Assessing the potential for rhizoremediation of PCB contaminated soils in northern regions using native tree species

Integrating Biochar, Bacteria, and Plants for Sustainable Remediation of Soils Contaminated with Organic Pollutants

The contamination of soil with organic pollutants has been accelerated by agricultural and industrial development and poses a major threat to global ecosystems and human health. Various chemical and physical techniques have been developed to remediate soils contaminated with organic pollutants, but challenges related to cost, efficacy, and toxic byproducts often limit their sustainability. Fortunately, phytoremediation, achieved through the use of plants and associated microbiomes, has shown great promise for tackling environmental pollution; this technology has been tested both in the laboratory and in the field. Plant-microbe interactions further promote the efficacy of phytoremediation, with plant growth-promoting bacteria (PGPB) often used to assist the remediation of organic pollutants. However, the efficiency of microbe-assisted phytoremediation can be impeded by (i) high concentrations of secondary toxins, (ii) the absence of a suitable sink for these toxins, (iii) nutrient limitations, (iv) the lack of continued release of microbial inocula, and (v) the lack of shelter or porous habitats for planktonic organisms. In this regard, biochar affords unparalleled positive attributes that make it a suitable bacterial carrier and soil health enhancer. We propose that several barriers can be overcome by integrating plants, PGPB, and biochar for the remediation of organic pollutants in soil. Here, we explore the mechanisms by which biochar and PGPB can assist plants in the remediation of organic pollutants in soils, and thereby improve soil health. We analyze the cost-effectiveness, feasibility, life cycle, and practicality of this integration for sustainable restoration and management of soil.

Mulching in lowland hay meadows drives an adaptive convergence of above- and below-ground traits reducing plasticity and improving biomass: A possible tool for enhancing phytoremediation

We aimed to understand the effect of mulching (i.e., cutting and leaving the crushed biomass to decompose in situ) on above- and below-ground plant functional traits and whether this practice may be a potential tool for enhancing the phytoremediation of lowland hay meadows. To this aim, we evaluated at the community level seven years of mulching application in a PCBs and HMs soil-polluted Site of National Interest (SIN Brescia-Caffaro) through the analysis of the floristic composition and the above- and below-ground plant traits. We found that the abandonment of agricultural activities led to a marked increase in the soil organic carbon and pH, and the over-imposed mulching additionally induced a slight increase in soil nutrients. Mulching favored the establishment of a productive plant community characterized by a more conservative-resource strategy, a higher biomass development, and lower plasticity through an adaptative convergence between above- and below-ground organs. In particular, the analysis of the root depth distribution highlighted the key role of roots living in the upper soil layer (10 cm). Mulching did not show a significant effect on plant species known to be effective in terms of PCB phytoremediation. However, the mulching application appears to be a promising tool for enhancing the root web that functions as the backbone for the proliferation of microbes devoted to organic contaminants' degradation and selects a two-fold number of plant species known to be metal-tolerant. However, besides these potential positive effects of the mulching application, favoring species with a higher biomass development, in the long term, may lead to a biodiversity reduction and thus to potential consequences also on the diversity of native species important for the phytoremediation.

Bioremediation strategies with biochar for polychlorinated biphenyls (PCBs)-contaminated soils: A review

Polychlorinated biphenyls (PCBs) are hazardous organic contaminants threatening human health and environmental safety due to their toxicity and carcinogenicity. Biochar (BC) is an eco-friendly carbonaceous material that can extensively be utilized for the remediation of PCBs-contaminated soils. In the last decade, many studies reported that BC is beneficial for soil quality enhancement and agricultural productivity based on its physicochemical characteristics. In this review, the potential of BC application in PCBs-contaminated soils is elaborated as biological strategies (e.g., bioremediation and phytoremediation) and specific mechanisms are also comprehensively demonstrated. Further, the synergy effects of BC application on PCBs-contaminated soils are discussed, in view of eco-friendly, beneficial, and productive aspects.

'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions

An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.

A new dataset of PCB half-lives in soil: Effect of plant species and organic carbon addition on biodegradation rates in a weathered contaminated soil

This paper presents a new dataset of Polychlorinated Biphenyls (PCBs) half-lives in soil. Data were obtained from a greenhouse experiment performed with an aged contaminated soil under semi-field conditions, collected from a National Relevance Site (SIN) located in Northern Italy (SIN Brescia-Caffaro). Ten different treatments (combination of seven plant species and different soil conditions) were considered together with the respective controls (soil without plants). PCB concentration reduction in soil was measured over a period of 18 months to evaluate the ability of plants to stimulate the biodegradation of these compounds. Tall fescue, tall fescue cultivated together with pumpkin and tall fescue amended with compost reduced more than the 50% of the 79 measured PCB congeners, including the most chlorinated ones (octa to deca-PCBs). However, the data obtained showed that no plant species was uniquely responsible for the effective degradation of all isomeric classes and congeners. The obtained half-lives ranged from 1.3 to 5.6 years and were up to a factor of 8 lower compared to generic HL values reported in literature. This highlighted the importance of cultivation and plant-microbe interactions in speeding up the PCB biodegradation. This new dataset could contribute to substantially improve the predictions of soil remediation time, multimedia fate and the long-range transport of PCBs. Additionally, the half-lives obtained here can also be used in the evaluation of the food chain transfer of these chemicals, and finally the exposure and potential for effects on ecosystems.

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.

Microcosm Experiment to Assess the Capacity of a Poplar Clone to Grow in a PCB-Contaminated Soil

Polychlorinated byphenyls (PCBs) are a class of Persistent Organic Pollutants extremely hard to remove from soil. The use of plants to promote the degradation of PCBs, thanks to synergic interactions between roots and the natural soil microorganisms in the rhizosphere, has been proved to constitute an effective and environmentally friendly remediation technique. Preliminary microcosm experiments were conducted in a greenhouse for 12 months to evaluate the capacity of the Monviso hybrid poplar clone, a model plant for phytoremediation, to grow in a low quality and PCB-contaminated soil in order to assess if this clone could be subsequently used in a field experiment. For this purpose, three different soil conditions (Microbiologically Active, Pre-sterilized and Hypoxic soils) were set up in order to assess the capacity of this clone to grow in the polluted soil in these different conditions and support the soil microbial community activity. The growth and physiology (chlorophyll content, chlorophyll fluorescence, ascorbate, phenolic compounds and flavonoid contents) of the poplar were determined. Moreover, chemical analyses were performed to assess the concentrations of PCB indicators in soil and plant roots. Finally, the microbial community was evaluated in terms of total abundance and activity under the different experimental conditions. Results showed that the poplar clone was able to grow efficiently in the contaminated soil and to promote microbial transformations of PCBs. Plants grown in the hypoxic condition promoted the formation of a higher number of higher-chlorinated PCBs and accumulated lower PCBs in their roots. However, plants in this condition showed a higher stress level than the other microcosms, producing higher amounts of phenolic, flavonoid and ascorbate contents, as a defence mechanism.

Rhizoremediation of weathered PCBs in a heavily contaminated agricultural soil: Results of a biostimulation trial in semi field conditions

This paper describes the results of a rhizoremediation greenhouse experiment planned to select the best plant species and soil management for the bioremediation of weathered polychlorinated biphenyls (PCBs). We evaluated the ability of different plant species to stimulate activity and diversity of the soil microbial community leading to the reduction of PCB concentrations in a heavily contaminated soil (at mg kg-1 dw level), of the national priority site for remediation (SIN) "Brescia-Caffaro" in Italy. Biostimulation was determined in large size (6kg) pots, to reflect semi-field conditions with a soil/root volume ratio larger than in most rhizoremediation experiments present in the literature. In total, 10 treatments were tested in triplicates comparing 7 plant species (grass and trees) and 5 soil/cultivation conditions (i.e., only one plant species, plant consociation, redox cycle, compost or ammonium thiosulfate addition) with the appropriate unplanted controls. After 18months of biostimulation the overall reduction of total PCBs varied between 14 and 20%. Microbial analysis revealed a shift in the microbial community structure over time and showed that all the planted treatments significantly enhanced microbial hydrolytic activity and the abundance of bacterial populations, including potential PCB degraders, in the soil surrounding plant roots. The plant species most effective in reducing the contaminant concentrations were Festuca arundinacea cultivated adding compost or in consociation with Cucurbita pepo ssp. pepo and Medicago sativa cultivated with Rhizobium spp. and mycorrhizal fungi; they reduced total PCB concentrations of about 20% and showed the significant depletion of a high number of PCB congeners (29, 37 and 23, respectively, out of the 79 measured). Our results suggest that these plant species are particularly efficient in increasing soil PCB bioavailability and in stimulating microbial degradation. They could be used in field rhizoremediation strategies to enhance the natural attenuation process and reduce PCB levels in historically contaminated sites.

Remediation potential of bacterial mixed cultures for polychlorinated biphenyls (PCBs) biodegradation

Remediation of polychlorinated biphenyls (PCBs) in minimal mineral water media in the presence of bacterial mixed cultures consisting of several individual strains is proposed. Starting from the fact that the properties and features of bacterial strains in mixed cultures can be supplemented and compensated, two-, three- and seven-membered mixed cultures (MC) were performed. The strains used for the construction of the MC were isolated from the waste canal of a former PCB producer. The highest biodegradation of 70 % of the sum of seven defined PCB congeners was achieved by two-membered MC containing the strains Rhodococcus sp. and Stenotrophomonas maltophilia added in the biomass ratio of 1 : 3 and 3 : 1. PCB biodegradation by a seven-membered MC was lower (58 %) but provided several benefits over the less-membered mixed cultures or the individual strains: similarity to naturally occurring microflora, easier preparation of the inocula, certain and repeatable results. Periodical reinoculation of the water media resulted to PCB biodegradation increase to 65 %. Seven-membered MC was applied to the historically PCB contaminated sediment as well, where a 59 % degradation of the sum of seven PCB congeners was determined.

Local fungi, willow and municipal compost effectively remediate petroleum-contaminated soil in the Canadian North

Low energy-input alternatives based on locally available products are needed for treating petroleum-hydrocarbon spills in northern regions. We tested the efficacy of three local biological components (municipal compost, white-rot fungus: Pleurotus ostreatus and willow: Salix planifolia) to remediate diesel-contaminated soils in a subarctic climate (Whitehorse, YT, Canada), and compared their efficacy to natural attenuation and chemical fertilizers (industry standard). After the first growing season, biologically amended treatments (BAT) that contained >2 biological components, had decreased 69-73% of the diesel's F2 fraction (C₁₀-C₁₆), which is more than natural attenuation or fertilizer (48 and 51%). By the third growing season, the BAT dropped below the Canadian Council of Ministers of the Environment's (CCME) Agricultural & Residential/Parkland guideline (<150 mg kg^-1) and 86% of willows had survived and developed extensive roots. MiSeq amplicon sequencing of fungal (ITS) and bacterial (16S) rRNA genes showed the BAT's microbial communities were significantly more abundant and diverse. We found 132 bacterial and 35 fungal genera unique to the BAT. Readily-available local biological components such as municipal compost, fungi and willows may provide an effective alternative to applications of imported chemical fertilizers for the bioremediation and revegetation of diesel-contaminated soil in northern environments.

Rhizoremediation half-lives of PCBs: Role of congener composition, organic carbon forms, bioavailability, microbial activity, plant species and soil conditions, on the prediction of fate and persistence in soil

Polychlorinated biphenyls (PCBs) are persistent organic pollutants widely produced and used in many countries until the increasing concern about their environmental risk lead to their ban in the 1980s. Although their emissions decreased, PCBs are nowadays still present in the environment and can be reemitted from reservoir compartments such as contaminated soils. In the last two decades, there has been a growing interest in bioremediation technologies that use plants and microorganisms (i.e. rhizoremediation) to degrade organic chemicals in contaminated sites. Different studies have been conducted to investigate the potential of plant-microbe interactions in the remediation of organic chemical contaminated soils. They range from short-term and laboratory/greenhouse experiments to long-term and field trials and, when correctly set up, they could provide useful data such as PCB rhizoremediation half-lives in soil. Such type of data are important input parameters for multimedia fate models that aim to estimate the time requested to achieve regulatory thresholds in a PCB contaminated site, allowing to draw up its remediation plan. This review focuses on the main factors influencing PCB fate, persistence and bioavailability in soil including PCB mixture congener composition, soil organic carbon forms, microorganism activity, plant species and soil conditions. Furthermore, it provides an estimate of rhizoremediation half-lives of the ten PCB families starting from the results of literature rhizoremediation experiments. Finally, guidance to perform appropriate experiments to obtain comparable, accurate and useful data for fate estimation is proposed.

Rhizoremediation of a dioxin-like PCB polluted soil by alfalfa: Dynamic characterization at temporal and spatial scale

This study investigates the temporal and spacial dissipation dynamics of a dioxin-like polychlorinated biphenyl (PCB 77) in the rhizosphere of alfalfa. A three-chamber rhizobox was designed to compare the PCB 77 dissipation efficiency in the rhizosphere, near-rhizosphere, and far-rhizosphere zones. Culture-independent techniques, including quantitative PCR (qPCR), Biolog-ECO plate, and denatured gradient gel electrophoresis (DGGE) were employed to investigate the variation of bacterial quantity, metabolic diversity and community structure in the alfalfa-rhizobium symbiosis rhizosphere at different rhizoremediation stages. PCB dissipation rates in different rhizosphere zones were in the order: rhizosphere (90.9%) > near-rhizosphere (80.5%) > far-rhizosphere (31.7%). The number of the bacterial 16S rRNA gene copies in the rhizosphere zone in the polluted treatment reached the highest value of all the treatments. Microbial metabolic diversity, as indicated by average well color development (AWCD) in both rhizosphere and near-rhizosphere zones, had recovered from the PCB 77 pollution. The soil bacterial community diversity improved greatly in the rhizosphere of alfalfa, with some new species appeared in the rhizosphere and near-rhizosphere zones. In conclusion, the dissipation of PCB 77, the quantity of total soil bacteria, soil microbial metabolic diversity, and soil microbial community structure were significantly improved in rhizosphere and near-rhizosphere zones of alfalfa.

Assessing the dynamic changes of rhizosphere functionality of Zea mays plants grown in organochlorine contaminated soils

The persistent organochlorine pesticides (OCPs) in soils are suspected to disturb soil biogeochemical cycles. This study addressed the dynamic changes in soil functionality under lindane and chlordecone exposures with or without maize plant. Decreases in soil ammonium concentration, potential nitrogen mineralization and microbial biomass were only OCP-influenced in bulk soils. OCPs appeared to inhibit the ammonification step. With plants, soil functionality under OCP stress was similar to controls demonstrating the plant influence to ensure the efficiency of C- and N-turnover in soils. Moreover, OCPs did not impact the microbial community physiological profile in all tested conditions. However, microbial community structure was OCP-modified only in the presence of plants. Abundances of gram-negative and saprophytic fungi increased (up to +93% and +55%, respectively) suggesting a plant stimulation of nutrient turnover and rhizodegradation processes. Nevertheless, intimate microbial/plant interactions appeared to be OCP-impacted with depletions in mycorrhizae and micro/meso-fauna abundances (up to -53% and -56%, respectively) which might have adverse effects on more long-term plant growth (3-4 months). In short-term experiment (28days), maize growth was similar to the control ones, indicating an enhanced plasticity of the soil functioning in the presence of plants, which could efficiently participate to the remediation of OCP-contaminated soils.

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.

Insight into the long-term effect of mangrove species on removal of polybrominated diphenyl ethers (PBDEs) from BDE-47 contaminated sediments

Polybrominated diphenyl ethers (PBDEs) have become ubiquitous environmental contaminants, particularly in mangrove wetlands. However, little is known about the long-term effect of mangrove plants on PBDE removal from contaminated sediments. A 12-month microcosm experiment was conducted to understand the effect of two mangrove species, namely Avicennia marina (Am) and Aegiceras corniculatum (Ac), on PBDE removal from the sediments spiked with 2000ngg^-1 dry weight of BDE-47, and to explore the microbial mechanism responsible for the planting-induced effects on BDE-47 removal. Results showed that planting of mangrove species, either Am or Ac, could accelerate BDE-47 removal from contaminated sediments during the 12months experiment, mainly through enhancing microbial degradation process. In particular, Am sediment had significantly higher BDE-47 degradation efficiency compared with Ac sediment, which may be mainly attributed to higher activities of urease and dehydrogenase, as well as higher 16S rRNA gene copies of total bacteria and organohalide-respiring bacteria (OHRB) in Am sediment. Moreover, planting could shift sediment bacterial community composition and selectively enrich some bacterial genera responsible for PBDE degradation. Such selective enrichment effect of Am on the potential PBDE-degrading bacteria differed distinctly from that of Ac. These results indicated that long-term planting of mangrove species, especially Am, could significantly promote BDE-47 removal from the contaminated sediments by enhancing microbial activity, increasing total bacterial and OHRB abundances and altering bacterial community composition.

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.

Microbiome Dynamics of a Polychlorobiphenyl (PCB) Historically Contaminated Marine Sediment under Conditions Promoting Reductive Dechlorination

The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD. A long-term microcosm study revealed that autochthonous bacteria were able to sustain the PCB dechlorination at a high extent and the successive addition of an external fermentable organic substrate (lactate) caused the further depletion of the high-chlorinated PCBs (up to 70%). Next Generation Sequencing was used to describe the core microbiome of the marine sediment and to follow the changes caused by the treatments. OTUs affiliated to sulfur-oxidizing ε-proteobacteria, Sulfurovum, and Sulfurimonas, were predominant in the original sediment and increased up to 60% of total OTUs after lactate addition. Other OTUs detected in the sediment were affiliated to sulfate reducing (δ-proteobacteria) and to organohalide respiring bacteria within Chloroflexi phylum mainly belonging to Dehalococcoidia class. Among others, Dehalococcoides mccartyi was enriched during the treatments even though the screening of the specific reductive dehalogenase genes revealed the occurrence of undescribed strains, which deserve further investigations. Overall, this study highlighted the potential of members of Dehalococcoidia class in reducing the contamination level of the marine sediment from Mar Piccolo with relevant implications on the selection of sustainable bioremediation strategies to clean-up the site.

Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

Differential Impacts of Willow and Mineral Fertilizer on Bacterial Communities and Biodegradation in Diesel Fuel Oil-Contaminated Soil

Despite decades of research there is limited understanding of how vegetation impacts the ability of microbial communities to process organic contaminants in soil. Using a combination of traditional and molecular assays, we examined how phytoremediation with willow and/or fertilization affected the microbial community present and active in the transformation of diesel contaminants. In a pot study, willow had a significant role in structuring the total bacterial community and resulted in significant decreases in diesel range organics (DRO). However, stable isotope probing (SIP) indicated that fertilizer drove the differences seen in community structure and function. Finally, analysis of the total variance in both pot and SIP experiments indicated an interactive effect between willow and fertilizer on the bacterial communities. This study clearly demonstrates that a willow native to Alaska accelerates DRO degradation, and together with fertilizer, increases aromatic degradation by shifting microbial community structure and the identity of active naphthalene degraders.

Synergistic Processing of Biphenyl and Benzoate: Carbon Flow Through the Bacterial Community in Polychlorinated-Biphenyl-Contaminated Soil

Aerobic mineralization of PCBs, which are toxic and persistent organic pollutants, involves the upper (biphenyl, BP) and lower (benzoate, BZ) degradation pathways. The activity of different members of the soil microbial community in performing one or both pathways, and their synergistic interactions during PCB biodegradation, are not well understood. This study investigates BP and BZ biodegradation and subsequent carbon flow through the microbial community in PCB-contaminated soil. DNA stable isotope probing (SIP) was used to identify the bacterial guilds involved in utilizing ¹³C-biphenyl (unchlorinated analogue of PCBs) and/or ¹³C-benzoate (product/intermediate of BP degradation and analogue of chlorobenzoates). By performing SIP with two substrates in parallel, we reveal microbes performing the upper (BP) and/or lower (BZ) degradation pathways, and heterotrophic bacteria involved indirectly in processing carbon derived from these substrates (i.e. through crossfeeding). Substrate mineralization rates and shifts in relative abundance of labeled taxa suggest that BP and BZ biotransformations were performed by microorganisms with different growth strategies: BZ-associated bacteria were fast growing, potentially copiotrophic organisms, while microbes that transform BP were oligotrophic, slower growing, organisms. Our findings provide novel insight into the functional interactions of soil bacteria active in processing biphenyl and related aromatic compounds in soil, revealing how carbon flows through a bacterial community.

Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons

The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.

The Role of Hydrology in the Polychlorinated Dibenzo--dioxin and Dibenzofuran Distributions in a Lowland River

Persistent organic pollutants such as polychlorinated dibenzo--dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are environmental contaminants that have widespread distribution and pose a serious threat to aquatic ecosystems. We conducted a study to quantify the distribution, patterns, and transport of PCDDs and PCDFs along the Pilica River in central Poland under different hydrological conditions to estimate the loads of these compounds and understand their fate in aquatic systems. Water samples were collected at five sampling points along the river that represent a range of hydrological conditions including flooding and stable and low water flows. Reduced river water flow was associated with lower average total and toxic equivalent (TEQ) concentrations of PCDDs plus PCDFs: 33.6 pg L and 4.21 pg TEQ L for flooding; 28.3 pg L and 3.6 pg TEQ L for stable flow; 18.4 pg L and 1.0 pg TEQ L for low-water flow. Similar results were observed for daily loadings of total and TEQ concentrations: the highest values were observed during flooding (331.1-839.4 mg d and 27.8-110.7 mg TEQ d), medium under stable hydrological conditions (55.8-121.0 mg d and 7.7-15.3 mg TEQ d), and the lowest values during low water flow (30.9 and 40.3 mg d and 1.4-2.4 mg TEQ d). The results demonstrate that diffuse sources of pollution play a key role during periods of high water flow (i.e., flooding season), whereas point sources of pollution, including municipal and industrial wastewater treatment plant discharges, mainly determine the PCDD and PCDF concentrations seen during low water periods.

Optimizing Polychlorinated Biphenyl Degradation by Flavonoid-Induced Cells of the Rhizobacterium Rhodococcus erythropolis U23A

There is evidence that many plant secondary metabolites may act as signal molecules to trigger the bacterial ability to metabolize polychlorinated biphenyls (PCBs) during the rhizoremediation process. However, the bases for the PCB rhizoremediation process are still largely unknown. The rhizobacterium Rhodococcus erythropolis U23A is unable to use flavanone as a growth substrate. However, on the basis of an assay that monitors the amount of 4-chlorobenzoate produced from 4-chlorobiphenyl by cells grown co-metabolically on flavanone plus sodium acetate, this flavonoid was previously found to be a potential inducer of the U23A biphenyl catabolic pathway. In this work, and using the same assay, we identified ten other flavonoids that did not support growth, but that acted as inducers of the U23A biphenyl pathway, and we confirmed flavonoid induction of the biphenyl catabolic pathway using quantitative real-time polymerase chain reaction (RT-qPCR) on the bphA gene. We also examined the effect of the growth co-substrate on flavonoid induction. Sodium acetate was replaced by glucose, mannose, sucrose, or mannitol, which are sugars found in plant root exudates. The data showed that the level of induction of strain U23A biphenyl-degrading enzymes was significantly influenced by the nature and concentration of the flavonoid in the growth medium, as well as by the substrate used for growth. Sucrose allowed for an optimal induction response for most flavonoids. Some flavonoids, such as flavone and isoflavone, were better inducers of the biphenyl catabolic enzymes than biphenyl itself. We also found that all flavonoids tested in this work were metabolized by strain U23A during co-metabolic growth, but that the metabolite profiles, as well as the level of efficiency of degradation, differed for each flavonoid. To obtain insight into how flavonoids interact with strain U23A to promote polychlorinated biphenyl (PCB) degradation, we determined the concentration of flavanone at which optimal PCB-degrading performance of strain U23A was achieved. We showed that it corresponded to the concentration required to fully induce the biphenyl catabolic pathway of the strain. Together, our data demonstrate that optimal PCB degradation during the rhizoremediation process will require the adjustment of several parameters, including the presence of the appropriate flavonoids at the proper concentrations and the presence of proper growth substrates that positively influence the ability of flavonoids to induce the pathway.

Microbial community analysis of switchgrass planted and unplanted soil microcosms displaying PCB dechlorination

Polychlorinated biphenyls (PCBs) pose potential risks to human and environmental health because they are carcinogenic, persistent, and bioaccumulative. In this study, we investigated bacterial communities in soil microcosms spiked with PCB 52, 77, and 153. Switchgrass (Panicum virgatum) was employed to improve overall PCB removal, and redox cycling (i.e., sequential periods of flooding followed by periods of no flooding) was performed in an effort to promote PCB dechlorination. Lesser chlorinated PCB transformation products were detected in all microcosms, indicating the occurrence of PCB dechlorination. Terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis showed that PCB spiking, switchgrass planting, and redox cycling affected the microbial community structure. Putative organohalide-respiring Chloroflexi populations, which were not found in unflooded microcosms, were enriched after 2 weeks of flooding in the redox-cycled microcosms. Sequences classified as Geobacter sp. were detected in all microcosms and were most abundant in the switchgrass-planted microcosm spiked with PCB congeners. The presence of possible organohalide-respiring bacteria in these soil microcosms suggests that they play a role in PCB dechlorination therein.

Enhanced Polychlorinated Biphenyl Removal in a Switchgrass Rhizosphere by Bioaugmentation with Burkholderia xenovorans LB400

Phytoremediation makes use of plants and associated microorganisms to clean up soils and sediments contaminated with inorganic and organic pollutants. In this study, switchgrass (Panicum virgatum) was used to test for its efficiency in improving the removal of three specific polychlorinated biphenyl (PCB) congeners (PCB 52, 77 and 153) in soil microcosms. The congeners were chosen for their ubiquity, toxicity, and recalcitrance. After 24 weeks of incubation, loss of 39.9 ± 0.41% of total PCB molar mass was observed in switchgrass treated soil, significantly higher than in unplanted soil (29.5 ± 3.4%) (p<0.05). The improved PCB removal in switchgrass treated soils could be explained by phytoextraction processes and enhanced microbial activity in the rhizosphere. Bioaugmentation with Burkholderia xenovorans LB400 was performed to further enhance aerobic PCB degradation. The presence of LB400 was associated with improved degradation of PCB 52, but not PCB 77 or PCB 153. Increased abundances of bphA (a functional gene that codes for a subunit of PCB-degrading biphenyl dioxygenase in bacteria) and its transcript were observed after bioaugmentation. The highest total PCB removal was observed in switchgrass treated soil with LB400 bioaugmentation (47.3 ± 1.22 %), and the presence of switchgrass facilitated LB400 survival in the soil. Overall, our results suggest the combined use of phytoremediation and bioaugmentation could be an efficient and sustainable strategy to eliminate recalcitrant PCB congeners and remediate PCB-contaminated soil.

Phytoremediation and bioremediation of polychlorinated biphenyls (PCBs): state of knowledge and research perspectives

This review summarizes the bioremediation and phytoremediation technologies proposed so far to detoxify PCB-contaminated sites. A critical analysis about the potential and limits of the PCB pollution treatment strategies by means of plants, fungi and bacteria are elucidated, including the new insights emerged from recent studies on the rhizosphere potential and on the implementation of simultaneous aerobic and anaerobic biodegradation processes. The review describes the biodegradation and phytoremediation processes and elaborates on the environmental variables affecting contaminant degradation rates, summarizing the amendments recommended to enhance PCB degradation. Additionally, issues connected with PCB toxicology, actual field remediation strategies and economical evaluation are discussed.

Paddy field--a natural sequential anaerobic-aerobic bioreactor for polychlorinated biphenyls transformation

The environmental pollution and health risks caused by the improper disposal of electric and electronic waste (e-waste) have become urgent issues for the developing countries. One of the typical pollutants, polychlorinated biphenyls (PCBs), is commonly found in farmland in Taizhou, a major hotspot of e-waste recycling in China. This study investigated the amount of PCB residue in local farmlands. Biotransformation of PCBs was further studied under different water management conditions in paddy field with or without rice cultivation, with a special focus on the alternating flooded and drying processes. It was found that paddy field improved the attenuation of PCBs, especially for highly chlorinated congeners. In the microcosm experiment, 40% or more of the initial total PCBs was removed after sequential flood-drying treatments, compared to less than 10% in the sterilized control and 20% in the constant-drying system. Variation in the quantity of PCBs degrading and dechlorinating bacterial groups were closely related to the alteration of anaerobic-aerobic conditions. These results suggested that alternating anoxic-oxic environment in paddy field led to the sequential aerobic-anaerobic transformation of PCBs, which provided a favorable environment for natural PCB attenuation.

Potential for Polychlorinated Biphenyl Biodegradation in Sediments from Indiana Harbor and Ship Canal

Polychlorinated biphenyls (PCBs) are carcinogenic, persistent, and bioaccumulative contaminants that pose risks to human and environmental health. In this study, we evaluated the PCB biodegradation of sediments from Indiana Harbor and Ship Canal (IHSC), a PCB-contaminated site (average PCB concentration = 12,570 ng/g d.w.). PCB congener profiles and bacterial community structure in a core sediment sample (4.57 m long) were characterized. Analysis of vertical PCB congener profile patterns in sediment and pore water strongly suggest that in situ dechlorination occurred in sediments. However, 16S rRNA genes from putative PCB-dechlorinating Chloroflexi were relatively more abundant in upper 2 m sediments, as were genes indicative of aerobic biodegradation potential (i.e. biphenyl dioxygenase (bphA)). Characterization of the bacterial community by terminal restriction fragment length polymorphism and comparison of these with sediment and pore water PCB congener profiles with the Mantel test revealed a statistical correlation (p<0.001). Sequences classified as Acinetobacter and Acidovorax were highly abundant in deep sediments. Overall, our results suggest that PCB dechlorination has already occurred, and that IHSC sediments have the potential for further aerobic and anaerobic PCB biodegradation.

Influence of plants on the distribution and composition of PBDEs in soils of an e-waste dismantling area: evidence of the effect of the rhizosphere and selective bioaccumulation

Rhizosphere effects on the distribution of PBDEs in e-waste contaminated soils were investigated. The geometric means of the PBDEs in the rhizosphere and non-rhizosphere soils were 32.6 ng/g and 12.2 ng/g, whereas the geometric means of the PBDEs in vegetable shoots and roots were 2.15 ng/g and 3.02 ng/g, respectively. PBDEs in soil at different distances from the root surface may first rise appreciably and then decrease to a non-rhizosphere level for long-term contaminated soils. Different PBDE compositions in roots and shoots indicated that PBDEs in shoots may be mainly taken up from the air. The ratios of BDE99/100 and BDE153/154 in plants and their corresponding soils were different. The bioaccumulations of BDEs 100 and 154 were much higher than those of BDEs 99 and 153, respectively. This indicated that the bioaccumulation was selective and influenced by the substitution pattern, with ortho-substituted isomers being more prevalent than meta-substituted isomers.

The role of root exuded low molecular weight organic anions in facilitating petroleum hydrocarbon degradation: current knowledge and future directions

Rhizoremediation is a bioremediation technique whereby enhanced microbial degradation of organic contaminants occurs within the plant root zone (rhizosphere). It is considered an effective and affordable 'green technology' for remediating soils contaminated with petroleum hydrocarbons (PHCs). This paper critically reviews the potential role of root exuded compounds in rhizoremediation, with emphasis on commonly exuded low molecular weight aliphatic organic acid anions (carboxylates). The extent to which remediation is achieved shows wide disparity among plant species. Therefore, plant selection is crucial for the advancement and widespread adoption of this technology. Root exudation is speculated to be one of the predominant factors leading to microbial changes in the rhizosphere and thus the potential driver behind enhanced petroleum biodegradation. Carboxylates can form a significant component of the root exudate mixture and are hypothesised to enhance petroleum biodegradation by: i) providing an easily degradable energy source; ii) increasing phosphorus supply; and/or iii) enhancing the contaminant bioavailability. These differing hypotheses, which are not mutually exclusive, require further investigation to progress our understanding of plant-microbe interactions with the aim to improve plant species selection and the efficacy of rhizoremediation.

Long-term Effects of Nutrient Addition and Phytoremediation on Diesel and Crude Oil Contaminated Soils in subarctic Alaska

Phytoremediation is a potentially inexpensive method of detoxifying contaminated soils using plants and associated soil microorganisms. The remote locations and cold climate of Alaska provide unique challenges associated with phytoremediation such as finding effective plant species that can achieve successful site clean-up despite the extreme environmental conditions and with minimal site management. A long-term assessment of phytoremediation was performed which capitalized on a study established in Fairbanks in 1995. The original study sought to determine how the introduction of plants (Festuca rubra, Lolium multiflorum), nutrients (fertilizer), or their combination would affect degradation of petroleum hydrocarbon (TPH) contaminated soils (crude oil or diesel) over time. Within the year following initial treatments, the plots subjected to both planting and/or fertilization showed greater overall decreases in TPH concentrations in both the diesel and crude oil contaminated soils relative to untreated plots. We re-examined this field site after 15 years with no active site management to assess the long-term effects of phytoremediation on colonization by native and non-native plants, their rhizosphere microbial communities and on petroleum removal from soil. Native and non-native vegetation had extensively colonized the site, with more abundant vegetation found on the diesel contaminated soils than the more nutrient-poor, more coarse, and acidic crude oil contaminated soils. TPH concentrations achieved regulatory clean up levels in all treatment groups, with lower TPH concentrations correlating with higher amounts of woody vegetation (trees & shrubs). In addition, original treatment type has affected vegetation recruitment to each plot with woody vegetation and more native plants in unfertilized plots. Bacterial community structure also varies according to the originally applied treatments. This study suggests that initial treatment with native tree species in combination with grasses could be an effective means for phytoremediating petroleum contaminated soils and promoting ecological recovery in cold regions.

Dechlorination of PCBs in the rhizosphere of switchgrass and poplar

Polychlorinated biphenyl (PCB) congeners (PCB 52, 77, and 153) singly and in mixture were spiked and aged in soil microcosms and subsequently planted with switchgrass (Panicum virgatum) or poplar (Populus deltoids x nigra DN34). The planted reactors showed significantly greater reductions in PCB parent compounds when compared to unplanted systems after 32 weeks. There was evidence of reductive dechlorination in both planted and unplanted systems, but the planted microcosms with fully developed roots and rhizospheres showed greater biotransformation than the unplanted reactors. These dechlorination products accounted for approximately all of the molar mass of parent compound lost. Based on the transformation products, reductive dechlorination pathways are proposed for rhizospheric biotransformation of PCB 52, 77, and 153. This is the first report of rhizosphere biotransformation pathways for reductive dechlorination in marginally aerobic, intermittently flooded soil as evidenced by a mass balance on transformation products.

Overview of in situ and ex situ remediation technologies for PCB-contaminated soils and sediments and obstacles for full-scale application

Polychlorinated biphenyls (PCB) are persistent organic pollutants used worldwide between the 1930s and 1980s. Although their use has been heavily restricted, PCB can be found in contaminated soils and sediments. The most frequent remediation solutions adopted are "dig and dump" and "dig and incinerate", but there are currently new methods that could be more sustainable alternatives. This paper takes a look into the remediation options available for PCB-contaminated soils and sediments, differentiating between biological, chemical, physical and thermal methods. The use of combined technologies was also reviewed. Most of them are still in an initial development stage and further research in different implementation issues is needed. There is no single technology that is the solution for PCB contamination problem. The successful remediation of a site will depend on proper selection, design and adjustment of the technology or combined technologies to the site characteristics.

Whole-genome sequence of Cupriavidus sp. strain BIS7, a heavy-metal-resistant bacterium

Cupriavidus sp. strain BIS7 is a Malaysian tropical soil bacterium that exhibits broad heavy-metal resistance [Co(II), Zn(II), Ni(II), Se(IV), Cu(II), chromate, Co(III), Fe(II), and Fe(III)]. It is particularly resistant to Fe(II), Fe(III), and Zn(II). Here we present the assembly and annotation of its genome.

Plant secondary metabolite-induced shifts in bacterial community structure and degradative ability in contaminated soil

The aim of the study was to investigate how selected natural compounds (naringin, caffeic acid, and limonene) induce shifts in both bacterial community structure and degradative activity in long-term polychlorinated biphenyl (PCB)-contaminated soil and how these changes correlate with changes in chlorobiphenyl degradation capacity. In order to address this issue, we have integrated analytical methods of determining PCB degradation with pyrosequencing of 16S rRNA gene tag-encoded amplicons and DNA-stable isotope probing (SIP). Our model system was set in laboratory microcosms with PCB-contaminated soil, which was enriched for 8 weeks with the suspensions of flavonoid naringin, terpene limonene, and phenolic caffeic acid. Our results show that application of selected plant secondary metabolites resulted in bacterial community structure far different from the control one (no natural compound amendment). The community in soil treated with caffeic acid is almost solely represented by Proteobacteria, Acidobacteria, and Verrucomicrobia (together over 99 %). Treatment with naringin resulted in an enrichment of Firmicutes to the exclusion of Acidobacteria and Verrucomicrobia. SIP was applied in order to identify populations actively participating in 4-chlorobiphenyl catabolism. We observed that naringin and limonene in soil foster mainly populations of Hydrogenophaga spp., caffeic acid Burkholderia spp. and Pseudoxanthomonas spp. None of these populations were detected among 4-chlorobiphenyl utilizers in non-amended soil. Similarly, the degradation of individual PCB congeners was influenced by the addition of different plant compounds. Residual content of PCBs was lowest after treating the soil with naringin. Addition of caffeic acid resulted in comparable decrease of total PCBs with non-amended soil; however, higher substituted congeners were more degraded after caffeic acid treatment compared to all other treatments. Finally, it appears that plant secondary metabolites have a strong effect on the bacterial community structure, activity, and associated degradative ability.

Plant-microorganism interactions in bioremediation of polychlorinated biphenyl-contaminated soil

During the second half of the last century a large amount of substances toxic for higher organisms was released to the environment. Physicochemical methods of pollutant removal are difficult and prohibitively expensive. Using biological systems such as microorganisms, plants, or consortia microorganisms-plants is easier, cheaper, and more environmentally friendly. The aim of this study was to isolate, characterize and identify microorganisms from contaminated soil and to find out the effect of plants on microbial diversity in the environment. Microorganisms were isolated by two approaches with the aim to find all cultivable species and those able to utilise biphenyl as a sole source of carbon and energy. The first approach was direct extraction and the second was isolation of bacteria after enrichment cultivation with biphenyl. Isolates were biochemically characterized by NEFERMtest 24 and then the composition of ribosomal proteins in bacterial cells was determined by MALDI-TOF mass spectrometry. Ribosomal proteins can be used as phylogenetic markers and thus MALDI-TOF MS can be exploited also for taxonomic identification because the constitution of ribosomal proteins in bacterial cells is specific for each bacterial species. Identification of microorganisms using this method is performed with the help of database Bruker Daltonics MALDI BioTyper. Isolated bacteria were analyzed from the point of the bphA gene presence. Bacteria with detected bphA gene were then taxonomically identified by 16S rRNA sequence. The ability of two different plant species, tobacco (Nicotiana tabacum) and nightshade (Solanum nigrum), to accumulate PCBs was studied as well. It was determined that various plant species differ in the PCBs accumulation from the contaminated soil. Also the content of PCBs in various plant tissues was compared. PCBs were detected in roots and aboveground biomass including leaves and berries.