during the wet and dry seasons, along with 55 deeper wells in neighboring villages. One of the two villages is located in a particularly sandy environment where recharge is rapid and shallow wells contain little arsenic. Shallow aquifers in the other village are capped with an impermeable clay layer, recharge is an order of magnitude slower, and arsenic levels are high. The fecal indicator E. coli was detected in 43% of shallow wells, compared with 12% of deeper wells. More shallow wells contained E. coli during the wet season (61%) than during the dry season (9%). In the wet season, a higher proportion of shallow wells in the village with low arsenic levels (72%) contained E. coli compared with the village having high arsenic levels (43%). Differences in arsenic and E. coli distributions between the two sites are likely due to the differences in permeability of near-surface sediments although differences in average well-depth between the two villages (9 ± 4 vs. 15 ± 3 m) may play a role as well. Hydrogeologic conditions that favor high levels of fecal contamination but low levels of arsenic in shallow groundwater should be taken into account during arsenic mitigation throughout South and Southeast Asia.

How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats

Geobacteraceae dominate many iron-reducing subsurface environments and are associated with biodegradation of organic pollutants. In order to enhance the understanding of the environmental role played by Geobacteraceae, the physiology of Geobacter metallireducens was investigated at the low growth rates found in its subsurface habitat. Cultivation in retentostats (a continuous culturing device with biomass retention) under electron acceptor and electron donor limitation enabled growth rates as low as 0.0008 h(-1). The maximum growth yield was between 0.05 and 0.09 C-mol biomass per C-mol acetate and comparable to that observed in batch experiments. Maintenance energy demand is among the lowest reported for heterotrophic bacteria, under both acetate and AQDS limitation. The cells were able to use alternative electron acceptors directly, without requiring de novo protein synthesis. We discuss how the extremely low maintenance energy demand and the ability to readily use alternative electron acceptors may help Geobacter species to become ubiquitous and dominant microorganisms in many iron-reducing subsurface settings.

Multi tracer test for the implementation of enhanced in-situ bioremediation at a BTEX-contaminated megasite

At the Centre for Environmental Research Leipzig-Halle (UFZ) research site in Zeitz, Germany, benzene contaminates the lower of two aquifers with concentrations of up to 20 mg/l. Since the benzene plume has a minimum length of approximately 1 km, enhanced natural attenuation measures are being considered as a remediation strategy. This study describes the performance and evaluation of a multi-species reactive tracer test using the tracers fluorescein and bromide as conservative tracers and toluene as reactive tracer. Sampling was performed over a period of six months using a detailed network of multilevel sampling wells. Toluene was only slightly retarded in comparison to bromide, whereas fluorescein was retarded considerably stronger. Therefore, it was not possible to use fluorescein as an in situ tracer for the determination of groundwater velocities. The ionic nature of fluorescein is assumed to be the major reason for its retardation. The results show that the infiltration conditions were suitable to produce a wide spreading of the tracer front along the full thickness of the aquifer. Thus, a large aquifer volume can be treated in future enhanced bioremediation measures. The total quantity of infiltrated toluene (24 l) was degraded under sulfate-reducing conditions over a flow path of 50 m. Benzylsuccinate was identified as a metabolite of toluene degradation under sulfate-reducing conditions at this site. The modelling results show that toluene degradation was described more accurately using Monod kinetics than first-order kinetics. Since toluene was only slightly retarded in comparison to bromide, sorption and desorption processes were considered to be negligible.

Change of collision efficiency with distance in bacterial transport experiments

Understanding the mechanisms of bacterial transport in aquifers is important in developing bioremediation strategies. Collision efficiency (alpha) is one important parameter used in modeling bacterial transport. This study was undertaken to measure change in alpha with distance by performing a bacterial transport experiment in Oyster, Virginia. Following injection of a bacterium, Comamonas sp., into a well, water samples were collected at various distances along the flowpath and injected into columns packed with homogenized South Oyster focus area sediment. Zeta potentials of the bacteria in the samples were measured. Values of alpha were determined at various locations in the field in two ways: based on field breakthrough concentrations at the sampling points and based on column breakthrough concentrations. The alpha values estimated from field breakthrough decreased with distance, whereas those estimated from column breakthrough increased with distance. Bacterial cell surface charge became progressively more negative with distance in the field. We hypothesize that the apparent contradiction between field and column alpha values was caused by differences in the flow of the two systems. Flow in the columns was forced to occur through fine-grained zones of iron and aluminum hydroxide coatings that selectively removed the most negatively charged bacteria. In contrast, in the field, the injected cells did not come into contact with the positively charged coatings because the bulk solution bypassed them due to heterogeneous hydraulic properties. These results suggest that laboratory-based models may underestimate bacterial transport distance in the field. A more realistic approach may be necessary to capture the degree of heterogeneity.

Absence of Spiroplasma or other bacterial 16s rRNA genes in brain tissue of hamsters with scrapie

Spiroplasma spp. have been proposed to be the etiological agents of the transmissible spongiform encephalopathies (TSEs). In a blind study, a panel of 20 DNA samples was prepared from the brains of uninfected hamsters or hamsters infected with the 263K strain of scrapie. The brains of the infected hamsters contained > or =10(10) infectious doses/g. The coded panel was searched for bacterial 16S rRNA gene sequences, using primers selective for spiroplasma sequences, primers selective for mollicutes in general, and universal bacterial primers. After 35 PCR cycles, no samples were positive for spiroplasma or any other bacterial DNA, while control Spiroplasma mirum genomic DNA, spiked at 1% of the concentration required to account for the scrapie infectivity present, was readily detected. After 70 PCR cycles, nearly all samples yielded amplified products which were homologous to various bacterial 16S rRNA gene sequences, including those of frequent environmental contaminants. These sequences were seen in uninfected as well as infected samples. Because the concentration of scrapie infectivity was at a known high level, it is very unlikely that a bacterial infection at the same concentration could have escaped detection. We conclude that the infectious agent responsible for TSE disease cannot be a spiroplasma or any other eubacterial species.

Microbial diversity in biofilms from corroding heating systems

Culture-independent investigations of the bacterial diversity and activity in district heating systems with and without corrosion did not make it possible to relate one group of microorganisms with the observed corrosion. Fluorescence in situ hybridization by oligonucleotide probes revealed the dominance of beta-proteobacteria, sulphate reducing prokaryotes and alpha-proteobacteria. Analysis of a clone library from one Danish heating (DH) system showed that the most sequences formed two clusters within the alpha-proteobacteria affiliated to the families Rhizobiaceae and Acetobacteraceae and two clusters within the beta-proteobacteria belonging to the family Comamonadaceae. Functional groups were determined by microautoradiography showing aerobic and anaerobic bacteria (sulphate reducing and methanogenic bacteria). The corrosion study showed that pitting corrosion rates were five to ten times higher than the general corrosion rates, suggesting the presence of biocorrosion. The results indicate that several bacterial groups could be involved in corrosion of DH system piping including sulphate reducing prokaryotes, Acidovorax (within the beta-proteobacteria), methanogenic bacteria and others.

Application of a vital fluorescent staining method for simultaneous, near-real-time concentration monitoring of two bacterial strains in an Atlantic coastal plain aquifer in Oyster, Virginia

Two differentially labeled bacterial strains were monitored in near-real time during two field-scale bacterial transport experiments in a shallow aquifer in July 2000 and July 2001. Comamonas sp. strain DA001 and Acidovorax sp. strain OY-107 were grown and labeled with the vital fluorescent stain TAMRA/SE (5 [and -6]-carboxytetramethylrhodamine, succinimidyl ester) or CFDA/SE (5 [and -6]-carboxyfluorescein diacetate, succinimidyl ester). Fluorescently labeled cells and a conservative bromide tracer were introduced into a suboxic superficial aquifer, followed by groundwater collection from down-gradient multilevel samplers. Cells were enumerated in the field by microplate spectrofluorometry, with confirmatory analyses for selected samples done in the laboratory by epifluorescence microscopy, flow cytometry, and ferrographic capture. There was general agreement in the results from all of the vital-stain-based enumeration methods, with differences ranging from <10% up to 40% for the analysis of identical samples between different tracking methods. Field analysis by microplate spectrofluorometry was robust and efficient, allowing thousands of samples to be analyzed in quadruplicate for both of the injected strains. The near-real-time data acquisition allowed adjustments to the predetermined sampling schedule to be made. The microplate spectrofluorometry data sets for the July 2000 and July 2001 experiments allowed the transport of the injected cells to be related to the site hydrogeology and injection conditions and enabled the assessment of differences in the transport of the two strains. This near-real-time method should prove effective for a number of microbial ecology applications.