Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation

Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub

Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.

Taxonomic and Functional Diversity of Rhizosphere Microbiome Recruited From Compost Synergistically Determined by Plant Species and Compost

Compost is frequently served as the first reservoir for plants to recruit rhizosphere microbiome when used as growing substrate in the seedling nursery. In the present study, recruitment of rhizosphere microbiome from two composts by tomato, pepper, or maize was addressed by shotgun metagenomics and 16S rRNA amplicon sequencing. The 16S rRNA amplicon sequencing analysis showed that 41% of variation in the rhizosphere bacterial community was explained by compost, in contrast to 23% by plant species. Proteobacterial genera were commonly recruited by all three plant species with specific selections for Ralstonia by tomato and Enterobacteria by maize. These findings were confirmed by analysis of 16S rRNA retrieved from the shotgun metagenomics library. Approximately 70% of functional gene clusters differed more than sevenfold in abundance between rhizosphere and compost. Functional groups associated with the sensing and up-taking of C3 and C4 carboxylic acids, amino acids, monosaccharide, production of antimicrobial substances, and antibiotic resistance were over-represented in the rhizosphere. In summary, compost and plant species synergistically shaped the composition of the rhizosphere microbiome and selected for functional traits associated with the competition on root exudates.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

'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.

Enhancement of polychlorinated biphenyl biodegradation by resuscitation promoting factor (Rpf) and Rpf-responsive bacterial community

The activities of indigenous bacterial communities in polychlorinated biphenyls (PCBs) contaminated environments is closely related to the efficiency of bioremediation processes. Using resuscitation promoting factor (Rpf) from Micrococcus luteus is a promising method for resuscitation and stimulation of functional bacterial populations under stressful conditions. This study aims to use the Rpf to accelerate the biodegradation of Aroclor 1242, and explore putative PCB degraders which were resuscitated by Rpf addition. The Rpf-responsive bacterial populations were investigated using culture-dependent and culture-independent approaches, respectively. The results confirm that Rpf was capable of enhancing PCB degradation of enriched cultures from PCB-contaminated soils, and improving the activities of cultures with low tolerance to PCBs. High-throughput 16S rRNA analysis displays that the Rpf greatly altered the composition and abundance of bacterial populations in the phylum Proteobacteria. Identification of the resuscitated strains further suggests that the Rpf-responsive population was mostly represented by Sphingomonas and Pseudomonas, which are most likely the key PCB-degraders for enhanced biodegradation of PCBs.

Bacterial diversity on an abandoned, industrial wasteland contaminated by polychlorinated biphenyls, dioxins, furans and trace metals

Most former industrial sites are contaminated by mixtures of trace elements and organic pollutants. Levels of pollutants do not provide information regarding their biological impact, bioavailability and possible interactions between substances. There is genuine interest in combining chemical analyses with biological investigations. We studied a brownfield where several industrial activities were carried out starting in the 1970s, (incineration of pyralene transformers, recovery of copper by burning cables in the open air). Four representative plots showing different levels of polychlorobiphenyls were selected. Organic and trace metal levels were measured together with soil pedological characteristics. The bacterial community structure and functional diversity were assessed by 16S metagenomics with deep sequencing and community-level physiological profiling. Additionally, a vegetation survey was performed. Polychlorobiphenyls (8 mg.kg^-1 to 1500 mg.kg^-1) were from 2.4 × 10³-fold to 6 × 10⁵-fold higher than the European background level of 2.5 μg.kg^-1. Polychlorinated dibenzo-p-dioxins and dibenzofurans ranged from 0.5 to 8.0 μg.kg^-1. The soil was also contaminated with trace metals, i.e., Cu > 187, Zn > 217 and Pb > 372 mg.kg^-1. Location within the study area, trace metal content and soil humidity were stronger determinants than organic pollutants of bacterial community structures and activities. Thus, the highest biological activity and the greatest bacteriological richness were observed in the plot that was less contaminated with trace metals, despite the high level of organic pollutants in the plot. Moreover, trace element pollution was associated with a relatively low presence of Actinobacteria and Rhizobia. The plot with the highest metal contamination was rich in metal-resistant bacteria such as Sphingomonadales, Geodermatophilaceae and KD4-96 (Chloroflexi phylum). Acidobacteria and Sphingomonadales, capable of resisting trace metals and degrading persistent organic pollutants, were dominant in the plots that had accumulated metal and organic contamination, but bacterial activity was lower in these plots than in the other plots.

Long-term willows phytoremediation treatment of soil contaminated by fly ash polycyclic aromatic hydrocarbons from straw combustion

A three-year experiment was conducted to investigate willows of Salix × smithiana Willd. (S. smithiana) phytoremediation of soil contaminated by polycyclic aromatic hydrocarbons (PAHs) derived by fly ash from biomass combustion. The total removal of ash PAHs in phytoremediation treatment was 50.9% after three consecutive years while the ash PAHs were decreased in natural attenuated soil by 9.9% in the end of the experiment. The ash and spiked PAHs with low and medium molecular weight were susceptible to be removed in higher rates than high molecular weight PAHs. Lower bioconcentration factors of individual PAHs were observed in willow shoots than in roots. The estimated relative direct removal of PAHs by S. smithiana in phytoremediation was significantly lower than 1% suggesting that the contribution of S. smithiana to take up PAHs from soil was negligible and the degradation of PAHs occurred mainly in soil. Phytoremediation using S. smithiana could be seen as a feasible and environmentally friendly approach of arable soils impacted by a PAH contaminated biomass fly ash.

Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls

Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (H_S and H_P) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L⁻¹ PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for H_S and H_P soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.

Degradation of 2, 2-Dichlorovinyl dimethyl phosphate (dichlorvos) through the rhizosphere interaction between Panicum maximum Jacq and some selected fungi

Many fungi have been reported to enhance the plant responses and degradation of several persistent pollutants in soils. In this study, five dominant fungi strains were identified from a pesticides polluted soil in Nigeria and screened for the expression of phosphoesterase (opd and mpd) and catechol 1, 2-dioxygenase (afk2 and afk4) genes using Reverse Transcriptase-PCR technique. Their rhizosphere interaction with plant (Panicum maximum) was further studied for the degradation of 2, 2 Dichlorovinyl dimethyl phosphate (dichlorvos). Fungal strains were mixed with Spent Mushroom Compost (SMC) of Pleurotus ostreatus in 1:100 w/w and then applied to a sterilized pesticide polluted soil (5 kg) at increasing concentrations of 10, 20, 30 and 40% with two controls (plant only and fungi-SMC mixture only). Degradation efficiency (DE), degradation rate (K₁) and half-life (t_1/2) of dichlorvos was calculated in each treatment after 90-day of planting. All the strains were registered at NCBI gene-bank with accession numbers KY693969, KY488464, KY488465, KY693971 and KY693972: they all possess the tested genes although mpd and opd were over-expressed in all the strains while afk2 and afk4 were moderately expressed. The plant-fungi-SMC interaction synergistically sped-up dichlorvos degradation rate in less time period, appreciable loss of dichlorvos at 72.23 and 82.70% DE were observed in 30 and 40% treatments respectively as compared to controls 1 and 2 having 62.20 ± 3.07 and 62.33 ± 4.69% DE respectively. In the same way, the 40% treatment gave the best k₁ and t_1/2 of 1.755 and 0.40 ± 0.02/day respectively.

Identification of biphenyl-metabolising microbes in activated biosludge using cultivation-independent and -dependent approaches

Microbes have important roles in removing organic pollutants in wastewater treatment plants (WWTPs), especially in mineralising recalcitrant persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs). However, the majority of the microorganisms that metabolise these pollutants in situ remain elusive owing to barriers of traditional techniques in unravel yet-to-be-cultivated microbes. In this study, DNA stable-isotope probing (SIP) coupled with high-throughput sequencing was applied to identify the microbes responsible for PCB degradation in the activated biosludge of a WWTP using ¹³C-labelled biphenyl (BP). Results of time-course SIP revealed different bacteria and archaea involved in BP metabolism, which dominated the BP-degrading community at different time points. BP degradation by the genera Spartobacteria, Alicyclobacillus, Flavobacterium and the order Cenarchaeales has not been reported previously. The abundance of biphenyl dioxygenase (bphA) genes increased over time and a novel bphA gene was identified from the ¹³C-heavy DNA fraction. In addition, three cultivable BP degraders were isolated, but did not participate in BP degradation in situ or contain the identified bphA genes. Taken together, these data reveal the huge potential and important roles of yet-to-be-cultivated microbes responsible for PCB degradation in activated biosludge, providing fundamental knowledge on WWTP management to remove POPs.

The biochemical response of willow plants (Salix viminalis L.) to the use of sewage sludge from various sizes of wastewater treatment plant

Sewage sludge production is increasing, as is the importance of its safe and sustainable disposal. The study examine the impact of fertilizing poor quality soil with sewage sludge from three sizes of wastewater treatment plants (WTP) (small, medium and large) located in Central Poland, applied in two doses (3 and 9tons per hectare), on biomass yield and selected biochemical parameters in willow plants. The WTPs were selected based on the size criterion given in Polish regulations. Three variables were analyzed in the leaves and roots of willow cuttings after twenty weeks of cultivation: the degree of oxidative reaction, assessed as thiobarbituric-acid-reactive substances (TBARS) content; catalase activity (CAT, EC 1.11.1.6), reflecting the efficiency of the antioxidative response; and changes in the concentration of proline, one of the major cellular osmoprotectants. For plants growing in poor-quality soil, sewage sludge administration results in a large increase of willow biomass by creating good conditions for plant growth associated with protection against oxidative damage, efficient functioning of the antioxidant system and maintenance of the osmotic balance between the soil environment and plant roots. The greatest increase was 204% of control in the case of 9tha^-1 sludge from the medium WTP. Biomass production correlated with the applied sludge dose. After sewage sludge application lipid peroxides were reduced in leaves (81%) and roots (69%), CAT activity was enhanced (to 855% in leaves) and proline level was increased in root tissues. The application of sewage sludge originating from small WTPs offers the best conditions than larger WTPs: sludge from large WTPs may cause oxidative damage and exceed the possibilities of plants to counteract stress factors, especially when used in high doses.

Interaction Between Plant Competition and Rhizospheric Bacterial Community Influence Secondary Succession of Abandoned Farmland on the Loess Plateau of China

Interactions between plant and soil communities have important implication for plant competition, development and succession. In order to explore the internal mechanism behind natural succession of abandoned farmland, we test the effect of plant-soil interaction on plant growth and competitive ability through performing a pot experiment, which included three grasses in different successional stages on the Loess Plateau of China (Setaria viridis, Stipa bungeana, and Bothriochloa ischaemum) in monoculture and all possible two- and three-way combinations, along with a plant-free control pot. The plants were harvested after about 4 months, and the rhizospheric soil was collected. The bacterial communities of the soils were analyzed by high-throughput sequencing of the 16S rRNA gene. Plant competition affected richness of bacterial communities. Proteobacteria and Bacteroidetes were generally higher and Actinobacteria and Acidobacteria were lower in relative abundance in the mixed treatments associated with B. ischaemum. Photosynthetic bacterium, Genus Rhodobacter family Rhodospirillaceae, affected the growth condition and increased the competitive ability of B. ischaemum. Differences in the amounts of soil organic carbon, water-soluble organic carbon and nitrate nitrogen and available phosphorus drove the differences in bacterial communities. Our study has an important significance for understanding the trend of natural succession on the abandoned farmland on the Loess Plateau of China.

The effect of sewage sludge application on soil properties and willow (Salix sp.) cultivation

The aim of the study was to determine the impact of sewage sludge from three wastewater treatment plants of different sizes (small, medium and large) applied in two doses (3 and 9 tons per hectare) on soil properties, determined as the content of organic carbon and humus fractions, bacterial abundance, phytotoxicity and PCDD/PCDF TEQ concentrations. The study also evaluated the impact of this sewage sludge on the biometric and physiological parameters and detoxification reaction of willow (Salix sp.) as a typical crop used for the remediation of soil following sludge application. The cultivation of willow on soil treated with sludge was found to result in a gradual increase of humus fractions, total organic carbon content and bacterial abundance as well as soil properties measured using Lepidium sativum. However, it also produced an initial increase of soil phytotoxicity, indicated by Sinapis alba and Sorghum sacharatum, and PCDD/PCDF Toxic Equivalent (TEQ) concentrations, which then fell during the course of the experiment, particularly in areas planted by willow. Although the soil phytotoxicity and PCDD/PCDF TEQ content of the sewage sludge-amended soil initially increased, sludge application was found to have a positive influence on willow, probably due to its high nutrient and carbon content. The obtained results reveal increases in willow biomass, average leaf surface area and leaf length as well as chlorophyll a+b content. Moreover, a strong decline was found in the activity of the detoxifying enzyme glutathione S-transferase (GSTs), a multifunctional enzyme involved in the metabolism of xenobiotics in plants, again demonstrating the used sludge had a positive influence on willow performance.

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

Enhanced anaerobic dechlorination of polychlorinated biphenyl in sediments by bioanode stimulation

The application of a low-voltage electric field as an electron donor or acceptor to promote the bioremediation of chlorinated organic compounds represents a promising technology meeting the demand of developing an efficient and cost-effective strategy for in situ treatment of PCB-contaminated sediments. Here, we reported that bioanode stimulation with an anodic potential markedly enhanced dechlorination of 2,3,4,5-tetrachlorobiphenyl (PCB 61) contained in the sediment at an electronic waste recycling site of Qingyuan, Guangdong, China. The 110-day incubation of the bioanode with a potential poised at 0.2 V relative to saturated calomel electrode enabled 58% transformation of the total PCB 61 at the initial concentration of 100 μmol kg(-1), while only 23% was reduced in the open-circuit reference experiment. The introduction of acetate to the bioelectrochemical reactor (BER) further improved PCB 61 transformation to 82%. Analysis of the bacterial composition showed significant community shifts in response to variations in treatment. At phylum level, the bioanode stimulation resulted in substantially increased abundance of Actinobacteria, Bacteroidetes, and Chloroflexi either capable of PCB dechlorination, or detected in the PCB-contaminated environment. At genus level, the BER contained two types of microorganisms: electrochemically active bacteria (EAB) represented by Geobacter, Ignavibacterium, and Dysgonomonas, and dechlorinating bacteria including Hydrogenophaga, Alcanivorax, Sedimentibacter, Dehalogenimonas, Comamonas and Vibrio. These results suggest that the presence of EAB can promote the population of dechlorinating bacteria which are responsible for PCB 61 transformation.

Identification of benzo[a]pyrene-metabolizing bacteria in forest soils by using DNA-based stable-isotope probing

DNA-based stable-isotope probing (DNA-SIP) was used in this study to investigate the uncultivated bacteria with benzo[a]pyrene (BaP) metabolism capacities in two Chinese forest soils (Mt. Maoer in Heilongjiang Province and Mt. Baicaowa in Hubei Province). We characterized three different phylotypes with responsibility for BaP degradation, none of which were previously reported as BaP-degrading microorganisms by SIP. In Mt. Maoer soil microcosms, the putative BaP degraders were classified as belonging to the genus Terrimonas (family Chitinophagaceae, order Sphingobacteriales), whereas Burkholderia spp. were the key BaP degraders in Mt. Baicaowa soils. The addition of metabolic salicylate significantly increased BaP degradation efficiency in Mt. Maoer soils, and the BaP-metabolizing bacteria shifted to the microorganisms in the family Oxalobacteraceae (genus unclassified). Meanwhile, salicylate addition did not change either BaP degradation or putative BaP degraders in Mt. Baicaowa. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD) genes were amplified, sequenced, and quantified in the DNA-SIP (13)C heavy fraction to further confirm the BaP metabolism. By illuminating the microbial diversity and salicylate additive effects on BaP degradation across different soils, the results increased our understanding of BaP natural attenuation and provided a possible approach to enhance the bioremediation of BaP-contaminated 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 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.

Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology

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

Culture-dependent and culture-independent characterization of potentially functional biphenyl-degrading bacterial community in response to extracellular organic matter from Micrococcus luteus

Biphenyl (BP)-degrading bacteria were identified to degrade various polychlorinated BP (PCB) congers in long-term PCB-contaminated sites. Exploring BP-degrading capability of potentially useful bacteria was performed for enhancing PCB bioremediation. In the present study, the bacterial composition of the PCB-contaminated sediment sample was first investigated. Then extracellular organic matter (EOM) from Micrococcus luteus was used to enhance BP biodegradation. The effect of the EOM on the composition of bacterial community was investigated by combining with culture-dependent and culture-independent methods. The obtained results indicate that Proteobacteria and Actinobacteria were predominant community in the PCB-contaminated sediment. EOM from M. luteus could stimulate the activity of some potentially difficult-to-culture BP degraders, which contribute to significant enhancement of BP biodegradation. The potentially difficult-to-culture bacteria in response to EOM addition were mainly Rhodococcus and Pseudomonas belonging to Gammaproteobacteria and Actinobacteria respectively. This study provides new insights into exploration of functional difficult-to-culture bacteria with EOM addition and points out broader BP/PCB degrading, which could be employed for enhancing PCB-bioremediation processes.

Bacterial degradation of Aroclor 1242 in the mycorrhizosphere soils of zucchini (Cucurbita pepo L.) inoculated with arbuscular mycorrhizal fungi

A greenhouse experiment was conducted to investigate the effects of zucchini (Cucurbita pepo L.), inoculated with the arbuscular mycorrhizal (AM) species Acaulospora laevis, Glomus caledonium, and Glomus mosseae, on the soil bacterial community responsible for Aroclor 1242 dissipation. The dissipation rates of Aroclor 1242 and soil bacteria abundance were much higher with the A. laevis and G. mosseae treatments compared to the non-mycorrhizal control. The biphenyl dioxygenase (bphA) and Rhodococcus-like 2,3-dihydroxybiphenyl dioxygenase (bphC) genes were more abundant in AM inoculated soils, suggesting that the bphA and Rhodococcus-like bphC pathways play an important role in Aroclor 1242 dissipation in the mycorrhizosphere. The soil bacterial communities were dominated by classes Betaproteobacteria and Actinobacteria, while the relative proportion of Actinobacteria was significantly (F=2.288, P<0.05) correlated with the PCB congener profile in bulk soil. Our results showed that AM fungi could enhance PCB dissipation by stimulating bph gene abundance and the growth of specific bacterial groups.

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.

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.

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.

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.

Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils

Total extracted DNA from two heavily polychlorobiphenyl-contaminated soils was analyzed with respect to biphenyl dioxygenase sequences and activities. This was done by PCR amplification and cloning of a DNA segment encoding the active site of the enzyme. The translated sequences obtained fell into three similarity clusters (I to III). Sequence identities were high within but moderate or low between the clusters. Members of clusters I and II showed high sequence similarities with well-known biphenyl dioxygenases. Cluster III showed low (43%) sequence identity with a biphenyl dioxygenase from Rhodococcus jostii RHA1. Amplicons from the three clusters were used to reconstitute and express complete biphenyl dioxygenase operons. In most cases, the resulting hybrid dioxygenases were detected in cell extracts of the recombinant hosts. At least 83% of these enzymes were catalytically active. Several amino acid exchanges were identified that critically affected activity. Chlorobiphenyl turnover by the enzymes containing the prototype sequences of clusters I and II was characterized with 10 congeners that were major, minor, or not constituents of the contaminated soils. No direct correlations were observed between on-site concentrations and rates of productive dioxygenations of these chlorobiphenyls. The prototype enzymes displayed markedly different substrate and product ranges. The cluster II dioxygenase possessed a broader substrate spectrum toward the assayed congeners, whereas the cluster I enzyme was superior in the attack of ortho-chlorinated aromatic rings. These results demonstrate the feasibility of the applied approach to functionally characterize dioxygenase activities of soil metagenomes via amplification of incomplete genes.

Evidence for shifts in the structure and abundance of the microbial community in a long-term PCB-contaminated soil under bioremediation

Although the impact of bioremediation of PCB-contaminated sites on the indigenous microbial community is a key question for soil restoration, it remains poorly understood. Therefore, a small-scale bioremediation assay made of (a) a biostimulation treatment with carvone, soya lecithin and xylose and (b) two bioaugmentation treatments, one with a TSZ7 mixed culture and another with a Rhodococcus sp. Z6 pure strain was set up. Changes in the structure of the global soil microbial community and in the abundances of different taxonomic phyla were monitored using ribosomal intergenic spacer analysis (RISA) and real-time PCR. After an 18-month treatment, the structure of the bacterial community in the bioremediated soils was significantly different from that of the native soil. The shift observed in the bacterial community structure using RISA analysis was in accordance with the monitored changes in the abundances of 11 targeted phyla and classes. Actinobacteria, Bacteriodetes and α- and γ-Proteobacteria were more abundant under all three bioremediation treatments, with Actinobacteria representing the dominant phylum. Altogether, our results indicate that bioremediation of PCB-contaminated soil induces significant changes in the structure and abundance of the total microbial community, which must be addressed to implement bioremediation practices in order to restore soil functions.

Laboratory research aimed at closing the gaps in microbial bioremediation

The industrial revolution, the first agricultural 'green revolution', and the development of antibiotics and therapeutic chemicals have brought significant and undeniable benefits to the human race. However, these advances demand high levels of energy, exploit natural resources and create large amounts of waste that creates an environmental burden for our planet. The pollution rate and character of many of the pollutants results in a rapid deterioration of the environment. Bioremediation functions to isolate and select microorganisms that operate under aerobic and anoxic conditions to remove these harmful pollutants. Current 'omics' technologies allow the exploitation of the catabolic potential of microbes without the need to cultivate them. Synthetic microbiology builds new catabolic pathways to remove recalcitrant pollutants from the environment.

Pseudomonas fluorescens F113 mutant with enhanced competitive colonization ability and improved biocontrol activity against fungal root pathogens

Motility is one of the most important traits for efficient rhizosphere colonization by Pseudomonas fluorescens F113rif (F113). In this bacterium, motility is a polygenic trait that is repressed by at least three independent pathways, including the Gac posttranscriptional system, the Wsp chemotaxis-like pathway, and the SadB pathway. Here we show that the kinB gene, which encodes a signal transduction protein that together with AlgB has been implicated in alginate production, participates in swimming motility repression through the Gac pathway, acting downstream of the GacAS two-component system. Gac mutants are impaired in secondary metabolite production and are unsuitable as biocontrol agents. However, the kinB mutant and a triple mutant affected in kinB, sadB, and wspR (KSW) possess a wild-type phenotype for secondary metabolism. The KSW strain is hypermotile and more competitive for rhizosphere colonization than the wild-type strain. We have compared the biocontrol activity of KSW with those of the wild-type strain and a phenotypic variant (F113v35 [V35]) which is hypermotile and hypercompetitive but is affected in secondary metabolism since it harbors a gacS mutation. Biocontrol experiments in the Fusarium oxysporum f. sp. radicis-lycopersici/Lycopersicum esculentum (tomato) and Phytophthora cactorum/Fragaria vesca (strawberry) pathosystems have shown that the three strains possess biocontrol activity. Biocontrol activity was consistently lower for V35, indicating that the production of secondary metabolites was the most important trait for biocontrol. Strain KSW showed improved biocontrol compared with the wild-type strain, indicating that an increase in competitive colonization ability resulted in improved biocontrol and that the rational design of biocontrol agents by mutation is feasible.

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.

Equilibrium sampling of persistent and bioaccumulative compounds in soil and sediment: comparison of two approaches to determine equilibrium partitioning concentrations in lipids

The equilibrium sampling in silicone is increasingly applied to measure freely dissolved concentrations and chemical activities within bioaccumulation research of hydrophobic organic chemicals. Two equilibrium methods were applied to PCB-contaminated soil and sediment, and directly calibrated with respect to equilibrium partitioning concentrations in lipids (C(lipid,partitioning)): (i) Solid phase microextraction in the headspace above the sample (HS-SPME) required optimization for its application to PCBs, and it was calibrated above external partitioning standards in olive oil. (ii) Equilibrium sampling with internally coated glass jars with varying thicknesses of silicone (PDMS) resulted in proportionality between coating and analyte mass, which confirmed several validity criteria. C(lipid,partitioning) was here determined as product of PDMS concentration and PDMS to lipid partition ratio. The results of the two methods were in good agreement and thus validated each other. Finally, the coated glass jar method was applied to field sediment containing invertebrates, which lead to C(lipid,partitioning) that were about two times higher than measured lipid-normalized concentrations in the organisms. Temperature differences and animal lipid structure were discussed as possible reasons for this discrepancy. Both methods combine high analytical performance, reduced equilibration times and new calibration possibilities, which makes them suited for bioaccumulation research and environmental monitoring.

The effects of individual PCB congeners on the soil bacterial community structure and the abundance of biphenyl dioxygenase genes

Polychlorinated biphenyls (PCBs) are toxic environmental contaminants that represent a class of 209 congeners characterized by different degrees of chlorination and substitution patterns. Most of experimental studies about microbial degradation of PCBs have been conducted on PCB mixtures, even though evidence accumulated in bacteria and other organisms shows that exposure to different congeners may have different biological effects. Microcosm experiments were conducted using aerobic agitated soil slurries individually exposed to PCB congeners with different degrees of chlorination: PCB-3, 15, 28, and 77, and the commercial mixture Aroclor 1242. After four weeks of incubation, PCBs were analyzed by gas chromatography/mass spectrometry (GC/MS) showing different transformation extents: With the exception of PCB-15 that was not significantly transformed (7%), biodegradation rates decreased with the degree of chlorination, from 75% for PCB-3 to 22% for PCB-77 and Aroclor 1242. The bacterial abundance, as measured by colony counting and 16S rDNA quantification by real-time PCR, was lower (of about 40%) in soil microcosms exposed to the higher-chlorinated congeners, PCB-28, PCB-77, and Aroclor 1242, as compared to non-exposed soils and soils exposed to the lower-chlorinated congeners, PCB-3 and PCB-15. The relative abundance of different taxonomic groups, as determined by real-time PCR, revealed an increase of β-Proteobacteria and Actinobacteria in all microcosms exposed to PCBs, as compared with non-exposed soil. In addition, exposure to PCB-77 and Aroclor 1242 resulted in a higher abundance of α-Proteobacteria and Acidobacteria. Globally, these results suggest that exposure to PCBs (and especially to higher-chlorinated congeners and Aroclor 1242) selected bacterial groups involving most known PCB degraders, i.e., β-Proteobacteria and Acidobacteria. The quantification of biphenyl dioxygenase (BPH) genes--involved in the aerobic degradation of PCBs--using real-time PCR showed that exposure to all PCB congeners and Aroclor 1242 resulted in a marked increase of two out of the four BPH genes tested, similarly suggesting the selection of PCB-degrading bacteria. This paper showed that exposure to different PCB congeners leads to different structures of the soil bacterial community and BPH genes expression patterns.

The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation.

Microbiological polyphasic approach for soil health evaluation in an Italian polluted site

The use of microorganisms as bioindicators of soil health is quite a new feature, rarely considered for the soil health evaluation in chronically-polluted industrial sites, and still suffering of the bias related to the technique applied. In this work we applied a microbiological polyphasic approach, relying on soil indigenous microorganisms as bioindicators and combining culture-dependent and -independent methods, in order to evaluate soil health of four sites (1a, 1b, 2a and 2b) inside a chemical factory with a centenary activity. Functional as well as structural aspects were comprehensively considered. Results were related to the kind of pollutants found in each site. Heavy metal pollution was recorded in sites 1b and 2b, while both organic and inorganic substances were detected in sites 1a and 2a. Based on the chemical and physical properties of the four soils, site 1b and 2b grouped together, while 1a and 2a were separated from the others. The density of the culturable bacteria was very low in site 2a, where only gram-positive were found. According to the identification of culturable bacteria, site 2a showed the lowest similarity with the other sites. Microbial activity was detected only in sites 1b and 2b. PCR-DGGE (Denaturing Gradient Gel Electrophoresis), was performed on the culturable, total and active microbial communities. Consistently with the identification of culturable bacterial strains, the molecular profile of the culturable fraction of site 2a, was clearly separated from the molecular profiles of other sites in cluster analysis. Molecular fingerprintings of the whole and active bacterial communities differed among the sites, but clustered according to the pollutants present in each site. The presence of possible key species in each site has been discussed according to the whole and active species. Since the results obtained by microbiological analysis are consistent with the chemical data, we suggest that the use of this microbiological polyphasic approach and of microorganisms as intrinsic bioindicators, can be suitable for the evaluation of soil health.

Vertical distribution and diversity of sulfate-reducing prokaryotes in the Pearl River estuarine sediments, Southern China

The vertical distribution and diversity of sulfate-reducing prokaryotes (SRPs) in a sediment core from the Pearl River Estuary was reported for the first time. The profiles of methane and sulfate concentrations along the sediment core indicated processes of methane production/oxidation and sulfate reduction. Phospholipid fatty acids analysis suggested that sulfur-oxidizing bacteria (SOB) might be abundant in the upper layers, while SRPs might be distributed throughout the sediment core. Quantitative competitive-PCR analysis indicated that the ratios of SRPs to total bacteria in the sediment core varied from around 2-20%. Four dissimilatory sulfite reductase (dsrAB) gene libraries were constructed and analyzed for the top layer (0-6 cm), middle layer (18-24 cm), bottom layer (44-50 cm) and the sulfate-methane transition zone (32-42 cm) sediments. Most of the retrieved dsrAB sequences (80.9%) had low sequence similarity with known SRP sequences and formed deeply branching dsrAB lineages. Meanwhile, bacterial 16S rRNA gene analysis revealed that members of the Proteobacteria were predominant in these sediments. Putative SRPs within Desulfobacteriaceae, Syntrophaceae and Desulfobulbaceae of Deltaproteobacteria, and putative SOB within Epsilonproteobacteria were detected by the 16S rRNA gene analysis. Results of this study suggested a variety of novel SRPs in the Pearl River Estuary sediments.

Bacterial responses and interactions with plants during rhizoremediation

With the increase in quality of life standards and the awareness of environmental issues, the remediation of polluted sites has become a priority for society. Because of the high economic cost of physico-chemical strategies for remediation, the use of biological tools for cleaning-up contaminated sites is a very attractive option. Rhizoremediation, the use of rhizospheric microorganisms in the bioremediation of contaminants, is the biotechnological approach that we explore in this minireview. We focus our attention on bacterial interactions with the plant surface, responses towards root exudates, and how plants and microbes communicate. We analyse certain strategies that may improve rhizoremediation, including the utilization of endophytes, and finally we discuss several rhizoremediation strategies that have opened ways to improve biodegradation.

Developing microbe-plant interactions for applications in plant-growth promotion and disease control, production of useful compounds, remediation and carbon sequestration

Interactions between plants and microbes are an integral part of our terrestrial ecosystem. Microbe–plant interactions are being applied in many areas. In this review, we present recent reports of applications in the areas of plant‐growth promotion, biocontrol, bioactive compound and biomaterial production, remediation and carbon sequestration. Challenges, limitations and future outlook for each field are discussed.

Transgenic plants to improve rhizoremediation of polychlorinated biphenyls (PCBs)

Recent investigations have shown that the three components of the biphenyl dioxygenase and the 2,3-dihydroxybiphenyl dioxygenase can be produced actively in transgenic plants. Both enzymes catalyze critical steps of the bacterial polychlorinated biphenyl (PCB) degrading pathway. On the basis of these observations, optimized plant-microbe bioremediation processes in which transgenic plants would initiate PCB metabolism and release the metabolites for further degradation by rhizobacteria has been proposed. Since this is still a relatively new approach for PCB remediation, its successful application will require efforts first, to engineer improved PCB-degrading enzymes; second, to co-ordinately express these enzymes' components in plants; and third, to better understand the mechanisms by which plants and rhizobacteria interact to degrade organic pollutants.

Rules of engagement: interspecies interactions that regulate microbial communities

Microbial communities comprise an interwoven matrix of biological diversity modified by physical and chemical variation over space and time. Although these communities are the major drivers of biosphere processes, relatively little is known about their structure and function, and predictive modeling is limited by a dearth of comprehensive ecological principles that describe microbial community processes. Here we discuss working definitions of central ecological terms that have been used in various fashions in microbial ecology, provide a framework by focusing on different types of interactions within communities, review the status of the interface between evolutionary and ecological study, and highlight important similarities and differences between macro- and microbial ecology. We describe current approaches to study microbial ecology and progress toward predictive modeling.