Rhizoremediation: a beneficial plant-microbe interaction

Fungal inoculation and elevated CO2 mediate growth of Lolium mutiforum and Phytolacca americana, metal uptake, and metal bioavailability in metal-contaminated soil: evidence from DGT measurement

Fungal inoculation and elevated CO2 may mediate plant growth and uptake of heavy metals, but little evidence from Diffusive Gradients in Thin-films (DGT) measurement has been obtained to characterize the process. Lolium mutiforum and Phytolacca americana were grown at ambient and elevated CO2 on naturally Cd and Pb contaminated soils inoculated with and without Trichoderma asperellum strain C3 or Penicillium chrysogenum strain D4, to investigate plant growth, metal uptake, and metal bioavailability responses. Fungal inoculation increased plant biomass and shoot/root Cd and Pb concentrations. Elevated CO2 significantly increased plants biomass, but decreased Cd and Pb concentrations in shoot/root to various extents, leading to a metal dilution phenomenon. Total Cd and Pb uptake by plants, and DGT-measured Cd and Pb concentrations in rhizosphere soils, were higher in all fungal inoculation and elevated CO2 treatments than control treatments, with the combined treatments having more influence than either treatment alone. Metal dilution phenomenon occurred because the increase in DGT-measured bioavailable metal pools in plant rhizosphere due to elevated CO2 was unable to match the increase in requirement for plant uptake of metals due to plant biomass increase.

Plant-bacteria partnerships for the remediation of hydrocarbon contaminated soils

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

Gut and root microbiota commonalities

Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

Bioaugmentation with Petroleum-Degrading Consortia Has a Selective Growth-Promoting Impact on Crop Plants Germinated in Diesel Oil-Contaminated Soil

Rhizoremediation is a complex type of green clean-up technology that involves both plants and the rhizosphere-associated microorganisms to decompose hazardous compounds. The success of the strategy strongly depends on plant tolerance towards the pollutant, as well as plant's interactions with the rhizospheric microbes. The microorganisms may be stimulated by the secreted root exudates, which results in an increased breakdown of contaminants in the rhizosphere. The main goal of this study was to establish a potential rhizoremediation combination for a diesel-polluted site. Inoculation of plant roots or seeds with indigenous rhizospheric populations is a common approach in the rhizoremediation. However, we introduced hydrocarbon-degrading consortia (M10, R3, and K52) that were previously isolated from crude oil-contaminated soil instead of indigenous microbes. Bioaugmentation with these petroleum degraders was applied to screen four high biomass crop species (Indian mustard, alfalfa, high erucic acid rapeseed, HEAR, and low erucic acid rapeseed, LEAR) for their tolerance towards diesel oil. At no pollution, a promoting effect of M10 bacteria could be observed on germination and root elongation of all plant species. Moreover, M10 consortiums increased the germination index at 6,000 mg diesel oil per kilogram dry soil in the case of Indian mustard, alfalfa, and HEAR. The latter species was found to increment its dry weight upon bioaugmentation with M10 bacteria and all diesel oil treatments (6,000 and 24,000 mg diesel oil per kilogram dry soil). The initial results indicate HEAR and the M10 bacterial consortium as a promising plant-microbe tandem for a long-term rhizoremediation process.

Microbial interactions in the arsenic cycle: adoptive strategies and applications in environmental management

Arsenic (As) is a nonessential element that is often present in plants and in other organisms. However, it is one of the most hazardous of toxic elements globally. In many parts of the world, arsenic contamination in groundwater is a serious and continuing threat to human health. Microbes play an important role in regulating the environmental fate of arsenic. Different microbial processes influence the biogeochemical cycling of arsenic in ways that affect the accumulation of different arsenic species in various ecosystem compartments. For example, in soil, there are bacteria that methylate arsenite to trimethylarsine gas, thereby releasing arsenic to the atmosphere.In marine ecosystems, microbes exist that can convert inorganic arsenicals to organic arsenicals (e.g., di- and tri-methylated arsenic derivatives, arsenocholine,arsenobetaine, arsenosugars, arsenolipids). The organo arsenicals are further metabolized to complete the arsenic cycle.Microbes have developed various strategies that enable them to tolerate arsenic and to survive in arsenic-rich environments. Such strategies include As exclusion from cells by establishing permeability barrier, intra- and extracellular sequestration,active efflux pumps, enzymatic reduction, and reduction in the sensitivity of cellular targets. These strategies are used either singly or in combination. In bacteria,the genes for arsenic resistance/detoxification are encoded by the arsenic resistance operons (ars operon).In this review, we have addressed and emphasized the impact of different microbial processes (e.g., arsenite oxidation, cytoplasmic arsenate reduction, respiratory arsenate reduction, arsenite methylation) on the arsenic cycle. Microbes are the only life forms reported to exist in heavy arsenic-contaminated environments. Therefore,an understanding of the strategies adopted by microbes to cope with arsenic stress is important in managing such arsenic-contaminated sites. Further future insights into the different microbial genes/proteins that are involved in arsenic resistance may also be useful for developing arsenic resistant crop plants.

Influence of different salt marsh plants on hydrocarbon degrading microorganisms abundance throughout a phenological cycle

The influence of Juncus maritimus, Phragmites australis, and Triglochin striata on hydrocarbon degrading microorganisms (HD) in Lima River estuary (NW Portugal) was investigated through a year-long plant life cycle. Sediments un-colonized and colonized (rhizosediments) by those salt marsh plants were sampled for HD, total cell counts (TCC), and total petroleum hydrocarbons (TPHs) assessment. Generally, TCC seemed to be markedly thriving by the presence of roots, but without significant (p > 0.05) differences among rhizosediments. Nevertheless, plants seemed to have a distinct influence on HD abundance, particularly during the flowering season, with higher HD abundance in the rhizosediments of the fibrous roots plants (J. maritimus < P. australis < T. striata). Our data suggest that different plants have distinct influence on the dynamics of HD populations within its own rhizosphere, particularly during the flowering season, suggesting a period of higher rhizoremediation activity. Additionally, during the vegetative period, plants with fibrous and dense root system tend to retain hydrocarbons around their belowground tissues more efficiently than plants with adventitious root system. Overall results indicate that fibrous root plants have a higher potential to promote hydrocarbons degradation, and that seasonality should be taken into account when designing long-term rhizoremediation strategies in estuarine areas.

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.

The role of biodegradation in limiting the accumulation of petroleum hydrocarbons in raingarden soils

Previous studies have indicated that raingardens are effective at removing petroleum hydrocarbons from stormwater. There are concerns, however, that petroleum hydrocarbons could accumulate in raingarden soil, potentially resulting in liability for the site owner. In this work, 75 soil samples were collected from 58 raingardens and 4 upland (i.e., control) sites in the Minneapolis, Minnesota area, representing a range of raingarden ages and catchment land uses. Total petroleum hydrocarbon (TPH) concentrations in the samples were quantified, as were 16S rRNA genes for Bacteria and two functional genes that encode for enzymes used in the degradation of petroleum hydrocarbons. TPH levels in all of the raingarden soil samples were low (<3 μg/kg) and not significantly different from one another. The TPH concentration in raingarden soil samples was, however, significantly greater (p ≤ 0.002) than TPH levels in upland sites. In addition, the number of copies of Bacteria 16S rRNA genes and functional genes were greater in the raingardens planted with deeply-rooted natives and cultivars than in raingardens containing simply turf grass or mulch (p < 0.036), suggesting that planted raingardens may be better able to assimilate TPH inputs. The ability of microorganisms present in the soil samples to degrade a representative petroleum hydrocarbon (naphthalene) was also investigated in batch experiments. A sub-set of the field sites was selected for re-sampling, and all soil samples tested (n = 8) were able to mineralize naphthalene. In these experiments the initial mineralization rate correlated with the number of copies of Bacteria 16S rRNA genes present.

Bacterial bio-resources for remediation of hexachlorocyclohexane

In the last few decades, highly toxic organic compounds like the organochlorine pesticide (OP) hexachlorocyclohexane (HCH) have been released into the environment. All HCH isomers are acutely toxic to mammals. Although nowadays its use is restricted or completely banned in most countries, it continues posing serious environmental and health concerns. Since HCH toxicity is well known, it is imperative to develop methods to remove it from the environment. Bioremediation technologies, which use microorganisms and/or plants to degrade toxic contaminants, have become the focus of interest. Microorganisms play a significant role in the transformation and degradation of xenobiotic compounds. Many Gram-negative bacteria have been reported to have metabolic abilities to attack HCH. For instance, several Sphingomonas strains have been reported to degrade the pesticide. On the other hand, among Gram-positive microorganisms, actinobacteria have a great potential for biodegradation of organic and inorganic toxic compounds. This review compiles and updates the information available on bacterial removal of HCH, particularly by Streptomyces strains, a prolific genus of actinobacteria. A brief account on the persistence and deleterious effects of these pollutant chemical is also given.

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.

Biological degradation and solubilisation of coal

This review focuses on ligninolytic fungi, soil bacteria, plants and root exudates in the degradation and solubilisation of low grade and waste coal and the interaction between these mutualistic biocatalysts. Coal represents a considerable portion of the total global fossil fuel reserve and continued demand for, and supply of this resource generates vast quantities of spoil and low grade waste. Large scale bioremediation technologies for the beneficiation of waste coal have unfortunately not yet been realised despite the many discoveries of microorganisms capable of lignite, lignin, and humic acid breakdown. Even so, solubilisation and depolymerization of low grade coal appears to involve either ligninolytic enzyme action or the production of alkaline substances or both. While the precise mechanism of coal biosolubilisation is unclear, a model for the phyto-biodegradation of low rank coal by mutualistic interaction between ligninolytic microorganisms and higher plants is proposed. Based on accumulated evidence this model suggests that solubilisation and degradation of lignite and waste coals commences upon plant root exudate and ligninolytic microorganism interaction, which is mutualistic, and includes soil bacteria and both mycorrhizal and non-mycorrhizal fungi. It is envisaged that this model and its further elaboration will aid in the development of functional technologies for commercial bioremediation of coal mine spoils, contribute to soil formation, and the overall biogeochemistry of organic carbon in the global ecosystem.

Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid

In this work, we explore the potential use of the Pseudomonas putida KT2440 strain for bioremediation of naphthalene-polluted soils. Pseudomonas putida strain KT2440 thrives in naphthalene-saturated medium, establishing a complex response that activates genes coding for extrusion pumps and cellular damage repair enzymes, as well as genes involved in the oxidative stress response. The transfer of the NAH7 plasmid enables naphthalene degradation by P. putida KT2440 while alleviating the cellular stress brought about by this toxic compound, without affecting key functions necessary for survival and colonization of the rhizosphere. Pseudomonas putida KT2440(NAH7) efficiently expresses the Nah catabolic pathway in vitro and in situ, leading to the complete mineralization of [(14)C]naphthalene, measured as the evolution of (14)CO(2), while the rate of mineralization was at least 2-fold higher in the rhizosphere than in bulk soil.

GFP-tagged multimetal-tolerant bacteria and their detection in the rhizosphere of white mustard

The introduction of rhizobacteria that tolerate heavy metals is a promising approach to support plants involved in phytoextraction and phytostabilisation. In this study, soil of a metal-mine wasteland was analyzed for the presence of metal-tolerant bacterial isolates, and the tolerance patterns of the isolated strains for a number of heavy metals and antibiotics were compared. Several of the multimetal-tolerant strains were tagged with a broad host range reporter plasmid (i.e. pPROBE-NT) bearing a green fluorescent protein marker gene (gfp). Overall, the metal-tolerant isolates were predominately Gram-negative bacteria. Most of the strains showed a tolerance to five metals (Zn, Cu, Ni, Pb and Cd), but with differing tolerance patterns. From among the successfully tagged isolates, we used the transconjugant Pseudomonas putida G25 (pPROBE-NT) to inoculate white mustard seedlings. Despite a significant decrease in transconjugant abundance in the rhizosphere, the gfp-tagged cells survived on the root surfaces at a level previously reported for root colonisers.

Rhizostabilization of metals in soils using Lupinus luteus inoculated with the metal resistant rhizobacterium Serratia sp. MSMC541

The aim of this work was to test Lupinus luteus plants, inoculated with metal resistant rhizobacteria, in order to phytostabilise metals in contaminated soils. The resistance to heavy metals of strains isolated from nodules of Lupinus plants was evaluated. The strain MSMC541 showed multi-resistance to several metals (up to 13.3 mM As, 2.2 mM Cd, 2.3 mM Cu, 9 mM Pb and 30 mM Zn), and it was selected for further characterization. Furthermore, this strain was able to biosorb great amounts of metals in cell biomass. 16S rDNA sequencing positioned this strain within the genus Serratia. The presence of arsenic resistance genes was confirmed by southern blot and PCR amplification. A rhizoremediation pot experiment was conducted using Lupinus luteus grown on sand supplemented with heavy metals and inoculated with MSMC541. Plant growth parameters and metal accumulation were determined in inoculated vs. non-inoculated Lupinus luteus plants. The results showed that inoculation with MSMC541 improved the plant tolerance to metals. At the same time, metal translocation to the shoot was significantly reduced upon inoculation. These results suggest that Lupinus luteus plants, inoculated with the metal resistant strain Serratia sp. MSMC541, have a great potential for phytostabilization of metal contaminated soils.

Transformation of pWWO in Rhizobium leguminosarum DPT to Engineer Toluene Degrading Ability for Rhizoremediation

Rhizoremediation of organic xenobiotics is based on interactions between plants and their associated micro-organisms. The present work was designed to engineer a bacterial system having toluene degradation ability along with plant growth promoting characteristics for effective rhizoremediation. pWWO harboring the genes responsible for toluene breakdown was isolated from Pseudomonas putida MTCC 979 and successfully transformed in Rhizobium DPT. This resulted in a bacterial strain (DPT(T)) which had the ability to degrade toluene as well as enhance growth of host plant. The frequency of transformation was recorded 5.7 × 10(-6). DPT produced IAA, siderophore, chitinase, HCN, ACC deaminase, solubilized inorganic phosphate, fixed atmospheric nitrogen and inhibited the growth of Fusarium oxysporum and Macrophomina phaseolina in vitro. During pot assay, 50 ppm toluene in soil was found to inhibit the germination of Cajanus cajan seeds. However when the seeds bacterized with toluene degrading P. putida or R. leguminosarum DPT were sown in pots, again no germination was observed. Non-bacterized as well as bacterized seeds germinated successfully in toluene free soil as control. The results forced for an alternative mode of application of bacteria for rhizoremediation purpose. Hence bacterial suspension was mixed with soil having 50 ppm of toluene. Germination index in DPT treated soil was 100% while in P. putida it was 50%. Untreated soil with toluene restricted the seeds to germinate.

Analysis and characterization of cultivable heavy metal-resistant bacterial endophytes isolated from Cd-hyperaccumulator Solanum nigrum L. and their potential use for phytoremediation

This study investigates the heavy metal-resistant bacterial endophytes of Cd-hyperaccumulator Solanum nigrum L. grown on a mine tailing by using cultivation-dependent technique. Thirty Cd-tolerant bacterial endophytes were isolated from roots, stems, and leaves of S. nigrum L. and classified by amplified ribosomal DNA-restriction analysis into 18 different types. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates belonged to four groups: Actinobacteria (43%), Proteobacteria (23%), Bacteroidetes (27%) and Firmicutes (7%). All the isolates were then characterized for their plant growth promoting traits as well as their resistances to different heavy metals; and the actual plant growth promotion and colonization ability were also assessed. Four isolates were re-introduced into S. nigrum L. under Cd stress and resulted in Cd phytotoxicity decrease, as dry weights of roots increased from 55% to 143% and dry weights of above-ground from 64% to 100% compared to the uninoculated ones. The total Cd accumulation of inoculated plants increased from 66% to 135% (roots) and from 22% to 64% (above-ground) compared to the uninoculated ones. Our research suggests that bacterial endophytes are a most promising resource and may be the excellent candidates of bio-inoculants for enhancing the phytoremediation efficiency.

Soil microbes and plant fertilization

With respect to the adverse effects of chemical fertilization on the environment and their related expenses, especially when overused, alternative methods of fertilization have been suggested and tested. For example, the combined use of chemical fertilization with organic fertilization and/or biological fertilization is among such methods. It has been indicated that the use of organic fertilization with chemical fertilization is a suitable method of providing crop plants with adequate amount of nutrients, while environmentally and economically appropriate. In this article, the importance of soil microbes to the ecosystem is reviewed, with particular emphasis on the role of plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, and endophytic bacteria in providing necessary nutrients for plant growth and yield production. Such microbes are beneficial to plant growth through colonizing plant roots and inducing mechanisms by which plant growth increases. Although there has been extensive research work regarding the use of microbes as a method of fertilizing plants, it is yet a question how the efficiency of such microbial fertilization to the plant can be determined and increased. In other words, how the right combination of chemical and biological fertilization can be determined. In this article, the most recent advances regarding the effects of microbial fertilization on plant growth and yield production in their combined use with chemical fertilization are reviewed. There are also some details related to the molecular mechanisms affecting the microbial performance and how the use of biological techniques may affect the efficiency of biological fertilization.

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.

Effect of plant species on the function and structure of the bacterial community in the rhizosphere of lead–zinc mine tailings in Zhejiang, China

To uncover the role played by pioneer plants in the natural succession of vegetation on heavy-metal mine tailings, it is important to explore the sensitive indicator of rhizosphere microbial community performance. We investigated the structure and function of rhizosphere bacterial communities of five pioneer plants growing on lead–zinc mine tailings in Zhejiang, China. Compared with the control, all five pioneer plants differentially affected the structure and function of rhizosphere bacterial communities. The number of bacteria, the activity of β-glucosidase and urease, and species richness indices were the highest in the rhizosphere of Erigeron annuus . The carbon utilization ability and the functional diversity indices were the highest in the rhizosphere of Lysimachia clethroides . There was no significant relationship between the functional or structural diversity indices and the bioavailable heavy-metal content among each species. Clustering analysis and the nonmetric dimensional scaling biplot showed that the rhizosphere bacterial communities of the five pioneer plants were different from those of control, indicating that plant species might be the main driver of microbial community composition on mine tailings. Both L. clethroides and E. annuus might be appropriate candidates for phytoremediation of mine tailings for higher soil microbial community function and species richness in rhizosphere.

Effect of multiple metal resistant bacteria from contaminated lake sediments on metal accumulation and plant growth

Naturally occurring bacteria play an important role in bioremediation of heavy metal pollutants in soil and wastewater. This study identified high levels of resistance to zinc, cesium, lead, arsenate and mercury in eight copper resistant Pseudomonas strains previously isolated from Torch Lake sediment. These strains showed variable susceptibility to different antibiotics. Furthermore, these metal resistant strains were capable of bioaccumulation of multiple metals and solubilization of copper. Bacterial strains TLC 3-3.5-1 and TLC 6-6.5-1 showed high bioaccumulation ability of Zn (up to 15.9 mg/g dry cell) and Pb (80.7 mg/g dry cell), respectively. All the strains produced plant growth promoting indole-3-acetic acid (IAA), iron chelating siderophore and solubilized mineral phosphate and metals. The effect of bacterial inoculation on plant growth and copper uptake by maize (Zea mays) and sunflower (Helianthus annuus) was investigated using one of the isolates (Pseudomonas sp. TLC 6-6.5-4) with higher IAA production and phosphate and metal solubilization, which resulted in a significant increase in copper accumulation in maize and sunflower, and an increase in the total biomass of maize. The multiple metal-resistant bacterial isolates characterized in our study have potential applications for remediation of metal contaminated soils in combination with plants and metal contaminated water.

Hyperaccumulators, arbuscular mycorrhizal fungi and stress of heavy metals

Use of plants, with hyperaccumulating ability or in association with soil microbes including the symbiotic fungi, arbuscular mycorrhiza (AM), are among the most common biological methods of treating heavy metals in soil. Both hyperaccumulating plants and AM fungi have some unique abilities, which make them suitable to treat heavy metals. Hyperaccumulator plants have some genes, being expressed at the time of heavy metal pollution, and can accordingly localize high concentration of heavy metals to their tissues, without showing the toxicity symptoms. A key solution to the issue of heavy metal pollution may be the proper integration of hyperaccumulator plants and AM fungi. The interactions between the soil microbes and the host plant can also be important for the treatment of soils polluted with heavy metals.

Rhizoremediation of lindane by root-colonizing Sphingomonas

We used a two‐step enrichment approach to isolate root‐colonizing hexachlorocyclohexane (HCH)‐degrading microorganisms. The first step consists of the use of classical liquid enrichment to isolate γ‐HCH degraders. The γ‐HCH‐degrading microbes were attached in mass to corn seeds sown in soil with γ‐HCH, and after plant development we rescued bacteria growing on root tips. Bacteria were then subjected to a second enrichment round in which growth on liquid medium with γ‐HCH and inoculation of corn seeds were repeated. We then isolated bacteria on M9 minimal medium with γ‐HCH from root tips. We were able to isolate four Sphingomonas strains, all of which degraded α‐, β‐, γ‐ and δ‐HCH. Two of the strains were particularly good colonizers of corn roots, reaching high cell density in vegetated soil and partly removing γ‐HCH. In contrast, these bacteria performed poorly in unplanted soils. This study supports the hypothesis that the removal of persistent toxic chemicals can be accelerated by combinations of plants and bacteria, a process generally known as rhizoremediation.

[Advance in bioremediation of polychlorinated biphenyls]

As one of the persistent organic pollutants, polychlorinated biphenyls are harmful to the environment and humans. Biodegradation is the most potential way to remove PCBs. Biodegradation can mainly be divided into microbial degradation, phytoremediation, plant and microbial combined remediation. Here, we introduced isolation of the PCBs-degrading strains, cloning and modification of the related degradation genes. Additionally, on the other hand, the natural remediation of plant, plant and microbial combined remediation, plant transgenic remediation were described.

Rhizosphere dynamics during phytoremediation of olive mill wastewater

The potential of phytoremediation as a treatment option for olive mill wastewater (OMW) was tested on five perennial tree species. Cupressus sempervirens and Quercus ilex proved tolerant to six-month OMW treatment followed by six-month water irrigation, whereas Salix sp. and Laurus nobilis and, later, Pinus mugo suffered from phytotoxic effects. Test plants were compared to controls after treatment and irrigation, by monitoring biochemical and microbiological variations in the rhizosphere soil. OMW-treated soils were exposed to 50-fold higher phenols concentrations, which, irrespective of whether the respective plants were OMW-resistant or susceptible, were reduced by more than 90% by the end of the irrigation cycle, owing to significantly increased laccase, peroxidase and β-glucosidase activities, recovery/acquisition of bacterial culturability and transitory development of specialized fungal communities sharing the presence of Geotrichum candidum. Of all results, the identification of Penicillium chrysogenum and Penicillium aurantiogriseum as dominant rhizosphere fungi was distinctive of OMW-tolerant species.

Influence of Rhizobium meliloti on phytoremediation of polycyclic aromatic hydrocarbons by alfalfa in an aged contaminated soil

Microbe-assisted phytoremediation is emerging as one of the most effective means by which plants and their associated rhizosphere microbes degrade organic contaminants in soils. A pot study was conducted to examine the effects of inoculation with Rhizobium meliloti on phytoremediation by alfalfa grown for 90 days in an agricultural soil contaminated with weathered polycyclic aromatic hydrocarbons (PAHs). Planting with uninoculated alfalfa (P) and alfalfa inoculated with R. meliloti (PR) significantly lowered the initial soil PAH concentrations by 37.2 and 51.4% respectively compared with unplanted control soil. Inoculation with R. meliloti significantly increased the counts of culturable PAH-degrading bacteria, soil microbial activity and the carbon utilization ability of the soil microbial community. The results suggest that the symbiotic association between alfalfa and Rhizobium can stimulate the rhizosphere microflora to degrade PAHs and its application may be a promising bioremediation strategy for aged PAH-contaminated soils.

Characterization of a copper-resistant symbiotic bacterium isolated from Medicago lupulina growing in mine tailings

A root nodule bacterium, Sinorhizobium meliloti CCNWSX0020, resistant to 1.4 mM Cu2+ was isolated from Medicago lupulina growing in mine tailings. In medium supplied with copper, this bacterium showed cell deformation and aggregation due to precipitation of copper on the cell surface. Genes similar to the copper-resistant genes, pcoR and pcoA from Escherichia coli, were amplified by PCR from a 1.4-Mb megaplasmid. Inoculation with S. meliloti CCNWSX0020 increased the biomass of M. lupulina grown in medium added 0 and 100 mg Cu2+ kg(-1) by 45.8% and 78.2%, respectively, and increased the copper concentration inside the plant tissues grown in medium supplied with 100 μM Cu2+ by 39.3%, demonstrating that it is a prospective symbiotic system for bioremediation purposes.

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.

Arbuscular mycorrhizal fungi restore normal growth in a white poplar clone grown on heavy metal-contaminated soil, and this is associated with upregulation of foliar metallothionein and polyamine biosynthetic gene expression

BACKGROUND AND AIMS

It is increasingly evident that plant tolerance to stress is improved by mycorrhiza. Thus, suitable plant-fungus combinations may also contribute to the success of phytoremediation of heavy metal (HM)-polluted soil. Metallothioneins (MTs) and polyamines (PAs) are implicated in the response to HM stress in several plant species, but whether the response is modulated by arbuscular mycorrhizal fungi (AMF) remains to be clarified. The aim of the present study was to check whether colonization by AMF could modify growth, metal uptake/translocation, and MT and PA gene expression levels in white poplar cuttings grown on HM-contaminated soil, and to compare this with plants grown on non-contaminated soil.

METHODS

In this greenhouse study, plants of a Populus alba clone were pre-inoculated, or not, with either Glomus mosseae or G. intraradices and then grown in pots containing either soil collected from a multimetal- (Cu and Zn) polluted site or non-polluted soil. The expression of MT and PA biosynthetic genes was analysed in leaves using quantitative reverse transcription-PCR. Free and conjugated foliar PA concentrations were determined in parallel.

RESULTS

On polluted soil, AMF restored plant biomass despite higher Cu and Zn accumulation in plant organs, especially roots. Inoculation with the AMF caused an overall induction of PaMT1, PaMT2, PaMT3, PaSPDS1, PaSPDS2 and PaADC gene expression, together with increased free and conjugated PA levels, in plants grown on polluted soil, but not in those grown on non-polluted soil.

CONCLUSIONS

Mycorrhizal plants of P. alba clone AL35 exhibit increased capacity for stabilization of soil HMs, together with improved growth. Their enhanced stress tolerance may derive from the transcriptional upregulation of several stress-related genes, and the protective role of PAs.

Sustainable biodegradation of phenol by Acinetobacter calcoaceticus P23 isolated from the rhizosphere of duckweed Lemna aoukikusa

Phenol-degrading bacteria were isolated from the rhizosphere of duckweed (Lemna aoukikusa) using an enrichment culture method. One of the isolates, P23, exhibited an excellent ability to degrade phenol and attach to a solid surface under laboratory conditions. Phylogenetic analysis revealed that P23 belongs to the genera Acinetobacter and has the highest similarity to Acinetobacter calcoaceticus. P23 rapidly colonized on the surface of sterilized duckweed roots and formed biofilms, indicating that the conditions provided by the root system of duckweed are favorable to P23. A long-term performance test (160 h) showed that continuous removal of phenol can be attributed to the beneficial symbiotic interaction between duckweed and P23. P23 is the first growth-promoting bacterium identified from Lemna aoukikusa. The results in this study suggest the potential usefulness of dominating a particular bacterium in the rhizosphere of duckweeds to achieve efficient and sustainable bioremediation of polluted water.

Isolation and characterization of pyrene metabolizing microbial consortia from the plant rhizoplane

Most research on the ecology of PAH degrading bacteria in the rhizosphere has focused on individual strains that grow on specific PAHs. Thus, there are fundamental questions as to importance of microbial consortia for PAH degradation in the plant rhizosphere. The study reported here characterized cultivable pyrene degrading rhizoplane microbial communities from two different plant species using a root printing technique on agar plates. Colonies were revealed by formation of clearing zones on medium containing a thin film of pyrene on the surface of a mineral nutrient agar. Prints of the rhizoplane colonies were obtained from roots of Melilotus officinalis (sweet yellow clover) and Andropogon gerardii (big bluestem) plants. Phylogenetic characterizations of selected pyrene degrading colonies were assessed by PCR-DGGE and DNA sequencing. Results showed that different populations of cultivable pyrene degraders were obtained from representative consortia that were examined. Many of the PAH degrading consortia consisted of mixtures of bacterial species that were unable to degrade pyrene by themselves. While this study focused on culturable PAH degraders, the results suggest that pyrene degradation in the rhizosphere commonly involves the activity of bacterial consortia in which various species of bacteria interact to achieve PAH degradation.

Influence of arbuscular mycorrhiza and Rhizobium on phytoremediation by alfalfa of an agricultural soil contaminated with weathered PCBs: a field study

A field experiment was conducted to study the effects of inoculation with the arbuscular mycorrhizal fungus Glomus caledonium and/or Rhizobium meliloti on phytoremediation of an agricultural soil contaminated with weathered PCBs by alfalfa grown for 180 days. Planting alfalfa (P), alfalfa inoculated with G. caledonium (P + AM), alfalfa inoculated with R. meliloti (P + R), and alfalfa co-inoculated with R. meliloti and G. caledonium (P+AM+R) decreased significantly initial soil PCB concentrations by 8.1, 12.0, 33.8, and 43.5%, respectively. Inoculation with R. meliloti and/or G. caledonium (P+AM+R) increased the yield of alfalfa, and the accumulation of PCBs in the shoots. Soil microbial counts and the carbon utilization ability of the soil microbial community increased when alfalfa was inoculated with R. meliloti and/or G. caledonium. Results of this field study suggest that synergistic interactions between AMF and Rhizobium may have great potential to enhance phytoremediation by alfalfa of an agricultural soil contaminated with weathered PCBs.

Review: In situ and bioremediation of organic pollutants in aquatic sediments

Organic pollutants in sediments are a worldwide problem because sediments act as sinks for hydrophobic, recalcitrant and hazardous compounds. Depending on biogeochemical processes these hydrocarbons are involved in adsorption, desorption and transformation processes and can be made available to benthic organisms as well as organisms in the water column through the sediment-water interface. Most of these recalcitrant hydrocarbons are toxic and carcinogenic, they may enter the food-chain and accumulate in biological tissue. Several approaches are being investigated or have been already used to remove organic hydrocarbons from sediments. This paper provides a review on types and sources of organic pollutants as well as their behavior in sediments. It presents the advantages and disadvantages of traditional sediment remediation techniques in use, such as dredging, capping and monitored natural attenuation. Furthermore, it describes new approaches with emphasis on bioremediation, like biostimulation, bioaugmentation and phytoremediation applied to sediments. These new techniques promise to be of lower impact and more cost efficient than traditional management strategies.

"In situ" phytostabilisation of heavy metal polluted soils using Lupinus luteus inoculated with metal resistant plant-growth promoting rhizobacteria

The aim of this work is the evaluation of metal phytostabilisation potential of Lupinus luteus inoculated with Bradyrhizobium sp. 750 and heavy metal resistant PGPRs (plant-growth promoting rhizobacteria), for in situ reclamation of multi-metal contaminated soil after a mine spill. Yellow lupines accumulated heavy metals mainly in roots (Cu, Cd and especially Pb were poorly translocated to shoots). This indicates a potential use of this plant in metal phytostabilisation. Furthermore, As accumulation was undetectable. On the other hand, zinc accumulation was 10-100 times higher than all other metals, both in roots and in shoots. Inoculation with Bradyrhizobium sp. 750 increased both biomass and nitrogen content, indicating that nitrogen fixation was effective in soils with moderate levels of contamination. Co-inoculation of lupines with a consortium of metal resistant PGPR (including Bradyrhizobium sp., Pseudomonas sp. and Ochrobactrum cytisi) produced an additional improvement of plant biomass. At the same time, a decrease in metal accumulation was observed, both in shoots and roots, which could be due to a protective effect exerted on plant rhizosphere. Our results indicate the usefulness of L. luteus inoculated with a bacterial consortium of metal resistant PGPRs as a method for in situ reclamation of metal polluted soils.

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.

Using soil bacteria to facilitate phytoremediation

In the past twenty years or so, researchers have endeavored to utilize plants to facilitate the removal of both organic and inorganic contaminants from the environment, especially from soil. These phytoremediation approaches have come a long way in a short time. However, the majority of this work has been done under more controlled laboratory conditions and not in the field. As an adjunct to various phytoremediation strategies and as part of an effort to make this technology more efficacious, a number of scientists have begun to explore the possibility of using various soil bacteria together with plants. These bacteria include biodegradative bacteria, plant growth-promoting bacteria and bacteria that facilitate phytoremediation by other means. An overview of bacterially assisted phytoremediation is provided here for both organic and metallic contaminants, with the intent of providing some insight into how these bacteria aid phytoremediation so that future field studies might be facilitated.

Genetic tools for tagging Gram-negative bacteria with mCherry for visualization in vitro and in natural habitats, biofilm and pathogenicity studies

Live-cell imaging techniques are essential to gain a better understanding of microbial functioning in natural systems, for example in biofilms. Autofluorescent proteins, such as the green fluorescent protein (GFP) and the red fluorescent protein (DsRed), are valuable tools for studying microbial communities in their natural environment. Because of the functional limitations of DsRed such as slow maturation and low photostability, new and improved variants were created such as mCherry. In this study, we developed genetic tools for labeling Gram-negative bacteria in order to visualize them in vitro and in their natural environment without the necessity of antibiotic pressure for maintenance. mcherry was cloned into two broad host-range cloning vectors and a pBK-miniTn7 transposon under the constitutive expression of the tac promoter. The applicability of the different constructs was shown in Escherichia coli, various Pseudomonas spp. and Edwardsiella tarda. The expression of mcherry was qualitatively analyzed by fluorescence microscopy and quantified by fluorometry. The suitability of the constructs for visualizing microbial communities was shown for biofilms formed on glass and tomato roots. In addition, it is shown that mCherry in combination with GFP is a suitable marker for studying mixed microbial communities.

Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils

In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.

Rhizosphere remediation of chlorpyrifos in mycorrhizospheric soil using ryegrass

The potential of ryegrass for rhizosphere bioremediation of chlorpyrifos in mycorrhizal soil was investigated by the green house pot culture experiments. The pot cultured soil amended at initial chlorpyrifos concentration of 10mg/kg was observed to be degraded completely within 7 days where the rest amended concentrations (25-100mg/kg) decreased rapidly under the influence of ryegrass mycorrhizosphere as the incubation progressed till 28 days. This bioremediation of chlorpyrifos in soil is attributed to the microorganisms associated with the roots in the ryegrass rhizosphere, therefore the microorganisms surviving in the rhizospheric soil spiked at highest concentration (100mg/kg) was assessed and used for isolation of chlorpyrifos degrading microorganisms. The potential degrader identified by 16s rDNA analysis using BLAST technique was Pseudomonas nitroreducens PS-2. Further, bioaugmentation for the enhanced chlorpyrifos biodegradation was performed using PS-2 as an inoculum in the experimental set up similar to the earlier. The heterotrophic bacteria and fungi were also enumerated from the inoculated and non-inoculated rhizospheric soils. In bioaugmentation experiments, the percentage dissipation of chlorpyrifos was 100% in the inoculated rhizospheric soil as compared to 76.24, 90.36 and 90.80% in the non-inoculated soil for initial concentrations of 25, 50 and 100mg/kg at the 14th, 21st and 28th day intervals respectively.