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

Oil-Contaminated Soil Remediation with Biodegradation by Autochthonous Microorganisms and Phytoremediation by Maize (Zea mays)

Biological methods are currently the most commonly used methods for removing hazardous substances from land. This research work focuses on the remediation of oil-contaminated land. The biodegradation of aliphatic hydrocarbons and PAHs as a result of inoculation with biopreparations B1 and B2 was investigated. Biopreparation B1 was developed on the basis of autochthonous bacteria, consisting of strains Dietzia sp. IN118, Gordonia sp. IN101, Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus globerulus IN113 and Raoultella sp. IN109, whereas biopreparation B2 was enriched with fungi, such as Aspergillus sydowii, Aspergillus versicolor, Candida sp., Cladosporium halotolerans, Penicillium chrysogenum. As a result of biodegradation tests conducted under ex situ conditions for soil inoculated with biopreparation B1, the concentrations of TPH and PAH were reduced by 31.85% and 27.41%, respectively. Soil inoculation with biopreparation B2 turned out to be more effective, as a result of which the concentration of TPH was reduced by 41.67% and PAH by 34.73%. Another issue was the phytoremediation of the pre-treated G6-3B2 soil with the use of Zea mays. The tests were carried out in three systems (system 1-soil G6-3B2 + Zea mays; system 2-soil G6-3B2 + biopreparation B2 + Zea mays; system 3-soil G6-3B2 + biopreparation B2 with γ-PGA + Zea mays) for 6 months. The highest degree of TPH and PAH reduction was obtained in system 3, amounting to 65.35% and 60.80%, respectively. The lowest phytoremediation efficiency was recorded in the non-inoculated system 1, where the concentration of TPH was reduced by 22.80% and PAH by 18.48%. Toxicological tests carried out using PhytotoxkitTM, OstracodtoxkitTM and Microtox® Solid Phase tests confirmed the effectiveness of remediation procedures and showed a correlation between the concentration of petroleum hydrocarbons in the soil and its toxicity. The results obtained during the research indicate the great potential of bioremediation practices with the use of microbial biopreparations and Zea mays in the treatment of soils contaminated with petroleum hydrocarbons.

A risk management framework for Gentle Remediation Options (GRO)

Gentle Remediation Options (GRO) are remediation measures involving plants, fungi, bacteria, and soil amendments that can be applied to manage risks at contaminated sites. Several studies and decision-support tools promote the wider range of benefits provided by GRO, but there is still skepticism regarding GRO implementation. Key issues that need to be better communicated are the various risk mitigation mechanisms, the required risk reduction for an envisioned land use, and the time perspective associated with the risk mitigation mechanisms. To increase the viability and acceptance of GRO, the phytomanagement approach implies the combination of GRO with beneficial green land use, gradually reducing risks and restoring ecosystem services. To strengthen the decision basis for GRO implementation in practice, this paper proposes a framework for risk management and communication of GRO applications to support phytomanagement strategies at contaminated sites. The mapping of the risk mitigation mechanisms is done by an extensive literature review and the Swedish national soil guideline value model is used to derive the most relevant human health exposure pathways and ecological risks for generic green land use scenarios. Results indicate that most of the expected risk mitigation mechanisms are supported by literature, but that knowledge gaps still exist. The framework is demonstrated to support the identification of GRO options for the case study site given two envisioned land uses: biofuel park and allotment garden. A more easily understandable risk management framework, as proposed here, is expected to act as a communication tool to educate decision-makers, regulatory bodies and other stakeholders for better understanding of risk mitigation mechanisms and preliminary timeframes of various GRO, particularly in the early stages of a brownfield redevelopment project.

Plant Growth Promoting and Stress Mitigating Abilities of Soil Born Microorganisms

Abiotic stresses affect the plant growth in different ways and at different developmental stages that reduce the crop yields. The increasing world population continually demands more crop yields; therefore it is important to use low-cost technologies against abiotic stresses to increase crop productivity. Soil microorganisms survive in the soil associated with plants in extreme condition. It was demonstrated that these beneficial microorganisms promote plant growth and development under various stresses. The soil microbes interact with the plant through rhizospheric or endophytic association and promote the plant growth through different processes such as nutrients mobilization, disease suppression, and hormone secretions. The microorganisms colonized in the rhizospheric region and imparted the abiotic stress tolerance by producing 1-aminocyclopropane-1- carboxylate (ACC) deaminase, antioxidant, and volatile compounds, inducing the accumulation of osmolytes, production of exopolysaccharide, upregulation or downregulation of stress genes, phytohormones and change the root morphology. A large number of these rhizosphere microorganisms are now patented. In the present review, an attempt was made to throw light on the mechanism of micro-organism that operates during abiotic stresses and promotes plant survival and productivity.

Oak (Quercus robur) Associated Endophytic Paenibacillus sp. Promotes Poplar (Populus spp.) Root Growth In Vitro

Soil fertilization is necessary for high-demand crop production in agriculture and forestry. Our current dependence on chemical fertilizers has significant harmful side effects. Biofertilization using microorganisms is a sustainable way to limit the need for chemical fertilizers in various enterprises. Most plant endophytic bacteria have thus far been unstudied for their plant growth promoting potential and hence present a novel niche for new biofertilizer strains. We isolated English oak (Quercus robur) endophytic bacteria and tested them for plant growth promoting traits (PGPTs) such as nitrogen fixation, phosphate mineralization/solubilization, siderophore and indole-3-acetic acid (IAA) production. We also investigated the effect the selected isolate had on poplar (Populus spp.) microshoot vegetative growth parameters in vitro. In total 48 bacterial strains were isolated, attributed to Bacillus, Delftia, Paenibacillus, Pantoea and Pseudomonas genera. All the isolates displayed at least three PGPTs, with 39.6% of the isolates displaying all five (all were Pseudomonas spp.) and 18.75% displaying four. Based on relative abundance, Paenibacillus sp. isolate was selected for the poplar microshoot inoculation study. The isolate had a significant positive effect on poplar microshoot root growth and development. Two tested poplar genotypes both had increased lateral root number and density, fresh and dry root biomass. Furthermore, one genotype had increased length and number of adventitious roots as well as a decrease in fresh aboveground biomass. The root enhancement was attributed to IAA production. We propose this isolate for further studies as a potential biofertilizer.

Isolation, Biochemical and Genomic Characterization of Glyphosate Tolerant Bacteria to Perform Microbe-Assisted Phytoremediation

The large-scale use of the herbicide glyphosate leads to growing ecotoxicological and human health concerns. Microbe-assisted phytoremediation arises as a good option to remove, contain, or degrade glyphosate from soils and waterbodies, and thus avoid further spreading to non-target areas. To achieve this, availability of plant-colonizing, glyphosate-tolerant and -degrading strains is required and at the same time, it must be linked to plant-microorganism interaction studies focusing on a substantive ability to colonize the roots and degrade or transform the herbicide. In this work, we isolated bacteria from a chronically glyphosate-exposed site in Argentina, evaluated their glyphosate tolerance using the minimum inhibitory concentration assay, their in vitro degradation potential, their plant growth-promotion traits, and performed whole genome sequencing to gain insight into the application of a phytoremediation strategy to remediate glyphosate contaminated agronomic soils. Twenty-four soil and root-associated bacterial strains were isolated. Sixteen could grow using glyphosate as the sole source of phosphorous. As shown in MIC assay, some strains tolerated up to 10000 mg kg^–1 of glyphosate. Most of them also demonstrated a diverse spectrum of in vitro plant growth-promotion traits, confirmed in their genome sequences. Two representative isolates were studied for their root colonization. An isolate of Ochrobactrum haematophilum exhibited different colonization patterns in the rhizoplane compared to an isolate of Rhizobium sp. Both strains were able to metabolize almost 50% of the original glyphosate concentration of 50 mg l^–1 in 9 days. In a microcosms experiment with Lotus corniculatus L, O. haematophilum performed better than Rhizobium, with 97% of glyphosate transformed after 20 days. The results suggest that L. corniculatus in combination with to O. haematophilum can be adopted for phytoremediation of glyphosate on agricultural soils. An effective strategy is presented of linking the experimental data from the isolation of tolerant bacteria with performing plant-bacteria interaction tests to demonstrate positive effects on the removal of glyphosate from soils.

A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus

In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.

Characterization of microbial community and resistance gene (CzcA) shifts in up-flow constructed wetlands-microbial fuel cell treating Zn (II) contaminated wastewater

The main aim of this work was to characterize the microbial community structure and resistance gene (CzcA) shifts in up-flow constructed wetlands-microbial fuel cell (CW-MFC) treating Zn (II) contaminated wastewater. Two CW-MFC devices were operated, i.e. the experimental group (EG) treating Zn (II) wastewater, and the control group (CG) treating Zn (II)-free wastewater. The results showed the CW-MFC combination exhibited good removal efficiency on Zn (II), while the average voltage, the power density and the removal rates (TP, TN, NH₄⁺-N and COD) significantly reduced (p < 0.05). The microbial community structure showed that the Zn (II) significantly reduced the abundance of some functional genus (p < 0.05), such as Ochrobactrum, Nitrosomonas, Pseudomonas and Dechloromonas. Zn (II) inhibited the microbial richness in the anode, but it played a positive role in the cathode. Anew, the expression of the CzcA in the CW-MFC was promoted by Zn (II), particularly in the cathode.

Influence of plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 using Helianthus annuus on degradation of endosulfan from contaminated soil

Endosulfan is a broad spectrum insecticide used in agriculture for protection of various food and non-food crops. It is persistent in nature and hence found in soil, air and water. The potential use of plants and microorganisms for the removal of endosulfan from soil was studied. Helianthus annuus plant was grown in soil spiked with 5, 10, 25 and 50 mg kg^-1 concentrations of endosulfan and inoculated with plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 for 40, 80 and 120 days. Potential of plant for endosulfan uptake was evaluated by investigating the endosulfan levels in plant tissues (root and shoot). The results indicated that endosulfan accumulation followed the pattern of root > shoot as well as decrease in uptake of endosulfan in root and shoot of a plant grown in bacterial inoculated soil as compared to un-inoculated soil. Bacterial inoculation had a positive effect on endosulfan degradation. Maximum degradation of 92% at 5 mg kg^-1 of endosulfan in soil was observed on inoculation with PRB101 after 120 days of inoculation. The results showed that plant growth promoting bacteria enhances plant biomass production. Lipid peroxidation was also estimated by determining the malondialdehyde (MDA) production, which is a biomarker of oxidative damage. Decrease in MDA formation by root and leaves of plants grown in the bacteria inoculated plant was also observed. The results suggested the effectiveness of plant growth promoting rhizobacteria to boost accumulation potential, biomass production and enhance remediation of endosulfan contaminated soil.

Effect of endosulfan tolerant bacterial isolates (Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42) with Helianthus annuus on remediation of endosulfan from contaminated soil

Endosulfan contaminated soil has become an important risk to the environment and human health worldwide. In the present study, endosulfan tolerant bacterial strain Delftia lacustris IITISM30 and Klebsiella aerogenes IITISM42 were isolated from pesticide stressed agricultural soil and tested for plant growth promoting activities. A pot experiment was performed using Helianthus annuus, grown in soil supplemented with endosulfan and inoculated with pure and consortium of bacterial strain IITISM30 and IITISM42. Inoculation increased plant biomass production and endosulfan degradation, maximum degradation (90% at 5 mg kg^-1 of soil) was observed by inoculation with a consortium of bacterial strain IITISM30 and IITISM42. Moreover, there was significantly less endosulfan accumulation was observed in roots and shoots of bacterial inoculated plants as compared to uninoculated plants. Decrease in production of malonialdehyde (MDA) was noticed on inoculation of a bacterial strain. The study demonstrated that inoculation of a consortium of endosulfan tolerant plant growth promoting bacterial isolates could more effectively remediate endosulfan contaminated soils and decrease endosulfan residues in plants, than individual strains. Moreover, it revealed that combined use of H. annuus and endosulfan tolerant bacterial isolates IITISM30 and IITISM42 has great potential for remediating endosulfan contaminated soil.

Endophyte-enhanced phytoremediation of DDE-contaminated using Cucurbita pepo: A field trial

Although the use of the pesticide 2,2-bis(p-chlorophenyl)-1,1,1-trichloroethane (DDT) was banned from the mid-1970s, its most abundant and recalcitrant degradation product, 2,2-bis(p-chlorophenyl)-1,1-dichloro-ethylene (DDE), is still present in terrestrial and aquatic ecosystems worldwide. Zucchini (Cucurbita pepo ssp. pepo) has been shown to accumulate high concentrations of DDE and was proposed for phytoremediation of contaminated soils. We performed a field trial covering a full plant life cycle. C. pepo plants inoculated with the plant growth-promoting endophytic strains Sphingomonas taxi UH1, Methylobacterium radiotolerans UH1, Enterobacter aerogenes UH1, or a consortium combining these 3 strains were grown on a DDE-contaminated field for 100 days. The effects of these inoculations were examined at both the plant level, by evaluating plant weight and plant DDE-content, and at the level of the cultivable and total endophytic communities. Inoculating plants with S. taxi UH1, M. radiotolerans UH1, and the consortium increased plant weight. No significant effects of the inoculations were observed on DDE-concentrations in plant tissues. However, the amount of DDE accumulated by C. pepo plants per growing season was significantly higher for plants that were inoculated with the consortium of the 3 strains. Therefore, inoculation of C. pepo with DDE-degrading endophytes might be promising for phytoremediation applications.

Seed Endophyte Microbiome of Crotalaria pumila Unpeeled: Identification of Plant-Beneficial Methylobacteria

Metal contaminated soils are increasing worldwide. Metal-tolerant plants growing on metalliferous soils are fascinating genetic and microbial resources. Seeds can vertically transmit endophytic microorganisms that can assist next generations to cope with environmental stresses, through yet poorly understood mechanisms. The aims of this study were to identify the core seed endophyte microbiome of the pioneer metallophyte Crotalaria pumila throughout three generations, and to better understand the plant colonisation of the seed endophyte Methylobacterium sp. Cp3. Strain Cp3 was detected in C. pumila seeds across three successive generations and showed the most dominant community member. When inoculated in the soil at the time of flowering, strain Cp3 migrated from soil to seeds. Using confocal microscopy, Cp3-mCherry was demonstrated to colonise the root cortex cells and xylem vessels of the stem under metal stress. Moreover, strain Cp3 showed genetic and in planta potential to promote seed germination and seedling development. We revealed, for the first time, that the seed microbiome of a pioneer plant growing in its natural environment, and the colonisation behaviour of an important plant growth promoting systemic seed endophyte. Future characterization of seed microbiota will lead to a better understanding of their functional contribution and the potential use for seed-fortification applications.

Hydrocarbon degradation potential and plant growth-promoting activity of culturable endophytic bacteria of Lotus corniculatus and Oenothera biennis from a long-term polluted site

Many endophytic bacteria exert beneficial effects on their host, but still little is known about the bacteria associated with plants growing in areas heavily polluted by hydrocarbons. The aim of the study was characterization of culturable hydrocarbon-degrading endophytic bacteria associated with Lotus corniculatus L. and Oenothera biennis L. collected in long-term petroleum hydrocarbon-polluted site using culture-dependent and molecular approaches. A total of 26 hydrocarbon-degrading endophytes from these plants were isolated. Phylogenetic analyses classified the isolates into the phyla Proteobacteria and Actinobacteria. The majority of strains belonged to the genera Rhizobium, Pseudomonas, Stenotrophomonas, and Rhodococcus. More than 90% of the isolates could grow on medium with diesel oil, approximately 20% could use n-hexadecane as a sole carbon and energy source. PCR analysis revealed that 40% of the isolates possessed the P450 gene encoding for cytochrome P450-type alkane hydroxylase (CYP153). In in vitro tests, all endophytic strains demonstrated a wide range of plant growth-promoting traits such as production of indole-3-acetic acid, hydrogen cyanide, siderophores, and phosphate solubilization. More than 40% of the bacteria carried the gene encoding for the 1-aminocyclopropane-1-carboxylic acid deaminase (acdS). Our study shows that the diversity of endophytic bacterial communities in tested plants was different. The results revealed also that the investigated plants were colonized by endophytic bacteria possessing plant growth-promoting features and a clear potential to degrade hydrocarbons. The properties of isolated endophytes indicate that they have the high potential to improve phytoremediation of petroleum hydrocarbon-polluted soils.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies.IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria.

Characterization of PM2.5-bound polycyclic aromatic hydrocarbons and its deposition in Populus tomentosa leaves in Beijing

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous constituents of air particulate matter and can be taken up by plants from the atmosphere. However, the purification of particulate-bound PAHs in the atmosphere by greening tree species has not been reported. In this study, we assess the concentrations, distribution, and sources of PM_2.5-bound PAHs at three representative sites of Beijing in April, July, and November (non-heating period) and analyze the correlation between PAHs in Populus tomentosa leaves and in atmospheric PM_2.5. The total PAH concentrations in PM_2.5 were in the range of 19.85 ± 13.59-42.01 ± 37.17 ng/m³ with mean value of 31.35 ng/m³ at the three sites, and the PM_2.5-bound PAHs concentrations in the two suburban sites (YF and YQ) were significantly higher than that in urban site (XZM) in November (autumn). At the three sites, the high molecular weight (HMW) PAHs in PM_2.5 were dominant, accounting for 54.09-64.90% of total PAHs and the concentration of HMW PAHs was, on average, 9.1 times higher than that of low molecular weight (LWM) PAHs. Principal component analysis combined with diagnostic ratio analysis indicated that vehicle emission, wood combustion, and industrial processes were the main sources for PM_2.5-bound PAHs in the non-heating period of Beijing. However, the LMW PAHs were dominant in P. tomentosa leaves. The concentrations of HMW PAHs (BbF, BkF, BaP, IcdP, and BghiP) in P. tomentosa leaves reached 26.11 ± 2.39, 41.42 ± 7.77, and 55.70 ± 12.33 ng/g at YQ, XZM, and YF in autumn, respectively, and were, on average, 2.1 times higher than those in April (spring) at the three sites. The ∑5PAHs concentration in P. tomentosa leaves accumulatively increased from spring to autumn, which was not related to the temporal variation of PM_2.5-bound PAHs. Nevertheless, the ∑5PAHs mean concentrations followed the order of YF > XZM > YQ. This trend was consistent with spatial distribution of atmosphere PM_2.5, indicating that HMW PAHs in leaves increased with the increase of atmosphere PM_2.5 concentration. Our results indicated that P. tomentosa may be used as a useful species for removing PAHs from the air and biomonitoring PAHs in atmosphere.

Bisphenol-A removal by the halophyte Juncus acutus in a phytoremediation pilot: Characterization and potential role of the endophytic community

A phytoremediation pilot emulating a shallow aquifer planted with Juncus acutus showed to be effective for remediating Bisphenol-A (BPA) contaminated groundwater. Biostimulation with root exudates, low molecular weight organic acids, of J. acutus did not improve BPA-degradation rates. Furthermore, the endophytic bacterial community of J. acutus was isolated and characterized. Many strains were found to possess increased tolerance to metals such as Zn, Ni, Pb and Cd. Moreover, several endophytic bacterial strains tolerated and even used BPA and/or two antibiotics (ciprofloxacin and sulfamethoxazole) as a sole carbon source. Our results demonstrate that the cultivable bacterial endophytic community of J. acutus is able to use organic contaminants as carbon sources, tolerates metals and is equipped with plant-growth promoting traits. Therefore, J. acutus has potential to be exploited in constructed wetlands when co-contamination is one of the restricting factors.

Plant-bacteria partnerships for the remediation of persistent organic pollutants

High toxicity, bioaccumulation factor and widespread dispersal of persistent organic pollutants (POPs) cause environmental and human health hazards. The combined use of plants and bacteria is a promising approach for the remediation of soil and water contaminated with POPs. Plants provide residency and nutrients to their associated rhizosphere and endophytic bacteria. In return, the bacteria support plant growth by the degradation and detoxification of POPs. Moreover, they improve plant growth and health due to their innate plant growth-promoting mechanisms. This review provides a critical view of factors that affect absorption and translocation of POPs in plants and the limitations that plant have to deal with during the remediation of POPs. Moreover, the synergistic effects of plant-bacteria interactions in the phytoremediation of organic pollutants with special reference to POPs are discussed.

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.

Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth

The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.

Cadmium-induced and trans-generational changes in the cultivable and total seed endophytic community of Arabidopsis thaliana

Trans-generational adaptation is important to respond rapidly to environmental challenges and increase overall plant fitness. Besides well-known mechanisms such as epigenetic modifications, vertically transmitted endophytic bacteria might contribute to this process. The cultivable and total endophytic communities of several generations of Arabidopsis thaliana seeds harvested from plants exposed to cadmium (Cd) or not exposed were investigated. The diversity and richness of the seed endophytic community decreased with an increasing number of generations. Aeromicrobium and Pseudonocardia were identified as indicator species in seeds from Cd-exposed plants, while Rhizobium was abundantly present in both seed types. Remarkably, Rhizobium was the only genus that was consistently detected in seeds of all generations, which suggests that the phenotypic characteristics were more important as selection criteria for which bacteria are transferred to the next plant generation than the actual genera. Production of IAA was an important trait for endophytes from both seed types, while ACC deaminase activity and Cd tolerance were mainly associated with seed endophytes from Cd-exposed plants. Understanding how different factors influence the seed endophytic community can help us to improve seed quality and plant growth through different biotechnological applications.

Exposure of Cucurbita pepo to DDE-contamination alters the endophytic community: A cultivation dependent vs a cultivation independent approach

2,2-bis(p-chlorophenyl)-1,1-dichloro-ethylene (DDE) is the most abundant and persistent degradation product of the pesticide 2,2-bis(p-chlorophenyl)-1,1,1-trichloroethane (DDT) and is encountered in contaminated soils worldwide. Both DDE and DDT are classified as Persistent Organic Pollutants (POPs) due to their high hydrophobicity and potential for bioaccumulation and biomagnification in the food chain. Zucchini (Cucurbita pepo ssp. pepo) has been shown to accumulate high concentrations of DDE and other POPs and has been proposed as a phytoremediation tool for contaminated soils. The endophytic bacteria associated with this plant may play an important role in the remedial process. Therefore, this research focuses on changes in endophytic bacterial communities caused by the exposure of C. pepo to DDE. The total bacterial community was investigated using cultivation-independent 454 pyrosequencing, while the cultivable community was identified using cultivation-dependent isolation procedures. For both procedures, increasing numbers of endophytic bacteria, as well as higher diversities of genera were observed when plants were exposed to DDE. Several bacterial genera such as Stenotrophomonas sp. and Sphingomonas sp. showed higher abundance when DDE was present, while, for example Pseudomonas sp. showed a significantly lower abundance in the presence of DDE. These findings suggest tolerance of different bacterial strains to DDE, which might be incorporated in further investigations to optimize phytoremediation with the possible use of DDE-degrading endophytes.

Transpiration and metabolisation of TCE by willow plants - a pot experiment

Willows were grown in glass cylinders filled with compost above water-saturated quartz sand, to trace the fate of TCE in water and plant biomass. The experiment was repeated once with the same plants in two consecutive years. TCE was added in nominal concentrations of 0, 144, 288, and 721 mg l(-1). Unplanted cylinders were set-up and spiked with nominal concentrations of 721 mg l(-1) TCE in the second year. Additionally, (13)C-enriched TCE solution (δ(13)C = 110.3 ‰) was used. Periodically, TCE content and metabolites were analyzed in water and plant biomass. The presence of TCE-degrading microorganisms was monitored via the measurement of the isotopic ratio of carbon ((13)C/(12)C) in TCE, and the abundance of (13)C-labeled microbial PLFAs (phospholipid fatty acids). More than 98% of TCE was lost via evapotranspiration from the planted pots within one month after adding TCE. Transpiration accounted to 94 to 78% of the total evapotranspiration loss. Almost 1% of TCE was metabolized in the shoots, whereby trichloroacetic acid (TCAA) and dichloroacetic acid (DCAA) were dominant metabolites; less trichloroethanol (TCOH) and TCE accumulated in plant tissues. Microbial degradation was ruled out by δ(13)C measurements of water and PLFAs. TCE had no detected influence on plant stress status as determined by chlorophyll-fluorescence and gas exchange.

Seasonal variation of bacterial endophytes in urban trees

Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.

Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

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

Characterization of the cultivable bacterial populations associated with field grown Brassica napus L.: an evaluation of sampling and isolation protocols

Plant-associated bacteria are intensively investigated concerning their characteristics for plant growth promotion, biocontrol mechanisms and enhanced phytoremediation efficiency. To obtain endophytes, different sampling and isolation protocols are used although their representativeness is not always clearly demonstrated. The objective of this study was to acquire representative pictures of the cultivable bacterial root, stem and leaf communities for all Brassica napus L. individuals growing on the same field. For each plant organ, genotypic identifications of the endophytic communities were performed using three replicates. Root replicates were composed of three total root systems, whereas stem and leaf replicates needed to consist of six independent plant parts in order to be representative. Greater variations between replicates were found when considering phenotypic characteristics. Correspondence analysis revealed reliable phenotypic results for roots and even shoots, but less reliable ones for leaves. Additionally, realistic Shannon-Wiener biodiversity indices were calculated for all three organs and showed similar Evenness factors. Furthermore, it was striking that all replicates and thus the whole plant contained Pseudomonas and Bacillus strains although aboveground and belowground plant tissues differed in most dominant bacterial genera and characteristics.

Mitigation measures for chromium-VI contaminated groundwater - The role of endophytic bacteria in rhizofiltration

A constructed wetland pilot with Juncus acutus L. plants was investigated for its rhizofiltration efficiency in treating Cr(VI)-contaminated groundwater. Measurements of Cr(VI) and total Cr were performed to estimate the rate of removal. In addition, Cr concentration in plant tissues was measured and the role of endophytic bacteria on plant's tolerance to Cr(VI) toxicity was investigated. The results support that J. acutus is able to rhizofiltrate Cr(VI) from contaminated water with up to 140μg/L while Cr content analysis in plant tissues revealed that the majority of Cr was accumulated by the plants. Moreover, two leaf (Acidovorax sp. strain U3 and Ralstonia sp. strain U36) isolated endophytic bacteria were found to tolerated 100mg/L Cr(VI) while nine root isolates showed resistance to 500mg/L Cr(VI). The endophytic bacteria Pseudomonas sp. strain R16 and Ochrobactrum sp. strain R24 were chosen for Cr(VI) reduction assays. All four strains exhibited a strong potential to reduce Cr(VI) to Cr(III) aerobically. Among them Pseudomonas sp. strain R16 was found able to completely reduced 100mg/L Cr(VI) after 150h of incubation. These results suggest that J. acutus is an excellent choice for CWs whose function is the removal of Cr(VI) from contaminated groundwater for subsequent use in crop irrigation.

Uptake of carbamazepine by rhizomes and endophytic bacteria of Phragmites australis

Carbamazepine is an antiepileptic and mood-stabilizing drug which is used widely in Europe and North America. In the environment, it is found as a persistent and recalcitrant contaminant, being one of the most prominent hazardous pharmaceuticals and personal care products in effluents of wastewater treatment plants. Phragmites australis is one of the species with both, the highest potential of detoxification and phytoremediation. It has been used successfully in the treatment of industrial and municipal wastewater. Recently, the identification of endophytic microorganisms from different plant species growing in contaminated sites has provided a list of candidates which could be used as bio-inoculants for bioremediation of difficult compounds. In this study, Phragmites australis plants were exposed to 5 mg/L of carbamazepine. After 9 days the plants had removed 90% of the initial concentration. Endophytic bacteria were isolated from these plants and further characterized. Phylogenetic analysis based on 16S rDNA sequencing revealed that the majority of these isolates belong to three groups: Proteobacteria, Actinobacteria, and Bacteroidetes. Carbamazepine uptake and plant growth promoting (PGP) traits were analyzed among the isolates. Ninety percent of the isolates produce indole acetic acid (IAA) and all of them possess at least one of the PGP traits tested. One isolate identified as Chryseobacterium taeanense combines good carbamazepine uptake and all of the PGP traits. Rhizobium daejeonense can remove carbamazepine and produces 23 μg/mL of IAA. Diaphorobacter nitroreducens and Achromobacter mucicolens are suitable for carbamazepine removal while both, Pseudomonas veronii and Pseudomonas lini show high siderophore production and phosphate solubilization. Alone or in combination, these isolates might be applied as inoculates in constructed wetlands in order to enhance the phytoremediation of carbamazepine during wastewater treatment.

Phytoremediation of Metal Contaminated Soil Using Willow: Exploiting Plant-Associated Bacteria to Improve Biomass Production and Metal Uptake

Short rotation coppice (SRC) of willow and poplar is proposed for economic valorization and concurrently as remediation strategy for metal contaminated land in northeast-Belgium. However, metal phytoextraction appears insufficient to effectuate rapid reduction of soil metal contents. To increase both biomass production and metal accumulation of SRC, two strategies are proposed: (i) in situ selection of the best performing clones and (ii) bioaugmentation of these clones with beneficial plant-associated bacteria. Based on field data, two experimental willow clones, a Salix viminalis and a Salix alba x alba clone, were selected. Compared to the best performing commercial clones, considerable increases in stem metal extraction were achieved (up to 74% for Cd and 91% for Zn). From the selected clones, plant-associated bacteria were isolated and identified. All strains were subsequently screened for their plant growth-promoting and metal uptake enhancing traits. Five strains were selected for a greenhouse inoculation experiment with the selected clones planted in Cd-Zn-Pb contaminated soil. Extraction potential tended to increase after inoculation of S. viminalis plants with a Rahnella sp. strain due to a significantly increased twig biomass. However, although bacterial strains showing beneficial traits in vitro were used for inoculation, increments in extraction potential were not always observed.

The Potential of the Ni-Resistant TCE-Degrading Pseudomonas putida W619-TCE to Reduce Phytotoxicity and Improve Phytoremediation Efficiency of Poplar Cuttings on A Ni-TCE Co-Contamination

To examine the potential of Pseudomonas putida W619-TCE to improve phytoremediation of Ni-TCE co-contamination, the effects of inoculation of a Ni-resistant, TCE-degrading root endophyte on Ni-TCE phytotoxicity, Ni uptake and trichloroethylene (TCE) degradation of Ni-TCE-exposed poplar cuttings are evaluated. After inoculation with P. putida W619-TCE, root weight of non-exposed poplar cuttings significantly increased. Further, inoculation induced a mitigation of the Ni-TCE phytotoxicity, which was illustrated by a diminished exposure-induced increase in activity of antioxidative enzymes. Considering phytoremediation efficiency, inoculation with P. putida W619-TCE resulted in a 45% increased Ni uptake in roots as well as a slightly significant reduction in TCE concentration in leaves and TCE evapotranspiration to the atmosphere. These results indicate that endophytes equipped with the appropriate characteristics can assist their host plant to deal with co-contamination of toxic metals and organic contaminants during phytoremediation. Furthermore, as poplar is an excellent plant for biomass production as well as for phytoremediation, the obtained results can be exploited to produce biomass for energy and industrial feedstock applications in a highly productive manner on contaminated land that is not suited for normal agriculture. Exploiting this land for biomass production could contribute to diminish the conflict between food and bioenergy production.

Endophytic bacteria: prospects and applications for the phytoremediation of organic pollutants

Recently, there has been an increased effort to enhance the efficacy of phytoremediation of contaminated environments by exploiting plant-microbe interactions. The combined use of plants and endophytic bacteria is an emerging approach for the clean-up of soil and water polluted with organic compounds. In plant-endophyte partnerships, plants provide the habitat as well as nutrients to their associated endophytic bacteria. In response, endophytic bacteria with appropriate degradation pathways and metabolic activities enhance degradation of organic pollutants, and diminish phytotoxicity and evapotranspiration of organic pollutants. Moreover, endophytic bacteria possessing plant growth-promoting activities enhance the plant's adaptation and growth in soil and water contaminated with organic pollutants. Overall, the application of endophytic bacteria gives new insights into novel protocols to improve phytoremediation efficiency. However, successful application of plant-endophyte partnerships for the clean-up of an environment contaminated with organic compounds depends on the abundance and activity of the degrading endophyte in different plant compartments. Although many endophytic bacteria have the potential to degrade organic pollutants and improve plant growth, their contribution to enhance phytoremediation efficiency is still underestimated. A better knowledge of plant-endophyte interactions could be utilized to increase the remediation of polluted soil environments and to protect the foodstuff by decreasing agrochemical residues in food crops.

Degradation, phytoprotection and phytoremediation of phenanthrene by endophyte Pseudomonas putida, PD1

Endophytes have been isolated from a large diversity of plants and have been shown to enhance the remediation efficiency of plants, but little information is available on the influence of endophytic bacteria on phytoremediation of widespread environmental contaminants such as polycyclic aromatic hydrocarbons (PAHs). In this study we selected a naturally occurring endophyte for its combined ability to colonize plant roots and degrade phenanthrene in vitro. Inoculation of two different willow clones and a grass with Pseudomonas putida PD1 was found to promote root and shoot growth and protect the plants against the phytotoxic effects of phenanthrene. There was an additional 25-40% removal of phenanthrene from soil by the willow and grasses, respectively inoculated with PD1 when compared to the uninoculated controls. Fluorescent microscopy using fluorescent protein tagging of PD1 confirmed the presence of bacteria inside the root tissue. Inoculation of willows with PD1 consistently improved the growth and health when grown in hydroponic systems with high concentrations of phenanthrene. To our knowledge this is the first time that the inoculation of willow plants has been shown to improve the degradation of PAHs and improve the health of the host plants, demonstrating the potential wide benefit to the field of natural endophyte-assisted phytoremediation.

Bacteria associated with yellow lupine grown on a metal-contaminated soil: in vitro screening and in vivo evaluation for their potential to enhance Cd phytoextraction

In order to stimulate selection for plant-associated bacteria with the potential to improve Cd phytoextraction, yellow lupine plants were grown on a metal-contaminated field soil. It was hypothesised that growing these plants on this contaminated soil, which is a source of bacteria possessing different traits to cope with Cd, could enhance colonisation of lupine with potential plant-associated bacteria that could then be inoculated in Cd-exposed plants to reduce Cd phytotoxicity and enhance Cd uptake. All cultivable bacteria from rhizosphere, root and stem were isolated and genotypically and phenotypically characterised. Many of the rhizobacteria and root endophytes produce siderophores, organic acids, indole-3-acetic acid (IAA) and aminocyclopropane-1-carboxylate (ACC) deaminase, as well as being resistant to Cd and Zn. Most of the stem endophytes could produce organic acids (73.8%) and IAA (74.3%), however, only a minor fraction (up to 0.7%) were Cd or Zn resistant or could produce siderophores or ACC deaminase. A siderophore- and ACC deaminase-producing, highly Cd-resistant Rhizobium sp. from the rhizosphere, a siderophore-, organic acid-, IAA- and ACC deaminase-producing highly Cd-resistant Pseudomonas sp. colonising the roots, a highly Cd- and Zn-resistant organic acid and IAA-producing Clavibacter sp. present in the stem, and a consortium composed of these three strains were inoculated into non-exposed and Cd-exposed yellow lupine plants. Although all selected strains possessed promising in vitro characteristics to improve Cd phytoextraction, inoculation of none of the strains (i) reduced Cd phytotoxicity nor (ii) strongly affected plant Cd uptake. This work highlights that in vitro characterisation of bacteria is not sufficient to predict the in vivo behaviour of bacteria in interaction with their host plants.

The effect of long-term Cd and Ni exposure on seed endophytes of Agrostis capillaris and their potential application in phytoremediation of metal-contaminated soils

We examined whether long-term Cd exposure leads to beneficial changes in the cultivable endophytic bacteria present in the seeds of Agrostis capillaris. Therefore the cultivable seed endophytes of Agrostis capillaris growing on a long-term Cd/Ni-contaminated plot (Cd/Ni seeds) were compared with those originating from a non-contaminated plot (control seeds). We observed plant- and contaminant-dependent effects on the population composition between control and Cd/Ni seeds. Also differences in phenotypic characteristics were found: endophytes from Cd/Ni seeds exhibited more ACC deaminase activity and production of siderophores and IAA, while endophytes from control seeds, very surprisingly, showed more metal tolerance. Finally, the 3 most promising seed endophytes were selected based on their metal tolerance and plant growth promoting potential, and inoculated in Agrostis capillaris seedlings. In case of non-exposed plants, inoculation resulted in a significantly improved plant growth; after inoculation of Cd-exposed plants an increased Cd uptake was achieved without affecting plant growth. This indicates that inoculation of Agrostis with its seed endophytes might be beneficial for its establishment during phytoextraction and phytostabilisation of Cd-contaminated soils.

Bacterial communities associated with Brassica napus L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison

Cultivable bacterial strains associated with field-grown Brassica napus L. (soil, rhizosphere and roots) from a trace elements (Cd, Zn and Pb) contaminated field and a non-contaminated control field were characterized genotypically and phenotypically. Correspondence analysis of the genotypic data revealed a correlation between soil and rhizosphere communities isolated from the same field, indicating that local conditions play a more important role in influencing the composition of (rhizosphere) soil bacterial communities than root exudates. In contrast, endophytic communities of roots showed a correlation between fields, suggesting that plants on the two fields contain similar obligate endophytes derived from a common seed endophytic community and/or can select bacteria from the rhizosphere. The latter seemed not very likely since, despite the presence of several potential endophytic taxa in the rhizosphere, no significant correlation was found between root and rhizosphere communities. The majority of Cd/Zn tolerant strains capable of phosphorus solubilization, nitrogen fixation, indole-3-acetic acid production and showing 1-aminocyclopropane-1-carboxylate deaminase capacity were found in the rhizosphere and roots of plants growing on the contaminated field.

Phytoremediation of hexachlorocyclohexane (HCH)-contaminated soils using Cytisus striatus and bacterial inoculants in soils with distinct organic matter content

The performance of Cytisus striatus in association with different microbial inoculant treatments on the dissipation of the insecticide hexachlorocyclohexane (HCH) was studied. Two soils with different organic matter (A and B soil) content were spiked with 0 or 65 mg HCH kg(-1). Plants were either not inoculated (NI), or inoculated with the endophyte Rhodococcus erythropolis ET54b and the HCH-degrader Sphingomonas sp. D4 separately or in combination (ET, D4 and ETD4). Unplanted pots were also established. HCH phytotoxicity was more pronounced in the B soil. Soil HCH concentrations in unplanted pots were similar to initial concentrations, whereas concentrations were reduced after plant growth: by 20% and 8% in A and B soil, respectively. Microbial inoculants also modified HCH dissipation, although effects were soil-dependent. Inoculation with the combination of strains (ETD4) led to a significant enhancement in HCH dissipation: up to 53% in the A soil and 43% in the B soil.

Laboratory-scale column study for remediation of TCE-contaminated aquifers using three-section controlled-release potassium permanganate barriers

A laboratory-scale study with a sand column was designed to simulate trichloroethylene (TCE) pollution in the aquifer environment with three-section controlled-release potassium permanganate (CRP) barriers. The main objective of this study was to evaluate the feasibility of CRP barriers in remediation of TCE in aquifers in a long-term and controlled manner. CRP particles with a 1:3 molar ratio of KMnO4 to stearic acid showed the best controlled-release properties in pure water, and the theoretical release time was 138.5 days. The results of TCE removal in the test column indicated that complete removal efficiency of TCE in a sand column by three-section CRP barriers could be reached within 15 days. The molar ratio of KMnO4 to TCE in the three-section CRP barriers was 16:1, which was much lower than 82:1 as required when KMnO4 solution is used directly to achieve complete destruction of TCE. This result revealed that the efficiency of CRP for remediation of TCE was highly improved after encapsulation.

Plant-associated bacteria and their role in the success or failure of metal phytoextraction projects: first observations of a field-related experiment

Phytoextraction has been reported as an economically and ecologically sound alternative for the remediation of metal-contaminated soils. Willow is a metal phytoextractor of interest because it allows to combine a gradual contaminant removal with production of biomass that can be valorized in different ways. In this work two willow clones growing on a metal-contaminated site were selected: 'Belgisch Rood' (BR) with a moderate metal extraction capacity and 'Tora' (TO) with a twice as high metal accumulation. All cultivable bacteria associated with both willow clones were isolated and identified using 16SrDNA ARDRA analysis followed by 16SrDNA sequencing. Further all isolated bacteria were investigated for characteristics that might promote plant growth (production of siderophores, organic acids and indol acetic acid) and for their metal resistance. The genotypic and phenotypic characterization of the isolated bacteria showed that the TO endophytic bacterial population is more diverse and contains a higher percentage of metal-resistant plant growth promoting bacteria than the endophytic population associated with BR. We hypothesize that the difference in the metal accumulation capacity between BR and TO clones might be at least partly related to differences in characteristics of their associated bacterial population.

Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils

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

Enhanced remediation of chlorpyrifos from soil using ryegrass (Lollium multiflorum) and chlorpyrifos-degrading bacterium Bacillus pumilus C2A1

The combined use of plants and associated microorganisms has great potential for remediating soil contaminated with organic compounds such as pesticides. The objective of this study was to determine whether the bacterial inoculation influences plant growth promotion and chlorpyrifos (CP) degradation and accumulation in different parts of the plant. Ryegrass was grown in soil spiked with CP and inoculated with a pesticide degrading bacterial strain Bacillus pumilus C2A1. Inoculation generally had a beneficial effect on CP degradation and plant biomass production, highest CP degradation (97%) was observed after 45 days of inoculation. Furthermore, inoculated strain efficiently colonized in the rhizosphere of inoculated plant and enhanced CP and its primary metabolite 3,5,6-trichloro-2-pyridinol (TCP) degradation. There was significantly less CP accumulation in roots and shoots of inoculated plants as compared to uninoculated plants. The results show the effectiveness of inoculated exogenous bacteria to boost the remediation of CP contaminated sites and decrease levels of toxic pesticide residues in crop plants.

Understanding the development of roots exposed to contaminants and the potential of plant-associated bacteria for optimization of growth

BACKGROUND AND SCOPE

Plant responses to the toxic effects of soil contaminants, such as excess metals or organic substances, have been studied mainly at physiological, biochemical and molecular levels, but the influence on root system architecture has received little attention. Nevertheless, the precise position, morphology and extent of roots can influence contaminant uptake. Here, data are discussed that aim to increase the molecular and ecological understanding of the influence of contaminants on root system architecture. Furthermore, the potential of plant-associated bacteria to influence root growth by their growth-promoting and stress-relieving capacities is explored.

METHODS

Root growth parameters of Arabidopsis thaliana seedlings grown in vertical agar plates are quantified. Mutants are used in a reverse genetics approach to identify molecular components underlying quantitative changes in root architecture after exposure to excess cadmium, copper or zinc. Plant-associated bacteria are isolated from contaminated environments, genotypically and phenotypically characterized, and used to test plant root growth improvement in the presence of contaminants.

KEY RESULTS

The molecular determinants of primary root growth inhibition and effects on lateral root density by cadmium were identified. A vertical split-root system revealed local effects of cadmium and copper on root development. However, systemic effects of zinc exposure on root growth reduced both the avoidance of contaminated areas and colonization of non-contaminated areas. The potential for growth promotion and contaminant degradation of plant-associated bacteria was demonstrated by improved root growth of inoculated plants exposed to 2,4-di-nitro-toluene (DNT) or cadmium.

CONCLUSIONS

Knowledge concerning the specific influence of different contaminants on root system architecture and the molecular mechanisms by which this is achieved can be combined with the exploitation of plant-associated bacteria to influence root development and increase plant stress tolerance, which should lead to more optimal root systems for application in phytoremediation or safer biomass production.

Endophytes and their potential to deal with co-contamination of organic contaminants (toluene) and toxic metals (nickel) during phytoremediation

The aim was to investigate if engineered endophytes that are capable of degrading organic contaminants, and deal with or ideally improve uptake and translocation of toxic metals, can improve phytoremediation of mixed organic-metal pollution. As a model system, yellow lupine was inoculated with the endophyte Burkholderia cepacia VM1468 possessing (a) the pTOM-Bu61 plasmid, coding for constitutive toluene/TCE degradation, and (b) the chromosomally inserted ncc-nre Ni resistance/sequestration system. As controls, plants were inoculated with B. vietnamiensis BU61 (pTOM-Bu61) and B. cepacia BU72 (containing the ncc-nre Ni resistance/sequestration system). Plants were exposed to mixes of toluene and Ni. Only inoculation with B. cepacia VM1468 resulted in decreased Ni and toluene phytotoxicity, as measured by a protective effect on plant growth and decreased activities of enzymes involved in antioxidative defence (catalase, guaiacol peroxidase, superoxide dismutase) in the roots. Besides, plants inoculated with B. cepacia VM1468 and B. vietnamiensis BU61 released less toluene through the leaves than non-inoculated plants and those inoculated with B. cepacia BU72. Ni-uptake in roots was slightly increased for B. cepacia BU72 inoculated plants. These results indicate that engineered endophytes have the potential to assist their host plant to deal with co-contamination of toxic metals and organic contaminants during phytoremediation.

Potential of the TCE-degrading endophyte Pseudomonas putida W619-TCE to improve plant growth and reduce TCE phytotoxicity and evapotranspiration in poplar cuttings

The TCE-degrading poplar endophyte Pseudomonas putida W619-TCE was inoculated in poplar cuttings, exposed to 0, 200 and 400 mg l(-1) TCE, that were grown in two different experimental setups. During a short-term experiment, plants were grown hydroponically in half strength Hoagland nutrient solution and exposed to TCE for 3 days. Inoculation with P. putida W619-TCE promoted plant growth, reduced TCE phytotoxicity and reduced the amount of TCE present in the leaves. During a mid-term experiment, plants were grown in potting soil and exposed to TCE for 3 weeks. Here, inoculation with P. putida W619-TCE had a less pronounced positive effect on plant growth and TCE phytotoxicity, but resulted in strongly reduced amounts of TCE in leaves and roots of plants exposed to 400 mg l(-1) TCE, accompanied by a lowered evapotranspiration of TCE. Dichloroacetic acid (DCAA) and trichloroacetic acid (TCAA), which are known intermediates of TCE degradation, were not detected.

Bisphenol A removal by the Dracaena plant and the role of plant-associating bacteria

Dracaena sanderiana and Dracaena fragrans plants, as representatives of native, tropical, evergreen plants with fibrous root systems, were evaluated for bisphenol A (BPA) tolerance and uptake capability. D. sanderiana demonstrated significantly higher BPA removal capability than D. fragrans. Therefore, it was chosen for further study. D. sanderiana tolerated BPA toxicity levels up to 80 microM, while higher BPA concentrations damaged the plant. In the sterile hydroponic system with an initial BPA concentration of 20 microM, the plant could uptake approximately 50% of the BPA. The plant's ability to translocate BPA was confirmed by the detection of BPA that accumulated at the roots and stems, but not at the leaves of the plant. Upon BPA exposure, the D. sanderiana secreted extracellular plant mucilage as a protective barrier to the toxic compound. In the non-sterile treatment, the BPA dissipation was contributed not only by the D. sanderiana plant, but also by the co-existing microbes. The BPA reached 85% of the initial concentration at 20 microM. Among the six plant-associating bacterial isolates, Bacillus cereus strain BPW4 and Enterobacter sp. strain BPW5 colonized the D. sanderiana root surface and facilitated BPA dissipation in the hydroponic treatment system. In addition, the success of the BPA treatment in the hazardous waste landfill leachate demonstrated the potential application of D. sanderiana plant in the phytoremediation of BPA contaminated wastewater or industrial leachate.

Bioaugmentation with engineered endophytic bacteria improves contaminant fate in phytoremediation

Phytoremediation of volatile organic contaminants often proves not ideal because plants and their rhizosphere microbes only partially degrade these compounds. Consequently, plants undergo evapotranspiration that contaminates the ambient air and, thus, undermines the merits of phytoremediation. Under laboratory conditions, endophytic bacteria equipped with the appropriate degradation pathways can improve in planta degradation of volatile organic contaminants. However, several obstacles must be overcome before engineered endophytes will be successful in field-scale phytoremediation projects. Here we report the first in situ inoculation of poplar trees, growing on a TCE-contaminated site, with the TCE-degrading strain Pseudomonas putida W619-TCE. In situ bioaugmentation with strain W619-TCE reduced TCE evapotranspiration by 90% under field conditions. This encouraging result was achieved after the establishment and enrichment of P. putida W619-TCE as a poplar root endophyte and by further horizontal gene transfer of TCE metabolic activity to members of the poplar's endogenous endophytic population. Since P. putida W619-TCE was engineered via horizontal gene transfer, its deliberate release is not restricted under European genetically modified organisms (GMO) regulations.