Impact of the microscale distribution of a Pseudomonas strain introduced into soil on potential contacts with indigenous bacteria

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

The Impact of the Antibiotic Fosfomycin on Wastewater Communities Measured by Flow Cytometry

Fosfomycin is a re-emergent antibiotic known to be effective against severe bacterial infections even when other antibiotics fail. To avoid overuse and thus the risk of new antibiotic resistance, the European Commission has recommended the intravenous use of fosfomycin only when other antibiotic treatments fail. A release of fosfomycin into the environment via wastewater from not only municipalities but also already from the producing pharmaceutical industry can seriously undermine a sustaining therapeutic value. We showed in long-term continuous-mode bioreactor cultivation and by using microbial community flow cytometry, microbial community ecology tools, and cell sorting that the micro-pollutant altered the bacterial wastewater community (WWC) composition within only a few generations. Under these conditions, fosfomycin was not readily degraded both at lower and higher concentrations. At the same time, operational reactor parameters and typical diversity parameters such as α- and intracommunity β-diversity did not point to system changes. Nevertheless, an intrinsic compositional change occurred, caused by a turnover process in which higher concentrations of fosfomycin selected for organisms known to frequently harbor antibiotic resistance genes. A gfp-labeled Pseudomonas putida strain, used as the model organism and a possible future chassis for fosfomycin degradation pathways, was augmented and outcompeted in all tested situations. The results suggest that WWCs, as complex communities, may tolerate fosfomycin for a time, but selection for cell types that may develop resistance is very likely. The approach presented allows very rapid assessment and visualization of the impact of antibiotics on natural or managed microbial communities in general and on individual members of these communities in particular.

Bioengineered Microbes for Soil Health Restoration - Present Status and Future

According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

Metal and metal(loids) removal efficiency using genetically engineered microbes: Applications and challenges

The environment is being polluted in different many with metal and metalloid pollution, mostly due to anthropogenic activity, which is directly affecting human and environmental health. Metals and metalloids are highly toxic at low concentrations and contribute primarily to the survival equilibrium of activities in the environment. However, because of non-degradable, they persist in nature and these metal and metalloids bioaccumulate in the food chain. Genetically engineered microorganisms (GEMs) mediated techniques for the removal of metals and metalloids are considered an environmentally safe and economically feasible strategy. Various forms of GEMs, including fungi, algae, and bacteria have been produced by recombinant DNA and RNA technologies, which have been used to eliminate metal and metalloids compounds from the polluted areas. Besides, GEMs have the potentiality to produce enzymes and other metabolites that are capable of tolerating metals stress and detoxify the pollutants. Thus, the aim of this review is to discuss the use of GEMs as advanced tools to produce metabolites, signaling molecules, proteins through genetic expression during metal and metalloids interaction, which help in the breakdown of persistent pollutants in the environment.

Effect of inoculation of Burkholderia sp. strain SJ98 on bacterial community dynamics and para-nitrophenol, 3-methyl-4-nitrophenol, and 2-chloro-4-nitrophenol degradation in soil

para-Nitrophenol (PNP), 3-methyl-4-nitrophenol (3M4NP), and 2-chloro-4-nitrophenol (2C4NP) are highly toxic compounds that have caused serious environmental issues. We inoculated an artificially contaminated soil with Burkholderia sp. strain SJ98, which has the ability to degrade PNP, 3M4NP, and 2C4NP, and quantified bioremediation. There was accelerated degradation of all nitrophenols in inoculated treatments compared to the un-inoculated treatments. The indigenous bacteria were able to degrade PNP, but not 3M4NP or 2C4NP. Real-time PCR targeting the catabolic gene pnpA showed that levels of strain SJ98 remained stable over the incubation period. High-throughput sequencing revealed that both contamination and bioaugmentation influenced the bacterial community structure. Bioaugmentation seemed to protect Kineosporia, Nitrososphaera, and Schlesneria from nitrophenol inhibition, as well as led to a sharp increase in the abundance of Nonomuraea, Kribbella, and Saccharopolyspora. There was a significant increase in the relative abundances of Thermasporomyces, Actinomadura, and Streptomyces in both contaminated and bioaugmented treatments; this indicated that these bacteria are likely directly related to nitrophenol degradation. To our knowledge, this is the first report of the simultaneous removal of PNP, 3M4NP, and 2C4NP using bioaugmentation. This study provides valuable insights into the bioremediation of soils contaminated with nitrophenols.

Mycelia as a focal point for horizontal gene transfer among soil bacteria

Horizontal gene transfer (HGT) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. The transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. HGT between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. Using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degree mycelial networks facilitate contact of and HGT between spatially separated bacteria. Our study shows that the network structures of mycelia promote bacterial HGT by providing continuous liquid films in which bacterial migration and contacts are favoured. This finding was confirmed by individual-based simulations, revealing that the tendency of migrating bacteria to concentrate in the liquid film around hyphae is a key factor for improved HGT along mycelial networks. Given their ubiquity, we propose that hyphae can act as focal point for HGT and genetic adaptation in soil.

Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner

The environmental stimulants and inhibitors of conjugal plasmid transfer in microbial communities are poorly understood. Specifically, it is not known whether exposure to stressors may cause a community to alter its plasmid uptake ability. We assessed whether metals (Cu, Cd, Ni, Zn) and one metalloid (As), at concentrations causing partial growth inhibition, modulate community permissiveness (that is, uptake ability) against a broad-host-range IncP-type plasmid (pKJK5). Cells were extracted from an agricultural soil as recipient community and a cultivation-minimal filter mating assay was conducted with an exogenous E. coli donor strain. The donor hosted a gfp-tagged pKJK5 derivative from which conjugation events could be microscopically quantified and transconjugants isolated and phylogenetically described at high resolution via FACS and 16S rRNA amplicon sequencing. Metal stress consistently decreased plasmid transfer frequencies to the community, while the transconjugal pool richness remained unaffected with OTUs belonging to 12 bacterial phyla. The taxonomic composition of the transconjugal pools was distinct from their respective recipient communities and clustered dependent on the stress type and dose. However, for certain OTUs, stress increased or decreased permissiveness by more than 1000-fold and this response was typically correlated across different metals and doses. The response to some stresses was, in addition, phylogenetically conserved. This is the first demonstration that community permissiveness is sensitive to metal(loid) stress in a manner that is both partially consistent across stressors and phylogenetically conserved.

Exploring the potential of novel biomixtures and Lentinula edodes fungus for the degradation of selected pesticides. Evaluation for use in biobed systems

An approach to reduce the contamination of water sources with pesticides is the use of biopurificaction systems. The active core of these systems is the biomixture. The composition of biomixtures depends on the availability of local agro-industrial wastes and design should be adapted to every region. In Portugal, cork processing is generally regarded as environmentally friendly and would be interesting to find applications for its industry residues. In this work the potential use of different substrates in biomixtures, as cork (CBX); cork and straw, coat pine and LECA (Light Expanded Clay Aggregates), was tested on the degradation of terbuthylazine, difenoconazole, diflufenican and pendimethalin pesticides. Bioaugmentation strategies using the white-rot fungus Lentinula edodes inoculated into the CBX, was also assessed. The results obtained from this study clearly demonstrated the relevance of using natural biosorbents as cork residues to increase the capacity of pesticide dissipation in biomixtures for establishing biobeds. Furthermore, higher degradation of all the pesticides was achieved by use of bioaugmented biomixtures. Indeed, the biomixtures inoculated with L. edodes EL1 were able to mineralize the selected xenobiotics, revelling that these white-rot fungi might be a suitable fungus for being used as inoculum sources in on-farm sustainable biopurification system, in order to increase its degradation efficiency. After 120 days, maximum degradation of terbuthylazine, difenoconazole, diflufenican and pendimethalin, of bioaugmented CBX, was 89.9%, 75.0%, 65.0% and 99.4%, respectively.. The dominant metabolic route of terbuthylazine in biomixtures inoculated with L. edodes EL1 proceeded mainly via hydroxylation, towards production of terbuthylazine-hydroxy-2 metabolite. Finally, sorption process to cork by pesticides proved to be a reversible process, working cork as a mitigating factor reducing the toxicity to microorganisms in the biomixture, especially in the early stages.

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.

Novel assay to measure the plasmid mobilizing potential of mixed microbial communities

Mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. Instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. While community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. Here, we present a novel framework and experimental method to estimate the mobilization potential of mixed communities. We compare the transfer frequency of a mobilizable plasmid to that of a mobilizing and conjugal plasmid measured for a model strain and for the assayed community. With Pseudomonas putida carrying the gfp-tagged mobilizable IncQ plasmid RSF1010 as donor strain, we conducted solid surface mating experiments with either a P. putida strain carrying the mobilizing IncP-1α plasmid RP4 or a model bacterial community that was extracted from the inner walls of a domestic shower conduit. Additionally, we estimated the permissiveness of the same community for RP4 using P. putida as donor strain. The permissiveness of the model community for RP4 [at 1.16 × 10^-4 transconjugants per recipient (T/R)] was similar to that previously measured for soil microbial communities. RSF1010 was mobilized by the model community at a frequency of 1.16 × 10^-5 T/R, only one order of magnitude lower than its permissiveness to RP4. This mobilization frequency is unexpectedly high considering that (i) mobilization requires the presence of mobilizing conjugal plasmids within the permissive fraction of the recipients; (ii) in pure culture experiments with P. putida retromobilization of RSF1010 through RP4 only took place in approximately half of the donors receiving the conjugal plasmid in the first step. Further work is needed to establish how plasmid mobilization potential varies within and across microbial communities. This method has the potential to provide such insights; in addition it allows for the direct isolation of in situ mobilizing plasmids together with their endogenous hosts.

Fine scale spatial variability of microbial pesticide degradation in soil: scales, controlling factors, and implications

Pesticide biodegradation is a soil microbial function of critical importance for modern agriculture and its environmental impact. While it was once assumed that this activity was homogeneously distributed at the field scale, mounting evidence indicates that this is rarely the case. Here, we critically examine the literature on spatial variability of pesticide biodegradation in agricultural soil. We discuss the motivations, methods, and main findings of the primary literature. We found significant diversity in the approaches used to describe and quantify spatial heterogeneity, which complicates inter-studies comparisons. However, it is clear that the presence and activity of pesticide degraders is often highly spatially variable with coefficients of variation often exceeding 50% and frequently displays non-random spatial patterns. A few controlling factors have tentatively been identified across pesticide classes: they include some soil characteristics (pH) and some agricultural management practices (pesticide application, tillage), while other potential controlling factors have more conflicting effects depending on the site or the pesticide. Evidence demonstrating the importance of spatial heterogeneity on the fate of pesticides in soil has been difficult to obtain but modeling and experimental systems that do not include soil's full complexity reveal that this heterogeneity must be considered to improve prediction of pesticide biodegradation rates or of leaching risks. Overall, studying the spatial heterogeneity of pesticide biodegradation is a relatively new field at the interface of agronomy, microbial ecology, and geosciences and a wealth of novel data is being collected from these different disciplinary perspectives. We make suggestions on possible avenues to take full advantage of these investigations for a better understanding and prediction of the fate of pesticides in soil.

Bioaugmentation with a consortium of bacterial nitrophenol-degraders for remediation of soil contaminated with three nitrophenol isomers

A consortium consisting of para-nitrophenol utilizer Pseudomonas sp. strain WBC-3, meta-nitrophenol utilizer Cupriavidus necator JMP134 and ortho-nitrophenol utilizer Alcaligenes sp. strain NyZ215 was inoculated into soil contaminated with three nitrophenol isomers for bioaugmentation. Accelerated removal of all nitrophenols was achieved in inoculated soils compared to un-inoculated soils, with complete removal of nitrophenols in inoculated soils occurring between 2 and 16 days. Real-time polymerase chain reaction (PCR) targeting nitrophenol-degradation functional genes indicated that the three strains survived and were stable over the course of the incubation period. The abundance of total indigenous bacteria (measured by 16S rRNA gene real-time PCR) was slightly negatively impacted by the nitrophenol contamination. Denaturing gradient gel electrophoresis profiles of total and group-specific indigenous community suggested a dynamic change in species richness occurred during the bioaugmentation process. Furthermore, Pareto-Lorenz curves and Community organization parameters indicated that the bioaugmentation process had little impact on species evenness within the microbial community.

Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat

Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.

Plasmid-mediated bioaugmentation for the degradation of chlorpyrifos in soil

To overcome the poor survival and low activity of the bacteria used for bioremediation, a plasmid-mediated bioaugmentation method was investigated, which could result in a persistent capacity for the degradation of chlorpyrifos in soil. The results indicate that the pDOC plasmid could transfer into soil bacteria, including members of the Pseudomonas and Staphylococcus genera. The soil bacteria acquired the ability to degrade chlorpyrifos within 5 days of the transfer of pDOC. The efficiency of the pDOC transfer in the soil, as measured by the chlorpyrifos degradation efficiency and the most probable number (MPN) of chlorpyrifos degraders, was influenced by the soil temperature, moisture level and type. The best performance for the transfer of pDOC was observed under conditions of 30°C and 60% water-holding capacity (WHC). The results presented in this paper show that the transfer of pDOC can enhance the degradation of chlorpyrifos in various soils, although the degradation efficiency did vary with the soil type. It may be concluded that the introduction of plasmids encoding enzymes that can degrade xenobiotics or donor strains harboring these plasmids is an alternative approach in bioaugmentation.

Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere

Benzoxazinoids, such as 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), are secondary metabolites in grasses. In addition to their function in plant defence against pests and diseases above-ground, benzoxazinoids (BXs) have also been implicated in defence below-ground, where they can exert allelochemical or antimicrobial activities. We have studied the impact of BXs on the interaction between maize and Pseudomonas putida KT2440, a competitive coloniser of the maize rhizosphere with plant-beneficial traits. Chromatographic analyses revealed that DIMBOA is the main BX compound in root exudates of maize. In vitro analysis of DIMBOA stability indicated that KT2440 tolerance of DIMBOA is based on metabolism-dependent breakdown of this BX compound. Transcriptome analysis of DIMBOA-exposed P. putida identified increased transcription of genes controlling benzoate catabolism and chemotaxis. Chemotaxis assays confirmed motility of P. putida towards DIMBOA. Moreover, colonisation essays in soil with Green Fluorescent Protein (GFP)-expressing P. putida showed that DIMBOA-producing roots of wild-type maize attract significantly higher numbers of P. putida cells than roots of the DIMBOA-deficient bx1 mutant. Our results demonstrate a central role for DIMBOA as a below-ground semiochemical for recruitment of plant-beneficial rhizobacteria during the relatively young and vulnerable growth stages of maize.

Dynamics of augmented soil system containing biphenyl with Dyellaginsengisoli LA-4

One high efficient biphenyl-degrading strain Dyella ginsengisoli LA-4 was inoculated into biphenyl-contaminated soil for bioaugmentation in this study. The results showed that bioaugmentation could accelerate the startup period of the biphenyl bioremediation process compared with the non-augmented one. PCR-DGGE fingerprints demonstrated that both of the diversity and pattern of microbial community were affected by the addition of strain LA-4 and biphenyl. Biphenyl-utilizing populations gradually increased and become the dominant species. The introduced strain LA-4 could be persistent and co-exist well with the indigenous populations. However, both of the strain LA-4 and indigenous microorganisms in the bioaugmented system would be partially inhibited by Zn(2+) and Ni(2+). This study suggests that it is feasible and potentially useful to remediate biphenyl-contaminated soil using bioaugmentation with D. ginsengisoli LA-4.

Biodegradation in a partially saturated sand matrix: compounding effects of water content, bacterial spatial distribution, and motility

Bacterial pesticide degraders are generally heterogeneously distributed in soils, leaving soil volumes devoid of degradation potential. This is expected to have an impact on degradation rates because the degradation of pollutant molecules in such zones will be contingent either on degraders colonizing these zones or on pollutant mass transfer to neighboring zones containing degraders. In a model system, we quantified the role exerted by water on mineralization rate in the context of a heterogeneously distributed degradation potential. Alginate beads colonized by Pseudomonas putida KT2440 were inserted at prescribed locations in sand microcosms so that the initial spatial distribution of the mineralization potential was controlled. The mineralization rate was strongly affected by the matric potential (decreasing rate with decreasing matric potential) and by the initial distribution of the degraders (more aggregated distributions being associated with lower rates). The mineralization was diffusion-limited, as confirmed with a mathematical model. In wet conditions, extensive cell dispersal was observed for the flagellated wild type and, albeit to a lesser extent, for a nonflagellated mutant, partially relieving the diffusion limitation. Dry conditions, however, sustained low mineralization rates through the combined effects of low pollutant diffusivity and limited degrader dispersal.

In situ bioremediation of organochlorine-pesticide-contaminated microcosm soil and evaluation by gene probe

BACKGROUND

Pesticide-formulating industries are contaminating the environment through various activities. Bioremediation is the best method for decontamination, as chemical and physical methods are not only costly but also not very effective in open field systems. In the present study, in situ bioremediation of organochlorine-contaminated soil was demonstrated by combined biostimulation and bioaugmentation strategies, followed by evaluation using a molecular method.

RESULTS

Three parameters were monitored: microbial biomass (colony-forming units (CFU) g(-1) soil), residual pesticides after treatment and catabolic genes from microcosm soil. Both the biostimulation and the bioaugmentation treatments showed an initial lag phase of 80 days towards colony-forming units. Gas chromatography of soil samples showed that concentrations of residual pesticides in the soil declined by up to 85-90% after 80 days, indicating their utilisation with time. On dot-blot hybridisation of the total DNA from the same soil samples, it was observed that catabolic genes tfdC (catechol 1,2-dioxygenase) and cm genes (chlorophenol monoxygenase) were predominant, whereas other catabolic genes such as catechol 2,3-dioxygenase (xylE) were negligible.

CONCLUSION

The strategy of in situ bioremediation and its evaluation by gene probe and also by conventional methods was demonstrated for organochlorine-pesticide-contaminated soil in open microcosms. It showed that bioaugmentation along with biostimulation was effective, although initial acclimatization for a period of almost 2-3 months was required in the open field systems.

Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73

The strain Pseudomonas putida ZWL73, which metabolizes 4-chloronitrobenzene (4CNB) by a partial-reductive pathway, was inoculated into lab-scale 4CNB-contaminated soil for bioaugmentation purposes in this study. The degradation of 4CNB was clearly stimulated, as indicated with the gradual accumulation of ammonium and chloride. Simultaneously, the diversity and quantity of cultivable heterotrophic bacteria decreased due to 4CNB contamination, while the quantity of 4CNB-resistant bacteria increased. During the bioaugmentation, denaturing gradient gel electrophoresis analysis showed the changes of diversity in dominant populations of intrinsic soil microbiota. The results showed that Alphaproteobacteria and Betaproteobacteria were not distinctly affected, but Actinobacteria were apparently stimulated. In addition, an interesting dynamic within Acidobacteria was observed, as well as an influence on ammonia-oxidizing bacteria population. These combined findings demonstrate that the removal of 4CNB in soils by inoculating strain ZWL73 is feasible, and that specific populations in soils rapidly changed in response to 4CNB contamination and subsequent bioaugmentation.

Flavobacterial community structure in a hardwater rivulet and adjacent forest soil, Harz Mountain, Germany

The great increase in the abundance and phylogenetic diversity of Flavobacterium spp. within a few hundred meters downstream of the discharge site of the Westerhöfer Bach, a hardwater rivulet, raised the question whether adjacent soil may serve as a reservoir of bacteria not detected in discharge water. To address this question, denaturing gradient gel electrophoresis (DGGE) analyses of the V3 region of Flavobacterium 16S rRNA genes were performed on DNA from nine soil samples and five rivulet sites. The resulting patterns were tested for the significance of differences between the sampling habitats using the nonparametric analysis of similarities and multidimensional scaling procedures. Even though both habitats were sampled in two consecutive years DGGE patterns of soil and downstream water samples showed significant overlap (R = 0.614). Sequencing of 57 DGGE bands resulted in 30 different sequences, which, on the basis of BLAST analyses, were between 96% and 100% similar to published clone, DGGE, and strain sequences from a wide range of different habitats. Forty-five percent of the highly similar sequences included those of isolates from the Westerhöfer Bach, while the other sequences were more closely related to clones and cultures from other habitats, especially agricultural soil. Based on these results we suggest that the increase in flavobacterial strain diversity and abundance in the rivulet may originate from soil microflora.

Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants

This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.