Please refer to other reviews that discussed aspects of this process . Rhizobacteria was shown to induce the accumulation of sesquiterperne synthase transcripts . Sesquiterperne, used in cosmetics and perfumery, is one component of vetiver root essential oil synthesis. The authors showed that the root associated bacteria metabolized the vetiver oil and produced additional compounds, which suggested that each distinct rhizobacteria community contributed to a signature composition of commercial vetiver oil. For two decades, it was thought that the plant pathogenic fungus Rhizopus microsporus produced the antimitotic polyketide macrolide rhizoxin. Partida-Martinez and Hertweck uncovered that it was actually an endosymbiont, Burkholderia sp., of the fungus that produced rhizoxin. The authors demonstrated that in the absence of Burkholderia, no rhizoxin was produced in the fungal culture. Transmission electron microscopy demonstrated that Burkholderia sp. was localized in the fungal cytosol . Rhizoxin inhibits mitosis and leads to cell cycle arrest, and has potential as an antitumor drug. Further investigation elucidated rhizoxin derivative structures and obtained stable analogues by inhibition of a putative P-450 monooxygenase . Ryan et al. summarized applications for bacterial endophytes, including production of bio-materials such as poly-3-hydroxybutyrate and poly-3-hydroxyalkanoate . Catalán et al. showed that diazotrophic endophyte Herbaspirillum seropedicae could accumulate 36% of its biomass as PHB and could constitute a cost-effective mean for producing bio-material.

Organic contaminants naturally biodegrade,plastic pots 30 liters except for chlorinated compounds such as polychorinated biphenyl and 4-chloronitrobenzene , which tend to be persistent and recalcitrant in the environment. Recent reports on chlorinated compound degrading rhizosphere bacteria are presented. Natural PCB-degrader bacterial populations were cultured from several plant species growing in a contaminated site. High numbers of culturable PCB-degrader colonies were isolated from roots of Austrian pine and goat willow . Most of the PCB metabolizing bacteria are Rhodococcus sp. However, the isolates were first selected based on cultivability and morphology thus possibly leading to a biased representation of PCB-degrading bacterial communities. In addition, since the PCB degradation capability of these strains was tested in liquid medium, the benefits of plant association was not addressed. Narasimhan et al. investigated the role of plant secondary compounds in stimulating rhizobacteria growth and PCB removal efficiency. The authors identified that the Arabidopsis root exudates consisted mostly of phenylpropanoids, such as flavonoids, lignins and indole compounds. Wild type and mutant Arabidopsis lines over producing flavonoids sustained higher counts of flavonoid-utilizing P. putida strain than bacteria grown on Arabidopsis mutant not producing flavonoids. More interestingly, close to 90% of PCB was degraded in soil adhering to the roots indicating that direct contact with roots and the exudates resulted in bacteria growth and bio-degradation enhancement. Genetically engineered microbes were also applied towards remediation. The PCB degradation efficiency of a recombinant strain of P. fluorescens expressing a bph operon under the control of nodulation genes from Sinorhizobium meliloti, was examined . Resting cell PCB-degradation experiments indicated that the recombinant strain metabolized different cogeners of PCB more efficiently than the Burkholderia sp. strain LB400. However, no plant-bacteria potted experiments were performed to measure PCB degradation. Böltner et al. enriched rhizosphere microbes and demonstrated that four Sphingomonas strains were capable of rhizoremediating hexachlorocyclohexane .

Potted experiments showed that 30% of lindane was removed with corn seedlings inoculated with the Sphingomonas strains. Whereas, in unplanted soil, sterile planted soil, and uninoculated-unplanted soil, less than 3% of lindane was removed. Liu et al. successfully inoculated a gfp-tagged strain of Comamonas sp. onto the roots of alfalfa as demonstrated by quantitative competitive -PCR and confocal laser scanning microscopy . The rhizosphere community shifted due to addition of 4CNB and the Comamonas strain was characterized using denaturing gradient gel electrophoresis . In outdoor potted experiments, the symbiosis enhanced phytotoxicity resistance, and removed 4CNB faster than the plant control without the strain in a 24-hour period. However, the control without the strain removed 60% of the 4CNB compared to 99% in experiment with strain inoculation. It seemed likely that if the experiment was extended beyond the 24-hour measurements, the 4CNB removal might be similar between the control and the treatment.However, certain volatile organic compounds such as trichloroethylene and BTEX are released into the atmosphere through the plant’s vascular system. The endophyte-plant interaction was used to degrade these volatile organic pollutants and minimize evapotranspiration . Barac et al. demonstrated that the genetically modified endophytic strain of Burkholderia cepacia together with yellow lupine reduced evapotranspiration of toluene by 50-70%, and reduced phytotoxicity. The same group inoculated poplar cuttings with two strains of B. cepacia, an endophyte and a soil isolate, expressing the toluene monooxygenase , and showed significantly less toluene being transpired in the poplar inoculated with the endophytic B. cepacia . In addition, the authors indicated evidence for horizontal gene transfer of the recombinant plasmid encoding the toluene degradation pathway from the inoculant B. cepacia to the endogenous microbial community, and suggested that it would be possible to eliminate selection of an appropriate endophyte since the bio-degradation gene will be transferred to the endogenous microorganisms.

However, the authors touched on the issue of low horizontal transfer efficiency but did not elaborate on solutions for the lack of control over the time scale of the transfer and recipients of the genes. The authors also did not comment on the risks associated with the spread of exogenous genes into a new environment. However, the risk caused by a gene originally isolated from the environment, such as the tom gene should be low compared to risks from synthetic genes. Moore et al. isolated endophytic bacteria from two poplar varieties that were grown at a field trial site phytoremediating BTEX in the groundwater. There were differences in spatial compartmentalization of strain localization in the root, shoot and leaves suggesting there were species-specific and non-specific associations between bacteria and plants. However, the study did not examine the reasons for the strain localization and association with the plants and whether remediation efficiency was affected by bacterial community. Heavy metal contamination is a persistent problem since the metals, unlike organic compounds, do not biodegrade. Several recent reviews address role of plant growth promoting rhizobacteria in metals remediation , and various plant bacteria systems that have been applied towards remediation of metals contamination . Removal of metals from soil or groundwater using rhizosphere bacteria and plants has been demonstrated recently. Willowseedlings inoculated with different strains of rhizosphere Streptomyces and Agromyces and the strains ability to produce indole acetic acid and siderophore was measured. No correlation was observed between IAA and siderophore production and metal accumulation. Only plants inoculated with Agromyces terreus exhibited reduced phytotoxicity due to cadmium and zinc. Metal accumulation in leaf biomass was measured . However, the data did not demonstrate a marked difference between the inoculated plants and the non-inoculated control. Perhaps,round plastic pots most of the phyto accumulated metals were immobilized in the roots where most of the rhizosphere strains would be located. No root metal concentrations were measured. Wu et al. utilized an engineered symbiosis between recombinant P. putida and sunflower plants for adsorption of cadmium. The recombinant P. putida expressed a synthetic phytochelatin, EC20, and exhibited inherent cadmium resistance. The inoculation of the P. putida strain enhanced plant growth and resulted in 40 % more cadmium accumulation from hydroponic solutions than the non-inoculated control. No field study was conducted. Ryan et al. demonstrated that a recombinant strain of P. fluorescens F113rifPCB with arsenic resistance genes and PCB degradation capabilities protected M. sativa when grown in soil supplemented with sodium arsenate. No arsenic removal nor PCB degradation efficiency were assessed with this plant-bacteria system. Since most of the metals tend to accumulate in the top 20 cm layer of the soil , grass species with high fine-root biomass providing large surface area for bacteria colonization and metal accumulation, in the top soil layer, would be ideal for remediation of metal contaminated sites. The plants serve as concentrators of metals, and further treatment of the plant biomass accumulated with metals would be required. Overall, the use of the plant-bacteria system would be more cost-effective than excavation of the soil contaminated with low levels of heavy metals. The successful demonstrations of laboratory-scale phyto- or rhizo- remediation do not always translate into adequate removal of contaminants in field-scale. The reasons include heterogeneity of the field site, unpredictability of environmental conditions, inability to sustain bacterial population and the remediating microbes being out competed by endogenous organisms. There are several reasons that plant-bacteria interactions are advantageous when applied to remediation. The plant-associated bacteria population would be more competitive than the native soil microorganisms since plant exudates provide nutrients.

Plants would act as natural pumps that draw contaminated soil pore water towards the plant-associated remediating bacteria. Rhizoremediation is an ideal strategy for cleanup of mixed-contaminants. Recombinant rhizosphere bacteria with specific genes targeting pollutants present at the site can be inoculated into plant roots. For example, Lee et al. engineered two strains of rhizobacteria with TCE degradation capability, and surface expression of synthetic phytochelatins for improved heavy metal resistance, thus enhancing the rate of TCE degradation. An excellent review by Gerhardt et al. addressed strategies to overcoming challenges of field application of phyto- or rhizo-remediation such as stressors to the microbes, complexity of the field conditions, regulatory acceptability and the use of genetically modified organisms . Research that look at the impact of GMOs on native bacteria and bacterial community changes post introduction of willow trees for rhizoremediation of PCB contamination are starting to emerge and will elucidate questions regarding the impact on the native microfauna. Studies that compare remediation efficiencies of natural attenuation, bio-augmentation, phytoremediation and rhizoremedation, under field conditions , assess bacterial colonization and activity on plant roots, and measure allometric relationships of tree trunk size and various root parameters provide invaluable information for determining field application options and evaluating contaminant removal. More extensive, long-term field comparisons of control plots with treatment plots for remediation efficiency are necessary to validate laboratory observations and to gain public and regulatory agency confidence for this promising application. Another application of plant-microbe interaction drawing increasing attention is carbon sequestration, where atmospheric C is deposited as plant root material, incorporated into the soil microorganisms and soil organic matter. It is hypothesized that increase in CO2 leads to an increase in rhizodeposition, and wider C/N ratio thus retarding decomposition . Several reviews are dedicated to presenting methods for measuring CO2 fluxes in different soil compartments , mechanism of root carbon stabilization , effects of elevated CO2 on below ground carbon storage , and carbon sequestration by roots . This nascent field is still at the exploratory stage where most of the research is focusing on understanding the effects of elevated CO2 levels on microbial community, below-ground plant material production, and biomass decomposition, as well as land management practices and plant species on the long term potential of C rhizodeposition. Several researchers explored the possibility of different land management practices to enhance C sequestration. Bailey et al. compared ex situ incubations of soil samples from five different ecosystems . The restored prairie samples had the highest total soil carbon and also the highest fungal-to-bacterial activities . The authors asserted that increased F:B ratios correlated with higher amount of carbon stored in the soil. Also, that invasive land management decreased fungal biomass and thus the carbon stored in the soil. Soil samples were collected and CO2 respiration experiments were conducted in a laboratory setting over a 6-hour period, thus the measurements might not be representative of field conditions. Heinemeyer et al. described contradicting results in their in situ study of the ability of Lodgepole pine associated mycorrhiza to store soil C over a period of 1- year, where the fungus was thought to return plant surplus C directly back to the atmosphere. Verburg et al. compared the net ecosystem carbon exchange between the atmosphere and two experimental non-native cheat grass varieties in a 2-year study in the Desert Research Institute’s Ecologically Controlled Enclosed Lysimeter Laboratories. They showed that fertilization increased C uptake initially, however, C loss through soil respiration was also enhanced. Bazot et al. found similar results, at a grassland ecosystem of Free Air CO2 Enrichment is Eschikon, Switzerland, where increased N supply to the plants enhanced allocation of fixed C to the shoots and reduced below ground carbon allocation and rhizodeposition.