Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants.

Phytoremediation of highly water soluble and volatile organic xenobiotics is often inefficient because plants do not completely degrade these compounds through their rhizospheres. This results in phytotoxicity and/or volatilization of chemicals through the leaves, which can cause additional environmental problems. We demonstrate that endophytic bacteria equipped with the appropriate degradation pathway improve the in planta degradation of toluene. We introduced the pTOM toluene-degradation plasmid of Burkholderia cepacia G4 into B. cepacia L.S.2.4, a natural endophyte of yellow lupine. After surface-sterilized lupine seeds were successfully inoculated with the recombinant strain, the engineered endophytic bacteria strongly degraded toluene, resulting in a marked decrease in its phytotoxicity, and a 50-70% reduction of its evapotranspiration through the leaves. This strategy promises to improve the efficiency of phytoremediating volatile organic contaminants.

DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria.

A denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of dsrB (dissimilatory sulfite reductase beta-subunit)-genes in sulfate-reducing communities. For this purpose a PCR primer pair was optimized for the amplification of a approximately 350 bp dsrB gene fragment that after DGGE gel electrophoresis enabled us to discriminate between dsrB genes of different SRB-subgroups,-genera and -species. The dsrB-DGGE method revealed considerable genetic diversity when applied to DNA extracts obtained from aquifer samples that were derived from monitoring wells of an in situ metal precipitation (ISMP) pilot project conducted at the site of a non-ferrous industry or from environmental heavy metal contaminated samples. The sequences of the excised and sequenced DGGE bands represented dsrB genes of different SRB-subgroups,-genera and -species, thus confirming the broad applicability of the PCR primer pair. Linking the results of the physico-chemical follow-up of the field and lab experiments to the dsrB-DGGE data will provide a better understanding of the contribution of the SRB populations to the ongoing ISMP processes.

Endophytic bacterial diversity in poplar trees growing on a BTEX-contaminated site: the characterisation of isolates with potential to enhance phytoremediation.

The diversity of endophytic bacteria found in association with poplar was investigated as part of a larger study to assess the possibility and practicality of using endophytic bacteria to enhance in situ phytoremediation. Endophytic bacteria were isolated from the root, stem and leaf of two cultivars of poplar tree growing on a site contaminated with BTEX compounds. They were further characterised genotypically by comparative sequence analysis of partial 16S rRNA genes and BOX-PCR genomic DNA fingerprinting, and phenotypically by their tolerance to a range of target pollutants, heavy metals and antibiotics. One hundred and 21 stable, morphologically distinct isolates were obtained, belonging to 21 genera, although six isolates could not be identified with confidence to a genus. The endophytic bacteria exhibited marked spatial compartmentalisation within the plant, suggesting there are likely to be species-specific and non-specific associations between bacteria and plants. A number of isolates demonstrated the ability to degrade BTEX compounds or to grow in the presence of TCE. This study demonstrates that within the diverse bacterial communities found in poplar several endophytic strains are present that have the potential to enhance phytoremediation strategies.

Column experiments to assess the effects of electron donors on the efficiency of in situ precipitation of Zn, Cd, Co and Ni in contaminated groundwater applying the biological sulfate removal technology.

BACKGROUND, AIMS AND SCOPE: In a previous study, we explored the use of acetate, lactate, molasses, Hydrogen Release Compound (HRC, which is based on a biodegradable poly-lactate ester), methanol and ethanol as carbon source and electron donor to promote bacterial sulfate reduction in batch experiments, this with regards to applying an in situ metal precipitation (ISMP) process as a remediation tool to treat heavy metal contaminated groundwater at the site of a nonferrous metal work company. Based on the results of these batch tests, column experiments were conducted with lactate, molasses and HRCI as the next step in our preliminary study for a go-no go decision for dimensioning an on site application of the ISMP process that applies the activity of the endogenous population of sulfate-reducing bacteria (SRB). Special attention was given to the sustainability of the metal precipitation process under circumstances of changing chemical oxygen demand (COD) to [SO4(2-)] ratios or disrupted substrate supply. METHODS: To optimize the ISMP process, an insight is needed in the composition and activity of the indigenous SRB community, as well as information on the way its composition and activity are affected by process conditions such as the added type of C-source/ electron donor, or the presence of other prokaryotes (e.g. fermenting bacteria, methane producing Archaea, acetogens). Therefore, the biological sulfate reduction process in the column experiments was evaluated by combining classical analytical methods [measuring heavy metal concentration, SO4(2-)-concentration, pH, dissolved organic carbon (DOC)] with molecular methods [denaturing gradient gel electrophoresis (DGGE) fingerprinting and phylogenetic sequence analysis] based on either the 16S rRNA-gene or the dsr (dissimilatory sulfite reductase) gene, the latter being a specific biomarker for SRB. RESULTS AND DISCUSSION: All carbon sources tested promoted SRB activity, which resulted within 8 weeks in a drastic reduction of the sulfate and heavy metal contents in the column effluents. However, unexpected temporal decreases in the efficiency of the ISMP process, accompanied by the release of precipitated metals, were observed for most conditions tested. The most dramatic observation of the failing ISMP process was observed within 12 weeks for the molasses amended column. Subsequent lowering the COD/ SO4(2-) ratio from 1.9 to 0.4 did not alter the outcome of sulfate reduction and metal precipitation efficiency in this set-up. Remarkably, after 6 months of inactivity, bacterial sulfate reduction was recovered in the molasses set up when the original COD/ SO4(2-) ratio of 1.9 was applied again. Intentional disruption of the lactate and HRC supplies resulted in an immediate stagnation of the ISMP processes and in a rapid release of precipitated metals into the column effluents. However, the ISMP process could be restored after substrate amendment. 16S rDNA-based DGGE analysis revealed that the SRB population, in accordance with the results of the previously performed batch experiments, consisted exclusively of members of the genus Desulfosporosinus. The community of Archaea was characterized by sequencing amplicons of archaeal and methanogen-specific PCR reactions. This approach only revealed the presence of non-thermophilic Crenarchaeota, a novel group of organisms which is only distantly related to methane producing Euryarchaeota. DGGE on the dsrB genes was successfully used to link the results of the ISMP process to the community composition of the sulfate reducing bacteria. CONCLUSIONS: In the case of an intentional disruption of substrate supply, the ISMP process failed most likely because the growth and activity of the indigenous SRB community stopped due to a lack of a carbon and electron donor. On the other hand, the cause of the sudden temporal shortcomings of the ISMP process in the presence of different substrates was not immediately clear. It was first thought to be the result of competition between methanogenic prokaryotes (MP) and sulfate reducers, since the formation of small amounts of CH4 (0.01-0.03 ppm ml(-1) was detected. However, the results of molecular analyzes indicate that methanogens do not constitute a major fraction of the microbial communities that were enriched in the column experiments. Therefore, we postulate that the SRB population becomes inhibited by the formed metal sulfides. RECOMMENDATION AND PERSPECTIVE: Our results indicate that the ISMP process is highly dependent on SRB-stimulation by substrate amendments and suggest that this remedial approach might not be viable for long-term application unless substrate amendments are continued and environmental conditions are strictly controlled. This will include the removal of affected aquifer material from the metal precipitation zone at the end of the remediation process, or removal of metal precipitates when the microbial activity decreases. Additional tests are necessary to investigate what will happen when clear groundwater passes through the reactive zone while no more C-sources are amended and all indigenous carbon is consumed. Also, the effects of dramatic increases in sulfate- or HM-concentrations on the SRB-community and the concomitant ISMP process need to be studied in more detail.

Batch-test study on the dechlorination of 1,1,1-trichloroethane in contaminated aquifer material by zero-valent iron.

Chlorinated aliphatic hydrocarbons are common groundwater contaminants. One possible remediation option is in-situ reductive dechlorination by zero-valent iron, either by direct injection or as reactive barriers. Chlorinated ethenes (tetrachloroethene: PCE; trichloroethene: TCE) have received extensive attention in this context. However, another common groundwater pollutant, 1,1,1-trichlorethane (TCA), has attracted much less attention. We studied TCA reduction by three types of granular zero-valent irons in a series of batch experiments using polluted groundwater, with and without added aquifer material. Two types of iron were able to reduce TCA completely with no daughter product concentration increases (1,1-dichloroethane: DCA; chloroethane: CA). One type of iron showed slower reduction, with intermediate rise of DCA and CA concentrations. When evaluating the formation of daughter products, the tests on the groundwater alone showed different results than the groundwater plus aquifer batches: DCA did not temporarily accumulate in the batches with added aquifer material, contrary to the batches without added aquifer material. 1,1-dichloroethene (DCE, also present in the groundwater as an abiotic degradation product of TCA) was also reduced slower in the batches without added aquifer material than in the batches with aquifer material. Redox potentials gradually decreased to low values in batches with aquifer material without iron, while the batches with groundwater alone maintained a constant higher redox potential. Either adsorption processes or microbiological activity in the samples could explain these phenomena. Polymerase Chain Reaction (PCR: a targeted gene probe technique) for chlorinated aliphatic compound (CAH)-degrading bacteria confirmed the presence of Dehalococcoides sp. (chloroethene-degraders) but was negative for Desulfobacterium autotrophicum (a known co-metabolic TCA degrader). DCA reduction was rate determining: first-order half-lives of 300-350 h were observed. TCA was fully removed within hours. CA is resistant to reduction by zero-valent iron but it is known to hydrolyze easily. Since CA did not accumulate in our batches, it may have disappeared by the latter mechanism or it may not have formed as a major daughter product.

Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34.

The four replicons of Cupriavidus metallidurans CH34 (the genome sequence was provided by the US Department of Energy-University of California Joint Genome Institute) contain two gene clusters putatively encoding periplasmic resistance to copper, with an arrangement of genes resembling that of the copSRABCD locus on the 2.1 Mb megaplasmid (MPL) of Ralstonia solanacearum, a closely related plant pathogen. One of the copSRABCD clusters was located on the 2.6 Mb MPL, while the second was found on the pMOL30 (234 kb) plasmid as part of a larger group of genes involved in copper resistance, spanning 17 857 bp in total. In this region, 19 ORFs (copVTMKNSRABCDIJGFLQHE) were identified based on the sequencing of a fragment cloned in an IncW vector, on the preliminary annotation by the Joint Genome Institute, and by using transcriptomic and proteomic data. When introduced into plasmid-cured derivatives of C. metallidurans CH34, the cop locus was able to restore the wild-type MIC, albeit with a biphasic survival curve, with respect to applied Cu(II) concentration. Quantitative-PCR data showed that the 19 ORFs were induced from 2- to 1159-fold when cells were challenged with elevated Cu(II) concentrations. Microarray data showed that the genes that were most induced after a Cu(II) challenge of 0.1 mM belonged to the pMOL30 cop cluster. Megaplasmidic cop genes were also induced, but at a much lower level, with the exception of the highly expressed MPL copD. Proteomic data allowed direct observation on two-dimensional gel electrophoresis, and via mass spectrometry, of pMOL30 CopK, CopR, CopS, CopA, CopB and CopC proteins. Individual cop gene expression depended on both the Cu(II) concentration and the exposure time, suggesting a sequential scheme in the resistance process, involving genes such as copK and copT in an initial phase, while other genes, such as copH, seem to be involved in a late response phase. A concentration of 0.4 mM Cu(II) was the highest to induce maximal expression of most cop genes.

Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene.

Poplar, a plant species frequently used for phytoremediation of groundwater contaminated with organic solvents, was inoculated with the endophyte Burkholderia cepacia VM1468. This strain, whose natural host is yellow lupine, contains the pTOM-Bu61 plasmid coding for constitutively expressed toluene degradation. Noninoculated plants or plants inoculated with the soil bacterium B. cepacia Bu61(pTOM-Bu61) were used as controls. Inoculation of poplar had a positive effect on plant growth in the presence of toluene and reduced the amount of toluene released via evapotranspiration. These effects were more dramatic for VM1468, the endophytic strain, than for Bu61. Remarkably, none of the strains became established at detectable levels in the endophytic community, but there was horizontal gene transfer of pTOM-Bu61 to different members of the endogenous endophytic community, both in the presence and in the absence of toluene. This work is the first report of in planta horizontal gene transfer among plant-associated endophytic bacteria and demonstrates that such transfer could be used to change natural endophytic microbial communities in order to improve the remediation of environmental insults.

Colonisation of poplar trees by gfp expressing bacterial endophytes.

With the exception of nitrogen fixing bacteria, there is little known about the colonisation patterns or population sizes of bacterial endophytes in deciduous trees. This study describes the isolation, identification, construction and re-colonisation patterns of three green fluorescent protein(gfp):kanamycin(R) labelled bacterial endophytes when re-introduced into poplar trees, their original host plant. Two of these endophytes showed considerable colonisation in the roots and stems of inoculated plants. gfp expressing cells of all three strains were observed to colonise the xylem tissue of the root. All three strains proved to be efficient rhizosphere colonisers, supporting the theory that the rhizosphere can serve as a source of bacterial endophytes.