Rhizoremediation of diesel-contaminated soil using the plant growth-promoting rhizobacterium Gordonia sp. S2RP-17

Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance

As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.

Inoculation effect of Pseudomonas sp. TF716 on N2O emissions during rhizoremediation of diesel-contaminated soil

The demand for rhizoremediation technology that can minimize greenhouse gas emissions while effectively removing pollutants in order to mitigate climate change has increased. The inoculation effect of N₂O-reducing Pseudomonas sp. TF716 on N₂O emissions and on remediation performance during the rhizoremediation of diesel-contaminated soil planted with tall fescue (Festuca arundinacea) or maize (Zea mays) was investigated. Pseudomonas sp. TF716 was isolated from the rhizosphere soil of tall fescue. The maximum N₂O reduction rate of TF716 was 18.9 mmol N₂O g dry cells⁻¹ h⁻¹, which is superior to the rates for previously reported Pseudomonas spp. When Pseudomonas sp. TF716 was added to diesel-contaminated soil planted with tall fescue, the soil N₂O-reduction potential was 2.88 times higher than that of soil with no inoculation during the initial period (0–19 d), and 1.08–1.13 times higher thereafter. However, there was no enhancement in the N₂O-reduction potential for the soil planted with maize following inoculation with strain TF716. In addition, TF716 inoculation did not significantly affect diesel degradation during rhizoremediation, suggesting that the activity of those microorganisms involved in diesel degradation was unaffected by TF716 treatment. Analysis of the dynamics of the bacterial genera associated with N₂O reduction showed that Pseudomonas had the highest relative abundance during the rhizoremediation of diesel-contaminated soil planted with tall fescue and treated with strain TF716. Overall, these results suggest that N₂O emissions during the rhizoremediation of diesel-contaminated soil using tall fescue can be reduced with the addition of Pseudomonas sp. TF716.

Simultaneous biodegradation of λ-cyhalothrin pesticide and Vicia faba growth promotion under greenhouse conditions

λ-cyhalothrin is a widely used synthetic pyrethroid insecticide and its persistence in plant, soil and water exerts a detrimental effect on humans as well as the environment. There are many studies regarding isolated bacteria capable of degrading λ-cyhalothrin in vitro. However, limited work has been done examining the microbial degradation of λ-cyhalothrin together with plant growth promotion under greenhouse conditions. In this study, 43 bacterial strains were isolated from heavily polluted soil with λ-cyhalothrin by the enrichment technique. The plant growth promotion characteristics of all isolates were evaluated. The results revealed that five isolates were potential in λ-cyhalothrin biodegradation at high concentration (1200 mg/L) within only 24 h together with their high plant growth promotion abilities. The morphological, biochemical and 16S rDNA sequence analyses identified the isolates as Bacillus subtilis strains. The GC/MS analysis revealed that the selected isolates reached high levels of degradation after only two days, the degradation percentage ranged from 95.72 to 99.52% after 48 h of incubation. Furthermore, the degradation pathway for complete detoxification and metabolism of λ-cyhalothrin was established. Moreover, greenhouse experiment was conducted, the results indicate that the application of seed coat significantly enhanced Vicia faba seedling growth and caused an increase from 38.4 to 40.2% percentage of fresh and dry weight, respectively compared to untreated control. All isolates were effective to remove the pesticide residues in Vicia faba seedlings and recorded the highest degradation percentage of 83.79 under greenhouse conditions. Therefore, it can be concluded that the Bacillus subtilis strains isolated in this study have a dual potential role in complete mineralization of λ-cyhalothrin residues in vivo as well as effective biofertilization for future use in sustainable agriculture.

Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits

The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca₃(PO₄)₂, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg⁻¹ h⁻¹). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.

Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans

Environmental pollution especially heavy metal-contaminated soils adversely affects the microbial communities associated with the rhizosphere and phyllosphere of plants growing in these areas. In the current study, we identified and characterized the rhizospheric and phyllospheric bacterial strains from Avena fatua and Brachiaria reptans with the potential for antimicrobial activity and heavy metal resistance. A total of 18 bacterial strains from the rhizosphere and phyllosphere of A. fatua and 19 bacterial strains from the rhizosphere and phyllosphere of B. reptans were identified based on 16S rRNA sequence analysis. Bacterial genera, including Bacillus, Staphylococcus, Pseudomonas, and Enterobacter were dominant in the rhizosphere and phyllosphere of A. fatua and Bacillus, Marinobacter, Pseudomonas, Enterobacter, and Kocuria, were the dominating bacterial genera from the rhizosphere and phyllosphere of B. reptans. Most of the bacterial strains were resistant to heavy metals (Cd, Pb, and Cr) and showed antimicrobial activity against different pathogenic bacterial strains. The whole-genome sequence analysis of Pseudomonas putida BR-PH17, a strain isolated from the phyllosphere of B. reptans, was performed by using the Illumina sequencing approach. The BR-PH17 genome contained a chromosome with a size of 5774330 bp and a plasmid DNA with 80360 bp. In this genome, about 5368 predicted protein-coding sequences with 5539 total genes, 22 rRNAs, and 75 tRNA genes were identified. Functional analysis of chromosomal and plasmid DNA revealed a variety of enzymes and proteins involved in antibiotic resistance and biodegradation of complex organic pollutants. These results indicated that bacterial strains identified in this study could be utilized for bioremediation of heavy metal-contaminated soils and as a novel source of antimicrobial drugs.

Bioremediation of petroleum contaminated soil through biosurfactant and Pseudomonas sp. SA3 amended design treatments

•

Potent PGP strain Pseudomonas sp SA3 was isolated from oil contaminated zone.

•

PGPR strain SA3 produce biosurfactant under petroleum stress.

•

Biosurfactant and strain SA3 amended treatments were developed.

•

Amended treatments effects the plant growth and pigments.

•

Treatment are efficient in reclamation of petroleum contaminated soil.

Toxicity of agricultural soil due to petroleum contamination has become a serious issue in recent times. Petrol oil exhibits toxic effects in agricultural crops due to the presence of various hazardous hydrocarbons. The degradation of petroleum hydrocarbon has been widely studied by the researchers that signify the requirement of effective treatments for the detoxification of petroleum contaminated soil and their reuse for growing crops. Hence, with this intention in the present study secondary metabolites “biosurfactant” (natural surfactant) along with the potent plant growth promoting (PGP) bacterial strain Pseudomonas sp. SA3 was used in the designed treatments for growing agricultural crop. The biosurfactant produced by the strain has the emulsification capacity of 43% and surface tension reduction ability to 34.5 mN/m whereas the plant growth promoting traits demonstrates 93.46 µg/mL phosphate solubilisation ability, siderophores (iron chelating compound) production upto 69.41% units and 81.41 µg/mL indole acetic acid  (IAA) production ability. Further, the results of the design treatments signifies that treatments amended with the strain SA3 and biosurfactant is effective in the management of petroleum contaminated soil indicating treatment EX 5 (1 kg soil + 1 L water + Pseudomonas sp. SA3 + 300 mL crude biosurfactant), as an efficient treatment in increment of phytochemical constituents and 10–15% enhancement in growth parameters as compared to negative control. Hence, the developed treatments can be efficaciously used for the management of petroleum contaminated soil for agronomy.

Bacterial bioaugmentation enhances hydrocarbon degradation, plant colonization and gene expression in diesel-contaminated soil

Environmental contamination by hydrocarbons is a major problem, and hydrocarbon accumulation in soil poses hazardous threat to ecosystems. Phytoremediation, which involves plants, is an encouraging technique for the removal of hydrocarbons from polluted soil and water. The purpose of this investigation was to examine whether bacterial inoculation enhanced the phytoremediation of hydrocarbons in diesel-contaminated soil vegetated with maize (Zea mays L.). The two cultivars of maize, MMRI Yellow and Pearl White, were planted in diesel-polluted soil (0, 1.5, 2.5, and 3.5 g diesel kg^-1 soil), and inoculated with the consortium of three alkane-degrading bacterial strains, Arthrobacter oxydans ITRH49, Pseudomonas sp. ITRI73 and Pseudomonas sp. MixRI75. Bacterial inoculation enhanced plant growth and hydrocarbon degradation. Between two cultivars, MMRI Yellow showed better growth and hydrocarbon degradation in the presence and absence of bacterial inoculation. Maximum hydrocarbon degradation (80%) was observed in the soil having minimum concentration of diesel (1.5 g kg^-1 soil), and vegetated with bacterial inoculated MMRI Yellow maize cultivar. Furthermore, more bacterial colonization, and abundance and expression of the alkane hydroxylase gene (alkB) were observed in the root interior than in the rhizosphere and shoot interior of the plants. The bacteria-mediated phytoremediation of soil contaminated with hydrocarbons suggested that the collective use of plants and bacteria was the most beneficial approach for the reclamation of diesel-contaminated soil in comparison with vegetation alone.

Phytotoxicity of petroleum hydrocarbons: Sources, impacts and remediation strategies

Extraction and exploration of petroleum hydrocarbons (PHs) to satisfy the rising world population's fossil fuel demand is playing havoc with human beings and other life forms by contaminating the ecosystem, particularly the soil. In the current review, we highlighted the sources of PHs contamination, factors affecting the PHs accumulation in soil, mechanisms of uptake, translocation and potential toxic effects of PHs on plants. In plants, PHs reduce the seed germination andnutrients translocation, and induce oxidative stress, disturb the plant metabolic activity and inhibit the plant physiology and morphology that ultimately reduce plant yield. Moreover, the defense strategy in plants to mitigate the PHs toxicity and other potential remediation techniques, including the use of organic manure, compost, plant hormones, and biochar, and application of microbe-assisted remediation, and phytoremediation are also discussed in the current review. These remediation strategies not only help to remediate PHs pollutionin the soil rhizosphere but also enhance the morphological and physiological attributes of plant and results to improve crop yield under PHs contaminated soils. This review aims to provide significant information on ecological importance of PHs stress in various interdisciplinary investigations and critical remediation techniques to mitigate the contamination of PHs in agricultural soils.

Rhizoremediation as a green technology for the remediation of petroleum hydrocarbon-contaminated soils

Rhizoremediation is increasingly becoming a green and sustainable alternative to physico-chemical methods for remediation of contaminated environments through the utilization of symbiotic relationship between plants and their associated soil microorganisms in the root zone. The overall efficiency can be enhanced by identifying suitable plant-microbe combinations for specific contaminants and supporting the process with the application of appropriate soil amendments. This approach not only involves promoting the existing activity of plants and soil microbes, but also introduces an adequate number of microorganisms with specific catabolic activity. Here, we reviewed recent literature on the main mechanisms and key factors in the rhizoremediation process with a particular focus on soils contaminated with total petroleum hydrocarbon (TPH). We then discuss the potential of different soil amendments to accelerate the remediation efficiency based on biostimulation and bioaugmentation processes. Notwithstanding some successes in well-controlled environments, rhizoremediation of TPH under field conditions is still not widespread and considered less attractive than physico-chemical methods. We catalogued the major pitfalls of this remediation approach at the field scale in TPH-contaminated sites and, provide some applicable situations for the future successful use of in situ rhizoremediation of TPH-contaminated soils.

Uptake and detoxification of diesel oil by a tropical soil Actinomycete Gordonia amicalis HS-11: Cellular responses and degradation perspectives

A tropical soil Actinomycete, Gordonia amicalis HS-11, has been previously demonstrated to degrade unsaturated and saturated hydrocarbons (squalene and n-hexadecane, respectively) in an effective manner. In present study, G. amicalis HS-11 degraded 92.85 ± 3.42% of the provided diesel oil [1% (v/v)] after 16 days of aerobic incubation. The effect of different culture conditions such as carbon source, nitrogen source, pH, temperature, and aeration on degradation was studied. During degradation, this Actinomycete synthesized surface active compounds (SACs) in an extracellular manner that brought about a reduction in surface tension from 69 ± 2.1 to 30 ± 1.1 mN m^-1 after 16 days. The morphology of cells grown on diesel was monitored by using a Field Emission Scanning Electron Microscope. Diesel-grown cells were longer and clumped with smooth surfaces, possibly due to the secretion of SACs. The interaction between the cells and diesel oil was studied by Confocal Laser Scanning Microscope. Some cells were adherent on small diesel droplets and others were present in the non-attached form thus confirming the emulsification ability of this organism. The fatty acid profiles of the organism grown on diesel oil for 48 h were different from those on Luria Bertani Broth. The genotoxicity and cytotoxicity of diesel oil before and after degradation were determined. Cytogenetic parameters such as mitotic index (MI); mitosis distribution and chromosomal aberration (type and frequency) were assessed. Oxidative stress was evaluated by measuring levels of catalase, superoxide dismutase and concentration of malondialdehyde. On the basis of these studies it was deduced that the degradation metabolites were relatively non-toxic.

Biodegradation of di-(2-ethylhexyl) phthalate by a newly isolated Gordonia sp. and its application in the remediation of contaminated soils

A bacterial strain (Gordonia sp. Lff) capable of efficiently degrading di-(2-ethylhexyl) phthalate (DEHP) was isolated from river sludge. The optimal pH and temperature for the degradation of DEHP by Lff were 7.0 and 35 °C, respectively. Lff could degrade high concentrations of DEHP (100-2000 mg/L) with a degradation efficiency of over 91.43%. The DEHP degradation curves fit well with first-order kinetics, with a half-life ranging from 0.598 to 0.746 d. Substrate inhibition analyses showed that the maximum specific degradation rate, half-saturation constant and inhibition constant were 0.8 d^-1, 45.8 mg/L and 462.18 mg/L, respectively. A detailed biodegradation pathway of DEHP was proposed based on GC-MS analysis. Furthermore, Lff could also efficiently degrade DEHP in soils. DEHP or DEHP plus Lff changed the bacterial community in soils, and Lff accelerated the shaping of the bacterial community. To the best of our knowledge, this study is the first to perform a detailed investigation into the biodegradation of DEHP in soil by Gordonia sp. and its effect on the soil bacterial community. These results suggest that Lff is an ideal candidate for the bioremediation of DEHP-contaminated environments.

Phytohormone Mediation of Interactions Between Plants and Non-Symbiotic Growth Promoting Bacteria Under Edaphic Stresses

The capacity of rhizoshere bacteria to influence plant hormonal status, by bacterial production or metabolism of hormones, is considered an important mechanism by which they promote plant growth, and productivity. Nevertheless, inoculating these bacteria into the plant rhizosphere may produce beneficial or detrimental results depending on bacterial effects on hormone composition and quantity in planta, and the environmental conditions under which the plants are growing. This review considers some effects of bacterial hormone production or metabolism on root growth and development and shoot physiological processes. We analyze how these changes in root and shoot growth and function help plants adapt to their growth conditions, especially as these change from optimal to stressful. Consistent effects are addressed, along with plant responses to specific environmental stresses: drought, salinity, and soil contamination (with petroleum in particular).

Petroleum degradation by endophytic Streptomyces spp. isolated from plants grown in contaminated soil of southern Algeria

Petroleum hydrocarbons are well known by their high toxicity and recalcitrant properties. Their increasing utilization around worldwide led to environmental contamination. Phytoremediation using plant-associated microbe is an interesting approach for petroleum degradation and actinobacteria have a great potential for that. For this purpose, our study aimed to isolate, characterize, and assess the ability of endophytic actinobacteria to degrade crude petroleum, as well as to produce plant growth promoting traits. Seventeen endophytic actinobacteria were isolated from roots of plants grown naturally in sandy contaminated soil. Among them, six isolates were selected on the basis of their tolerance to petroleum on solid minimal medium and characterized by 16S rDNA gene sequencing. All petroleum-tolerant isolates belonged to the Streptomyces genus. Determination by crude oil degradation by gas chromatorgraph-flame ionization detector revealed that five strains could use petroleum as sole carbon and energy source and the petroleum removal achieved up to 98% after 7 days of incubation. These isolates displayed an important role in the degradation of the n-alkanes (C₆-C₃₀), aromatic and polycyclic aromatic hydrocarbons. All strains showed a wide range of plant growth promoting features such as siderophores, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase, nitrogen fixation and indole-3-acetic acid production as well as biosurfactant production. This is the first study highlighting the petroleum degradation ability and plant growth promoting attributes of endophytic Streptomyces. The finding suggests that the endophytic actinobacteria isolated are promising candidates for improving phytoremediation efficiency of petroleum contaminated soil.

An insight into the ecology, diversity and adaptations of Gordonia species

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Effects of solution chemistry on antimicrobial activities of silver nanoparticles against Gordonia sp

Silver nanoparticles (NPs) are the largest and fastest growing category of nanotechnology-based medicines and consumer products. Silver can have great toxicity to some aquatic organisms and, as a biocidal agent, may also damage or alter the most abundant and vulnerable beneficial microorganisms in the environment, such as Gordonia sp. However, considering the complex chemical background of natural waters, silver NPs can have complicated interactions with background chemicals such as chloride, surfactants, and dissolved natural organic matters (NOM). The results of this study show that the average particle size and dispersivity of silver NPs and the surface characteristics play an important role in the toxicity of silver NPs. Aggregation was enhanced for silver NPs in 10mM NaNO3, but not much in 10mM NaCl due to reactions with chloride. However, the presence of 3mM sodium dodecyl sulfate (SDS) or 8mgC/L Suwannee River (SR) NOM appeared to reduce the aggregation of silver NPs. Regarding the bactericidal effect of silver NPs, solubility analysis suggests silver NPs inactivate Gordonia sp. differently from Ag(+) and/or a slow release of Ag(+) from silver NPs. When the silver NP concentration was raised from 7.3 to 29.2mg/L in DI water, the log inactivation rate of Gordonia sp. increased from 0.16±0.04 to 0.45±0.13. However, with 29.2mg/L silver NPs the log inactivation rate reached 1.40±0.26 in 3mM SDS. The presence of SRNOM mitigated the bactericidal efficacy of silver NPs due to surface coating/adsorption. On the other hand, 10mM NaCl reduced the log inactivation rate to 0.07±0.07 due to the formation of likely less toxic silver chloride species, such as AgCl, AgCl2(-), AgCl3(2-), and AgCl4(3-).

From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects

Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate

The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ.

Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan

Three microbial strains were isolated from the rhizosphere of alfalfa (Medicago sativa), grass mixture (Festuca rubra, 75 %; Lolium perenne, 20 %; Poa pratensis, 10 %), and rape (Brassica napus) on the basis of their high capacity to use crude oil as the sole carbon and energy source. These isolates used an unusually wide spectrum of hydrocarbons as substrates (more than 80), including n-alkanes with chain lengths ranging from C12 to C32, monomethyl- and monoethyl-substituted alkanes (C12-C23), n-alkylcyclo alkanes with alkyl chain lengths from 4 to 18 carbon atoms, as well as substituted monoaromatic and diaromatic hydrocarbons. These three strains were identified as Gordonia rubripertincta and Rhodococcus sp. SBUG 1968. During their transformation of this wide range of hydrocarbon substrates, a very large number of aliphatic, alicyclic, and aromatic acids was detected, 44 of them were identified by GC/MS analyses, and 4 of them are described as metabolites for the first time. Inoculation of plant seeds with these highly potent bacteria had a beneficial effect on shoot and root development of plants which were grown on oil-contaminated sand.

Effect of plant growth-promoting bacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) inoculation on oats in saline-alkali soil contaminated by petroleum to enhance phytoremediation

To investigate the effect of plant growth-promoting bacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) on phytoremediation in saline-alkali soil contaminated by petroleum, saline-alkali soil samples were artificially mixed with different amount of oil, 5 and 10 g/kg, respectively. Pot experiments with oat plants (Avena sativa) were conducted under greenhouse condition for 60 days. Plant biomass, physiological parameters in leaves, soil enzymes, and degradation rate of total petroleum hydrocarbon were measured. The result demonstrated that petroleum inhibited the growth of the plant; however, inoculation with PGPR in combination with AMF resulted in an increase in dry weight and stem height compared with noninoculated controls. Petroleum stress increased the accumulation of malondialdehyde (MDA) and free proline and the activities of the antioxidant enzyme such as superoxide dismutase, catalase, and peroxidase. Application of PGPR and AMF augmented the activities of three enzymes compared to their respective uninoculated controls, but decreased the MDA and free proline contents, indicating that PGPR and AMF could make the plants more tolerant to harmful hydrocarbon contaminants. It also improved the soil quality by increasing the activities of soil enzyme such as urease, sucrase, and dehydrogenase. In addition, the degradation rate of total petroleum hydrocarbon during treatment with PGPR and AMF in moderately contaminated soil reached a maximum of 49.73%. Therefore, we concluded the plants treated with a combination of PGPR and AMF had a high potential to contribute to remediation of saline-alkali soil contaminated with petroleum.

Photosynthetic and Ultrastructure Parameters of Maize Plants are Affected During the Phyto-Rhizoremediation Process of Degraded Metal Working Fluids

A phyto-rhizoremediation system using corn and esparto fiber as rooting support to remediate degraded metal working fluids (dMWFs) has been developed in the present study. In order to improve the process, plants were inoculated at the root level with bacteria either individually, and with a consortium of strains. All strains used were able to grow with MWFs. The results show that this system significantly lowers the Chemical Oxygen Demand below legal limits within 5 days. However, results were only improved with the bacterial consortium. Despite the effectiveness of the phyto-rhizoremediation process, plants are damaged at the photosynthetic level according to the photosynthetic parameters measured, as well as at the ultrastructure of the vascular cylinder and the Bundle Sheath Cells. Interestingly, the bacterial inoculation protects against this damage. Therefore, it seems that that the inoculation with bacteria can protect the plants against these harmful effects.

Microbe-assisted phytoremediation of hydrocarbons in estuarine environments

Estuaries are sinks for various anthropogenic contaminants, such as petroleum hydrocarbons, giving rise to significant environmental concern. The demand for organisms and processes capable of degrading pollutants in a clean, effective, and less expensive process is of great importance. Phytoremedition approaches involving plant/bacteria interactions have been explored as an alternative, and halophyte vegetation has potential for use in phytoremedition of hydrocarbon contamination. Studies with plant species potentially suitable for microbe-assisted phytoremediation are widely represented in scientific literature. However, the in-depth understanding of the biological processes associated with the re-introduction of indigenous bacteria and plants and their performance in the degradation of hydrocarbons is still the limiting step for the application of these bioremediation solutions in a field context. The intent of the present review is to summarize the sources and effects of hydrocarbon contamination in estuarine environments, the strategies currently available for bioremediation (potential and limitations), and the perspectives of the use of halophyte plants in microbe-assisted phytoremediation approaches.

Gordonia sp.: a salt tolerant bacterial inoculant for growth promotion of pearl millet under saline soil conditions

In the resent study, a diazotrophic bacterial isolate JPA2 having the ability to tolerate salinity (6 % NaCl) and plant growth-promoting features was isolated from rhizospheric soil of weed Chenopodium murale growing in saline soil of Pindara (EC 11.47 dS m⁻¹), district Jind (Haryana). The nitrogen fixing ability of the isolate was confirmed by nifH gene amplification and acetylene reduction assay (38.9 nmol ethylene h⁻¹ mg⁻¹ protein). The potential of strain JPA2 to promote growth of pearl millet was investigated by inoculation experiment which showed significant increase in plant height (51.1, 39.9 and 28.8 %) and dry weight (55.9, 36.4 and 35.5 %) over uninoculated control plants at EC 0, 6, 8 dS m⁻¹, respectively. The strain JPA2 was Gram +ve and identified as Gordonia sp. on the basis of partial 16S rRNA gene sequencing and biochemical characterization. It is concluded that salt tolerant diazotrophic Gordonia sp. can be considered as a beneficial microbe for agriculture in saline soils.

Effect of PGPR Serratia marcescens BC-3 and AMF Glomus intraradices on phytoremediation of petroleum contaminated soil

Soil contamination caused by petroleum hydrocarbons has become a worldwide environmental problem. Microorganism combined with phytoremediation appears to be more effective for removal and/or degradation of petroleum hydrocarbons from impacted soils. The current study investigated the effect of inoculated with PGPR Serratia marcescens BC-3 alone or in combination with AMF Glomus intraradices on the phytoremediation of petroleum-contaminated soil. Pot experiments were conducted to analyze the effect on plant and soil for 90 days in greenhouse. The inoculation treatments showed higher plant biomass and antioxidant enzyme activities than the non inoculation control. Inoculation treatments also improved rhizosphere microbial populations in petroleum contaminated soil. The degradation rate of total petroleum hydrocarbons with PGPR and AMP co-inoculation treatment was up to 72.24 %. The results indicated that plant combined with microorganisms for remediation of petroleum hydrocarbons would be a feasible method.

Rhizosphere effects of PAH-contaminated soil phytoremediation using a special plant named Fire Phoenix

The rhizosphere effect of a special phytoremediating species known as Fire Phoenix on the degradation of polycyclic aromatic hydrocarbons (PAHs) was investigated, including changes of the enzymatic activity and microbial communities in rhizosphere soil. The study showed that the degradation rate of Σ8PAHs by Fire Phoenix was up to 99.40% after a 150-day culture. The activity of dehydrogenase (DHO), peroxidase (POD) and catalase (CAT) increased greatly, especially after a 60-day culture, followed by a gradual reduction with an increase in the planting time. The activity of these enzymes was strongly correlated to the higher degradation performance of Fire Phoenix growing in PAH-contaminated soils, although it was also affected by the basic characteristics of the plant species itself, such as the excessive, fibrous root systems, strong disease resistance, drought resistance, heat resistance, and resistance to barren soil. The activity of polyphenoloxidase (PPO) decreased during the whole growing period in this study, and the degradation rate of Σ8PAHs in the rhizosphere soil after having planted Fire Phoenix plants had a significant (R(2)=0.947) negative correlation with the change in the activity of PPO. Using an analysis of the microbial communities, the results indicated that the structure of microorganisms in the rhizosphere soil could be changed by planting Fire Phoenix plants, namely, there was an increase in microbial diversity compared with the unplanted soil. In addition, the primary advantage of Fire Phoenix was to promote the growth of flora genus Gordonia sp. as the major bacteria that can effectively degrade PAHs.

Rhizosphere effect of Scirpus triqueter on soil microbial structure during phytoremediation of diesel-contaminated wetland

Though phytoremediation has been widely used to restore various contaminated sites, it is still unclear how soil microbial communities respond microecologically to plants and pollutants during the process. In this paper, batch microcosms imitating in situ phytoremediation of petroleum-contaminated wetland by Scirpus triqueter were set up to monitor the influence of plant rhizosphere effect on soil microbes. Palmitic acid, one of the main root exudates of S. triqueter, was added to strengthen rhizosphere effect. Abundances of certain microbial subgroups were quantified by phospholipid fatty acid profiles. Results showed that diesel removal extents were significantly higher in the rhizosphere (57.6 +/-4.2-65.5 +/- 6.9%) than those in bulk soil (27.8 +/-6.5-36.3 +/- 3.2%). In addition, abundances of saturated, monounsaturated, and polyunsaturated fatty acids were significantly higher (P < 0.05) in planted soil than those in the bulk soil. When it was less than 15,000 mg diesel kg soil-1, increasing diesel concentration led to higher abundances of fungi, Gram-positive and Gram-negative bacteria. The addition of palmitic acid amplified the rhizosphere effect on soil microbial populations and diesel removal. Principal component analysis revealed that plant rhizosphere effect was the dominant factor affecting microbial structure. These results provided new insights into plant-microbe-pollutant coactions responsible for diesel degradation, and they were valuable to facilitate phytoremediation of diesel contamination in wetland habitats.

Combined use of alkane-degrading and plant growth-promoting bacteria enhanced phytoremediation of diesel contaminated soil

Inoculation of plants with pollutant-degrading and plant growth-promoting microorganisms is a simple strategy to enhance phytoremediation activity. The objective of this study was to determine the effect of inoculation of different bacterial strains, possessing alkane-degradation and 1-amino-cyclopropane-1 -carboxylic acid (ACC) deaminase activity, on plant growth and phytoremediation activity. Carpet grass (Axonopus affinis) was planted in soil spiked with diesel (1% w/w) for 90 days and inoculated with different bacterial strains, Pseudomonas sp. ITRH25, Pantoea sp. BTRH79 and Burkholderia sp. PsJN, individually and in combination. Generally, bacterial application increased total numbers of culturable hydrocarbon-degrading bacteria in the rhizosphere ofcarpet grass, plant biomass production, hydrocarbon degradation and reduced genotoxicity. Bacterial strains possessing different beneficial traits affect plant growth and phytoremediation activity in different ways. Maximum bacterial population, plant biomass production and hydrocarbon degradation were achieved when carpet grass was inoculated with a consortium of three strains. Enhanced plant biomass production and hydrocarbon degradation were associated with increased numbers of culturable hydrocarbon-degrading bacteria in the rhizosphere of carpet grass. The present study revealed that the combined use of different bacterial strains, exhibiting different beneficial traits, is a highly effective strategy to improve plant growth and phytoremediation activity.

Spent metal working fluids produced alterations on photosynthetic parameters and cell-ultrastructure of leaves and roots of maize plants

In this work we assess the capacity of maize (Zea mays) plants to phytoremediate spent metal working fluids (MWFs) and its effects on photosynthesis and ultrastructure of mesophyll and root cells. A corn-esparto fibre system patented by us has been used to phytoremediate MWFs in hydroponic culture. Furthermore, a plant growth promoting rhizobacteria (PGPR) has been used to improve the process. The results show that this system is capable of significantly reducing the chemical oxygen demand, under local legislation limits. However, plant systems are really damaged, mainly its photosynthetic system, as shown by the photosynthetical parameters. Nevertheless, strain inoculated improves these parameters, especially Hill reaction. The ultrastructure of photosynthetic apparatus was also affected. Chloroplast number decreased and becomes degraded in the mesophyll of MWFs treated plants. In some cases even plasmolysis of chloroplast membrane was detected. Early senescence symptoms were detected in root ultrastructural study. Severe cellular damage was observed in the parenchymal root cells of plants grown with MWFs, while vascular bundles cell remained unchanged. It seems that the inoculation minimises the damage originated by the MWFs pollutants, appearing as less degenerative organelles and higher chloroplast number than in non-inoculated ones.

Inoculum pretreatment affects bacterial survival, activity and catabolic gene expression during phytoremediation of diesel contaminated soil

Plant-bacteria partnership is a promising approach for remediating soil contaminated with organic pollutants. The colonization and metabolic activity of an inoculated microorganism depend not only on environmental conditions but also on the physiological condition of the applied microorganisms. This study assessed the influence of different inoculum pretreatments on survival, gene abundance and catabolic gene expression of an applied strain (Pantoea sp. strain BTRH79) in the rhizosphere of ryegrass vegetated in diesel contaminated soil. Maximum bacterium survival, gene abundance and expression were observed in the soil inoculated with bacterial cells that had been pregrown on complex medium, and hydrocarbon degradation and genotoxicity reduction were also high in this soil. These findings propose that use of complex media for growing plant inocula may enhance bacterial survival and colonization and subsequently the efficiency of pollutant degradation.

Combined phytoremediation of metal-working fluids with maize plants inoculated with different microorganisms and toxicity assessment of the phytoremediated waste

The aim of this study was to validate the effectiveness of a phytoremediation procedure for metal-working fluids (MWFs) with maize plants growing in hydroponic culture in which the roots grow on esparto fibre and further improve bioremediation potential of the system with root beneficial bacteria, seeking a synergistic effect of the plant-microorganism combination. Chemical oxygen demand (COD), pH, total and type of hydrocarbons measured after phytoremediation indicated that the process with maize plants was successful, as demonstrated by the significant decrease in the parameters measured. This effect was mainly due to the plant although inoculated microorganisms had a relevant effect on the type of remaining hydrocarbons. The success of the phytoremediation process was further confirmed by two toxicity tests, one of them based on chlorophyll fluorescence measurements on maize plants and another one based on cyanobacteria, using a bioluminescent toxicity bioassay; both tests demonstrated that the phytoremediated waste was significantly less toxic than the initial non-phytoremediated MWFs.

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.

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.

The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential

This review about the genus Gordonia provides a current overview of recent research on a young genus that was introduced in the year 1997 ( Stackebrandt et al., 1997 ). This emerging genus has attracted increasing environmental, industrial, biotechnological and medical interest during the last few years, in particular due to the capabilities of its members to degrade, transform, and synthesize organic compounds as well as to the pathogenic effects that have been described in many case studies. The number of publications about Gordonia has increased significantly after the year 2004 (the year of the first Gordonia review published by Arenskötter et al.) describing 13 new validly published species (type strains), many newly described physiological and metabolic capabilities, new patent applications and many new case reports of bacterial infections. Members of the genus Gordonia are widely distributed in nature and it is therefore important to unravel the species richness and metabolic potential of gordoniae in future studies to demonstrate their environmental impact especially on the degradation of persistent organic compounds and their ecological participation in the carbon cycle of organic material in soil and water. This review summarizes mainly the current state of importance and potential of the members of this genus for the environmental and biotechnological industry ("the strengthsâ) and briefly its pathogenic impact to humans ("the weaknessesâ).