Rhizosphere competitiveness of trichloroethylene-degrading, poplar-colonizing recombinant bacteria

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Agronomic Approaches for Characterization, Remediation, and Monitoring of Contaminated Sites

With a view to conserving or improving soil ecosystem services, environment-friendly techniques, such as bio- and phytoremediation, can effectively be used for the characterization, risk assessment, and remediation of contaminated agricultural sites. Polyannual vegetation (meadows, poplar, and cane stands) is widely considered the most efficient tool for remediation (extraction of bioavailable fraction of contaminants), for undertaking safety measures (reducing the mobility of contaminants towards other environmental compartments), and for restoring the ecosystem services of contaminated agricultural sites (biomass production, groundwater protection, C storage, landscape quality improvement, and cultural and educational services). The roles of agronomic approaches will be reviewed by focusing on the various steps in the whole remediation process: (i) detailed environmental characterization; (ii) phytoremediation for reducing risks for the environment and human health; (iii) agronomic management for improving efficiency of phytoremediation; and (iv) biomass recycling in the win-win perspective of the circular economy.

Surfactant enhanced pyrene degradation in the rhizosphere of tall fescue (Festuca arundinacea)

The present study was conducted to evaluate the effect of two non ionic surfactants (Tween 80 and Triton X-100), a biosurfactant (Lecithin), and randomly methylated-β-cyclodextrins (RAMEB) on the remediation of pyrene from soil planted with tall fescue (Festuca arundinacea). Soils with pyrene concentration of about 243 mg kg(-1) was grown with tall fescue and were individually amended with 0, 200, 600, 1000, and 1500 mg kg(-1) of Tween 80, Triton X-100, biosurfactant, and RAMEB. The results show that all surfactants significantly increased plant biomass compared to unamended soil. Dehydrogenase activity was also stimulated as a result of surfactant addition. Only 3.9 and 3.2 % of pyrene was decreased in the uncovered and covered abiotic sterile control, suggesting that microbial degradation was the main removal mechanism of pyrene from soil. In the planted treatment receiving no surfactant, the remediation of pyrene was 45 % which is significantly higher than that of corresponding unplanted control soil, suggesting that the cultivation of tall fescue alone could enhance the overall remediation of pyrene in soil. All surfactants had significantly higher rates of pyrene remediation compared to the unamended planted soil. Generally, RAMEB displayed the highest remediation rates, i.e., 64.4-79.1 % followed by the Triton X-100, i.e., 60.1-74.8 %. The positive impact of surfactants on pyrene remediation could possibly be because of their capacities to increase its bioavailability in soil. The evidence from this study suggests that the addition of surfactants could enhance phytoremediation of PAHs polluted soil.

Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif

Deletion of Gly-720 and Tyr-721 from a highly conserved GYxxØ trafficking signal in the SIVmac239 envelope glycoprotein cytoplasmic domain, producing a virus termed ΔGY, leads to a striking perturbation in pathogenesis in rhesus macaques (Macaca mulatta). Infected macaques develop immune activation and progress to AIDS, but with only limited and transient infection of intestinal CD4(+) T cells and an absence of microbial translocation. Here we evaluated ΔGY in pig-tailed macaques (Macaca nemestrina), a species in which SIVmac239 infection typically leads to increased immune activation and more rapid progression to AIDS than in rhesus macaques. In pig-tailed macaques, ΔGY also replicated acutely to high peak plasma RNA levels identical to those for SIVmac239 and caused only transient infection of CD4(+) T cells in the gut lamina propria and no microbial translocation. However, in marked contrast to rhesus macaques, 19 of 21 pig-tailed macaques controlled ΔGY replication with plasma viral loads of <15 to 50 RNA copies/ml. CD4(+) T cells were preserved in blood and gut for up to 100 weeks with no immune activation or disease progression. Robust antiviral CD4(+) T cell responses were seen, particularly in the gut. Anti-CD8 antibody depletion demonstrated CD8(+) cellular control of viral replication. Two pig-tailed macaques progressed to disease with persisting viremia and possible compensatory mutations in the cytoplasmic tail. These studies demonstrate a marked perturbation in pathogenesis caused by ΔGY's ablation of the GYxxØ trafficking motif and reveal, paradoxically, that viral control is enhanced in a macaque species typically predisposed to more pathogenic manifestations of simian immunodeficiency virus (SIV) infection.

IMPORTANCE

The pathogenesis of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) reflects a balance between viral replication, host innate and adaptive antiviral immune responses, and sustained immune activation that in humans and Asian macaques is associated with persistent viremia, immune escape, and AIDS. Among nonhuman primates, pig-tailed macaques following SIV infection are predisposed to more rapid disease progression than are rhesus macaques. Here, we show that disruption of a conserved tyrosine-based cellular trafficking motif in the viral transmembrane envelope glycoprotein cytoplasmic tail leads in pig-tailed macaques to a unique phenotype in which high levels of acute viral replication are followed by elite control, robust cellular responses in mucosal tissues, and no disease. Paradoxically, control of this virus in rhesus macaques is only partial, and progression to AIDS occurs. This novel model should provide a powerful tool to help identify host-specific determinants for viral control with potential relevance for vaccine development.

Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

The remediation of polluted sites has become a priority for society because of increase in quality of life standards and the awareness of environmental issues. Over the past few decades there has been avid interest in developing in situ strategies for remediation of environmental contaminants, because of the high economic cost of physicochemical strategies, the biological tools for remediation of these persistent pollutants is the better option. Major foci have been considered on persistent organic chemicals i.e. polyaromatic hydrocarbons (PAHs) due to their ubiquitous occurrence, recalcitrance, bioaccumulation potential and carcinogenic activity. Rhizoremediation, a specific type of phytoremediation that involves both plants and their associated rhizospheric microbes is the creative biotechnological approach that has been explored in this review. Moreover, in this review we showed the significance of rhizoremediation of PAHs from other bioremediation strategies i.e. natural attenuation, bioaugmentation and phytoremediation and also analyze certain environmental factor that may influence the rhizoremediation technique. Numerous bacterial species were reported to degrade variety of PAHs and most of them are isolated from contaminated soil, however few reports are available from non contaminated soil. Pseudomonas aeruginosa , Pseudomons fluoresens , Mycobacterium spp., Haemophilus spp., Rhodococcus spp., Paenibacillus spp. are some of the commonly studied PAH-degrading bacteria. Finally, exploring the molecular communication between plants and microbes, and exploiting this communication to achieve better results in the elimination of contaminants, is a fascinating area of research for future perspective.

Engineering the soil bacterium Pseudomonas putida for arsenic methylation

Accumulation of arsenic has potential health risks through consumption of food. Here, we inserted the arsenite [As(III)] S-adenosylmethionine methyltransferase (ArsM) gene into the chromosome of Pseudomonas putida KT2440. Recombinant bacteria methylate inorganic arsenic into less toxic organoarsenicals. This has the potential for bioremediation of environmental arsenic and reducing arsenic contamination in food.

Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils

Plant-bacteria partnerships have been extensively studied and applied to improve crop yield. In addition to their application in agriculture, a promising field to exploit plant-bacteria partnerships is the remediation of soil and water polluted with hydrocarbons. Application of effective plant-bacteria partnerships for the remediation of hydrocarbons depend mainly on the presence and metabolic activities of plant associated rhizo- and endophytic bacteria possessing specific genes required for the degradation of hydrocarbon pollutants. Plants and their associated bacteria interact with each other whereby plant supplies the bacteria with a special carbon source that stimulates the bacteria to degrade organic contaminants in the soil. In return, plant associated-bacteria can support their host plant to overcome contaminated-induced stress responses, and improve plant growth and development. In addition, plants further get benefits from their associated-bacteria possessing hydrocarbon-degradation potential, leading to enhanced hydrocarbon mineralization and lowering of both phytotoxicity and evapotranspiration of volatile hydrocarbons. A better understanding of plant-bacteria partnerships could be exploited to enhance the remediation of hydrocarbon contaminated soils in conjunction with sustainable production of non-food crops for biomass and biofuel production.

Pseudomonas aeruginosa PAO1 virulence factors and poplar tree response in the rhizosphere

Whole-transcriptome analysis was used here for the first time in the rhizosphere to discern the genes involved in the pathogenic response of Pseudomonas aeruginosa PAO1 as well as to discern the response of the poplar tree. Differential gene expression shows that 185 genes of the bacterium and 753 genes of the poplar tree were induced in the rhizosphere. Using the P. aeruginosa transcriptome analysis, isogenic knockout mutants, and two novel plant assays (poplar and barley), seven novel PAO1 virulence genes were identified (PA1385, PA2146, PA2462, PA2463, PA2663, PA4150 and PA4295). The uncharacterized putative haemolysin repressor, PA2463, upon inactivation, resulted in greater poplar virulence and elevated haemolysis while this mutant remained competitive in the rhizosphere. In addition, disruption of the haemolysin gene itself (PA2462) reduced the haemolytic activity of P. aeruginosa, caused less cytotoxicity and reduced barley virulence, as expected. Inactivating PA1385, a putative glycosyl transferase, reduced both poplar and barley virulence. Furthermore, disrupting PA2663, a putative membrane protein, reduced biofilm formation by 20-fold. Inactivation of PA3476 (rhlI) increased virulence with barley as well as haemolytic activity and cytotoxicity, so quorum sensing is important in plant pathogenesis. Hence, this strategy is capable of elucidating virulence genes for an important pathogen.

Hydrocarbon degradation and plant colonization by selected bacterial strains isolated from Italian ryegrass and birdsfoot trefoil

AIMS

To assess the degradation potential and plant colonization capacity of four alkane-degrading strains (ITSI10, ITRI15, ITRH76 and BTRH79) in combination with birdsfoot trefoil and Italian ryegrass and to evaluate the diversity of indigenous alkane-degrading soil bacteria in the rhizo- and endosphere.

METHODS AND RESULTS

Contaminated soil was prepared by spiking agricultural soil with 10 g diesel fuel per kg soil. Italian ryegrass (Lolium multiflorum var. Taurus) and birdsfoot trefoil (Lotus corniculatus var. Leo) were inoculated with four alkane-degrading strains. Hydrocarbon degradation (up to 57%) was observed in all inoculated treatments of vegetated and unvegetated samples. Italian ryegrass in combination with compost and BTRH79 showed highest degradation, while birdsfoot trefoil performed best with compost and strain ITSI10. Cultivation-based as well as cultivation-independent analysis showed that both strains were competitive colonizers.

CONCLUSIONS

The combination between vegetation, inoculation with well-performing degrading bacteria and compost amendment was an efficient approach to reduce hydrocarbon contamination. Two Pantoea sp. strains, ITSI10 and BTRH79, established well in the plant environment despite the presence of a variety of other, indigenous alkane-degrading bacteria.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study suggests that the application of degrading bacterial strains, which are able to compete with the native microflora and to tightly associate with plants, are promising candidates to be used for phytoremediation applications.

Enhanced phytoremediation potential of polychlorinated biphenyl contaminated soil from e-waste recycling area in the presence of randomly methylated-beta-cyclodextrins

The crude recycling of electronic and electric waste (e-waste) is now creating soil pollution problems with organic compounds such as polychlorinated biphenyls (PCBs). The present study aimed to compare the phytoremediation potential of four plant species (rice, alfalfa, ryegrass and tall fescue) for PCBs contaminated soil from Taizhou city, one of the largest e-waste recycling centers in China. In addition, the enhanced effects of randomly methylated-beta-cyclodextrins (RAMEB) on PCBs phytoremediation potential were evaluated. Higher PCBs removal percentages of 25.6-28.5% in rhizosphere soil were observed after 120 days, compared with those of the non-rhizosphere (10.4-16.9%) and unplanted controls (7.3%). The average PCBs removal percentages of four plant species increased from 26.9% to 37.1% in the rhizosphere soil with addition of RAMEB. Meanwhile, relatively high microbial counts and dehydrogenase activity were detected in planted soils and a stimulatory effect by RAMEB addition was found. The present study indicated that all the plant candidates were feasible for phytoremediation of PCBs contaminated soil from the e-waste recycling area, and tall fescue with RAMEB amendment seemed as a promising remediation strategy. High PCBs removal percentage was due to the increased PCBs bioavailability as well as biostimulation of microbial communities after plantation and RAMEB addition.

Bacteria associated with oak and ash on a TCE-contaminated site: characterization of isolates with potential to avoid evapotranspiration of TCE

BACKGROUND, AIM, AND SCOPE

Along transects under a mixed woodland of English Oak (Quercus robur) and Common Ash (Fraxinus excelsior) growing on a trichloroethylene (TCE)-contaminated groundwater plume, sharp decreases in TCE concentrations were observed, while transects outside the planted area did not show this remarkable decrease. This suggested a possibly active role of the trees and their associated bacteria in the remediation process. Therefore, the cultivable bacterial communities associated with both tree species growing on this TCE-contaminated groundwater plume were investigated in order to assess the possibilities and practical aspects of using these common native tree species and their associated bacteria for phytoremediation. In this study, only the cultivable bacteria were characterized because the final aim was to isolate TCE-degrading, heavy metal resistant bacteria that might be used as traceable inocula to enhance bioremediation.

MATERIALS AND METHODS

Cultivable bacteria isolated from bulk soil, rhizosphere, root, stem, and leaf were genotypically characterized by amplified rDNA restriction analysis (ARDRA) of their 16S rRNA gene and identified by 16S rRNA gene sequencing. Bacteria that displayed distinct ARDRA patterns were screened for heavy metal resistance, as well as TCE tolerance and degradation, as preparation for possible future in situ inoculation experiments. Furthermore, in situ evapotranspiration measurements were performed to investigate if the degradation capacity of the associated bacteria is enough to prevent TCE evapotranspiration to the air.

RESULTS AND DISCUSSION

Between both tree species, the associated populations of cultivable bacteria clearly differed in composition. In English Oak, more species-specific, most likely obligate endophytes were found. The majority of the isolated bacteria showed increased tolerance to TCE, and TCE degradation capacity was observed in some of the strains. However, in situ evapotranspiration measurements revealed that a significant amount of TCE and its metabolites was evaporating through the leaves to the atmosphere.

CONCLUSIONS AND PERSPECTIVES

The characterization of the isolates obtained in this study shows that the bacterial community associated with Oak and Ash on a TCE-contaminated site, was strongly enriched with TCE-tolerant strains. However, this was not sufficient to degrade all TCE before it reaches the leaves. A possible strategy to overcome this evapotranspiration to the atmosphere is to enrich the plant-associated TCE-degrading bacteria by in situ inoculation with endophytic strains capable of degrading TCE.

Bacterial responses and interactions with plants during rhizoremediation

With the increase in quality of life standards and the awareness of environmental issues, the remediation of polluted sites has become a priority for society. Because of the high economic cost of physico-chemical strategies for remediation, the use of biological tools for cleaning-up contaminated sites is a very attractive option. Rhizoremediation, the use of rhizospheric microorganisms in the bioremediation of contaminants, is the biotechnological approach that we explore in this minireview. We focus our attention on bacterial interactions with the plant surface, responses towards root exudates, and how plants and microbes communicate. We analyse certain strategies that may improve rhizoremediation, including the utilization of endophytes, and finally we discuss several rhizoremediation strategies that have opened ways to improve biodegradation.

The neuroendocrine hormone norepinephrine increases Pseudomonas aeruginosa PA14 virulence through the las quorum-sensing pathway

It has been proposed that the gastrointestinal tract environment containing high levels of neuroendocrine hormones is important for gut-derived Pseudomonas aeruginosa infections. In this study, we report that the hormone norepinephrine increases P. aeruginosa PA14 growth, virulence factor production, invasion of HCT-8 epithelial cells, and swimming motility in a concentration-dependent manner. Transcriptome analysis of P. aeruginosa exposed to 500 microM, but not 50 microM, norepinephrine for 7 h showed that genes involved in the regulation of the virulence determinants pyocyanin, elastase, and the Pseudomonas quinolone signal (PQS, 2-heptyl-3-hydroxy-4-quinolone) were upregulated. The production of rhamnolipids, which are also important in P. aeruginosa infections, was not significantly altered in suspension cultures upon exposure to 500 microM norepinephrine but decreased on semisolid surfaces. Swarming motility, a phenotype that is directly influenced by rhamnolipids, was also decreased upon 500 microM norepinephrine exposure. The increase in the transcriptional activation of lasR but not that of rhlR and the increase in the levels of PQS suggest that the effects of norepinephrine are mediated primarily through the las quorum-sensing pathway. Together, our data strongly suggest that norepinephrine can play an important role in gut-derived infections by increasing the pathogenicity of P. aeruginosa PA14.

Effects of pig manure compost and nonionic-surfactant Tween 80 on phenanthrene and pyrene removal from soil vegetated with Agropyron elongatum

This paper evaluates the effects of pig manure compost (PMC) and Tween 80 on the removal of phenanthrene (PHE) and pyrene (PYR) from soil cultivated with Agropyron elongatum. Soils spiked with about 300 mg kg(-1) of PHE and PYR were individually amended with 0%, 2.5%, 5% and 7.5% (dry wt) of PMC or 0, 20 and 100 mg kg(-1) of Tween 80. Unplanted and sterile microcosms were prepared as the controls. PAH concentration, total organic matter (TOM), dissolved organic carbon (DOC), total heterotrophic and PAH degrading microbial populations in soil were quantified before and after 60d period. The results indicated that A. elongatum could significantly enhance PYR removal (from 46% to 61%) but had less impact on PHE removal (from 96% to 97%). Plant uptake of the PAHs was insignificant. Biodegradation was the key mechanism of PAH removals (<3% losses in the sterile control). Increase in PMC or Tween 80 levels increased the removal of PYR but not of PHE. Maximal PYR removal of 79% and 92% were observed in vegetated soil receiving 100 mg kg(-1) Tween 80 and 7.5% PMC, respectively. Enhanced PYR removal in soil receiving PMC could be explained by the elevated levels of DOC, TOM and microbial populations as suggested by Pearson correlation test. While the positive effect of Tween 80 on PYR removal could probably due to its capacities to enhance PYR bioavailability in soil. This paper suggests that the addition of either PMC or nonionic-surfactant Tween 80 could facilitate phytoremediation of PAH contaminated soil.

Enhancing phytoremediation through the use of transgenics and endophytes

In the last decade, there has been an increase in research on improving the ability of plants to remove environmental pollution. Genes from microbes, plants, and animals are being used successfully to enhance the ability of plants to tolerate, remove, and degrade pollutants. Through expression of specific bacterial genes in transgenic plants, the phytotoxic effects of nitroaromatic pollutants were overcome, resulting in increased removal of these chemicals. Overexpression of mammalian genes encoding cytochrome P450s led to increased metabolism and removal of a variety of organic pollutants and herbicides. Genes involved in the uptake or detoxification of metal pollutants were used to enhance phytoremediation of this important class of pollutants. Transgenic plants containing specific bacterial genes converted mercury and selenium to less toxic forms. In addition to these transgenic approaches, the use of microbes that live within plants, termed endophytes, also led to improved tolerance to normally phytotoxic chemicals and increased removal of the pollutants. Bacteria that degraded a herbicide imparted resistance to the herbicide when inoculated into plants. In another study, plants harboring bacteria capable of degrading toluene were more tolerant to normally phytotoxic concentrations of the chemical, and transpired less of it into the atmosphere. This review examines the recent advances in enhancing phytoremediation through transgenic plant research and through the use of symbiotic endophytic microorganisms within plant tissues.

Potassium and sodium transporters of Pseudomonas aeruginosa regulate virulence to barley

We investigated the role of three uncharacterized cation transporters of Pseudomonas aeruginosa PAO1 as virulence factors for barley: PA1207, PA5021, and PA2647. PAO1 displayed reduced barley virulence with inactivated PA1207, PA5021, and PA2647 as well as with one known Na(+)/H(+) antiporter, PA1820. Using the Escherichia coli LB2003 mutant lacking three K(+) uptake systems, the expression of the PA5021 gene repressed LB2003 growth with low K(+), but the strain acquired tolerance to high K(+). In contrast, the expression of the PA1207 gene enhanced growth of LB2003 with low K(+) but repressed its growth with high K(+); therefore, the PA5021 protein exports K(+), while the PA1207 protein imports K(+). The PA5021 mutant of P. aeruginosa also showed impaired growth at 400 mM KCl and at 400 mM NaCl; therefore, the PA5021 protein may also export Na(+). The loss of the PA5021 protein also decreased production of the virulence factor pyocyanin; corroborating this result, pyocyanin production decreased in wild-type PAO1 under high salinity. Whole-genome transcriptome analysis showed that PAO1 induced more genes in barley upon infection compared to the PA5021 mutant. Additionally, PAO1 infection induced water stress-related genes in barley, which suggests that barley may undergo water deficit upon infection by this pathogen.

Promotion of pyrene degradation in rhizosphere of alfalfa (Medicago sativa L.)

Pot experiment was conducted to evaluate the phytoremediation of pyrene-contaminated soil using alfalfa (Medicago sativa L.). Alfalfa biomasses, microbial viable counts, dehydrogenase activity, residual pyrene concentration and pyrene removal percentage were determined after 60 days of alfalfa growth. The results indicated that pyrene had an inhibitive effect on alfalfa growth, and higher pyrene concentration seriously affected alfalfa growth. In addition, the inhibitive effect on the root was more severe than that on the shoot. When pyrene concentration reached 492 mg kg(-1) in soil, the shoot and root biomasses were only 34% and 22% of those of alfalfa growing in non-spiked soil, respectively. The rhizospheric bacterial and fungi counts were 5.0-7.5 and 1.8-2.3 times higher than those in non-rhizosphere soil, respectively. The residual concentrations of pyrene in the rhizosphere soil were lower than those in the non-rhizosphere soil. After 60 days, 69-85% and 59-80% of spiked pyrene disappeared from the rhizosphere and non-rhizosphere soils, respectively. The removal percentage decreased with increasing pyrene concentration. However, the average removal of pyrene in the rhizosphere soil was 6% higher than that in the non-rhizosphere soil. Therefore, the presence of alfalfa roots was effective in promoting the phytoremediation of freshly added pyrene into the soil.

Engineering TCE-degrading rhizobacteria for heavy metal accumulation and enhanced TCE degradation

Many superfund sites are currently co-contaminated with organic pollutants such as trichloroethene (TCE) and heavy metals. A promising strategy to address these mixed-waste situations is the use of TCE-degrading rhizobacteria that will survive and thrive in soil heavily polluted with heavy metals. In this work, a gene coding for the metal-binding peptide, EC20, was introduced into rhizobacteria engineered for TCE degradation, resulting in strains with both metal accumulation and TCE degradation capabilities. EC20 was displayed onto the cell surface of Pseudomonas strain Pb2-1 and Rhizobium strain 10320D using an ice-nucleation protein (INP) anchor. Expression of EC20 was confirmed by Western blot analysis and cells with EC20 expression showed sixfold higher cadmium accumulation than non-engineered strains in the presence of 16 microM CdCl(2). As expected, the TCE degradation rate was reduced in the presence of cadmium for cells without EC20 expression. However, expression of EC20 (higher cadmium accumulation) completely restored the level of TCE degradation. These results demonstrated that EC20 expression enhanced not only cadmium accumulation but also reduced the toxic effect of cadmium on TCE degradation. We expect that similar improvements will be observed when these engineered rhizobacteria are inoculated onto plant roots.

Engineering plant-microbe symbiosis for rhizoremediation of heavy metals

The use of plants for rehabilitation of heavy-metal-contaminated environments is an emerging area of interest because it provides an ecologically sound and safe method for restoration and remediation. Although a number of plant species are capable of hyperaccumulation of heavy metals, the technology is not applicable for remediating sites with multiple contaminants. A clever solution is to combine the advantages of microbe-plant symbiosis within the plant rhizosphere into an effective cleanup technology. We demonstrated that expression of a metal-binding peptide (EC20) in a rhizobacterium, Pseudomonas putida 06909, not only improved cadmium binding but also alleviated the cellular toxicity of cadmium. More importantly, inoculation of sunflower roots with the engineered rhizobacterium resulted in a marked decrease in cadmium phytotoxicity and a 40% increase in cadmium accumulation in the plant root. Owing to the significantly improved growth characteristics of both the rhizobacterium and plant, the use of EC20-expressing P. putida endowed with organic-degrading capabilities may be a promising strategy to remediate mixed organic-metal-contaminated sites.

Biotechnological potential within the genus Burkholderia

Many species within the genus Burkholderia possess significant biotechnological potential in bioremediation and biological control. Here we provide a description of the Burkholderia strains being investigated for their ability to degrade major xenobiotic pollutants and update information on their taxonomy, metabolic capacity and genomes.

Characterization of phenol and trichloroethene degradation by the rhizobium Ralstonia taiwanensis

Ralstonia taiwanensis is a root nodule bacterium originally isolated from Mimosa sp. in southern Taiwan. Some strains of R. taiwanensis demonstrated the ability to grow on medium containing phenol as the sole carbon source, especially strain TJ86, which was able to survive and grow at phenol concentrations of up to 900 mg/l. The dependence of the phenol degradation rate on the phenol concentration can be described by Haldane's model with a low KS (the apparent half-saturation constant) of 5.46 microM and an extremely high KSI (the apparent inhibition constant) 9075 microM. The optimal phenol degradation rate was 61 micromol/min/g cell, which occurred at a phenol concentration of 228 microM. The phenol-limited growth kinetics of TJ86 by Andrews's model also followed a similar trend to that of phenol degradation, indicating the close links between phenol degradation and cell growth. Strain TJ86 also achieved 100 and 40% degradation for soil samples amended with 500 and 1000 microg phenol/g soil (dry weight) within 9 days, respectively. Moreover, strain TJ86 cometabolically degraded trichloroethene (TCE) after being cultivated with media containing phenol or m-cresol as the carbon substrate. The sequence of the large-subunit phenol hydroxylase (LmPH) gene obtained from TJ86 displayed high homology to that of other phenol-utilizing bacteria. Results from kinetic and phylogenetic analyses suggest that strain TJ86 most likely belongs to group I phenol-degrading bacteria which are considered to be efficient TCE degraders. It is proposed that the symbiotic relationship between rhizobia R. taiwanensis and its host plant Mimosa sp. may have the potential for rhizoremediation of aquatic and soil environments contaminated by phenol and TCE.

Spatial distribution of bacterial communities and phenanthrene degradation in the rhizosphere of Lolium perenne L

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria.

Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation

Trichloroethylene (TCE) is the most frequently detected groundwater contaminant, and 1-naphthol is an important chemical manufacturing intermediate. Directed evolution was used to increase the activity of toluene ortho-monooxygenase (TOM) of Burkholderia cepacia G4 for both chlorinated ethenes and naphthalene oxidation. When expressed in Escherichia coli, the variant TOM-Green degraded TCE (2.5 +/- 0.3 versus 1.39 +/- 0.05 nmol/min/mg of protein), 1,1-dichloroethylene, and trans-dichloroethylene more rapidly. Whole cells expressing TOM-Green synthesized 1-naphthol at a rate that was six times faster than that mediated by the wild-type enzyme at a concentration of 0.1 mM (0.19 +/- 0.03 versus 0.029 +/- 0.004 nmol/min/mg of protein), whereas at 5 mM, the mutant enzyme was active (0.07 +/- 0.03 nmol/min/mg of protein) in contrast to the wild-type enzyme, which had no detectable activity. The regiospecificity of TOM-Green was unchanged, with greater than 97% 1-naphthol formed. The beneficial mutation of TOM-Green is the substitution of valine to alanine in position 106 of the alpha-subunit of the hydroxylase, which appears to act as a smaller "gate" to the diiron active center. This hypothesis was supported by the ability of E. coli expressing TOM-Green to oxidize the three-ring compounds, phenanthrene, fluorene, and anthracene faster than the wild-type enzyme. These results show clearly that random, in vitro protein engineering can be used to improve a large multisubunit protein for multiple functions, including environmental restoration and green chemistry.