Rhizoremediation: a beneficial plant-microbe interaction

Rhizosphere Microbial Response to Multiple Metal(loid)s in Different Contaminated Arable Soils Indicates Crop-Specific Metal-Microbe Interactions

In this study, we sampled rhizosphere soils from seven different agricultural fields adjacent to mining areas and cultivated with different crops (corn, rice, or soybean), to study the interactions among the innate microbiota, soil chemical properties, plants, and metal contamination. The rhizosphere bacterial communities were characterized by Illumina sequencing of the 16S rRNA genes, and their interactions with the local environments, including biotic and abiotic factors, were analyzed. Overall, these soils were heavily contaminated with multiple metal(loid)s, including V, Cr, Cu, Sb, Pb, Cd, and As. The interactions between environmental parameters and microbial communities were identified using multivariate regression tree analysis, canonical correspondence analysis, and network analysis. Notably, metal-microbe interactions were observed to be crop specific. The rhizosphere communities were strongly correlated with V and Cr levels, although these sites were contaminated from Sb and Zn/Pb mining, suggesting that these two less-addressed metals may play important roles in shaping the rhizosphere microbiota. Members of Gaiellaceae cooccurred with other bacterial taxa (biotic interactions) and several metal(loid)s, suggesting potential metal(loid) resistance or cycling involving this less-well-known taxon.IMPORTANCE The rhizosphere is the "hub" for plant-microbe interactions and an active region for exchange of nutrients and energy between soil and plants. In arable soils contaminated by mining activities, the rhizosphere may be an important barrier resisting metal uptake. Therefore, the responses of the rhizosphere microbiota to metal contamination involve important biogeochemical processes, which can affect metal bioavailability and thus impact food safety. However, understanding these processes remains a challenge. The current study illustrates that metal-microbe interactions may be crop specific and some less-addressed metals, such as V and Cr, may play important roles in shaping bacterial communities. The current study provides new insights into metal-microbe interactions and contributes to future implementation and monitoring efforts in contaminated arable soils.

Intracellular Polyphosphate Levels in Gluconacetobacter diazotrophicus Affect Tolerance to Abiotic Stressors and Biofilm Formation

Gluconacetobacter diazotrophicus is a plant growth-promoting bacterium that is used as a bioinoculant. Phosphate (Pi) modulates intracellular polyphosphate (polyP) levels in Escherichia coli, affecting cellular fitness and biofilm formation capacity. It currently remains unclear whether environmental Pi modulates polyP levels in G. diazotrophicus to enhance fitness in view of its technological applications. In high Pi media, cells accumulated polyP and degraded it, thereby improving survival, tolerance to environmental stressors, biofilm formation capacity on abiotic and biotic surfaces, and competence as a growth promoter of strawberry plants. The present results support the importance of Pi and intracellular polyP as signals involved in the survival of G. diazotrophicus.

PGPR Reduce Root Respiration and Oxidative Stress Enhancing Spartina maritima Root Growth and Heavy Metal Rhizoaccumulation

The present study aims to unravel ecophysiological mechanisms underlying plant-microbe interactions under natural abiotic stress conditions, specifically heavy metal pollution. Effect of plant growth promoting rhizobacteria (PGPR) bioaugmentation on Spartina maritima in vivo root respiration and oxidative stress was investigated. This autochthonous plant is a heavy metal hyperaccumulator cordgrass growing in one of the most polluted estuaries in the world. The association with native PGPR is being studied with a view to their biotechnological potential in environmental decontamination. As a novelty, the oxygen-isotope fractionation technique was used to study the in vivo activities of cytochrome oxidase (COX) and alternative oxidase (AOX) pathways. Inoculated plants showed decreased antioxidant enzymatic activities and in vivo root respiration rates. The reduction in respiratory carbon consumption and the stress alleviation may explain the increments observed in S. maritima root biomass and metal rhizoaccumulation after inoculation. For the first time, plant carbon balance and PGPR are interrelated to explain the effect of rhizobacteria under abiotic stress.

Long-term biodegradation of aged saline-alkali oily sludge with the addition of bulking agents and microbial agents

Huge amount of aged oily sludge was generated during the drilling and transportation of crude oil. Sometimes, the sludge exhibited characters of combined pollution, such as saline-alkali oily sludge. Orthogonal experiments of L₁₆(4⁵) were conducted to evaluate the long-term effects of total petroleum hydrocarbons (TPH) concentration, microbial agents (Oil Gator and ZL) and bulking agents (peat and wheat bran) on the biodegradation of aged saline-alkali oily sludge. Compared with the control group, the significant improvement in the removal rate of TPH was exhibited with the addition of microbial agents and bulking agents after 231 days of the experimental period. Based on the values of mean range (R), it was revealed that the predominant influencing factor of the bioremediation was TPH concentration. After biostimulation and bioaugmentation, the quantity of petroleum hydrocarbon-degrading bacteria in the oily sludge increased by 2-4 orders of magnitude. Furthermore, the bioremediation improved the microbial diversity based on the analysis of PCR-DGGE. It was inferred that the addition of microbial agents and bulking agents reconstructed the microbial ecological niche. The principal component analysis indicated that the differentiation of the microbial community was generated by the biostimulation and bioaugmentation in comparison with the control samples.

The Fate of Chemical Pollutants with Soil Properties and Processes in the Climate Change Paradigm—A Review

Heavy metal(loid)s and organic contaminants are two major groups of pollutants in soils. The fate and exposure of such pollutants in soil depends on their chemical properties, speciation, and soil properties. Soil properties and processes that control the toxicological aspects of pollutants include temperature, moisture, organic matter, mineral fractions, and microbial activities. These processes are vulnerable to climate change associated with global warming, including increased incidences of extreme rainfall, extended dry periods, soil erosion, and a rise in sea level. Here we explain evidence that relates to the effects of climate change-driven soil processes on the mobility, transport, and storage of pollutants in soil. The review found that changes in climate could increase human exposure to soil contaminants mainly due to processes involving soil organic carbon (SOC), surface runoff, redox state, and microbial community. However, uncertainties remain in relation to the extent of contaminant toxicity to human health, which is linked to global change drivers.

Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation

Phytoremediation is a green and sustainable alternative to physico-chemical methods for contaminated soil remediation. One of the flavours of phytoremediation is rhizoremediation, where plant roots stimulate soil microbes to degrade organic contaminants. This approach is particularly interesting as it takes advantage of naturally evolved interaction mechanisms between plant and microorganisms and often results in a complete mineralization of the contaminants (i.e. transformation to water and CO2 ). However, many biotic and abiotic factors influence the outcome of this interaction, resulting in variable efficiency of the remediation process. The difficulty to predict precisely the timeframe associated with rhizoremediation leads to low adoption rates of this green technology. Here, we review recent literature related to rhizoremediation, with a particular focus on soil organisms. We then expand on the potential of rhizoremediation to be a model plant-microbe interaction system for microbiome manipulation studies.

Compared the physiological response of two petroleum tolerant-contrasting plants to petroleum stress

Petroleum not only benefits the world economy but also contaminates the soil. In order to select the plants tolerant to petroleum, the physiological response of two petroleum tolerant-contrasting plants, Mirabilis jalapa and Orychophragmus violace, were investigated in variation of petroleum-contaminated soils (0, 5, 10, 20, and 40 g petroleum per kg soil) for 120 d. Petroleum degradation rate, seeds germination rate, free proline, and superoxide dismutase and peroxidase activities of M. jalapa were higher than that of O. violace under petroleum stress. However, the decrease rate of soluble protein, plant height, chlorophyll, and root fresh weight was greater in O. violace as compared to M. jalapa. Pearson correlation coefficient analysis was conducted, which indicated that the higher tolerance of M. jalapa was correlated with the higher level of free proline and antioxidative enzyme activities. Besides, the 10 g petroleum per kg soil may be appropriate for petroleum-tolerant plants selection, in which petroleum significantly restrain growth in O. violace but not in M. jalapa.

Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked With the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere

Agricultural soils are becoming contaminated with synthetic chemicals like polyaromatic compounds, petroleum hydrocarbons, polychlorinated biphenyls (PCBs), phenols, herbicides, insecticides and fungicides due to excessive dependency of crop production systems on the chemical inputs. Microbial degradation of organic pollutants in the agricultural soils is a continuous process due to the metabolic multifunctionalities and enzymatic capabilities of the soil associated communities. The plant rhizosphere with its complex microbial inhabitants and their multiple functions, is amongst the most live and dynamic component of agricultural soils. We analyzed the metatranscriptome data of 20 wheat rhizosphere samples to decipher the taxonomic microbial communities and their multifunctionalities linked with the degradation of organic soil contaminants. The analysis revealed a total of 21 different metabolic pathways for the degradation of aromatic compounds and 06 for the xenobiotics degradation. Taxonomic annotation of wheat rhizosphere revealed bacteria, especially the Proteobacteria, actinobacteria, firmicutes, bacteroidetes, and cyanobacteria, which are shown to be linked with the degradation of aromatic compounds as the dominant communities. Abundance of the transcripts related to the degradation of aromatic amin compounds, carbazoles, benzoates, naphthalene, ketoadipate pathway, phenols, biphenyls and xenobiotics indicated abundant degradation capabilities in the soils. The results highlighted a potentially dominant role of crop rhizosphere associated microbial communities in the remediation of contaminant aromatic compounds.

Enhanced and Complete Removal of Phenylurea Herbicides by Combinational Transgenic Plant-Microbe Remediation

The synergistic relationships between plants and their rhizospheric microbes can be used to develop a combinational bioremediation method, overcoming the constraints of individual phytoremediation or a bioaugmentation method. Here, we provide a combinational transgenic plant-microbe remediation system for a more efficient removal of phenylurea herbicides (PHs) from contaminated sites. The transgenic Arabidopsis thaliana plant synthesizing the bacterial N-demethylase PdmAB in the chloroplast was developed. The constructed transgenic Arabidopsis plant exhibited significant tolerance to isoproturon (IPU), a typical PH, and it took up the IPU through the roots and transported it to leaves, where the majority of the IPU was demethylated to 3-(4-isopropylphenyl)-1-methylurea (MDIPU). The produced intermediate was released outside the roots and further metabolized by the combinationally inoculated MDIPU-mineralizing bacterium Sphingobium sp. strain 1017-1 in the rhizosphere, resulting in an enhanced and complete removal of IPU from soil. Mutual benefits were built for both the transgenic Arabidopsis plant and strain 1017-1. The transgenic Arabidopsis plant offered strain 1017-1 a suitable accommodation, and in return, strain 1017-1 protected the plant from the phytotoxicity of MDIPU. The biomass of the transgenic Arabidopsis plant and the residence of the inoculated degrading microbes in the combinational treatment increased significantly compared to those in their respective individual transgenic plant treatment or bioaugmentation treatment. The influence of the structure of bacterial community by combinational treatment was between that of the two individual treatments. Overall, the combination of two approaches, phytoremediation by transgenic plants and bioaugmentation with intermediate-mineralizing microbes in the rhizosphere, represents an innovative strategy for the enhanced and complete remediation of pollutant-contaminated sites.IMPORTANCE Phytoremediation of organic pollutant-contaminated sites using transgenic plants expressing bacterial enzyme has been well described. The major constraint of transgenic plants transferred with a single catabolic gene is that they can also accumulate/release intermediates, still causing phytotoxicity or additional environmental problems. On the other hand, bioaugmentation with degrading strains also has its drawbacks, including the instability of the inoculated strains and low bioavailability of pollutants. In this study, the synergistic relationship between a transgenic Arabidopsis plant expressing the bacterial N-demethylase PdmAB in the chloroplast and the inoculated intermediate-mineralizing bacterium Sphingobium sp. strain 1017-1 in the rhizosphere is used to develop an intriguing bioremediation method. The combinational transgenic plant-microbe remediation system shows a more efficient and complete removal of phenylurea herbicides from contaminated sites and can overcome the constraints of individual phytoremediation or bioaugmentation methods.

The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil

Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.

Degradation of phenol via ortho-pathway by Kocuria sp. strain TIBETAN4 isolated from the soils around Qinghai Lake in China

Based on the feature of high-altitude permafrost topography and the diverse microbial ecological communities of the Qinghai-Tibetan Plateau, soil samples from thirteen different collection points around Qinghai lake were collected to screen for extremophilic strains with the ability to degrade phenol, and one bacterial strain recorded as TIBETAN4 that showed effective biodegradation of phenol was isolated and identified. TIBETAN4 was closely related to Kocuria based on its observed morphological, molecular and biochemical characteristics. TIBETAN4 grew well in the LB medium at pH 7–9 and 0–4% NaCl showing alkalophilicity and halophilism. The isolate could also tolerate up to 12.5 mM phenol and could degrade 5 mM phenol within 3 days. It maintained a high phenol degradation rate at pH 7–9 and 0–3% NaCl in MSM with 5 mM phenol added as the sole carbon source. Moreover, TIBETAN4 could maintain efficient phenol degradation activity in MSM supplemented with both phenol and glucose and complex water environments, including co-culture Penicillium strains or selection of non-sterilized natural lake water as a culture. It was found that TIBETAN4 showed enzymatic activity of phenol hydroxylase and catechol 1,2-dioxygenase after induction by phenol and the corresponding genes of the two enzymes were detected in the genome of the isolate, while catechol 2,3-dioxygenase or its gene was not, which means there could be a degradation pathway of phenol through the ortho-pathway. The Q-PCR results showed that the transcripts of both the phenol hydroxylase gene and catechol 1,2-dioxygenase gene were up-regulated under the stimulation of phenol, demonstrating again that the strain degraded phenol via ortho-degradation pathway.

Enhancement of toxic Cr (VI), Fe, and other heavy metals phytoremediation by the synergistic combination of native Bacillus cereus strain and Vetiveria zizanioides L

Bioremediation of Cr (VI), Fe, and other heavy metals (HMs) through plant-microbes interaction is one of the efficient strategies due to its high efficiency, low cost, and ecofriendly nature. The aim of the study was to isolate, characterize, and assess the potential of rhizospheric bacteria to enhance growth and metal accumulation by the chromium hyperaccumulator Vetiveria zizanoides. The bacterial strain isolated from mine tailings was identified to be Bacillus cereus (T1B3) strain exhibited plant growth-promoting traits including, 1-aminocyclopropane-1-carboxylate deaminase, indole acetic acid, and siderophores production, nitrogen fixation, and P solubilization. Removal capacity (mg L^-1) of T1B3 strain was 82% for Cr⁺⁶ (100), 92% for Fe (100), 67% for Mn(50), 36% for Zn (50), 31% for Cd (30), 25% for Cu (30), and 43% for Ni (50) during the active growth cycle in HM-amended, extract medium. Results indicate that inoculating the native V. zizanioides with T1B3 strain improves its phytoremediation efficiency of HMs. The mineralogical characteristics of chromite ore tailings and soil were also confirmed by X-ray diffraction, Fourier Transform Infrared, scanning electron microscope-energy dispersive spectroscopy analysis.

Bacterial community structure and diversity responses to the direct revegetation of an artisanal zinc smelting slag after 5 years

This comparative field study examined the responses of bacterial community structure and diversity to the revegetation of zinc (Zn) smelting waste slag with eight plant species after 5 years. The microbial community structure of waste slag with and without vegetation was evaluated using high-throughput sequencing. The physiochemical properties of Zn smelting slag after revegetation with eight plant rhizospheres for 5 years were improved compared to those of bulk slag. Revegetation significantly increased the microbial community diversity in plant rhizospheres, and at the phylum level, Proteobacteria, Acidobacteria, and Bacteroidetes were notably more abundant in rhizosphere slags than those in bulk waste slag. Additionally, revegetation increased the relative abundance of plant growth-promoting rhizobacteria such as Flavobacterium, Streptomyces, and Arthrobacter as well as symbiotic N₂ fixers such as Bradyrhizobium. Three dominant native plant species (Arundo donax, Broussonetia papyrifera, and Robinia pseudoacacia) greatly increased the quality of the rhizosphere slags. Canonical correspondence analysis showed that the differences in bacterial community structure between the bulk and rhizosphere slags were explained by slag properties, i.e., pH, available copper (Cu) and lead (Pb), moisture, available nitrogen (N), phosphorus (P), and potassium (K), and organic matter (OM); however, available Zn and cadmium (Cd) contents were the slag parameters that best explained the differences between the rhizosphere communities of the eight plant species. The results suggested that revegetation plays an important role in enhancing bacterial community abundance and diversity in rhizosphere slags and that revegetation may also regulate microbiological properties and diversity mainly through changes in heavy metal bioavailability and physiochemical slag characteristics.

Culture-independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil-bioremediation

To analyze microbial communities in environmental samples, this study combined Denaturing Gradient Gel Electrophoresis of amplified 16S rRNA-genes in total genomic DNA extracts from those samples with gene sequencing. The environmental samples studied were oily seawater and soil samples, that had been bioaugmented with natural materials rich in hydrocarbonoclastic bacteria. This molecular approach revealed much more diverse bacterial taxa than the culture-dependent method we had used in an earlier study for the analysis of the same samples. The study described the dynamics of bacterial communities during bioremediation. The main limitation associated with this molecular approach, namely of not distinguishing hydrocarbonoclastic taxa from others, was overcome by consulting the literature for the hydrocarbonoclastic potential of taxa related to those identified in this study. By doing so, it was concluded that the hydrocarbonoclastic bacterial taxa were much more diverse than those captured by the culture-dependent approach. The molecular analysis also revealed the frequent occurrence of nifH-genes in the total genomic DNA extracts of all the studied environmental samples, which reflects a nitrogen-fixation potential. Nitrogen fertilization is long known to enhance microbial oil-bioremediation. The study revealed that bioaugmentation using plant rhizospheres or soil with long history of oil-pollution was more effective in oil-removal in the desert soil than in seawater microcosms.

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation

Contaminated soils are frequently characterized by the simultaneous presence of organic and inorganic contaminants, as well as a poor biological and nutritional status. Rhizoremediation, the combined use of phytoremediation and bioremediation, has been proposed as a Gentle Remediation Option to rehabilitate multi-contaminated soils. Recently, newer techniques, such as the application of metallic nanoparticles, are being deployed in an attempt to improve traditional remediation options. In order to implement a phytomanagement strategy on calcareous alkaline peri-urban soils simultaneously contaminated with several metals and diesel, we evaluated the effectiveness of Brassica napus L., a profitable crop species, assisted with organic amendment and zero-valent iron nanoparticles (nZVI). A two-month phytotron experiment was carried out using two soils, i.e. amended and unamended with organic matter. Soils were artificially contaminated with Zn, Cu and Cd (1500, 500 and 50mgkg^-1, respectively) and diesel (6000mgkg^-1). After one month of stabilization, soils were treated with nZVI and/or planted with B. napus. The experiment was conducted with 16 treatments resulting from the combination of the following factors: amended/unamended, contaminated/non-contaminated, planted/unplanted and nZVI/no-nZVI. Soil physicochemical characteristics and biological indicators (plant performance and soil microbial properties) were determined at several time points along the experiment. Carbonate content of soils was the crucial factor for metal immobilization and, concomitantly, reduction of metal toxicity. Organic amendment was essential to promote diesel degradation and to improve the health and biomass of B. napus. Soil microorganisms degraded preferably diesel hydrocarbons of biological origin (biodiesel). Plants had a remarkable positive impact on the activity and functional diversity of soil microbial communities. The nZVI were ineffective as soil remediation tools, but did not cause any toxicity. We concluded that rhizoremediation with B. napus combined with an organic amendment is promising for the phytomanagement of calcareous soils with mixed (metals and diesel) contamination.

Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation

Chlorophenols are widespread and of environmental concern due to their toxic and carcinogenic properties. Development of less costly and less technically challenging remediation methods are needed; therefore, we developed a formulation based on micronized vermiculite that, when air-dried, resulted in a granular product containing the 4-chlorophenol (4-CP)-degrading Gram-positive bacterium Arthrobacter chlorophenolicus A6. This formulation and stabilization method yielded survival rates of about 60% that remained stable in storage for at least 3 months at 4 °C. The 4-CP degradation by the formulated and desiccated A. chlorophenolicus A6 cells was compared to that of freshly grown cells in controlled-environment soil microcosms. The stabilized cells degraded 4-CP equally efficient as freshly grown cells in two different set-ups using both hygienized and non-treated soils. The desiccated microbial product was successfully employed in an outdoor pot trial showing its effectiveness under more realistic environmental conditions. No significant phytoremediation effects on 4-CP degradation were observed in the outdoor pot experiment. The 4-CP degradation kinetics from both the microcosms and the outdoor pot trial were used to generate a predictive model of 4-CP biodegradation potentially useful for larger-scale operations, enabling better bioremediation set-ups and saving of resources. This study also opens up the possibility of formulating and stabilizing also other Arthrobacter strains possessing different desirable pollutant-degrading capabilities.

Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture

The progression of life in all forms is not only dependent on agricultural and food security but also on the soil characteristics. The dynamic nature of soil is a direct manifestation of soil microbes, bio-mineralization, and synergistic co-evolution with plants. With the increase in world's population the demand for agriculture yield has increased tremendously and thereby leading to large scale production of chemical fertilizers. Since the use of fertilizers and pesticides in the agricultural fields have caused degradation of soil quality and fertility, thus the expansion of agricultural land with fertile soil is near impossible, hence researchers and scientists have sifted their attention for a safer and productive means of agricultural practices. Plant growth promoting rhizobacteria (PGPR) has been functioning as a co-evolution between plants and microbes showing antagonistic and synergistic interactions with microorganisms and the soil. Microbial revitalization using plant growth promoters had been achieved through direct and indirect approaches like bio-fertilization, invigorating root growth, rhizoremediation, disease resistance etc. Although, there are a wide variety of PGPR and its allies, their role and usages for sustainable agriculture remains controversial and restricted. There is also variability in the performance of PGPR that may be due to various environmental factors that might affect their growth and proliferation in the plants. These gaps and limitations can be addressed through use of modern approaches and techniques such as nano-encapsulation and micro-encapsulation along with exploring multidisciplinary research that combines applications in biotechnology, nanotechnology, agro biotechnology, chemical engineering and material science and bringing together different ecological and functional biological approaches to provide new formulations and opportunities with immense potential.

A review of germination and early growth as a proxy for plant fitness under petrogenic contamination - knowledge gaps and recommendations

Germination-an important stage in the life cycle of plants-is susceptible to the presence of soil contaminants. Since the early 1990s, the use of germination tests to screen multiple plant species to select candidates for phytoremediation has received much attention. This is due to its inexpensive methodology and fast assessment relative to greenhouse or field growth studies. Surprisingly, no comprehensive synthesis is available of these studies in the scientific literature. As more plant species are added to phytoremediation databases, it is important to encapsulate the knowledge thus far and revise protocols. In this review, we have summarised previously-documented effects of petroleum hydrocarbons on germination and seedling growth. The methods and materials of previous studies are presented in tabulated form. Common practice includes the use of cellulose acetate filter paper, plastic Petri dishes, and low numbers of seeds and replicates. A general bias was observed for the screening of cultivated crops as opposed to native species, even though the latter may be better suited to site conditions. The relevance of germination studies as important ecotoxicological tools is highlighted with the proposed use of root imaging software. Screening of novel plant species, particularly natives, is recommended with selection focussed on (i) species phylogeny, (ii) plant morphological and functional traits, and (iii) tolerance towards harsh environmental stresses. Recommendations for standardised protocols for germination and early growth monitoring are made in order to improve the robustness of statistical modelling and species selection in future phytoremediation evaluations and field programs.

New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts

Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. Graphical Abstract ᅟ.

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve

Pristine forest ecosystems provide a unique perspective for the study of plant-associated microbiota since they host a great microbial diversity. Although the Amazon forest is one of the hotspots of biodiversity around the world, few metagenomic studies described its microbial community diversity thus far. Understanding the environmental factors that can cause shifts in microbial profiles is key to improving soil health and biogeochemical cycles. Here we report a taxonomic and functional characterization of the microbiome from the rhizosphere of Brosimum guianense (Snakewood), a native tree, and bulk soil samples from a pristine Brazilian Amazon forest reserve (Cuniã), for the first time by the shotgun approach. We identified several fungi and bacteria taxon significantly enriched in forest rhizosphere compared to bulk soil samples. For archaea, the trend was the opposite, with many archaeal phylum and families being considerably more enriched in bulk soil compared to forest rhizosphere. Several fungal and bacterial decomposers like Postia placenta and Catenulispora acidiphila which help maintain healthy forest ecosystems were found enriched in our samples. Other bacterial species involved in nitrogen (Nitrobacter hamburgensis and Rhodopseudomonas palustris) and carbon cycling (Oligotropha carboxidovorans) were overrepresented in our samples indicating the importance of these metabolic pathways for the Amazon rainforest reserve soil health. Hierarchical clustering based on taxonomic similar microbial profiles grouped the forest rhizosphere samples in a distinct clade separated from bulk soil samples. Principal coordinate analysis of our samples with publicly available metagenomes from the Amazon region showed grouping into specific rhizosphere and bulk soil clusters, further indicating distinct microbial community profiles. In this work, we reported significant shifts in microbial community structure between forest rhizosphere and bulk soil samples from an Amazon forest reserve that are probably caused by more than one environmental factors such as rhizosphere and soil depth.

Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites

Derelict mines pose potential risks to environmental health. Several factors such as soil structure, organic matter, and nutrient content are the greatly affected qualities in mined soils. Soil microbial communities are an important element for successful reclamation because of their major role in nutrient cycling, plant establishment, geochemical transformations, and soil formation. Yet, microorganisms generally remain an undervalued asset in mined sites. The microbial diversity in derelict mine sites consists of diverse species belonging to four key phyla: Proteobacteria, Acidobacteria, Firmicutes, and Bacteroidetes. The activity of plant symbiotic microorganisms including root-colonizing rhizobacteria and ectomycorrhizal fungi of existing vegetation in the mined sites is very high since most of these microbes are extremophiles. This review outlines the importance of microorganisms to soil health and the rehabilitation of derelict mines and how microbial activity and diversity can be exploited to better plan the soil rehabilitation. Besides highlighting the major breakthroughs in the application of microorganisms for mined site reclamation, we provide a critical view on plant-microbiome interactions to improve revegetation at the mined sites. Also, the need has been emphasized for deciphering the molecular mechanisms of adaptation and resistance of rhizosphere and non-rhizosphere microbes in abandoned mine sites, understanding their role in remediation, and subsequent harnessing of their potential to pave the way in future rehabilitation strategies for mined sites.

Different genotypes of Silene vulgaris (Moench) Garcke grown on chromium-contaminated soils influence root organic acid composition and rhizosphere bacterial communities

Plant-microbe interactions are considered to be important processes determining the efficiency of phytoremediation of heavy metal-contaminated soils. However, relatively little is known about how these interactions are influenced by chromium (Cr) contamination. The effect of Cr stress on metal uptake, root organic acid composition, and rhizosphere bacterial communities was studied using two genotypes of the metallophyte Silene vulgaris, which have shown different tolerance to Cr(VI). The results indicated that root biomass and shoot biomass were not significantly influenced by Cr treatment, but metal uptake in shoots and roots was significantly impacted by the genotype. Principal component analyses (PCA) showed that variation in organic acids oxalic, citric, malic, formic, lactic, acetic, and succinic differed between genotypes. Changes in root organic acid contents in response to Cr revealed a significant increase of oxalic acid in genotype SV-21. The denaturing gradient gel electrophoresis (DGGE) cluster analysis showed that the community structure (determined by PCR-DGGE) was affected by plant genotype and, to a lesser extent, by Cr contamination, the first being the most influential factor shaping the rhizosphere microbiome. Under Cr pollution, a shift in the relative abundance of specific taxa was found and dominant phylotypes were identified as Variovorax in SV-21 and Chitinophaga niastensis, Pontibacter sp., and Ramlibacter sp. in SV-38. These results provided the basis for further studies aimed at the combined use of plants and soil microorganisms in the remediation of Cr-polluted soils.

Bacterial endophytes enhance phytostabilization in soils contaminated with uranium and lead

The combined use of plants and bacteria is a promising approach for the remediation of polluted soil. In the current study, the potential of bacterial endophytes in partnership with Leptochloa fusca (L.) Kunth was evaluated for the remediation of uranium (U)- and lead (Pb)-contaminated soil. L. fusca was vegetated in contaminated soil and inoculated with three different endophytic bacterial strains, Pantoea stewartii ASI11, Enterobacter sp. HU38, and Microbacterium arborescens HU33, individually as well as in combination. The results showed that the L. fusca can grow in the contaminated soil. Bacterial inoculation improved plant growth and phytoremediation capacity: this manifested in the form of a 22-51% increase in root length, 25-62% increase in shoot height, 10-21% increase in chlorophyll content, and 17-59% more plant biomass in U- and Pb-contaminated soils as compared to plants without bacterial inoculation. Although L. fusca plants showed potential to accumulate U and Pb in their root and shoot on their own, bacterial consortia further enhanced metal uptake capacity by 53-88% for U and 58-97% for Pb. Our results indicate that the combination of L. fusca and endophytic bacterial consortia can effectively be used for the phytostabilization of both U- and Pb-contaminated soils.

Characterization and degradation potential of diesel-degrading bacterial strains for application in bioremediation

Bioremediation of polluted soils is a promising technique with low environmental impact, which uses soil organisms to degrade soil contaminants. In this study, 19 bacterial strains isolated from a diesel-contaminated soil were screened for their diesel-degrading potential, biosurfactant (BS) production, and biofilm formation abilities, all desirable characteristics when selecting strains for re-inoculation into hydrocarbon-contaminated soils. Diesel-degradation rates were determined in vitro in minimal medium with diesel as the sole carbon source. The capacity to degrade diesel range organics (DROs) of strains SPG23 (Arthobacter sp.) and PF1 (Acinetobacter oleivorans) reached 17-26% of total DROs after 10 days, and 90% for strain GK2 (Acinetobacter calcoaceticus). The amount and rate of alkane degradation decreased significantly with increasing carbon number for strains SPG23 and PF1. Strain GK2, which produced BSs and biofilms, exhibited a greater extent, and faster rate of alkane degradation compared to SPG23 and PF1. Based on the outcomes of degradation experiments, in addition to BS production, biofilm formation capacities, and previous genome characterizations, strain GK2 is a promising candidate for microbial-assisted phytoremediation of diesel-contaminated soils. These results are of particular interest to select suitable strains for bioremediation, not only presenting high diesel-degradation rates, but also other characteristics which could improve rhizosphere colonization.

Bacteria facilitate prey retention by the pitcher plant Darlingtonia californica

Bacteria are hypothesized to provide a variety of beneficial functions to plants. Many carnivorous pitcher plants, for example, rely on bacteria for digestion of captured prey. This bacterial community may also be responsible for the low surface tensions commonly observed in pitcher plant digestive fluids, which might facilitate prey capture. I tested this hypothesis by comparing the physical properties of natural pitcher fluid from the pitcher plant Darlingtonia californica and cultured 'artificial' pitcher fluids and tested these fluids' prey retention capabilities. I found that cultures of pitcher leaves' bacterial communities had similar physical properties to raw pitcher fluids. These properties facilitated the retention of insects by both fluids and hint at a previously undescribed class of plant-microbe interaction.

Coliform Bacteria for Bioremediation of Waste Hydrocarbons

Raw, domestic sewage of Kuwait City contained about 106 ml-1 colony forming units of Enterobacter hormaechei subsp. oharae (56.6%), Klebsiella spp. (36%), and Escherichia coli (7.4%), as characterized by their 16S rRNA-gene sequences. The isolated coliforms grew successfully on a mineral medium with crude oil vapor as a sole source of carbon and energy. Those strains also grew, albeit to different degrees, on individual n-alkanes with carbon chains between C9 and C36 and on the individual aromatic hydrocarbons, toluene, naphthalene, phenanthrene, and biphenyl as sole sources of carbon and energy. These results imply that coliforms, like other hydrocarbonoclastic microorganisms, oxidize hydrocarbons to the corresponding alcohols and then to aldehydes and fatty acids which are biodegraded by β-oxidation to acetyl CoA. The latter is a well-known key intermediate in cell material and energy production. E. coli cells grown in the presence of n-hexadecane (but not in its absence) exhibited typical intracellular hydrocarbon inclusions, as revealed by transmission electron microscopy. Raw sewage samples amended with crude oil, n-hexadecane, or phenanthrene lost these hydrocarbons gradually with time. Meanwhile, the numbers of total and individual coliforms, particularly Enterobacter, increased. It was concluded that coliform bacteria in domestic sewage, probably in other environmental materials too, are effective hydrocarbon-biodegrading microorganisms.

Alleviation of Heavy Metal Stress in Plants and Remediation of Soil by Rhizosphere Microorganisms

Increasing concentration of heavy metals (HM) due to various anthropogenic activities is a serious problem. Plants are very much affected by HM pollution particularly in contaminated soils. Survival of plants becomes tough and its overall health under HM stress is impaired. Remediation of HM in contaminated soil is done by physical and chemical processes which are costly, time-consuming, and non-sustainable. Metal–microbe interaction is an emerging but under-utilized technology that can be exploited to reduce HM stress in plants. Several rhizosphere microorganisms are known to play essential role in the management of HM stresses in plants. They can accumulate, transform, or detoxify HM. In general, the benefit from these microbes can have a vast impact on plant’s health. Plant–microbe associations targeting HM stress may provide another dimension to existing phytoremediation and rhizoremediation uses. In this review, applied aspects and mechanisms of action of heavy metal tolerant-plant growth promoting (HMT-PGP) microbes in ensuring plant survival and growth in contaminated soils are discussed. The use of HMT-PGP microbes and their interaction with plants in remediation of contaminated soil can be the approach for the future. This low input and sustainable biotechnology can be of immense use/importance in reclaiming the HM contaminated soils, thus increasing the quality and yield of such soils.

Rhizosphere effect is stronger than PAH concentration on shaping spatial bacterial assemblages along centimetre-scale depth gradients

At centimetre scale, soil bacterial assemblages are shaped by both abiotic (edaphic characteristics and pollutants) and biotic parameters. In a rhizobox experiment carried out on planted industrial soil contaminated with polycyclic aromatic hydrocarbons (PAHs), we previously showed that pollution was distributed randomly with hot and cold spots. Therefore, in the present study, we investigated the effect of this patchy PAH distribution on the bacterial community assemblage and compared it with that of root depth gradients found in the rhizosphere of either alfalfa or ryegrass. Sequencing of 16S rRNA amplicons revealed a higher bacterial diversity in ryegrass rhizosphere and enrichment in specific taxa by the 2 plant species. Indeed, Bacteroidetes, Firmicutes, and Gammaproteobacteria were globally favored in alfalfa, whereas Acidimicrobiia, Chloroflexi, Alpha-, and Betaproteobacteria were globally favored in ryegrass rhizosphere. The presence of alfalfa created depth gradients of root biomass, carbohydrate, and pH, and actually shaped the bacterial assemblage, favoring Actinobacteria near the surface and Gemmatimonadetes and Proteobacteria at greater depths. Contrarily, the bacterial assemblage was homogeneous all along depths of the ryegrass root system. With both plant species, the PAH content and random distribution had no significant effect on bacterial assemblage. Globally, at centimeter scale, bacterial community assemblages were mostly shaped by soil physical and chemical depth gradients induced by root growth but not by patchy PAH content.

Secondary compound hypothesis revisited: Selected plant secondary metabolites promote bacterial degradation of cis-1,2-dichloroethylene (cDCE)

Cis-1,2-dichloroethylene (cDCE), which is a common hazardous compound, often accumulates during incomplete reductive dechlorination of higher chlorinated ethenes (CEs) at contaminated sites. Simple monoaromatics, such as toluene and phenol, have been proven to induce biotransformation of cDCE in microbial communities incapable of cDCE degradation in the absence of other carbon sources. The goal of this microcosm-based laboratory study was to discover non-toxic natural monoaromatic secondary plant metabolites (SPMEs) that could enhance cDCE degradation in a similar manner to toluene and phenol. Eight SPMEs were selected on the basis of their monoaromatic molecular structure and widespread occurrence in nature. The suitability of the SPMEs chosen to support bacterial growth and to promote cDCE degradation was evaluated in aerobic microbial cultures enriched from cDCE-contaminated soil in the presence of each SPME tested and cDCE. Significant cDCE depletions were achieved in cultures enriched on acetophenone, phenethyl alcohol, p-hydroxybenzoic acid and trans-cinnamic acid. 16S rRNA gene sequence analysis of each microbial community revealed ubiquitous enrichment of bacteria affiliated with the genera Cupriavidus, Rhodococcus, Burkholderia, Acinetobacter and Pseudomonas. Our results provide further confirmation of the previously stated secondary compound hypothesis that plant metabolites released into the rhizosphere can trigger biodegradation of environmental pollutants, including cDCE.

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates

Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant–microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.

The role of artificial root exudate components in facilitating the degradation of pyrene in soil

Root exudates play an important role in the phytoremediation of soils contaminated by organic pollutants, but how root exudate components affect the remediation process is not well understood. In this study, we explored the effects and mechanisms of the major root exudates, including glucose, organic acids, and serine, in the rhizoremediation of pyrene-contaminated soil. The results showed that glucose increased the degradation of pyrene (54.3 ± 1.7%) most significantly compared to the organic acids (45.5 ± 2.5%) and serine (43.2 ± 0.1%). Glucose could significantly facilitate the removal of pyrene in soil through promoting dehydrogenase activity indicated by a positive correlation between the removal efficiency of pyrene and the soil dehydrogenase activity (p < 0.01). Furthermore, root exudates were able to change soil microbial community, particularly the bacterial taxonomic composition, thereby affecting the biodegradation of pyrene. Glucose could alter soil microbial community and enhance the amount of Mycobacterium markedly, which is dominant in the degradation of pyrene. These findings provide insights into the mechanisms by which root exudates enhance the degradation of organic contaminants and advance our understanding of the micro-processes involved in rhizoremediation.

Plant-growth promoting Candida sp. AVGB4 with capability of 4-nitroaniline biodegradation under drought stress

This study focused on rhizospheric yeast capable of degrading a priority pollutant, 4-nitroaniline (4-NA), under drought stress. Candida sp. AVGB4 (AVGB4) inhabiting in soil was isolated and characterized with plant-growth promoting (PGP) traits. 4-NA-dependent growth kinetic and biodegradation kinetics were analyzed and revealed 4-NA complete degradation and tolerance property. AVGB4 proliferation, PGP activities, and 4-NA degradation activity were well maintained under drought stress induced by PEG-6000 incorporation, and could be strengthened in the presence of succinate, an organic compound generally found in plant root exudates. The in vitro experiments proved that AVGB4 significantly enhanced plant growth and increased the shoot and root biomass of Vigna radiata plant in the absence or presence of 4-NA. The overall results including cytogenotoxicity and phytotoxicity test with legumes indicated that not only AVGB4 was capable of 4-NA detoxification facilitating plants to cope with chemical-toxicity stress, but it also has advantageous role in promoting plant growth and sustainable rhizoremediation of 4-NA contaminated sites.

Isolation and characterization of Magnetospirillum sp. strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model

Previously, Planted Fixed-Bed Reactors (PFRs) have been used to investigate microbial toluene removal in the rhizosphere of constructed wetlands. Aerobic toluene degradation was predominant in these model systems although bulk redox conditions were hypoxic to anoxic. However, culture-independent approaches indicated also that microbes capable of anaerobic toluene degradation were abundant. Therefore, we aimed at isolating anaerobic-toluene degraders from one of these PFRs. From the obtained colonies which consisted of spirilli-shaped bacteria, a strain designated 15–1 was selected for further investigations. Analysis of its 16S rRNA gene revealed greatest similarity (99%) with toluene-degrading Magnetospirillum sp. TS-6. Isolate 15–1 grew with up to 0.5 mM of toluene under nitrate-reducing conditions. Cells reacted to higher concentrations of toluene by an increase in the degree of saturation of their membrane fatty acids. Strain 15–1 contained key genes for the anaerobic degradation of toluene via benzylsuccinate and subsequently the benzoyl-CoA pathway, namely bssA, encoding for the alpha subunit of benzylsuccinate synthase, bcrC for subunit C of benzoyl-CoA reductase and bamA for 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Finally, most members of a clone library of bssA generated from the PFR had highest similarity to bssA from strain 15–1. Our study provides insights about the physiological capacities of a strain of Magnetospirillum isolated from a planted system where active rhizoremediation of toluene is taking place.

Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships

Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.

Bacillus aryabhattai SRB02 tolerates oxidative and nitrosative stress and promotes the growth of soybean by modulating the production of phytohormones

Plant growth promoting rhizobacteria (PGPR) are diverse, naturally occurring bacteria that establish a close association with plant roots and promote the growth and immunity of plants. Established mechanisms involved in PGPR-mediated plant growth promotion include regulation of phytohormones, improved nutrient availability, and antagonistic effects on plant pathogens. In this study, we isolated a bacterium from the rhizospheric soil of a soybean field in Chungcheong buk-do, South Korea. Using 16S rRNA sequencing, the bacterium was identified as Bacillus aryabhattai strain SRB02. Here we show that this strain significantly promotes the growth of soybean. Gas chromatography-mass spectrometry analysis showed that SRB02 produced significant amounts of abscisic acid, indole acetic acid, cytokinin and different gibberellic acids in culture. SRB02-treated soybean plants showed significantly better heat stress tolerance than did untreated plants. These plants also produced consistent levels of ABA under heat stress and exhibited ABA-mediated stomatal closure. High levels of IAA, JA, GA12, GA4, and GA7, were recorded in SRB02-treated plants. These plants produced longer roots and shoots than those of control plants. B. aryabhattai SRB02 was found to be highly tolerant to oxidative stress induced by H2O2 and MV potentiated by high catalase (CAT) and superoxide dismutase (SOD) activities. SRB02 also tolerated high nitrosative stress induced by the nitric oxide donors GSNO and CysNO. Because of these attributes, B. aryabhattai SRB02 may prove to be a valuable resource for incorporation in biofertilizers and other soil amendments that seek to improve crop productivity.

Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects

Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.

Phyto-rhizoremediation of polychlorinated biphenyl contaminated soils: An outlook on plant-microbe beneficial interactions

Polychlorinated biphenyls (PCBs) are toxic chemicals, recalcitrant to degradation, bioaccumulative and persistent in the environment, causing adverse effects on ecosystems and human health. For this reason, the remediation of PCB-contaminated soils is a primary issue to be addressed. Phytoremediation represents a promising tool for in situ soil remediation, since the available physico-chemical technologies have strong environmental and economic impacts. Plants can extract and metabolize several xenobiotics present in the soil, but their ability to uptake and mineralize PCBs is limited due to the recalcitrance and low bioavailability of these molecules that in turn impedes an efficient remediation of PCB-contaminated soils. Besides plant degradation ability, rhizoremediation takes into account the capability of soil microbes to uptake, attack and degrade pollutants, so it can be seen as the most suitable strategy to clean-up PCB-contaminated soils. Microbes are in fact the key players of PCB degradation, performed under both aerobic and anaerobic conditions. In the rhizosphere, microbes and plants positively interact. Microorganisms can promote plant growth under stressed conditions typical of polluted soils. Moreover, in this specific niche, root exudates play a pivotal role by promoting the biphenyl catabolic pathway, responsible for microbial oxidative PCB metabolism, and by improving the overall PCB degradation performance. Besides rhizospheric microbial community, also the endophytic bacteria are involved in pollutant degradation and represent a reservoir of microbial resources to be exploited for bioremediation purposes. Here, focusing on plant-microbe beneficial interactions, we propose a review of the available results on PCB removal from soil obtained combining different plant and microbial species, mainly under simplified conditions like greenhouse experiments. Furthermore, we discuss the potentiality of "omics" approaches to identify PCB-degrading microbes, an aspect of paramount importance to design rhizoremediation strategies working efficiently under different environmental conditions, pointing out the urgency to expand research investigations to field scale.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Bioremediation techniques-classification based on site of application: principles, advantages, limitations and prospects

Environmental pollution has been on the rise in the past few decades owing to increased human activities on energy reservoirs, unsafe agricultural practices and rapid industrialization. Amongst the pollutants that are of environmental and public health concerns due to their toxicities are: heavy metals, nuclear wastes, pesticides, green house gases, and hydrocarbons. Remediation of polluted sites using microbial process (bioremediation) has proven effective and reliable due to its eco-friendly features. Bioremediation can either be carried out ex situ or in situ, depending on several factors, which include but not limited to cost, site characteristics, type and concentration of pollutants. Generally, ex situ techniques apparently are more expensive compared to in situ techniques as a result of additional cost attributable to excavation. However, cost of on-site installation of equipment, and inability to effectively visualize and control the subsurface of polluted sites are of major concerns when carrying out in situ bioremediation. Therefore, choosing appropriate bioremediation technique, which will effectively reduce pollutant concentrations to an innocuous state, is crucial for a successful bioremediation project. Furthermore, the two major approaches to enhance bioremediation are biostimulation and bioaugmentation provided that environmental factors, which determine the success of bioremediation, are maintained at optimal range. This review provides more insight into the two major bioremediation techniques, their principles, advantages, limitations and prospects.

Phytoremediation of fuel oil and lead co-contaminated soil by Chromolaena odorata in association with Micrococcus luteus

Phytoremediation is widely promoted as a cost-effective technology for treating heavy metal and total petroleum hydrocarbon (TPH) co-contaminated soil. This study investigated the concurrent removal of TPHs and Pb in co-contaminated soil (27,000 mg kg(-1) TPHs, 780 mg kg(-1) Pb) by growing Siam weed (Chromolaena odorata) in a pot experiment for 90 days. There were four treatments: co-contaminated soil; co-contaminated soil with C. odorata only; co-contaminated soil with C. odorata and Micrococcus luteus inoculum; and co-contaminated soil with M. luteus only. C. odorata survived and grew well in the co-contaminated soil. C. odorata with M. luteus showed the highest Pb accumulation (513.7 mg kg(-1)) and uptake (7.7 mg plant(-1)), and the highest reduction percentage of TPHs (52.2%). The higher TPH degradation in vegetated soils indicated the interaction between the rhizosphere microorganisms and plants. The results suggested that C. odorata together with M. luteus and other rhizosphere microorganisms is a promising candidate for the removal of Pb and TPHs in co-contaminated soils.

From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.