Plant compounds that induce polychlorinated biphenyl biodegradation by Arthrobacter sp. strain B1B

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

The Partial Contribution of Constructed Wetland Components (Roots, Gravel, Microorganisms) in the Removal of Phenols: A Mini Review

Constructed wetlands (CW) have attracted growing interest in wastewater treatment research in the last 20 years, and have been investigated intensively worldwide. Many of the basic processes occurring in CWs have been qualitatively established; however, much quantitative knowledge is still lacking. In this mini review, the proportionate contributions of the different system components to removal of contaminants are examined. The main objective of this mini review is to provide a more in-depth assessment of the interactions between the porous bed, plants, and microorganisms during the removal of organic contaminants from the water in a subsurface flow CW system. In addition, a unique technique to study the partial contribution to the total removal of contaminants in a CW is described. Future studies in this field will expand our knowledge of any synergistic or antagonistic interactions between the components and facilitate improved CW construction and operation. Here, phenol will be used as a model industrial organic contaminant to illustrate our current understanding of the contributions of the different components to total removal. I will also discuss the various factors influencing the efficacy of bacteria, whether planktonic or as biofilm (on porous bed or plant roots), in subsurface flow CWs.

Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 Is Both Induced by Phenolics and Monoterpenes and Involved in Their Transformation

The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.

An endophytic bacterial strain, Enterobacter cloacae TMX-6, enhances the degradation of thiamethoxam in rice plants

Thiamethoxam (TMX) has been widely used over the last two decades. TMX residue in the environment has drawn great public attention. An endophytic bacterial strain, TMX-6, capable of degrading TMX was isolated from wild Ophiopogon japonicus and was identified as Enterobacter cloacae by morphology and 16S ribosomal DNA sequence analysis. After being marked with green fluorescent protein plasmid, TMX-6 was successfully inoculated in the rice plants (Oryza sativa L.). The numbers of TMX-6 in non-TMX treated rice plants ranged from 3.9 to 4.6 log CFU g^-1 in the roots, and from 2.7 to 4.0 log CFU g^-1 in the shoots; while ranged from 3.9 to 5.3 log CFU g^-1 in roots and from 2.7 to 4.1 log CFU g^-1 in shoots of TMX treated rice plants. Nearly 28%, 33%, 77% and 99% of TMX was removed from the hydroponic medium (HM), HM with strain TMX-6, HM with uninoculated rice and HM with inoculated rice, respectively, at the end of a 21-day (d) experiment period, and the correspondent half-lives of TMX were 46.2, 38.5, 9.9 and 4.7 d, respectively. Eleven TMX metabolites were identified in both inoculated and uninoculated rice plants through metabolomics data analysis. The intensity of TMX- NH, TMX-urea and clothianidin increased more than 3 times in inoculated rice plants on day 6. This demonstrates the usefulness of the strain TMX-6 to enhance the degradation of TMX-contaminated substrates and reduce levels of toxic insecticides in crop plants.

Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil

The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.

Chemically degraded soil rehabilitation process using medicinal and aromatic plants: review

In recent decades, the increasing number of degraded lands worldwide makes their rehabilitation essential and crucial. Various techniques have emerged to fulfill these needs but most of them are expensive and difficult to be applied. Revegetation is a cost effective, environmental friendly, and aesthetically pleasing approach suitable for degraded areas. However, the use of edible crops, especially for areas with heavy metals (HM) contamination, is not ecologically suitable because the HM may enter the food chain. Alternatively, non-edible, fast-growing, deep-rooting, and metal-stabilizing plants with high biomass, which can produce high-value products hold a great potential and have been regarded as potential candidates of edible crops. This current review presents the benefits of using aromatic and medicinal plants (AMPs) and their associated microorganisms for revegetation of degraded sites as they are high-value economic crops. We discussed the effect of various stress on productivity of secondary metabolites in AMPs in addition to the potential health risk with human consumption of these plants and their products. A focus was also given to the effect of HM stress on the essential oil (EO) content of certain AMPs. Reported data showed that AMPs growing on HM-contaminated soils are safe products to use as they are not significantly contaminated themselves by HM.

Evaluation of biphenyl- and polychlorinated-biphenyl (PCB) degrading Rhodococcus sp. MAPN-1 on growth of Morus alba by pot study

This study focused on isolation of bacteria with biphenyl/polychlorinated biphenyl (PCB) degrading ability from the rhizosphere of Morus alba (mulberry plant). Repetitive enrichment of rhizospheric soil samples with biphenyl resulted in the isolation of Rhodococcus sp. MAPN-1, identified by 16S rRNA gene sequence analysis. The bacterium showed growth on five different aromatic compounds (naphthalene, salicylic acid, benzoic acid, dibenzofuran and anthracene). Benzoic acid was detected as the major metabolite during biphenyl degradation using high-performance thin-layer chromatography (HPTLC) with R_f 0.42 at 254 nm. Further GC-MS/MS study showed 95% and 15% degradation of biphenyl and dichlorobiphenyl, respectively. A pot study was conducted to evaluate the effect of presence of biphenyl on M. alba and the role of biphenyl degrader Rhodococcus sp. MAPN-1 in relation to phytoremediation. Morus alba twigs in biphenyl spiked soil (100 mg/kg and 300 mg/kg) inoculated with Rhodococcus sp. MAPN-1 showed growth, whereas, growth of plants (control) was adversely affected in biphenyl-spiked uninoculated soil. It is the first report of isolation of Rhodococcus sp. MAPN-1 from the rhizosphere of Morus alba, its capability to degrade biphenyl, thereby showing a positive effect on the plant growth grown in biphenyl spiked soil.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

The Origin, Succession, and Predicted Metabolism of Bacterial Communities Associated with Leaf Decomposition

Community ecologists have traditionally treated individuals within a species as uniform, with individual-level biodiversity rarely considered as a regulator of community and ecosystem function. In our study system, we have documented clear evidence of within-species variation causing local ecosystem adaptation to fluxes across ecosystem boundaries. In this striking pattern of a “home-field advantage,” leaves from individual trees tend to decompose most rapidly when immediately adjacent to their parent tree. Here, we merge community ecology experiments with microbiome approaches to describe how bacterial communities adjust to within-species variation in leaves over spatial scales of less than a kilometer. The results show that bacterial community compositional changes facilitate rapid ecosystem responses to environmental change, effectively maintaining high rates of carbon and nutrient cycling through ecosystems.

Intraspecific variation in plant nutrient and defensive traits can regulate ecosystem-level processes, such as decomposition and transformation of plant carbon and nutrients. Understanding the regulatory mechanisms of ecosystem functions at local scales may facilitate predictions of the resistance and resilience of these functions to change. We evaluated how riverine bacterial community assembly and predicted gene content corresponded to decomposition rates of green leaf inputs from red alder trees into rivers of Washington State, USA. Previously, we documented accelerated decomposition rates for leaves originating from trees growing adjacent to the site of decomposition versus more distant locales, suggesting that microbes have a “home-field advantage” in decomposing local leaves. Here, we identified repeatable stages of bacterial succession, each defined by dominant taxa with predicted gene content associated with metabolic pathways relevant to the leaf characteristics and course of decomposition. “Home” leaves contained bacterial communities with distinct functional capacities to degrade aromatic compounds. Given known spatial variation of alder aromatics, this finding helps explain locally accelerated decomposition. Bacterial decomposer communities adjust to intraspecific variation in leaves at spatial scales of less than a kilometer, providing a mechanism for rapid response to changes in resources such as range shifts among plant genotypes. Such rapid responses among bacterial communities in turn may maintain high rates of carbon and nutrient cycling through aquatic ecosystems.

The stimulating role of syringic acid, a plant secondary metabolite, in the microbial degradation of structurally-related herbicide, MCPA

The ability of microorganisms to degrade xenobiotics can be exploited to develop cost-effective and eco-friendly bioremediation technologies. Microorganisms can degrade almost all organic pollutants, but this process might be very slow in some cases. A promising way to enhance removal of recalcitrant xenobiotics from the environment lies in the interactions between plant exudates such as plant secondary metabolites (PSMs) and microorganisms. Although there is a considerable body of evidence that PSMs can alter the microbial community composition and stimulate the microbial degradation of xenobiotics, their mechanisms of action remain poorly understood. With this in mind, our aim was to demonstrate that similarity between the chemical structures of PSMs and xenobiotics results in higher micropollutant degradation rates, and the occurrence of corresponding bacterial degradative genes. To verify this, the present study analyses the influence of syringic acid, a plant secondary metabolite, on the bacterial degradation of an herbicide, 4-chloro-2-methylphenoxyacetic acid (MCPA). In particular, the presence of appropriate MCPA degradative genes, MCPA removal efficiency and changes in samples phytotoxicity have been analyzed. Significant MCPA depletion was achieved in samples enriched with syringic acid. The results confirmed not only greater MCPA removal from the samples upon spiking with syringic acid, and thus decreased phytotoxicity, but also the presence of a greater number of genes responsible for MCPA biodegradation. 16S rRNA gene sequence analysis revealed ubiquitous enrichment of the β-proteobacteria Rhodoferax, Achromobacter, Burkholderia and Cupriavidus. The obtained results provide further confirmation that plant metabolites released into the rhizosphere can stimulate biodegradation of xenobiotics, including MCPA.

Biodegradation of persistent environmental pollutants by Arthrobacter sp

Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.

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

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

Bacteria Associated to Plants Naturally Selected in a Historical PCB Polluted Soil Show Potential to Sustain Natural Attenuation

The exploitation of the association between plants and microorganisms is a promising approach able to boost natural attenuation processes for soil clean-up in vast polluted areas characterized by mixed chemical contamination. We aimed to explore the selection of root-associated bacterial communities driven by different plant species spontaneously established in abandoned agricultural soils within a historical polluted site in north Italy. The site is highly contaminated by chlorinated persistent organic pollutants, mainly constituted by polychlorobiphenyls (PCBs), together with heavy metals and metalloids, in variable concentrations and uneven distribution. The overall structure of the non-vegetated and root-associated soil fractions bacterial communities was described by high-throughput sequencing of the 16S rRNA gene, and a collection of 165 rhizobacterial isolates able to use biphenyl as unique carbon source was assayed for plant growth promotion (PGP) traits and bioremediation potential. The results showed that the recruitment of specific bacterial communities in the root-associated soil fractions was driven by both soil fractions and plant species, explaining 21 and 18% of the total bacterial microbiome variation, respectively. PCR-based detection in the soil metagenome of bacterial bphA gene, encoding for the biphenyl dioxygenase α subunit, indicated that the soil in the site possesses metabolic traits linked to PCB degradation. Biphenyl-utilizing bacteria isolated from the rhizosphere of the three different plant species showed low phylogenetic diversity and well represented functional traits, in terms of PGP and bioremediation potential. On average, 72% of the strains harbored the bphA gene and/or displayed catechol 2,3-dioxygenase activity, involved in aromatic ring cleavage. PGP traits, including 1-aminocyclopropane-1-carboxylic acid deaminase activity potentially associated to plant stress tolerance induction, were widely distributed among the isolates according to in vitro assays. PGP tested in vivo on tomato plants using eleven selected bacterial isolates, confirmed the promotion and protection potential of the rhizosphere bacteria. Different spontaneous plant species naturally selected in a historical chronically polluted site showed to determine the enrichment of peculiar bacterial communities in the soil fractions associated to the roots. All the rhizosphere communities, nevertheless, hosted bacteria with degradation/detoxification and PGP potential, putatively sustaining the natural attenuation process.

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

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

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.

Degradation of phenanthrene by Novosphingobium sp. HS2a improved plant growth in PAHs-contaminated environments

At the same time that the European Union (EU) policy recommend to direct efforts towards reductions of heavy metals, polycyclic aromatic hydrocarbons (PAHs) and mining residues, there is the need to increase the cultivable areas within Europe to cope with the increasing demands for food and energy crops. Bioremediation is a good technique for the restoration of contaminated soils; however, it has not been used extensively because of the variability of the outcome. This variability is frequently due to a bad establishment of foreign degrading populations in soil. We have demonstrated that Novosphingobium sp. HS2aR (i) is able to compete with other root colonizers and with indigenous bacteria, (ii) is able to establish in high numbers in the contaminated environments and (iii) is able to remove more than 90 % of the extractable phenanthrene in artificially contaminated soils. Furthermore, we have demonstrated that the capacity to remove phenanthrene is linked to the ability to promote plant growth in contaminated environments. The fact that the presence of Novosphingobium sp. HS2aR improves the growth of plants in contaminated soil suggests that it may be a useful strain for utilization in amelioration of soil quality while improving the growth of economically important energy crops, thus adding value to the bioremediation strategy.

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.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

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.

Biodegradation of polychlorinated biphenyls (PCBs) by the novel identified cyanobacterium Anabaena PD-1

Polychlorinated biphenyls (PCBs), a class of hazardous pollutants, are difficult to dissipate in the natural environment. In this study, a cyanobacterial strain Anabaena PD-1 showed good resistance against PCB congeners. Compared to a control group, chlorophyll a content decreased 3.7% and 11.7% when Anabaena PD-1 was exposed to 2 and 5 mg/L PCBs for 7 d. This cyanobacterial strain was capable of decomposing PCB congeners which was conclusively proved by determination of chloride ion concentrations in chlorine-free medium. After 7 d, the chloride ion concentrations in PCB-treated groups (1, 2, 5 mg/L) were 3.55, 3.05, and 2.25 mg/L, respectively. The genetic information of strain PD-1 was obtained through 16S rRNA sequencing analysis. The GenBank accession number of 16S rRNA of Anabaena PD-1 was KF201693.1. Phylogenetic tree analysis clearly indicated that Anabaena PD-1 belonged to the genus Anabaena. The degradation half-life of Aroclor 1254 by Anabaena PD-1 was 11.36 d; the total degradation rate for Aroclor 1254 was 84.4% after 25 d. Less chlorinated PCB congeners were more likely to be degraded by Anabaena PD-1 in comparison with highly chlorinated congeners. Meta- and para-chlorines in trichlorodiphenyls and tetrachlorobiphenyls were more susceptible to dechlorination than ortho-chlorines during the PCB-degradation process by Anabaena PD-1. Furthermore, Anabaena PD-1 can decompose dioxin-like PCBs. The percent biodegradation of 12 dioxin-like PCBs by strain PD-1 ranged from 37.4% to 68.4% after 25 days. Results above demonstrate that Anabaena PD-1 is a PCB-degrader with great potential for the in situ bioremediation of PCB-contaminated paddy soils.

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.

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity

Although oilfields harbor a wide diversity of microorganisms with various metabolic potentials, our current knowledge about oil-degrading bacteria is limited because the vast majority of oil-degrading bacteria remain uncultured. In the present study, microbial communities in nine oil-contaminated soils collected from Daqing and Changqing, two of the largest oil fields in China, were characterized through highthroughput sequencing of 16S rRNA genes. Bacteria related to the phyla Proteobacteria and Actinobacteria were dominant in four and three samples, respectively. At the genus level, Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium, and Rhodococcus were frequently detected in nine soil samples. Many of the dominant genera were phylogenetically related to the known oil-degrading species. The correlation between physiochemical parameters within the microbial communities was also investigated. Canonical correspondence analysis revealed that soil moisture, nitrate, TOC, and pH had an important impact in shaping the microbial communities of the hydrocarbon-contaminated soil. This study provided an in-depth analysis of microbial communities in oilcontaminated soil and useful information for future bioremediation of oil contamination.

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.

A hydroponic system for growing gnotobiotic vs. sterile plants to study phytoremediation processes

In some phytoremediation studies it is desirable to separate and define the specific contribution of plants and root-colonizing bacteria towards contaminant removal. Separating the influence of plants and associated bacteria is a difficult task for soil root environments. Growing plants hydroponically provides more control over the biological factors in contaminant removal. In this study, a hydroponic system was designed to evaluate the role of sterile plant roots, rhizodeposition, and root-associated bacteria in the removal of a model contaminant, phenol. A strain of Pseudomonas pseudoalcaligenes that grows on phenol was inoculated onto plant roots. The introduced biofilm persisted in the root zone and promoted phenol removal over non-augmented controls. These findings indicate that this hydroponic system can be a valuable tool for phytoremediation studies that investigate the effects of biotic and abiotic factors on pollution remediation.

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.

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.

An evidence-based systematic review of spearmint by the natural standard research collaboration

An evidence-based systematic review of spearmint (Mentha spicata, Mentha viridis) including written and statistical analysis of scientific literature, expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Enhanced dissipation of polycyclic aromatic hydrocarbons in the presence of fresh plant residues and their extracts

The feasibility of using fresh plant residues and their extracts to stimulate the bio-dissipation of polycyclic aromatic hydrocarbons (PAHs) were highlighted. Wood chip, bamboo leave, orange peel and their water-extractable organic matter (WEOM) were chosen as amendment materials. Effect of WEOM on bio-dissipation (bioaccumulation and biodegradation) of phenanthrene and pyrene from water by two bacteria were investigated. Orange peel extract demonstrated the highest efficiency for stimulating PAHs removal by bacterium B1 (Pseudomonas putida), while bamboo leave extract was the best one to enhance PAHs bio-dissipation by bacterium B2 (unidentified bacterium isolated from PAHs-contaminated soil). Amended the actual contaminated soil with 1% plant residues, PAHs dissipation were increased by 15-20%, 20-39%, 14-24%, 12-23% and 17-26%, respectively, for 2-, 3-, 4-, 5- and 6-ring PAHs via stimulating indigenous microbial degradation activity. Bamboo leave exhibited the most effective one to stimulate dissipation of PAHs in contaminated soil.

Plant exudates promote PCB degradation by a rhodococcal rhizobacteria

Rhodococcus erythropolis U23A is a polychlorinated biphenyl (PCB)-degrading bacterium isolated from the rhizosphere of plants grown on a PCB-contaminated soil. Strain U23A bphA exhibited 99% identity with bphA1 of Rhodococcus globerulus P6. We grew Arabidopsis thaliana in a hydroponic axenic system, collected, and concentrated the plant secondary metabolite-containing root exudates. Strain U23A exhibited a chemotactic response toward these root exudates. In a root colonizing assay, the number of cells of strain U23A associated to the plant roots (5.7 × 10⁵ CFU g⁻¹) was greater than the number remaining in the surrounding sand (4.5 × 10⁴ CFU g⁻¹). Furthermore, the exudates could support the growth of strain U23A. In a resting cell suspension assay, cells grown in a minimal medium containing Arabidopsis root exudates as sole growth substrate were able to metabolize 2,3,4'- and 2,3',4-trichlorobiphenyl. However, no significant degradation of any of congeners was observed for control cells grown on Luria-Bertani medium. Although strain U23A was unable to grow on any of the flavonoids identified in root exudates, biphenyl-induced cells metabolized flavanone, one of the major root exudate components. In addition, when used as co-substrate with sodium acetate, flavanone was as efficient as biphenyl to induce the biphenyl catabolic pathway of strain U23A. Together, these data provide supporting evidence that some rhodococci can live in soil in close association with plant roots and that root exudates can support their growth and trigger their PCB-degrading ability. This suggests that, like the flagellated Gram-negative bacteria, non-flagellated rhodococci may also play a key role in the degradation of persistent pollutants.

Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil

Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases.

Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil

Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases.

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

Rhizosphere bioremediation of polychlorinated biphenyls (PCBs) offers a potentially inexpensive approach to remediating contaminated soils that is particularly attractive in remote regions including the Arctic. We assessed the abilities of two tree species native to Alaska, Salix alaxensis (felt-leaf willow) and Picea glauca (white spruce), to promote microbial biodegradation of PCBs via the release of phytochemicals upon fine root death. Crushed fine roots, biphenyl (PCB analogue) or salicylate (willow secondary compound) were added to microcosms containing soil spiked with PCBs and resultant PCB disappearance, soil toxicity and microbial community changes were examined. After 180d, soil treated with willow root crushates showed a significantly greater PCB loss than untreated soils for some PCB congeners, including the toxic congeners, PCB 77, 105 and 169, and showed a similar PCB loss pattern (in both extent of degradation and congeners degraded) to biphenyl-treated microcosms. Neither P. glauca (white spruce) roots nor salicylate enhanced PCB loss, indicating that biostimulation is plant species specific and was not mediated by salicylate. Soil toxicity assessed using the Microtox bioassay indicated that the willow treatment resulted in a less toxic soil environment. Molecular microbial community analyses indicated that biphenyl and salicylate promoted shifts in microbial community structure and composition that differed distinctly from each other and from the crushed root treatments. The biphenyl utilizing bacterium, Cupriavidus spp. was isolated from the soil. The findings suggest that S. alaxensis may be an effective plant for rhizoremediation by altering microbial community structure, enhancing the loss of some PCB congeners and reducing the toxicity of the soil environment.

Accelerated biodegradation of pyrene and benzo[a]pyrene in the Phragmites australis rhizosphere by bacteria-root exudate interactions

We investigated the biodegradation of pyrene and benzo[a]pyrene in Phragmites australis rhizosphere sediment. We collected P. australis plants, rhizosphere sediments, and unvegetated sediments from natural aquatic sites and conducted degradation experiments using sediments spiked with pyrene or benzo[a]pyrene. Accelerated removal of pyrene and benzo[a]pyrene was observed in P. australis rhizosphere sediments with plants, whereas both compounds persisted in unvegetated sediments without plants and in autoclaved rhizosphere sediments with sterilized plants, suggesting that the accelerated removal resulted largely from biodegradation by rhizosphere bacteria. Initial densities of pyrene-utilizing bacteria were substantially higher in the rhizosphere than in unvegetated sediments, but benzo[a]pyrene-utilizing bacteria were not detected in rhizosphere sediments. Mycobacterium gilvum strains isolated from rhizosphere sediments utilized pyrene aerobically as a sole carbon source and were able to degrade benzo[a]pyrene when induced with pyrene. Phragmites australis root exudates containing phenolic compounds supported growth as a carbon source for the one Mycobacterium strain tested, and induced benzo[a]pyrene-degrading activity of the strain. The stimulatory effect on benzo[a]pyrene biodegradation and the amounts of phenolic compounds in root exudates increased when P. australis was exposed to pyrene. Our results show that Mycobacterium-root exudate interactions can accelerate biodegradation of pyrene and benzo[a]pyrene in P. australis rhizosphere sediments.

Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates

To determine whether the diversity of phenanthrene-degrading bacteria in an aged polycyclic aromatic hydrocarbon (PAH) contaminated soil is affected by the addition of plant root exudates, DNA stable isotope probing (SIP) was used. Microcosms of soil with and without addition of ryegrass exudates and with ¹³C-labelled phenanthrene (PHE) were monitored over 12 days. PHE degradation was slightly delayed in the presence of added exudate after 4 days of incubation. After 12 days, 68% of added PHE disappeared both with and without exudate. Carbon balance using isotopic analyses indicated that a part of the ¹³C-PHE was not totally mineralized as ¹³CO₂ but unidentified ¹³C-compounds (i.e. ¹³C-PHE or ¹³C-labelled metabolites) were trapped into the soil matrix. Temporal thermal gradient gel electrophoresis (TTGE) analyses of 16S rRNA genes were performed on recovered ¹³C-enriched DNA fractions. 16S rRNA gene banding showed the impact of root exudates on diversity of PHE-degrading bacteria. With PHE as a fresh sole carbon source, Pseudoxanthomonas sp. and Microbacterium sp. were the major PHE degraders, while in the presence of exudates, Pseudomonas sp. and Arthrobacter sp. were favoured. These two different PHE-degrading bacterial populations were also distinguished through detection of PAH-ring hydroxylating dioxygenase (PAH-RHD(α)) genes by real-time PCR. Root exudates favoured the development of a higher diversity of bacteria and increased the abundance of bacteria containing known PAH-RHD(α) genes.

Efficiency of phenol biodegradation by planktonic Pseudomonas pseudoalcaligenes (a constructed wetland isolate) vs. root and gravel biofilm

In the last two decades, constructed wetland systems gained increasing interest in wastewater treatment and as such have been intensively studied around the world. While most of the studies showed excellent removal of various pollutants, the exact contribution, in kinetic terms, of its particular components (such as: root, gravel and water) combined with bacteria is almost nonexistent. In the present study, a phenol degrader bacterium identified as Pseudomonas pseudoalcaligenes was isolated from a constructed wetland, and used in an experimental set-up containing: plants and gravel. Phenol removal rate by planktonic and biofilm bacteria (on sterile Zea mays roots and gravel surfaces) was studied. Specific phenol removal rates revealed significant advantage of planktonic cells (1.04 × 10(-9) mg phenol/CFU/h) compared to root and gravel biofilms: 4.59 × 10(-11)-2.04 × 10(-10) and 8.04 × 10(-11)-4.39 × 10(-10) (mg phenol/CFU/h), respectively. In batch cultures, phenol biodegradation kinetic parameters were determined by biomass growth rates and phenol removal as a function of time. Based on Haldane equation, kinetic constants such as μ(max) = 1.15/h, K(s) = 35.4 mg/L and K(i) = 198.6 mg/L fit well phenol removal by P. pseudoalcaligenes. Although P. pseudoalcaligenes planktonic cells showed the highest phenol removal rate, in constructed wetland systems and especially in those with sub-surface flow, it is expected that surface associated microorganisms (biofilms) will provide a much higher contribution in phenol and other organics removal, due to greater bacterial biomass. Factors affecting the performance of planktonic vs. biofilm bacteria in sub-surface flow constructed wetlands are further discussed.

Dissipation gradients of phenanthrene and pyrene in the Rice rhizosphere

An experiment was conducted to reveal the effects of rice cultivation as well as polycyclic aromatic carbohydrates (PAHs) degrading bacterium (Acinetobacter sp.) on the dissipation gradients of two PAHs (PHE and PYR) in the rhizosphere. The results showed that the presence of rice root and bacteria significantly accelerated the dissipation rate of PHE and PYR. The root exudates contributed to the formation of dissipation gradients of PHE and PYR along the vertical direction of roots, with a higher dissipation rate in the rhizosphere and near rhizosphere zone than the soil far away the rhizosphere.

The Influence of Aromatic Plants on Microbial Biomass and Respiration in a Natural Ecosystem

The influence of three aromatic plant species, laurel (Laurus nobilisL.), myrtle (Myrtus communisL.), and French lavender (Lavandula stoechasL.), on top soil microbial biomass, respiration rates, and bacterial colonies was investigated. Fresh, mature plant material was introduced into a typical Mediterranean habitat in Northern Greece. The essential oil chemical compositions from the aromatics used in the study were evaluated by GC-MS analysis. The major compounds constitutingL. nobilisessential oil were 1,8-cineole (48.1%), eugenol (12.3%), and α-pinene (6.0%);M. communisoil consisted of α-pinene (31.2%), myrtenyl acetate (19.3%), and 1,8-cineole (16.1%); andL. stoechasconsisted of fenchone (46.7%), camphor (9.9%), and 1,8-cineole (9.0%).L. nobilispresented the highest inhibition against bacterial colonies (44.9%) and lowered soil respiration and microbial biomass when compared to control soils. In contrast,M. comunnisandL. stoechaswere found to augment bacterial activity by 85.9% and 63.8%, respectively, and to increase soil respiration (1.5-fold) and microbial biomass (2.5-fold) compared to control soil samples. These two plants are proposed for further investigations in biodegradation programs.

Phytoremediation of polychlorinated biphenyls: new trends and promises

Transgenic plants and associated bacteria constitute a new generation of genetically modified organisms for efficient and environment-friendly treatment of soil and water contaminated with polychlorinated biphenyls (PCBs). This review focuses on recent advances in phytoremediation for the treatment of PCBs, including the development of transgenic plants and associated bacteria. Phytoremediation, or the use of higher plants for rehabilitation of soil and groundwater, is a promising strategy for cost-effective treatment of sites contaminated by toxic compounds, including PCBs. Plants can help mitigate environmental pollution by PCBs through a range of mechanisms: besides uptake from soil (phytoextraction), plants are capable of enzymatic transformation of PCBs (phytotransformation); by releasing a variety of secondary metabolites, plants also enhance the microbial activity in the root zone, improving biodegradation of PCBs (rhizoremediation). However, because of their hydrophobicity and chemical stability, PCBs are only slowly taken up and degraded by plants and associated bacteria, resulting in incomplete treatment and potential release of toxic metabolites into the environment. Moreover, naturally occurring plant-associated bacteria may not possess the enzymatic machinery necessary for PCB degradation. To overcome these limitations, bacterial genes involved in the metabolism of PCBs, such as biphenyl dioxygenases, have been introduced into higher plants, following a strategy similar to the development of transgenic crops. Similarly, bacteria have been genetically modified that exhibit improved biodegradation capabilities and are able to maintain stable relationships with plants. Transgenic plants and associated bacteria bring hope for a broader and more efficient application of phytoremediation for the treatment of PCBs.