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,vertical rack 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. The plots were enriched with CO2 for 9 years in this study. At the same Swiss FACE facility, changes in microorganism structural diversity and function were also examined after 9 years of CO2 enrichment in monocultures and mixed cultures of Trifolium repens L. cv. Milkanowa and Lolium perenne L. cv. Bastion with and without N treatments . The authors concluded that increased atmospheric CO2 stimulated microbial enzymatic activities and changed structural diversity. Subsequently, the increase in microbial activity led to higher mineralization rate of soil organic matter and thus would reduce the C sequestered in the soil. However, the soil C concentrations were not quantified in this study. Long term effects are essential for assessing the applicability of plant rhizosphere C sequestration potential, and are investigated in the following field studies. Ingram et al. investigated microbial community changes to cattle grazing practices over a 10 year period at the High Plains Grasslands Research Station . The authors found that even moderate grazing impacted microbial community structures and vegetation composition that could lead to loss of soil organic C to the atmosphere. In the heavily grazed area, there was a 30% loss of soil organic C and the measured Nmineralization rate was the lowest among the different grazing regimes.

A 5 year study of loblolly pine associated fungi at a FACE site resulted in an increase in fungal biomass and a shift in distribution to deeper soils . Leake et al. presented a comprehensive study on C fluxes from plants to soil microbiota using 13CO2 pulse labeling on a Scottish upland grassland over a period of 4 years. It was found that there were two distinct pools of soil carbon: one with fast turnover and one with slow turnover time. Mycorrhizal mycelial system contributed to the pool with the fast turnover, by consuming approximately 9% of the fixed C, and returning much of it to the atmosphere within 16 hours. Liming was found to increase shoot and root productivity. However, liming enhanced soil respiration and microbial biomass production, thus decreasing the amounts of C retained in the soil. Bremer et al. compared soil organic C 6 and 12 years after a crop rotation study commenced and found that the C sequestration of the different soil treatments did not increase after the first 6 years for the carbon conserving practices. However,vertical farming hydroponic fertilized grass continued to gain soil organic C over the 12 year period. Niklaus and Falloon studied the capacity of calcareous grassland exposed to high levels of CO2 for 6 years and found that the C sequestration potential was limited due to processes that were unaccounted for such as increased soil moisture due to reduced leaf conductance, soil disaggregation due to increased moisture and accelerated soil organic matter decomposition. A 30 year soil C projection modeling using field measurements was used to assessing affects of ambient and elevated CO2 level . The results did not support the hypothesis that decreased litter quality due to increased CO2 level would lead to lower decomposition rate . The authors suggested that it would be more effective to reduce the rate of decomposition, rather than increase storage of plant litter C.The studies presented in this review do not encompass all possible plant microbe C sequestration research available. However, most of the studies discussed here indicate that optimal conditions for below ground C storage have not been found. There are many possible direct and indirect effects on the below ground C pools and processes resulting from elevated CO2 and increased temperature . Microbial activity is affected by increased temperature leading to increased N availability and net primary production. There might be differences in C sequestration capacity for different plant species, and whether they are perennial or annual.

The water content of the soil and Nlimitation would affect microbial mineralization of organic soil C. The challenges may lie in improving measurement methods of C stored below ground and de convoluting the myriads of confounding factors that could affect C and N cycling. In addition, the scale of the application required to have an impact on the atmospheric C level is unclear at this point. More long term and standardized studies, under different environmental conditions, of below ground carbon fluxes, integrating models and measurements are needed. C sequestration through plant microbe interaction is still in its exploratory phase. As more worldwide attention is drawn towards mitigating elevated atmospheric C level, hopefully more global collaborative interdisciplinary research efforts will be directed towards assessing the conditions required for successful application of plant microbe C sequestration. Nitrogen is an essential macro nutrient for plant growth and development and most terrestrial plants absorb nitrate as their main nitrogen source. In agricultural systems, nitrate supply directly affects plant growth and crop productivity. In many developed and developing countries, excessive nitrogen fertilizer is applied in agriculture, while the nitrogen use efficiency of crops is low. Therefore, a large fraction of the applied nitrogen cannot be taken up by plants and is lost into the environment, resulting in serious problems such as eutrophication and nitrate pollution of underground water. These problems must be addressed. One approach is to improve the NUE of crops, which could reduce the load of nitrogen fertilizers on farm land and natural ecosystems. Elucidating the mechanisms and the underlying network of nitrate regulation would provide a theoretical basis and guiding framework for improving NUE.A part of the nitrate imported into cells is reduced and assimilated into amino acid through a series of enzymes including nitrate reductase , nitrite reductase , glutamine synthase , and glutamate synthase . Nitrate acts as a nutrient and as an important signal to regulate gene expression, plant growth, and development. Nitrate signaling can be divided into short term and long term effects. The short term effect is referred to as the primary nitrate response, in view of the fact that many genes can be regulated after a short period of exposure to nitrate inputs. Indeed, some genes involved in nitrate transport and reduction are induced in a matter of minutes. The long term effects include the impact of nitrate on plant growth and development after a longer period of time, including effects on the morphogenesis of roots, plant flowering, seed dormancy, stomatal closure independent of abscisic acid, the circadian rhythm, and the transport of auxin. Among these aspects, the effects of nitrate on root development are well studied and several essential genes involved in this process have been identified. Here we review the genes involved in the primary nitrate response and describe their functions in nitrate signaling . Then we summarize the relationship between nitrate availability and root system architecture and the roles of the characterized genes that control root growth and development in response to local and systemic nitrate signals .In the late 1990s, molecular components involved in nitrate signaling were identified in bacteria and fungi. In Escherichia coli, both NARX and NARQ containing a P box domain were found to be responsible for nitrate binding and could activate the nitrate regulating proteins NarL and NarP, which are essential for nitrate sensing. Therefore, these two genes are nitrate regulators in E. coli. In fungi, two transcription factors NirA and Nit4 have been identified as important nitrate regulators. NirA is needed for the expression of nitrate reductase and Nit4 may interact with nitrate reductase directly. Both proteins were demonstrated to activate their target genes that can respond to nitrate. In plants, some genes encoding proteins required for nitrate assimilation, transport, and energy and carbon metabolism are rapidly induced after nitrate treatment. These are regarded as primary nitrate responsive genes. Scientists have characterized a few of the regulators playing important roles in primary nitrate responses, mainly by employing methodologies in forward and reverse genetics as well as systems biology. NRT1.1, also called CHL1 and NPF6.3, belongs to the NRT1/PTR family. Previously, NRT1.1 was identified as a dual affinity nitrate transporter working in both low and high nitrate concentrations. Subsequently, it was shown that NRT1.1 controlled root architecture by acting as a potential nitrate sensor. Then in 2009 it was found that NRT1.1 is involved in the primary nitrate response. Using a forward genetic screen, the Crawford lab identified a mutant with a defective response to nitrate, and the mutation was localized to NRT1.1. Characterization of the mutant revealed that expression of the primary nitrate responsive genes NIA1, NiR, and NRT2.1 was significantly inhibited when plants were grown in the presence of ammonium. Interestingly, the regulatory role of NRT1.1 was lost when ammonium was absent because the expression of these nitrate responsive genes was restored in the mutant without ammonium, indicating that other nitrate sensor were present and dominated in the absence of ammonium. The Tsay lab also showed that a null mutant of NRT1.1, chl15, lost both nitrate uptake and primary nitrate response functions. They then described an allele of NRT1.1that was defective in nitrate uptake but not nitrate regulation. These results indicate that the primary nitrate response was defective in the mutant chl15 but not in chl19, and the function of NRT1.1 in nitrate signaling is independent of its uptake activity, thereby identifying NRT1.1 as a nitrate sensor.