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

Phytoremediation of trichloroethylene in the soil/groundwater environment: Progress, problems, and potential

Trichloroethylene (TCE) poses a significant environmental threat in groundwater and soil, necessitating effective remediation strategies. Phytoremediation offers a cost-effective and environmentally friendly approach to remediation. However, the mechanisms governing plant uptake, volatilisation, and degradation of TCE remain poorly understood. This review explores the mechanisms of TCE phytoremediation, metabolic pathways, and influencing factors, emphasizing future research directions to improve the understanding of TCE phytoremediation. The results showed that although the proportion of TCE phytovolatilisation is limited, it is important at sites chronically contaminated with TCE. The rhizosphere is a key microzone for pollutant redox reactions that significantly enhance its effectiveness when its characteristics are fully utilised and manipulated through reinforcement. Future research should focus on manipulating microbial communities through methods such as the application of endophytic bacteria and genetic modification. However, practical applications are in their infancy and further investigation is needed. Furthermore, many findings are based on non-uniform parameters or unstandardised methods, making them difficult to compare. Therefore, future studies should provide more standardised experimental parameters and employ accurate and standardised methods to develop suitable prediction models, enhancing data comparability and deepening our understanding of plant detoxification mechanisms.

The mechanisms of yeast extracellular metabolites in stimulating microbial degradation of trichloroethylene: Physiological characteristics and omics analysis

The biodegradation of Trichloroethylene (TCE) is limited by low microbial metabolic capacity but can be enhanced through biostimulation strategies. This study explored the physiological effects and potential molecular mechanisms of the yeast Yarrowia lipolytica extracellular metabolites (YEMs) on the degradation of TCE by Acinetobacter LT1. Results indicated that YEMs stimulated the efficiency of strain LT1 by 50.28%. At the physiological level, YEMs exhibited protective effects on cell morphology, reduced oxidative stress, lessened membrane damage, and enhanced energy production and conversion. Analysis of omics results revealed that the regulation of various metabolic pathways by YEMs improved the degradation of TCE. Furthermore, RT-qPCR showed that the genes encoding YhhW protein in TCE stress and YEMs stimulation groups were 1.72 and 3.22 times the control group, respectively. Molecular docking results showed that the conformation of YhhW after binding to TCE changed into a more active form, which enhanced enzyme activity. Therefore, it is speculated that YhhW is the primary degradative enzyme involved in the process of YEMs stimulating strain LT1 to degrade TCE. These results reveal how YEMs induce strain LT1 to enhance TCE degradation.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants

Over the past decades, the atmospheric CO₂ concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.

Phytoremediation, Bioaugmentation, and the Plant Microbiome

Understanding plant biology and related microbial ecology as a means to phytoremediate soil and groundwater contamination has broadened and advanced the field of environmental engineering and science over the past 30 years. Using plants to transform and degrade xenobiotic organic pollutants delivers new methods for environmental restoration. Manipulations of the plant microbiome through bioaugmentation, endophytes, adding various growth factors, genetic modification, and/or selecting the microbial community via insertion of probiotics or phages for gene transfer are future areas of research to further expand this green, cost-effective, aesthetically pleasing technology─phytoremediation.

Plant Growth-Promoting Activities of Bacteria Isolated from an Anthropogenic Soil Located in Agrigento Province

Bacteria producers of plant growth-promoting (PGP) substances are responsible for the enhancement of plant development through several mechanisms. The purpose of the present work was to evaluate the PGP traits of 63 bacterial strains that were isolated from an anthropogenic soil, and obtained by modification of vertisols in the Sicily region (Italy) seven years after creation. The microorganisms were tested for the following PGP characteristics: indole acetic acid (IAA), NH3, HCN and siderophore production, 1-aminocyclopropane-1-carboxylate deaminase activity (ACC) and phosphate solubilization. The results of principal component analysis (PCA) showed that Bacillus tequilensis SI 319, Brevibacterium frigoritolerans SI 433, Pseudomonas lini SI 287 and Pseudomonas frederiksbergensis SI 307 expressed high levels of IAA and production of ACC deaminase enzyme, while for the rest of traits analyzed the best performances were registered with Pseudomonas genus, in particular for the strains Pseudomonas atacamensis SI 443, Pseudomonas reinekei SI 441 and Pseudomonas granadensis SI 422 and SI 450. The in vitro screening provided enough evidence for future in vivo growth promotion tests of these eight strains.

Combined Bioremediation of Bensulfuron-Methyl Contaminated Soils With Arbuscular Mycorrhizal Fungus and Hansschlegelia zhihuaiae S113

Over the past decades, because of large-scale bensulfuron-methyl (BSM) application, environmental residues of BSM have massively increased, causing severe toxicity in rotation-sensitive crops. The removal of BSM from the environment has become essential. In this study, the combined bioremediation of the arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices and BSM-degrading strain Hansschlegelia zhihuaiae S113 of BSM-polluted soil was investigated. BSM degradation by S113 in the maize rhizosphere could better promote AMF infection in the roots of maize, achieving an infection rate of 86.70% on the 36th day in the AMF + S113 + BSM group. Similarly, AMF enhanced the colonization and survival of S113 in maize rhizosphere, contributing 4.65 × 105 cells/g soil on the 15th day and 3.78 × 104 cells/g soil on the 20th day to a population of colonized-S113 (based possibly on the strong root system established by promoting plant-growth AMF). Both S113 and AMF coexisted in rhizosphere soil. The BSM-degrading strain S113 could completely remove BSM at 3 mg/kg from the maize rhizosphere soil within 12 days. AMF also promoted the growth of maize seedlings. When planted in BSM-contaminated soil, maize roots had a fresh weight of 2.59 ± 0.26 g in group S113 + AMF, 2.54 ± 0.20 g in group S113 + AMF + BSM, 2.02 ± 0.16 g in group S113 + BSM, and 2.61 ± 0.25 g in the AMF group, all of which exceeded weights of the control group on the 36th day except for the S113 + BSM group. Additionally, high-throughput sequencing results indicated that simultaneous inoculation with AMF and strain S113 of BSM-polluted maize root-soil almost left the indigenous bacterial community diversity and richness in maize rhizosphere soil unaltered. This represents a major advantage of bioremediation approaches resulting from the existing vital interactions among local microorganisms and plants in the soil. These findings may provide theoretical guidance for utilizing novel joint-bioremediation technologies, and constitute an important contribution to environmental pollution bioremediation while simultaneously ensuring crop safety and yield.

Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g^–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Study on the community structure and function of anaerobic granular sludge under trichloroethylene stress

Trichloroethylene (TCE) is one of the most common groundwater pollutants. It is carcinogenic, teratogenic, mutagenic and poses a serious threat to human health and the environment. Therefore, reducing the environmental toxicity of TCE is of great significance. Anaerobic sludge was cultured and acclimated in an upflow anaerobic sludge blanket (UASB) reactor in this study. The Chemical Oxygen Demand (COD) concentration of the influent was approximately 2500 mg L^-1, and the TCE concentration of the influent ranged from 1.46 mg L^-1 to 73 mg L^-1. After biodegradation of the anaerobic microflora, the COD removal rate was approximately 85%, and the TCE removal rate was over 85%. The microbial community of anaerobic sludge was analysed by 16 S rDNA clone libray and 454 high-throughput sequencing. Through analysis of the sequencing results, we found that there were a variety of acid-forming bacteria, anaerobic dechlorinating bacteria, and methanogenic bacteria. Based on the analysis of microflora function, it was speculated that the TCE metabolic pathway took place in UASB reactors. Desulfovibrio and Syntrophobacter provided an anaerobic environment, and acid-forming bacteria metabolise organic compounds into hydrogen. With Dehalobacter and Geobacter, TCE as an electron acceptor is dechlorinated and reduced under the anaerobic environment, in which hydrogen acts as an electron donor. By this, we clarified the metabolic pathway for improving TCE bioremediation.

Diversity and functional characteristics of endophytic bacteria from two grass species growing on an oil-contaminated site in the Yellow River Delta, China

Phragmites australis and Chloris virgata are native, dominant, salt-tolerant grass species that grow in the Yellow River Delta, China, and have potential applications in the phytoremediation of petroleum-polluted saline soil. The characteristics of endophytic bacterial communities of Phragmites australis and Chloris virgata and their functions in hydrocarbon degradation and plant growth promotion have been studied using both high-throughput sequencing and conventional microbial techniques. Through 16S rRNA gene amplicon sequencing, we found five bacterial phyla that were dominant among the endophytic bacterial communities of the two grass species, including Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Tenericutes. The phylum Proteobacteria was common among the endophytic bacterial communities of the two grass species. The diversity in the endophytic bacterial community of Chloris virgata was generally higher than that in the community of Phragmites australis. Thirty-eight hydrocarbon-degrading endophytic bacteria were isolated from the two grasses via culturing techniques. Based on phylogenetic analyses, the bacterial isolates were classified into the phyla Proteobacteria, Firmicutes, and Actinobacteria. The majority of strains belonged to the genera Bacillus and Pseudomonas. More than 70% of the isolates of hydrocarbon-degrading endophytes exhibited the ability to stimulate plant growth. These isolates mainly belonged to Bacillus sp., Pseudomonas sp., Beijerinckia sp., Serratia sp., Acinetobacter sp., Microbacterium sp., and Rhizobium sp. Altogether, the present study revealed that Phragmites australis and Chloris virgata growing on petroleum-polluted saline soil in the Yellow River Delta harbor several diverse species of endophytic bacteria and serve as novel sources of beneficial bacteria and hydrocarbon degradation.

The Response of the Associations of Grass and Epichloë Endophytes to the Increased Content of Heavy Metals in the Soil

The rapid development of civilization increases the area of land exposed to the accumulation of toxic compounds, including heavy metals, both in water and soil. Endophytic fungi associated with many species of grasses are related to the resistance of plants to biotic and abiotic stresses, which include heavy metals. This paper reviews different aspects of symbiotic interactions between grass species and fungal endophytes from the genera Epichloë with special attention paid to the elevated concentration of heavy metals in growing substrates. The evidence shows the high resistance variation of plant endophyte symbiosis on the heavy metals in soil outcome. The fungal endophytes confer high heavy metal tolerance, which is the key feature in its practical application with their host plants, i.e., grasses in phytoremediation.

Biotechnology and nanotechnology for remediation of chlorinated volatile organic compounds: current perspectives

Chlorinated volatile organic compounds (CVOCs) are persistent organic pollutants which are harmful to public health and the environment. Many CVOCs occur in substantial quantities in groundwater and soil, even though their use has been more carefully managed and restricted in recent years. This review summarizes recent data on several innovative treatment solutions for CVOC-affected media including bioremediation, phytoremediation, nanoscale zero-valent iron (nZVI)-based reductive dehalogenation, and photooxidation. There is no optimally developed single technology; therefore, the possibility of using combined technologies for CVOC remediation, for example bioremediation integrated with reduction by nZVI, is presented. Some methods are still in the development stage. Advantages and disadvantages of each treatment strategy are provided. It is hoped that this paper can provide a basic framework for selection of successful CVOC remediation strategies.

Colonization and performance of a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 on root surfaces of white clover

Some rhizosphere bacteria could colonize on the root surface of plants, or even form biofilm to promote plant growth, enhance plant resistance to harsh external environments and block the soil contamination. In this study, to explore the effects of pyrene-degrading bacterium on root surface on plant uptake of pyrene, a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 was isolated from the root surface of Eleusine indica L. Gaertn. in PAH-contaminated fields; after antibiotic labeling, it was colonized onto the root surface of white clover (Trifolium repens L.), and its distribution and performance were monitored under different levels of pyrene contamination. Strain Pyr9 could degrade 98% of pyrene (with an initial concentration of 50 mg L^-1) in culture solution within 8 d; it also owns a variety of plant growth promoting characteristics and appreciable tolerance to harsh environments. The transcription of pyrene catabolic genes in Pyr9 enhanced obviously when induced by pyrene. Pyr9 colonized and grew well on the root surface of white clover via root inoculation; some cells could even enter into the root tissues and move to the shoots. Compared with the Pyr9-free treatment, the pyrene contents in the roots and shoots of Pyr9-inoculated white clover decreased by 25%-30% and 33%-42%, respectively. Correspondingly, the pyrene accumulation and translocation factors in white clover decreased as well. These results indicate that Pyr9 would be a good potential to circumvent plant pyrene pollution. This research may provide a theoretical basis and technical support for the safety of agricultural products and human health in PAH-contaminated sites.

Role of environmental factors in shaping the soil microbiome

The soil microbiome comprises one of the most important and complex components of all terrestrial ecosystems as it harbors millions of microbes including bacteria, fungi, archaea, viruses, and protozoa. Together, these microbes and environmental factors contribute to shaping the soil microbiome, both spatially and temporally. Recent advances in genomic and metagenomic analyses have enabled a more comprehensive elucidation of the soil microbiome. However, most studies have described major modulators such as fungi and bacteria while overlooking other soil microbes. This review encompasses all known microbes that may exist in a particular soil microbiome by describing their occurrence, abundance, diversity, distribution, communication, and functions. Finally, we examined the role of several abiotic factors involved in the shaping of the soil microbiome.

The knowledge domain and emerging trends in phytoremediation: a scientometric analysis with CiteSpace

As a cost-effective, environmentally friendly remediation technology, phytoremediation is defined as the use of green plants to remove pollutants from the environment or render them harmless and has been applied to a variety of contaminated sites throughout the world. There is a prominent phenomenon in which publications about phytoremediation increase each year and involve an increasing number of subject categories. This paper adopts the scientometric analysis method to assess the current state and explore the trends of phytoremediation research based on the bibliographic records retrieved from the Web of Science Core Collection (WoSCC). The results of this paper clearly answer the following questions. (1) What are the publishing characteristics of research on the topic of phytoremediation? What are the characteristics of academic collaboration in phytoremediation research? (2) What are the characteristics and development trends of phytoremediation research? (3) What are the hotspots and frontiers of phytoremediation research? Overall, the research method provides a new approach for the assessment of the performance of phytoremediation research. These results may help new researchers quickly integrate into the field of phytoremediation, as they can easily grasp the frontiers of phytoremediation research and obtain more valuable scientific information. This study also provides references for the follow-up research of relevant researchers.

Narrative of a versatile and adept species Pseudomonas putida

Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.

Bacterial succession in oil-contaminated soil under phytoremediation with poplars

Petroleum hydrocarbons (PHCs) continue to be among the most common pollutants in soil worldwide. Phytoremediation has become a sustainable way of dealing with PHC contamination. We conducted the off-site phytoremediation of PHC-polluted soil from an oil tanker truck accident, where poplars were used for the phytoremediation of the oil-polluted soil in a boreal climate during a seven-year treatment. The succession of bacterial communities over the entire phytoremediation process was monitored using microbial ecological tools relying on high-throughput 16S rRNA gene sequencing. Upon the successful depletion of PHCs from soil, endophytic communities were analyzed in order to assess the complete plant-associated microbiome after the ecological recovery. The rhizosphere-associated soil exhibited different bacterial dynamics than unplanted soil, but both soils experienced succession of bacteria over time, with diversity being negatively correlated with PHC concentration. In the relatively short growing season in North Europe, seasonal variations in environmental conditions were identified that contributed to the dynamics of bacterial communities. Overall, our study proved that phytoremediation using poplar trees can be used to assist in the removal of PHCs from soils in boreal climate conditions and provides new insight into the succession patterns of bacterial communities associated with these plants.

Endophytic Bacteria in in planta Organopollutant Detoxification in Crops

Microbe-assisted organopollutant removal, or in planta crop decontamination, is based on an interactive system between organopollutant-degrading endophytic bacteria (DEB_OP) and crops in alleviating organic toxins in plants. This script focuses on the fast-growing body of literature that has recently bloomed in organopollutant control in agricultural plants. The various facets of DEB_OP under study include their colonization, distribution, plant growth-promoting mechanisms, and modes of action in the detoxification process in plants. Also, an assessment of the biotechnological advances, advantages, and bottlenecks in accelerating the implementation of this decontamination strategy will be undertaken. The highlighted key research directions from this review will shape the future of agro-environmental sustainability and preservation of human health.

Endophytic Bacillus megaterium BM18-2 mutated for cadmium accumulation and improving plant growth in Hybrid Pennisetum

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The endophytic Bacillus megaterium isolated from Hybrid Pennisetum is promising isolate for Cd bioremediation.

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The mutated strain BM18-2 showed higher capacity to resist Cd until 70 μM and improving plant growth.

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Six different genes of BM18-2 are involved in Cd resistance mechanism.

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Hybrid Pennisetum inoculated with BM18-2 showed higher amount of growth and toleranc to Cd toxicity than uninoculated plants.

Hybrid Pennisetum (Pennisetum americanum × P. purpureum Schumach L.) is a tall and rapidly growing perennial C₄ bunch grass. It has been considered as a promising plant for phytoremediation of heavy metal-contaminated soil due to its high biomass, high resistance to environmental stress, pests and diseases. Heavy metal bioavailability level is the most important parameter for measurement of the phytoremediation efficiency. Endophytic bacteria were used to further enhance phytoremediation of heavy metals through bioaccumulation or bioabsorption process. In the present study, the endophytic Bacillus megaterium strain ‘BM18’ isolated from hybrid Pennisetum was screened under 10-70 μM cadmium (Cd) stress for Cd-resistant mutant colonies. And one such mutant colony‘BM18-2’ was obtained from the screen. Comparably, ‘BM18-2’ was more Cd-tolerant and had higher Cd removal ability than the original strain‘BM18’. The amount of IAA and ammonia production, and phosphate solubilization were 1.09, 1.23 and 1.24 times in ‘BM18-2’ than those of ‘BM18’, respectively. Full genome sequencing of these two strains revealed 6 different genes: BM18GM000901, BM18GM005669 and BM18GM005870 encoding heavy metal efflux pumps, BM18GM003487 and BM18GM005818 encoding transcriptional regulators for metal stress biosensor and BM18GM001335 encoding a replication protein. Inoculation with ‘BM18-2’ or ‘BM18’ both significantly reduced the toxic effect of Cd on hybrid Pennisetum, while the effect of ‘BM18-2’ on plant growth promotion in the presence of Cd was significantly better that of ‘BM18’. Therefore, the mutated strain ‘BM18-2’ could be used as a potential agent for Cd bioremediation, improving growth and Cd absorption of hybrid Pennisetum in Cd contaminated soil.

Natural attenuation of naphthalene along the river-bank infiltration zone of the Liao River, Shenyang, China

In this study, the natural attenuation of naphthalene during riverbank infiltration was examined using batch experiments. The results indicated that, as the grain size and the permeability coefficient decreased, the natural attenuation rate of naphthalene increased, and it was highest in loam (62%) and lowest in coarse sand (20%). The half-life of naphthalene was longest in coarse sand (700 d) and shortest in mild clay (250 d). Facultative anaerobes such as Methylophilaceae accounted for about 70% of the total bacteria and played a major role in naphthalene degradation. A high total organic carbon concentration and large specific surface area can promote natural attenuation of naphthalene. Moreover, the adsorption to riverbank sediment in the hyporheic zone and bioremediation by indigenous microorganisms can effectively eliminate naphthalene during river water infiltration to the riverbank aquifer.

Investigation on microbial community in remediation of lead-contaminated soil by Trifolium repensL

Trifolium repensL. is a plant with strong adaptability and large biomass, which possess great potential for phytoremediation. However, little is known concerning its remediation effects and changes in rhizosphere microbial activity and community structure under heavy metal pressure. The aims of this study were to evaluate lead accumulation of Trifolium repensL., study microbial lead resistance, metabolism and community structure characteristics in rhizosphere soils. The accumulated Pb concentration of Trifolium repensL. was observed in 100 and 500 mg/kg Pb contained soil at 55.81 and 90.3 mg/kg, respectively, which cause the decrease of acid-soluble fractions in rhizosphere soil. In the progress of lead-contaminated soil phytoremediation by Trifolium repensL., Pb resistance and metabolic activities of microorganisms have been prompted gradually. In addition, the microbial community composition and abundance were investigated using Illumina sequencing and quantitative PCR. The result showed that after phytoremediation, beneficial microorganisms, such as Flavisolibacter, Kaistobacter, and Pseudomonas, increased, becoming the dominant genera. This study has provided insight into the distribution and activity of the microbial community.

Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review

Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.

Belowground Microbiota and the Health of Tree Crops

Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.

Colonization on Cucumber Root and Enhancement of Chlorimuron-ethyl Degradation in the Rhizosphere by Hansschlegelia zhihuaiae S113 and Root Exudates

The colonization of Hansschlegelia zhihuaiae S113 and its degradation of the herbicide chlorimuron-ethyl in the cucumber rhizosphere was investigated. The results reveal that S113 colonized the cucumber roots (2.14 × 10⁵cells per gram of roots) and were able to survive in the rhizosphere (maintained for 20 d). The root exudates promoted colonization on roots and increased the degradation of chlorimuron-ethyl by S113. Five organic acids in cucumber-root exudates were detected and identified by HPLC. Citric acid and fumaric acid significantly stimulated S113 colonization on cucumber roots, with 18.4 and 15.5% increases, respectively, compared with the control. After irrigation with an S113 solution for 10 days, chlorimuron-ethyl could not be detected in the roots, seedlings, or rhizosphere soil, which allowed for improved cucumber growth. Therefore, the degradation mechanism of chlorimuron-ethyl residues by S113 in the rhizosphere could be applied in situ for the bioremediation of chlorimuron-ethyl contaminated soil to ensure crop safety.

Metalaxyl Effects on Antioxidant Defenses in Leaves and Roots of Solanum nigrum L

Overuse of pesticides has resulted in environmental problems, threating public health through accumulation in food chains. Phytoremediation is a powerful technique to clean up contaminated environments. However, it is necessary to unravel the metabolic mechanisms underlying phytoremediation in order to increase the efficiency of this process. Therefore, growth, physiological and biochemical responses in leaves and roots of Solanum nigrum L. exposed to the commonly used fungicide metalaxyl were investigated. This species shows characteristics that make it valuable as a potential tool for the remediation of organic pollutants. We found that once inside the plant, metalaxyl altered carbon metabolism, which resulted in a reduction of growth and lower biomass accumulation due to impairment of carbohydrate production (total soluble sugar, starch, rubisco) and increased photorespiration (glycolate oxidase, Gly/Ser ratio). A significant increase of antioxidant defenses (polyphenols, flavonoids, tocopherols, ascorbate, glutathione, superoxide dismutase, catalase, peroxidases, monodehydroascorbate- and dehydroascorbate reductase, gluthatione reductase) kept reactive oxygen species (ROS) levels under control (superoxide anion) leaving cell membranes undamaged. The results suggest that enhancing carbon assimilation and antioxidant capacity may be target parameters to improve this species' phytoremediation capacities. Highlights • Metalaxyl inhibits growth by reducing photosynthesis and inducing photorespiration • Elevated antioxidant defenses protect metalaxyl-treated plants from oxidative damage • Ascorbate and glutathione are key antioxidants in metalaxyl tolerance.

Degradation of chlorpyrifos by an endophytic bacterium of the Sphingomonas genus (strain HJY) isolated from Chinese chives (Allium tuberosum)

The degradation of chlorpyrifos (CP) by an endophytic bacterial strain (HJY) isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng) was investigated. Strain HJY was identified as Sphingomonas sp. based on morphological, physiological, and biochemical tests and a 16S rDNA sequence analysis. Approximately 96% of 20 mg L^-1 CP was degraded by strain HJY over 15 days in liquid minimal salts medium (MSM). The CP degradation rate could also be increased by glucose supplementation. The optimal conditions for the removal of 20 mg L^-1 CP by strain HJY in MSM were 2% inoculum density, pH 6.0, and 30-35°C. The CP degradation rate constant and half-life were 0.2136 ± 0.0063 d^-1 and 3.2451 ± 0.0975 d, respectively, under these conditions, but were raised to 0.7961 ± 0.1925 d^-1 and 0.8707 ± 0.3079 d with 1% glucose supplementation. The detection of metabolic products and screening for degrading genes indicated that O,O-diethyl O-3,5,6-trichloropyridinol was the major degradation product from CP, while it was likely that some functional genes were undetected and the mechanism responsible for CP degradation by strain HJY remained unknown. Strain HJY is potentially useful for the reduction of CP residues in Chinese chives and may be used for the in situ phytoremediation of CP.

Enhanced degradation of chlorpyrifos in rice (Oryza sativa L.) by five strains of endophytic bacteria and their plant growth promotional ability

Endophytic bacteria reside in plant tissues, such as roots, stems, leaves and seeds. Most of them can stimulate plant growth or alleviate phytotoxicity of pollutants. There are handful species with dual functions stimulating plant growth and degrading pollutants have been reported. Five endophytic bacteria were isolated from chlorpyrifos (CP) treated rice plants and identified as Pseudomonas aeruginosa strain RRA, Bacillus megaterium strain RRB, Sphingobacterium siyangensis strain RSA, Stenotrophomonas pavanii strain RSB and Curtobacterium plantarum strain RSC according to morphological characteristics, physiological and biochemical tests, and 16S rDNA phylogeny. All of them possessed some plant growth promotional traits, including indole acetic acid and siderophore production, secretion of phosphate solubilization and 1-aminocyclopropane-1-carboxylate deaminase. The bacteria were marked with the green fluorescent protein (gfp) gene and successfully colonized into rice plants. All isolates were able to degrade CP in vitro and in vivo. The five isolates degraded more than 90% of CP in 24 h when the initial concentration was lower than 5 mg/L. CP degradation was significantly enhanced in the infested rice plants and rice grains. The final CP residual was reduced up to 80% in the infested rice grains compared to the controls. The results indicate that these isolates are promising bio-inoculants for the removal or detoxification of CP residues in rice plants and grains.

Colonization of Paracoccus sp. QCT6 and Enhancement of Metribuzin Degradation in Maize Rhizosphere Soil

Strain QCT6, capable of degrading metribuzin, was isolated from metribuzin-contaminated soil. The isolate was identified as Paracoccus sp. according to its physiological characteristics, biochemical tests, and 16S rRNA gene phylogenetic analysis. In liquid culture, 86.4% of 50 mg/L metribuzin was removed by strain QCT6 after incubation for 7 days. The product of metribuzin degradation by QCT6 was identified as deamino-metribuzin, which has reduced phytotoxicity on the growth of maize. After being marked with the gfp gene, the colonization and distribution of gfp-tagged QCT6 were directly observed with a confocal laser scanning microscope. The QCT6 strain showed good colonization ability on maize roots and was maintained for at least 20 days in rhizosphere soil. After root irrigation with gfp-tagged QCT6, 75.7% of 15 mg/L metribuzin was removed from the maize rhizosphere soil. This metribuzin-degrading strain QCT6 has strong potential applications for in situ bioremediation of soil contaminated with metribuzin.

Enhanced Degradation of TCE on a Superfund Site Using Endophyte-Assisted Poplar Tree Phytoremediation

Trichloroethylene (TCE) is a widespread environmental pollutant common in groundwater plumes associated with industrial manufacturing areas. We had previously isolated and characterized a natural bacterial endophyte, Enterobacter sp. strain PDN3, of poplar trees, that rapidly metabolizes TCE, releasing chloride ion. We now report findings from a successful three-year field trial of endophyte-assisted phytoremediation on the Middlefield-Ellis-Whisman Superfund Study Area TCE plume in the Silicon Valley of California. The inoculated poplar trees exhibited increased growth and reduced TCE phytotoxic effects with a 32% increase in trunk diameter compared to mock-inoculated control poplar trees. The inoculated trees excreted 50% more chloride ion into the rhizosphere, indicative of increased TCE metabolism in planta. Data from tree core analysis of the tree tissues provided further supporting evidence of the enhanced rate of degradation of the chlorinated solvents in the inoculated trees. Test well groundwater analyses demonstrated a marked decrease in concentration of TCE and its derivatives from the tree-associated groundwater plume. The concentration of TCE decreased from 300 μg/L upstream of the planted area to less than 5 μg/L downstream of the planted area. TCE derivatives were similarly removed with cis-1,2-dichloroethene decreasing from 160 μg/L to less than 5 μg/L and trans-1,2-dichloroethene decreasing from 3.1 μg/L to less than 0.5 μg/L downstream of the planted trees. 1,1-dichloroethene and vinyl chloride both decreased from 6.8 and 0.77 μg/L, respectively, to below the reporting limit of 0.5 μg/L providing strong evidence of the ability of the endophytic inoculated trees to effectively remove TCE from affected groundwater. The combination of native pollutant-degrading endophytic bacteria and fast-growing poplar tree systems offers a readily deployable, cost-effective approach for the degradation of TCE, and may help mitigate potential transfer up the food chain, volatilization to the atmosphere, as well as direct phytotoxic impacts to plants used in this type of phytoremediation.

Opinion: Taking phytoremediation from proven technology to accepted practice

Phytoremediation is the use of plants to extract, immobilize, contain and/or degrade contaminants from soil, water or air. It can be an effective strategy for on site and/or in situ removal of various contaminants from soils, including petroleum hydrocarbons (PHC), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), solvents (e.g., trichloroethylene [TCE]), munitions waste (e.g., 2,4,6-trinitrotoluene [TNT]), metal(loid)s, salt (NaCl) and radioisotopes. Commercial phytoremediation technologies appear to be underutilized globally. The primary objective of this opinion piece is to discuss how to take phytoremediation from a proven technology to an accepted practice. An overview of phytoremediation of soil is provided, with the focus on field applications, to provide a frame of reference for the subsequent discussion on better utilization of phytoremediation. We consider reasons why phytoremediation is underutilized, despite clear evidence that, under many conditions, it can be applied quite successfully in the field. We offer suggestions on how to gain greater acceptance for phytoremediation by industry and government. A new paradigm of phytomanagement, with a specific focus on using phytoremediation as a "gentle remediation option" (GRO) within a broader, long-term management strategy, is also discussed.

The endophytic bacterium Serratia sp. PW7 degrades pyrene in wheat

This research was conducted to isolate polycyclic aromatic hydrocarbon-degrading (PAH-degrading) endophytic bacteria and investigate their potential in protecting plants against PAH contamination. Pyrene-degrading endophytic bacteria were isolated from plants grown in PAH-contaminated soil. Among these endophytic bacteria, strain PW7 (Serratia sp.) isolated from Plantago asiatica was selected to investigate the suppression of pyrene accumulation in Triticum aestivum L. In the in vitro tests, strain PW7 degraded 51.2% of the pyrene in the media within 14 days. The optimal biodegradation conditions were pH 7.0, 30 °C, and MS medium supplemented with additional glucose, maltose, sucrose, and peptones. In the in vivo tests, strain PW7 successfully colonized the roots and shoots of inoculated (E⁺) wheat plants, and its colonization decreased pyrene accumulation and pyrene transportation from roots to shoots. Remarkably, the concentration of pyrene in shoots decreased much more than that in roots, suggesting that strain PW7 has the potential for protecting wheat against pyrene contamination and mitigating the threat of pyrene to human health via food consumption.

Isolation, Colonization, and Chlorpyrifos Degradation Mediation of the Endophytic Bacterium Sphingomonas Strain HJY in Chinese Chives (Allium tuberosum)

The endophyte-plant interaction can benefit the host in many different ways. An endophytic bacterium strain (HJY) capable of degrading chlorpyrifos (CP) was isolated from Chinese chives (Allium tuberosum Rottl. ex Spreng). The isolated bacterium HJY classified as Sphingomonas sp. strain HJY could use CP as the sole carbon source. After being marked with the gfp gene, the colonization and distribution of strain HJY-gfp were directly observed in different tissues of Chinese chives with a confocal laser scanning microscope. The inoculation of strain HJY-gfp in Chinese chives resulted in a higher degradation of CP inside the plants than in uninoculated plants. With drench application, up to 70 and 66% of CP were removed from shoots and roots of inoculated Chinese chives, respectively. Moreover, up to 75% of CP was removed from the soil containing plants inoculated with HJY-gfp. With foliage application, the applied concentration of chlorpyrifos affected the degradation performance of strain HJY in Chinese chives. Significant differences were observed only between inoculated and uninoculated Chinese chives with the low applied concentration of CP. Together, other than natural endophyte-assisted plant protection for food safety, the interaction of HJY and plant may be also a promising strategy for in situ bioremediation of soil contaminated with CP.

Native rhizobia from Zn mining soil promote the growth of Leucaena leucocephala on contaminated soil

Plants on contaminated mining soils often show a reduced growth due to nutrient depletion as well as trace elements (TEs) toxicity. Since those conditions threat plant's survival, plant growth-promoting rhizobacteria (PGPRs), such as rhizobia, might be of crucial importance for plant colonization on TE-contaminated soils. Native rhizobia from mining soils are promising candidates for bioaugmented phytoremediation of those soils as they are adapted to the specific conditions. In this work, rhizobia from Zn- and Cd-contaminated mining soils were in vitro screened for their PGP features [organic acids, indole-3-acetic acid (IAA), and siderophore (SID) production; 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity; and Ca₃(PO₄)₂ solubilization] and Zn and Cd tolerance. In addition, some type and reference rhizobia strains were included in the study as well. The in vitro screening indicated that rhizobia and other native genera have great potential for phytoremediation purposes, by exerting, besides biological N₂ fixation, other plant growth-promoting traits. Leucaena leucocephala-Mesorhizobium sp. (UFLA 01-765) showed multielement tolerance and an efficient symbiosis on contaminated soil, decreasing the activities of antioxidative enzymes in shoots. This symbiosis is a promising combination for phytostabilization.

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.

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.

Biodegradation of Mixed PAHs by PAH-Degrading Endophytic Bacteria

Endophytic bacteria can promote plant growth, induce plant defence mechanisms, and increase plant resistance to organic contaminants. The aims of the present study were to isolate highly PAH-degrading endophytic bacteria from plants growing at PAH-contaminated sites and to evaluate the capabilities of these bacteria to degrade polycyclic aromatic hydrocarbons (PAHs) in vitro, which will be beneficial for re-colonizing target plants and reducing plant PAH residues through the inoculation of plants with endophytic bacteria. Two endophytic bacterial strains P₁ (Stenotrophomonas sp.) and P₃ (Pseudomonas sp.), which degraded more than 90% of phenanthrene (PHE) within 7 days, were isolated from Conyza canadensis and Trifolium pretense L., respectively. Both strains could use naphthalene (NAP), PHE, fluorene (FLR), pyrene (PYR), and benzo(a)pyrene (B(a)P) as the sole sources of carbon and energy. Moreover, these bacteria reduced the contamination of mixed PAHs at high levels after inoculation for 7 days; strain P₁ degraded 98.0% NAP, 83.1% FLR, 87.8% PHE, 14.4% PYR, and 1.6% B(a)P, and strain P₃ degraded 95.3% NAP, 87.9% FLR, 90.4% PHE, 6.9% PYR, and negligible B(a)P. Notably, the biodegradation of PAHs could be promoted through additional carbon and nitrogen nutrients; therein, beef extract was suggested as the optimal co-substrate for the degradation of PAHs by these two strains (99.1% PHE was degraded within 7 days). Compared with strain P₁, strain P₃ has more potential for the use in the removal of PAHs from plant tissues. These results provide a novel perspective in the reduction of plant PAH residues in PAH-contaminated sites through inoculating plants with highly PAH-degrading endophytic bacteria.

Potential of Endophytic Bacterium Paenibacillus sp. PHE-3 Isolated from Plantago asiatica L. for Reduction of PAH Contamination in Plant Tissues

Endophytes are ubiquitous in plants, and they may have a natural capacity to biodegrade polycyclic aromatic hydrocarbons (PAHs). In our study, a phenanthrene-degrading endophytic Paenibacillus sp. PHE-3 was isolated from P. asiatica L. grown in a PAH-contaminated site. The effects of environmental variables on phenanthrene biodegradation by strain PHE-3 were studied, and the ability of strain PHE-3 to use high molecular weight PAH (HMW-PAH) as a sole carbon source was also evaluated. Our results indicated that pH value of 4.0–8.0, temperature of 30 °C–42 °C, initial phenanthrene concentration less than 100 mg·L⁻¹, and some additional nutrients are favorable for the biodegradation of phenanthrene by strain PHE-3. The maximum biodegradation efficiency of phenanthrene was achieved at 99.9% after 84 h cultivation with additional glutamate. Moreover, the phenanthrene biodegradation by strain PHE-3 was positively correlated with the catechol 2,3-dioxygenase activity (ρ = 0.981, p < 0.05), suggesting that strain PHE-3 had the capability of degrading HMW-PAHs. In the presence of other 2-, 3-ringed PAHs, strain PHE-3 effectively degraded HMW-PAHs through co-metabolism. The results of this study are beneficial in that the re-colonization potential and PAH degradation performance of endophytic Paenibacillus sp. PHE-3 may be applied towards reducing PAH contamination in plants.

Variable Nitrogen Fixation in Wild Populus

The microbiome of plants is diverse, and like that of animals, is important for overall health and nutrient acquisition. In legumes and actinorhizal plants, a portion of essential nitrogen (N) is obtained through symbiosis with nodule-inhabiting, N2-fixing microorganisms. However, a variety of non-nodulating plant species can also thrive in natural, low-N settings. Some of these species may rely on endophytes, microorganisms that live within plants, to fix N2 gas into usable forms. Here we report the first direct evidence of N2 fixation in the early successional wild tree, Populus trichocarpa, a non-leguminous tree, from its native riparian habitat. In order to measure N2 fixation, surface-sterilized cuttings of wild poplar were assayed using both 15N2 incorporation and the commonly used acetylene reduction assay. The 15N label was incorporated at high levels in a subset of cuttings, suggesting a high level of N-fixation. Similarly, acetylene was reduced to ethylene in some samples. The microbiota of the cuttings was highly variable, both in numbers of cultured bacteria and in genetic diversity. Our results indicated that associative N2-fixation occurred within wild poplar and that a non-uniformity in the distribution of endophytic bacteria may explain the variability in N-fixation activity. These results point to the need for molecular studies to decipher the required microbial consortia and conditions for effective endophytic N2-fixation in trees.

Endophytic Phytoaugmentation: Treating Wastewater and Runoff Through Augmented Phytoremediation

Limited options exist for efficiently and effectively treating water runoff from agricultural fields and landfills. Traditional treatments include excavation, transport to landfills, incineration, stabilization, and vitrification. In general, treatment options relying on biological methods such as bioremediation have the ability to be applied in situ and offer a sustainable remedial option with a lower environmental impact and reduced long-term operating expenses. These methods are generally considered ecologically friendly, particularly when compared to traditional physicochemical cleanup options. Phytoremediation, which relies on plants to take up and/or transform the contaminant of interest, is another alternative treatment method which has been developed. However, phytoremediation is not widely used, largely due to its low treatment efficiency. Endophytic phytoaugmentation is a variation on phytoremediation that relies on augmenting the phytoremediating plants with exogenous strains to stimulate associated plant-microbe interactions to facilitate and improve remediation efficiency. In this review, we offer a summary of the current knowledge as well as developments in endophytic phytoaugmentation and present some potential future applications for this technology. There has been a limited number of published endophytic phytoaugmentation case studies and much remains to be done to transition lab-scale results to field applications. Future research needs include large-scale endophytic phytoaugmentation experiments as well as the development of more exhaustive tools for monitoring plant-microbe-pollutant interactions.

Towards an Enhanced Understanding of Plant-Microbiome Interactions to Improve Phytoremediation: Engineering the Metaorganism

Phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. However, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. A number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely understood. Moreover, current approaches that target the plant host, and environment separately to improve phytoremediation, potentially overlook microbial functions and properties that are part of the multiscale complexity of the plant-environment wherein biodegradation takes place. In contrast, in situ studies of phytoremediation research at the metaorganism level (host and microbiome together) are lacking. Here, we discuss a competition-driven model, based on recent evidence from the metagenomics level, and hypotheses generated by microbial community ecology, to explain the establishment of a catabolic rhizosphere microbiome in a contaminated soil. There is evidence to ground that if the host provides the right level and mix of resources (exudates) over which the microbes can compete, then a competitive catabolic and plant-growth promoting (PGP) microbiome can be selected for as long as it provides a competitive superiority in the niche. The competition-driven model indicates four strategies to interfere with the microbiome. Specifically, the rhizosphere microbiome community can be shifted using treatments that alter the host, resources, environment, and that take advantage of prioritization in inoculation. Our model and suggestions, considering the metaorganism in its natural context, would allow to gain further knowledge on the plant-microbial functions, and facilitate translation to more effective, and predictable phytotechnologies.

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.

Inoculation methods using Rhodococcus erythropolis strain P30 affects bacterial assisted phytoextraction capacity of Nicotiana tabacum

In this study different bacterial inoculation methods were tested for tobacco plants growing in a mine-soil contaminated with Pb, Zn, and Cd. The inoculation methods evaluated were: seed inoculation, soil inoculation, dual soil inoculation event, and seed+soil inoculation. Each inoculum was added at two bacterial densities (10(6) CFUs mL(-1) and 10(8) CFUs mL(-1)). The objectives were to evaluate whether or not the mode of inoculation or the number of applied microorganisms influences plant response. The most pronounced bacterial-induced effect was found for biomass production, and the soil inoculation treatment (using 10(6) CFUs mL(-1)) led to the highest increase in shoot dry weight yield (up to 45%). Bacterial-induced effects on shoot metal concentrations were less pronounced; although a positive effect was found on shoot Pb concentration when using 10(8) CFUs mL(-1) in the soil inoculation (29% increase) and in the seed+soil inoculation (34% increase). Also shoot Zn concentration increased by 24% after seed inoculation with 10(6) CFUs mL(-1). The best effects on the total metal yield were not correlated with an increasing number of inoculated bacteria. In fact the best results were found after a single soil inoculation using the lower cellular density of 10(6) CFUs mL(-1).

Natural attenuation of 1,2,4-trichlorobenzene in shallow aquifer at the Luhuagang's landfill site, Kaifeng, China

The natural attenuation of 1,2,4-trichlorobenzene (1,2,4-TCB) in shallow aquifer was investigated at the Luhuagang's landfill site (LLS), where the subsoil and shallow aquifer have been contaminated by certain chemicals owning to a lack of protective structures and leachate collection systems. Batch natural attenuation experiments and molecular biology experiments were conducted to study the natural attenuation characteristics of 1,2,4-TCB, the relative contributions of the primary natural attenuation processes and the functional microorganisms degrading 1,2,4-TCB, respectively. The results indicated that the relationship between degradation rate and 1,2,4-TCB concentrations was in line with first-order decay kinetics, and the natural attenuation rate of 1,2,4-TCB in the three media followed the order silt>fine sand>medium sand, which was related to the size of the media and the microbial population. The relative contribution of adsorption to natural attenuation was 97.7%, 98.2%, and 95.7% in unsterilized silt, fine sand and medium sand, respectively, and that of biodegradation was 2.3%, 1.8%, and 4.3%, respectively. These properties are related to the characteristics of the pollutants and the specific conditions at the contaminated sites, such as the characteristics of the aquifer media and microbial communities. The functional microorganisms degrading 1,2,4-TCB at the site were proved to be primarily Pseudomonas sp. This study indicates the feasibility of bioremediation (bioaugmentation and biostimulation) by indigenous microorganisms to treat 1,2,4-TCB contamination at the site.