Noninvasive quantitative measurement of bacterial growth in porous media under unsaturated-flow conditions

Quantifying bacterial concentration in water and sand media during flow-through experiments using a non-invasive, real-time, and efficient method

Monitoring the dynamics of bacteria in porous media is of great significance to understand the bacterial transport and the interplay between bacteria and environmental factors. In this study, we reported a non-invasive, real-time, and efficient method to quantify bioluminescent bacterial concentration in water and sand media during flow-through experiments. First, 27 column experiments were conducted, and the bacterial transport was monitored using a real-time bioluminescent imaging system. Next, we quantified the bacterial concentration in water and sand media using two methods-viable count and bioluminescent count. The principle of the bioluminescent count in sand media was, for a given bioluminescence image, the total number of bacteria was proportionally allocated to each segment according to its bioluminescence intensity. We then compared the bacterial concentration for the two methods and found a good linear correlation between the bioluminescent count and viable count. Finally, the effects of porous media surface coating, pore water velocity, and ionic strength on the bioluminescent count in sand media were investigated, and the results showed that the bioluminescence counting accuracy was most affected by surface coating, followed by ionic strength, and was hardly affected by pore water velocity. Overall, the study proved that the bioluminescent count was a reliable method to quantify bacterial concentration in water (10⁶ to 2 × 10⁸ cell mL^-1) or sand media (5 × 10⁶-5 × 10⁸ cell cm^-3). This approach also offers a new way of thinking for in situ bacterial enumeration in two-dimensional devices such as 2D flow cells, microfluidic devices, and rhizoboxes.

Quantitative 3D comparison of biofilm imaged by X-ray micro-tomography and two-photon laser scanning microscopy

Optical imaging techniques for biofilm observation, like laser scanning microscopy, are not applicable when investigating biofilm formation in opaque porous media. X-ray micro-tomography (X-ray CMT) might be an alternative but it finds limitations in similarity of X-ray absorption coefficients for the biofilm and aqueous phases. To overcome this difficulty, barium sulphate was used in Davit et al. (2011) to enable high-resolution 3D imaging of biofilm via X-ray CMT. However, this approach lacks comparison with well-established imaging methods, which are known to capture the fine structures of biofilms, as well as uncertainty quantification. Here, we compare two-photon laser scanning microscopy (TPLSM) images of Pseudomonas Aeruginosa biofilm grown in glass capillaries against X-ray CMT using an improved protocol where barium sulphate is combined with low-gelling temperature agarose to avoid sedimentation. Calibrated phantoms consisting of mono-dispersed fluorescent and X-ray absorbent beads were used to evaluate the uncertainty associated with our protocol along with three different segmentation techniques, namely hysteresis, watershed and region growing, to determine the bias relative to image binarization. Metrics such as volume, 3D surface area and thickness were measured and comparison of both imaging modalities shows that X-ray CMT of biofilm using our protocol yields an accuracy that is comparable and even better in certain respects than TPLSM, even in a nonporous system that is largely favourable to TPLSM.

Visualisation study on Pseudomonas migulae AN-1 transport in saturated porous media

Influence of granular size and groundwater flow rate on transport of Pseudomonas migulae AN-1 in saturated porous media was non-invasively and visually investigated with a novel imaging technique based on our previously established green fluorescent protein-tagging approach. AN-1 was transported faster than water was. The finer the media were, the greater the enhancement of bacterial velocity was. Mass recovery (MR) increased, while deposition rate coefficient (K_c) decreased, with increasing granular size. Similar and linear trends of MR and K_c, respectively, were quantitatively observed with increasing water flow rate. The images revealed that the initial shape of bacterial plume after injection was a narrow strip along the injection well and an ellipsoid in the lower part of the injection well in medium and coarse sand, respectively. Bacterial plume migrated horizontally in medium sand, but shifted slightly downward in coarse sand. Under similar conditions, the fluorescent area carrying AN-1 in medium sand was larger than that carrying AN-1 in coarse sand during the same period. The visualisation method of this study captured both the movement of free-state and retained bacteria that adhered to sediments. A continuous biological zone composed of planktonic and retained AN-1 was observed. These findings are significant for actual bioremediation.

Pseudomonas fluorescens HK44: lessons learned from a model whole-cell bioreporter with a broad application history

Initially described in 1990, Pseudomonas fluorescens HK44 served as the first whole-cell bioreporter genetically endowed with a bioluminescent (luxCDABE) phenotype directly linked to a catabolic (naphthalene degradative) pathway. HK44 was the first genetically engineered microorganism to be released in the field to monitor bioremediation potential. Subsequent to that release, strain HK44 had been introduced into other solids (soils, sands), liquid (water, wastewater), and volatile environments. In these matrices, it has functioned as one of the best characterized chemically-responsive environmental bioreporters and as a model organism for understanding bacterial colonization and transport, cell immobilization strategies, and the kinetics of cellular bioluminescent emission. This review summarizes the characteristics of P. fluorescens HK44 and the extensive range of its applications with special focus on the monitoring of bioremediation processes and biosensing of environmental pollution.

Draft genome sequence of the polycyclic aromatic hydrocarbon-degrading, genetically engineered bioluminescent bioreporter Pseudomonas fluorescens HK44

Pseudomonas fluorescens strain HK44 (DSM 6700) is a genetically engineered lux-based bioluminescent bioreporter. Here we report the draft genome sequence of strain HK44. Annotation of ∼6.1 Mb of sequence indicates that 30% of the traits are unique and distributed over five genomic islands, a prophage, and two plasmids.

Noninvasive quantitative measurement of colloid transport in mesoscale porous media using time lapse fluorescence imaging

We demonstrate noninvasive quantitative imaging of colloid and solute transport at millimeter to decimeter (meso-) scale. Ultraviolet (UV) excited fluorescent solute and colloid tracers were independently measured simultaneously during co-advection through saturated quartz sand. Pulse-input experiments were conducted at constant flow rates and ionic strengths 10(-3), 10(-2) and 10(-1) M NaCl. Tracers were 1.9 microm carboxylate latex microspheres and disodium fluorescein. Spatial moments analysis was used to quantify relative changes in mass distribution of the colloid and solute tracers over time. The solute advected through the sand at a constant velocity proportional to flow rate and was described well by a conservative transport model (CXTFIT). In unfavorable deposition conditions increasing ionic strength produced significant reduction in colloid center of mass transport velocity over time. Velocity trends correlated with the increasing fraction of colloid mass retained along the flowpath. Attachment efficiencies (defined by colloid filtration theory) calculated from nondestructive retained mass data were 0.013 +/- 0.03, 0.09 +/- 0.02, and 0.22 +/- 0.05 at 10(-3), 10(-2), and 10(-1) M ionic strength, respectively, which compared well with previously published data from breakthrough curves and destructive sampling. Mesoscale imaging of colloid mass dynamics can quantify key deposition and transport parameters based on noninvasive, nondestructive, spatially high-resolution data.

Real-time, in situ monitoring of bioactive zone dynamics in heterogeneous systems

Successful implementation of in situ bioremediation is contingent upon understanding how physicochemical and microbial factors affect the formation and dynamics of microbially active regions known as bioactive zones (BAZs). This study demonstrates how a novel fiber optic detection system can be used to test hypotheses concerning real-time, in situ BAZ formation and dynamics. This study focuses on naphthalene transport in saturated porous media containing defined physicochemical and microbial heterogeneities. Biological activity was measured using a lux reporter bacterium, Pseudomonas putida RB1353, that bioluminesces during naphthalene catabolism. Results show that the presence of defined heterogeneities drives the development of BAZs at material-property interfaces where the confluence of naphthalene, dissolved oxygen, and sufficient microbial density is optimal. Thus, despite successful transport of P. putida RB1353 into a sterile low-permeability region containing substrate, BAZ formation in this region was limited by local physicochemical conditions (e.g., naphthalene and dissolved oxygen bioavailability). In another instance, transport of P. putida RB1353 occurred against advective flow, resulting in BAZ formation upgradient of inoculated regions. Defined systems such as this can be used as a basis for predicting localization of activity in complex subsurface systems.

Illuminating reactive microbial transport in saturated porous media: demonstration of a visualization method and conceptual transport model

We demonstrate a method to study reactive microbial transport in saturated translucent porous media using the bacteria Pseudomonas fluorescens 5RL genetically engineered to carry a plasmid with bioluminescence genes inducible by salicylate. Induced bacteria were injected into a cryolite grain filled chamber saturated with a sterile non-growth-promoting (phosphorus limited) chemical mixture containing salicylate as an aromatic hydrocarbon analogue. The amount of light produced by the bacteria serves as an estimator of the relative efficiency of aerobic biodegradation since bioluminescence is dependent on both salicylate and oxygen but only consumes oxygen. Bioluminescence was captured with a digital camera and analyzed to study the evolving spatial pattern of the bulk oxygen consuming reactions. As fluid flow transported the bacteria through the chamber, bioluminescence was observed to initially increase until an oxygen depletion zone developed behind the advective front. Bacterial transport was modeled with the advection dispersion equation and oxygen concentration was modeled assuming bacterial consumption via Monod kinetics with consideration of additional effects of rate-limited mass transfer from residual gas bubbles. Consistent with previous measurements, bioluminescence was considered proportional to oxygen consumed. Using the observed bioluminescence, model parameters were fit that were consistent with literature values and produced results in good agreement with the experimental data. These findings demonstrate potential for using this method to investigate the complex spatial and temporal dynamics of reactive microbial transport in saturated porous media.

Marker and reporter genes: illuminating tools for environmental microbiologists

Fluorescent and luminescent marker and reporter genes provide easily detectable phenotypes to microbial cells and are therefore valuable tools for the study of microorganisms in the environment. Although these tools are becoming widely adopted, there are still issues that remain to be solved, such as the dependence of the reporter output on the physiological status of the cell. Eventually it might be the use of marker and reporter genes themselves that will contribute towards better understanding of the physiological status of specific microbial populations in nature.