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Applied and Environmental Microbiology, March 2003, p. 1721-1727, Vol. 69, No. 3
0099-2240/03/$08.00+0 DOI: 10.1128/AEM.69.3.1721-1727.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Martina Hausner,2 and Stefan Wuertz1*
Department of Civil and Environmental Engineering, University of California, Davis, Davis, California 95616,1 Institute of Water Quality Control and Waste Management, Technical University of Munich, 85748 Garching, Germany2
Received 5 March 2002/ Accepted 22 August 2002
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However, for a system to be able to degrade xenobiotic compounds, the biocatalysts that are needed for degradation of a specific compound need to be present in the system (22). If reactors lack the desired biocatalysts, they need to be bioaugmented to obtain efficient degradation. By addition of exogenous optimally constructed bacteria (11, 43) or functionally adapted bacterial consortia (18) and communities (47), enrichment of the total gene pool can be obtained. Likewise, a reactor can be augmented by in situ gene transfer (42). It is surprising that in spite of several successes, few studies have evaluated bioaugmentation by horizontal gene transfer in activated sludge wastewater treatment reactors (33, 34, 50) or activated sludge microcosms (16, 36, 41). When plasmids carrying catabolic genes were integrated into indigenous bacterial organisms, increased and more rapid degradation of the target compound was observed (33, 34, 36). Likewise, there is little information available regarding bioaugmentation of biofilm reactors by in situ gene transfer by bacterial conjugation (1, 4, 12, 15, 53). Conjugation inside a biofilm matrix offers a great advantage in terms of both gene transfer frequency (1, 15, 19) and subsequent transconjugant stability (15). Still, the effect of in situ natural genetic transformation in order to obtain bioenhancement in activated sludge- or biofilm-based biological process engineering systems has not been studied.
To investigate the feasibility of bioaugmentation by genetic transformation, in situ natural genetic transformation was investigated with a model system consisting of biofilm-cultured Acinetobacter sp. strain BD413 (24) with the autonomously replicating gfp-carrying plasmid pGAR1 (19) as the transforming DNA. Acinetobacter species are ubiquitous, strictly aerobic, nonmotile organisms that can be isolated from soil, water, or wastewater (23). Acinetobacter strains can degrade recalcitrant aromatic and alicyclic compounds, as well as some aromatic amino acids, mineral oils, and synthetic polymers (3, 5, 7, 40). In addition, Acinetobacter strains produce biosurfactants, like emulsan (25, 45) and alasan (2), that enhance the bioavailability of poorly soluble compounds. Furthermore, Acinetobacter sp. strain BD413 (24) is amenable to gene manipulation by conjugation, transformation, and transduction (23), and this property makes the strain particularly interesting as a tool for biologically enhancing the catabolic properties of hazardous waste treatment facilities.
In this study the following conditions were investigated to determine their effects on natural genetic transformation in a model biofilm: biofilm age, free DNA concentration, and growth of the biofilm in the presence or absence of cells in the bulk fluid.
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Transformation in biofilms.
Transformation of biofilms was performed by the methods described by Wuertz et al. (54). Biofilms of Acinetobacter sp. strain BD413 were grown in a flow cell containing four separate flow channels (4 by 4 by 40 mm) for 3 days in rich Luria-Bertani medium by using a flow rate of 2.4 ml/h after DNA was added with minimal medium M9 (0.2% gluconate). Transformation involved incubation of DNA during 1 h of continuous flow with DNA-containing medium, unless indicated otherwise. After overnight incubation in minimal medium M9 (0.2% gluconate) without DNA at a flow rate of 2.4 ml/h, which allowed expression of the received gene, biofilms were prepared for microscopic monitoring.
Microscopic monitoring, image acquisition, and data processing.
Biofilm cells in Acinetobacter sp. strain BD413 monoculture biofilms undergoing transformation were visualized with the general nucleic acid stain Syto 60 (Molecular Probes, Eugene, Oreg.) and were detected with an LSM 410 CLSM (Zeiss, Jena, Germany). The 633-nm laser line and a 665-nm long-pass emission filter were used to detect cells stained with Syto 60. The 488-nm laser line and a 515-nm long-pass emission filter were used for detection of cells expressing gfp (Clontech). Automated image acquisition and data processing were performed by the methods described by Wuertz et al. (54).
Colocalization experiments.
Pure-culture BD413(pGAR1) biofilms grown for 46 h in selective minimal medium (minimal medium M9 containing 0.2% gluconate and 20 µg of tetracycline per ml) were stained with Syto 60 to test colocalization of the two signals. Approximately 18.5% of the signals in the BD413(pGAR1) biofilm were colocalized GFP and Syto 60 signals, 22.6% were single Syto 60 signals, and 58.9% were single GFP signals. Therefore, in transformation experiments the total cell volume was obtained by adding the Syto 60 signals and the GFP signals and subtracting the overlapping signals. GFP signals were considered transformants. Potential underestimation of the 22.6% GFP signals was not considered during calculation of the results because it was not possible to check whether cells still contained the introduced plasmid. When no DNA was added to the medium, no signals were detectable with CLSM settings for detection of GFP signals in two separate tests. In an additional test, signals were obtained by using the 515-nm long-pass emission filter, but no overlap was detectable with the Syto 60 settings. These false-positive signals might have been due to autofluorescent impurities in the inlet medium and could be clearly distinguished from fluorescence-expressing cells on the basis of form and size. Hence, to avoid overestimation of GFP due to autofluorescent impurities, images had to be checked manually to discard possible false-positive signals on the basis of form and size.
Mathematical parameters.
The mathematical equations describing volumes and transformation frequency are given below.
Calculation of the volume of transformants and the volume of recipients was based on the following equation:
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where VX,e is total volume of transformants or recipients (in cubic micrometers), Xi is the area covered by cells of interest at position i (in square micrometers), zi is the distance from the substratum at position i (in micrometers), i is the scanning position in the z direction starting at the biofilm substratum, and e is the last scanned position in a biofilm in the z direction.
The equation was adapted as follows with the trapezoidal rule to obtain a more correct approximation of the numerical integral as described by Kuehn et al. (28):
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The transformation frequency (TF) was the fraction of transformant volume per total cell volume: TF = VT,e/VR,e, where VT,e is the volume of transformants obtained with equation 2 (in cubic micrometers) and VR,e is the volume of recipients obtained with equation 2 (in cubic micrometers).
Below, transfer frequencies are expressed as the volume of transgenic cells per volume of recipient cells, unless indicated otherwise.
To obtain a reproducible estimate of the normalized distance from the substratum, we limited the total cell volume and biofilm thickness to contain 98% of the scanned biomass (VR,e) starting from the substratum towards the biofilm-bulk fluid interface within the biofilm volume investigated. The normalized distance from the substratum was calculated by dividing the distance from the biofilm attachment surface by the biofilm thickness: di = zi/zk for VR,k
VR,e x 0.98, where VR,k is the volume of recipients calculated with equation 2 limited to 98% of the total scanned biomass (in cubic micrometers), di is the normalized distance from the substratum at position i (in micrometers), zi is the distance from the substratum at position i (in micrometers), zk is the biofilm thickness or distance from the substratum at position k (in micrometers), and k is the position in a biofilm where VR,k reached 98% of VR,e.
Reproducibility of in situ natural genetic transformation in monoculture Acinetobacter sp. strain BD413 biofilms.
Biofilms should be observed noninvasively and with confidence that reliable and reproducible results will be obtained. Direct in situ detection of large areas is, therefore, desirable. A study to determine statistically representative areas of Pseudomonas fluorescens biofilms showed that a minimal area of 1 x 105 µm2 should be scanned to obtain reproducible results in biofilm investigations (27). In the present study a minimal area of 2.4 x 105 µm2 was scanned to monitor a biofilm volume of at least 1.2 x 107 µm3. The standard transformation frequencies with 0.2 µg of pGAR1/ml, derived from four separate experiments monitoring a minimum volume of 1.2 x 107 µm3, ranged from logarithmic values of -3.5 to -3.1, with a mean value of -3.3 and a standard deviation of 0.15. In contrast to the standard method in which planktonic cells are used (38), the in situ method in which CLSM was used provided reliable and reproducible results.
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View this table: [in a new window] |
TABLE 1. Transformation frequencies obtained for biofilms of different ages exposed to 0.2 µg of plasmid pGAR1 DNA/ml for different periods of timea
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FIG. 1. Microscopic images showing pGAR1 transformants in 3-day-old (A) and 1-day-old (B) Acinetobacter sp. strain BD413 biofilms. The black and white images show GFP signals (panels I) or Syto 60-stained cells (panels II). Superimposed single optical images (panels III) show gfp transformants (yellow, green) against a background of recipient Acinetobacter sp. strain BD413 biofilm cells (red). The edges of each image correspond to a length of 90 µm.
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The DNA concentration in the inlet medium ranged from 1 x 10-9 to 1.5 µg of pGAR1/ml. The transformation frequency increased as a function of DNA concentration within the range of DNA concentrations investigated (Fig. 2).
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FIG. 2. Transformation in monoculture strain BD413 biofilms with pGAR1 DNA at various concentrations in the inlet medium expressed as a semilog plot. The insert shows the same data points on a log-log scale.
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With low concentrations of pGAR1 in the feed, transformants were formed at the biofilm attachment surface. Exposure to increasing amounts of pGAR1 resulted in gradual accumulation of transformants at the bottom of the biofilm (Fig. 3), where the biofilm density was the greatest, and not in the middle or upper part of the biofilm. If it were true that the fraction of competent cells is homogeneously distributed inside a biofilm, most transformants would be found in the layers with the highest biofilm density and the transformation frequency would be equally high throughout the biofilm. However, this was observed only 5 of 10 times. Hence, other factors may have contributed to the distribution of frequencies detected.
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FIG. 3. Distribution profiles for the volume of gfp transformants as a function of the normalized distance from the substratum when organisms were exposed to 1 x 10-9 µg of DNA/ml (), 1 x 10-7 µg of DNA/ml ( ), 1 x 10-4 µg of DNA/ml ( ), 1 x 10-1 µg of DNA/ml ( ), and 1.5 µg of DNA/ml (*).
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Next, we investigated the effect of prestarvation on transformation of biofilm cells grown in the presence of cells in the bulk phase. Suspended cells were removed as described above by rinsing with 0.01 M MgSO4. The biofilm was then starved by feeding the flow cell either with a continuous supply of minimal medium M9 without a carbon source or with a salt solution (0.01 M MgSO4) for 24 h. Subsequent transformation was done with identical experimental transformation steps, as described above. Transformation was observed at low but measurable frequencies (9.1 x 10-5 and 1.9 x 10-5 for biofilms starved in the presence of minimal medium M9 and in the presence of the salt solution, respectively).
When biofilms that were grown with cells present in the inlet medium were rinsed with 0.01 M MgSO4 and subsequently fed with cell-free rich medium for 24 h before transformation, again no transformation was observed in the biofilms.
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The DNA concentration in the inlet was positively correlated with increasing transformation frequency. Natural genetic transformation occurred readily at high frequencies in monoculture Acinetobacter sp. strain BD413 biofilms. When 1.2 µg of pGAR1/ml was used, transformation frequencies as high as 2.4 x 10-3 were observed. Furthermore, it was possible to obtain detectable transformation frequencies with minute amounts (as little as 1 fg of pGAR1/ml) in biofilms. The lowest tested DNA concentration used for transformation of Acinetobacter sp. strain BD413 reported previously was approximately 1 ng of DNA/ml (38). Transfer frequencies even higher than those reported here may be obtainable if a feed with a DNA concentration greater than 10 µg of pGAR1/ml is added to a biofilm. For bioaugmentation via gene transfer, however, it is not necessary to have maximum transformation frequencies. Even if transfer frequencies are low, transformants may undergo cell division, and the transgenic strain could therefore still establish itself in a reactor system. In such a case, low but significant transfer frequencies should be enough to obtain successful bioaugmentation.
It was interesting that an increased DNA concentration in the influent resulted in accumulation of transformants in the biofilm substratum. However, it seems odd that most transformation events take place at the biofilm base. This observation implies that free DNA first has to diffuse through the biofilm before competent cells take up and subsequently replicate the integrated plasmid. It is possible that immobilization of cells was responsible for the occurrence of most transformation events at the bottom of the biofilm. The location of transformation events seemed to be simply a matter of chance, and the probability increased with increasing cell density at a certain distance from the substratum. In the case of monoculture Acinetobacter sp. strain BD413 biofilms the cell density was greatest near the biofilm attachment surface. Therefore, the chance for transformation was greater near the biofilm substratum. This suggests that the chances for transformation to occur are highest in a tightly packed biofilm (a biofilm with a low porosity value). However, it is not correct that porous biofilms are ill suited for transformation. Young biofilms, for example, are very porous (Fig. 1), and they allowed transformation at increased rates due to enhanced competency levels during exponential growth. Porosity plays an important role only in mature biofilms. Therefore, it is necessary to investigate the true impact of biofilm density and porosity on natural genetic transformation. If density played an important part in natural genetic transformation, anthropogenic manipulation of the factors that decrease biofilm porosity could lead to enhanced occurrence of transformation events. van Loosdrecht et al. (51) included flow rate, nutrient loading rate, and growth rate of the biofilm cells as parameters that influence biofilm thickness and porosity. In addition, cell-to-cell signaling molecules influence biofilm structure (10) and may indirectly influence transformation events.
Another important parameter in this study was the mode of growth in which the biofilm itself emerged. In many biofilm investigations scientists use batch-grown biofilms in 96-well microtiter plates (9, 39). In contrast to batch-grown biofilms, biofilms grown in flow chambers are in continuous contact with fresh medium that does not contain suspended cells. One needs to consider that biofilms grown in different modes could possess different qualities. In the present study, differences in the transformability of Acinetobacter sp. strain BD413 biofilm cells grown in the presence and in the absence of cells in the bulk fluid were observed. The presence of high numbers of cells in the surrounding medium inhibited transformation in biofilms (Hendrickx, results not shown). Likewise, when biofilms developed in the presence of high numbers of cells in the bulk fluid but were rinsed to eliminate cells present in the surrounding medium before they were exposed to naked DNA, transformation was strongly inhibited. Also, differences in the morphotypes of the bacterial cells were observed. Acinetobacter sp. displays two different morphotypes, the bacillar morphotype and the coccoid morphotype (21). In biofilms fed with cell-free medium, both the bacillar and coccoid forms were detected. In contrast, when biofilms were allowed to emerge in the presence of medium containing suspended bacterial cells, the cells exhibited almost exclusively the bacillar morphotype.
As determined by microscopy, batch-cultured stationary-phase Acinetobacter sp. strain BD413 cells also displayed the bacillar morphotype when the organism was grown in rich medium. Hence, it is possible that the lack of transformability in biofilms grown in the presence of cells in the bulk fluid is due to increased attachment of bacterial cells that have entered the stationary phase (and hence have become noncompetent) in the surrounding medium.
Biofilms grown in biofilm reactors may encounter many passing free-floating bacteria. This would discourage bioaugmentation by in situ transformation if the problem of inhibited gene transfer due to the presence of suspended cells during biofilm ontogenesis were unsolvable. Rinsing a biofilm to remove most cells present in the drifting fraction, followed by a starvation period, could reinduce in situ transformation when the cells are exposed to a nutrient-containing substrate with plasmid DNA. James and coworkers (21) discovered that upon starvation, bacillar cells revert to the coccoid form by reduction division, resulting in conservation of biomass but increased cell number. In this study the CLSM investigation revealed that the biofilms treated with starvation-inducing medium contained many cells with the coccoid morphotype, as observed when biofilms were grown in the absence of cells in the bulk fluid. Thus, all signs suggest that coccoid cells are the competent cells and bacillar cells are not competent for DNA uptake. Still, when cell shape was checked as a function of distance from the substratum, it was observed that cells at the biofilm substratum had the bacillar shape, while the prominent morphotype of cells at the biofilm-medium interface was coccoid (Hendrickx, data not shown). However, most transformants were formed at the biofilm substratum, where most bacillus-shaped cells resided. Further experiments are therefore needed to establish if other parameters related to the amount or location of bacillus-shaped or coccoid cells can be correlated with transformation frequency.
Nevertheless, the observed differences in transformation frequency in biofilms grown in the presence and in the absence of planktonic cells show that care should be taken in designing biofilm experiments. In addition to the effects of standard environmental parameters (temperature, pH, nutrient content, substratum, moisture content, biotic and abiotic stresses, flow rate, etc.), the results might differ considerably depending on whether the biofilms are grown under batch or continuous-flow conditions.
It should be noted that the experiments which we performed were not designed to prove the general feasibility of in situ biofilm cell transformation with any highly competent soil bacterium in naturally occurring biofilms. Our results do indicate that transformation has potential as a tool for bioaugmentation of biofilm reactors. It is interesting that transformation with Acinetobacter sp. strain BD413 resulted in transformation frequencies in nonsterile groundwater and wet soil microcosms that were as high as those obtained under sterile conditions (32). Likewise, transformation of Acinetobacter sp. strain BD413 biofilm cells embedded in river epilithon was not inhibited by the presence of indigenous organisms (52). It can be speculated that the presence of an ambient community in wastewater treatment systems should have few negative effects on transformation of Acinetobacter sp. strain BD413 cells. Future research should elucidate the efficiency of transforming cells which reside in natural biofilms inside bioreactors and other systems.
Present adress: Laboratory for Microbiology, Radioactive Waste and Cleanup, Belgian Nuclear Research Center, Mol, Belgium. ![]()
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