Bacterial responses and interactions with plants during rhizoremediation

Transfer and Degradation of PAHs in the Soil-Plant System: A Review

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, persistent organic pollutants that threaten ecosystems and human health. Consistent monitoring is essential to minimize the entry of PAHs into plants and reduce food chain contamination. PAHs infiltrate plants through multiple pathways, causing detrimental effects and triggering diverse plant responses, ultimately increasing either toxicity or tolerance. Primary plant detoxification processes include enzymatic transformation, conjugation, and accumulation of contaminants in cell walls/vacuoles. Plants also play a crucial role in stimulating microbial PAHs degradation by producing root exudates, enhancing bioavailability, supplying nutrients, and promoting soil microbial diversity and activity. Thus, synergistic plant-microbe interactions efficiently decrease PAHs uptake by plants and, thereby, their accumulation along the food chain. This review highlights PAHs uptake pathways and their overall fate as contaminants of emerging concern (CEC). Understanding plant uptake mechanisms, responses to contaminants, and interactions with rhizosphere microbiota is vital for addressing PAH pollution in soil and ensuring food safety and quality.

Lack of kinship with anaerobes is a kind of short-sightedness of agricultural and environmental microbiologists

Due to limited diffusion, active root respiration and intense microbial metabolism, rhizosphere and deeper layer of bulk soil often face hypoxic or anaerobic conditions. The majority of the data on plant growth promotion (PGP) and rhizoremediation have been obtained in aerobic conditions using aerobic or facultative anaerobic microbes neglecting anaerobes and actual soil oxygen conditions. Data obtained with a nutrient-rich medium from an aerobic condition do not exactly translate in oxygen-stressed oligotrophic environments of soil, leading to failure of hypothesis and microbial technology for PGP and pollutants remediation. Anaerobes are key players in the soil ecosystems and participate in the different biogeochemical processes of ecological and environmental significance. This Opinion article aims to divert the attention of agricultural and environmental Microbiologists towards neglected anaerobes and anaerobic processes to develop successful and sustainable PGP and pollutants removal by rhizospheric microorganisms.

Seed-Encapsulation of Desiccation-Tolerant Microorganisms for the Protection of Maize from Drought: Phenotyping Effects of a New Dry Bioformulation

Droughts and high temperatures deeply affect crop production. The use of desiccation-tolerant (or xerotolerant) microorganisms able to protect plants from droughts represents a promising alternative. These xerotolerant microorganisms have previously been used to modulate plant responses and improve their tolerance to drought. In addition, these microorganisms could be stored and used in dry formats, which would improve their viability and resilience at a much lower cost than current market alternatives. In the present study we analyze the possibility of using strains of xerotolerant Actinobacteria in encapsulated format on seeds. Under this formulation, we carried out greenhouse with farming soil with maize plants. Under greenhouse conditions, the plants showed greater resistance to drought, as well as increased growth and production yield, but not as well in field trials. This alternative could represent a useful tool to improve water efficiency in crops for drought-affected areas or affected by water scarcity.

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

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

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

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

Frenemies: Interactions between Rhizospheric Bacteria and Fungi from Metalliferous Soils

Is it possible to improve the efficiency of bioremediation technologies? The use of mixed cultures of bacteria and fungi inoculated at the rhizosphere level could promote the growth of the associated hyperaccumulating plant species and increase the absorption of metals in polluted soils, broadening new horizons on bioremediation purposes. This work investigates interactions between Ni-tolerant plant growth-promoting bacteria and fungi (BF) isolated from the rhizosphere of a hyperaccumulating plant. The aim is to select microbial consortia with synergistic activity to be used in integrated bioremediation protocols. Pseudomonas fluorescens (Pf), Streptomyces vinaceus (Sv) Penicillium ochrochloron (Po), and Trichoderma harzianum group (Th) were tested in mixes (Po-Sv, Po-Pf, Th-Pf, and Th-Sv). These strains were submitted to tests (agar overlay, agar plug, and distance growth co-growth tests), tailored for this aim, on Czapek yeast agar (CYA) and tryptic soy agar (TSA) media and incubated at 26 ± 1 °C for 10 days. BF growth, shape of colonies, area covered on plate, and inhibition capacity were evaluated. Most BF strains still exhibit their typical characters and the colonies separately persisted without inhibition (as Po-Sv) or with reciprocal confinement (as Th-Sv and Th-Pf). Even if apparently inhibited, the Po-Pf mix really merged, thus obtaining morphological traits representing a synergic co-growth, where both strains reached together the maturation phase and developed a sort of mixed biofilm. Indeed, bacterial colonies surround the mature fungal structures adhering to them without any growth inhibition. First data from in vivo experimentation with Po and Pf inocula in pot with metalliferous soils and hyperaccumulator plants showed their beneficial effect on plant growth. However, there is a lack of information regarding the effective co-growth between bacteria and fungi. Indeed, several studies, which directly apply the co-inoculum, do not consider suitable microorganisms consortia. Synergic rhizosphere BFs open new scenarios for plant growth promotion and soil bioremediation.

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.

Nicotiana tabacum-associated bioengineered Pseudomonas putida can enhance rhizoremediation of soil containing 2,4-dinitrotoluene

Rhizoremediation processes are based on plant-bacteria interactions and can be effectively used for cleaning many pollutants from the environment to overcome the constraints of individual phytoremediation. Here, 1 mM and 1.5 mM concentrations of 2,4-dinitrotoluene (2,4-DNT) degrading Pseudomonas putida (P. putida) strain KT.DNT and various growth stages of Nicotiana tabacum (N. tabacum) were initially assayed in in vitro tissue culture system and the best conditions for the association of plant-rhizobacterium were ascertained to remediation of the soil contaminated with 2,4-DNT. 5-days old N. tabacum plants inoculated with 2 × 106 cfu/mL bacterial inoculum for 3 weeks were preferred for rhizoremediation experiments as they showed a nearly threefold increase in the fresh and dry biomass in comparison to noninoculated ones. When these seedlings were planted either alone or together with P. putida KT2440 or P. putida KT.DNT in soils contaminated with 1 mM and 1.5 mM of 2,4-DNT, the maximum degradation rate of 98% and ~ 93% were determined at the end of 14 days by KT.DNT inoculated tobacco plants. Our results indicate that it would be advantageous to use the 2,4-DNT-degrading bacterium inoculated with N. tabacum plants to accelerate and enhance the cleanup of soil contaminated with 2,4-DNT.

Phytoremediation potential of heavy metal accumulator plants for waste management in the pulp and paper industry

The present manuscript has focused on the heavy metal; accumulation potential by common native plants i.e. Chenopodium album L., Ricinus communis, Ranunculus sceleratus, and Rumex dentatus growing on the disposed of pulp and paper mill effluent sludge. The sludge showed the abundance of benzene propanoic acid tert- butyldimethylsilyl ester, Octadecanoic acid, TMS, Hexadecanoic acid, TMS, cinnamic acid-α-phenyl-TMS ester, β-sitosterol TMS, 4-mercaptobenzoic acid as residual complex organic compounds along with heavy metals Fe (98.30 mg/L-1), Zn (51.00 mg/L-1), Cu (3.21 mg/L-1), Cd (9.11 mg/L-1), Mn (18.27 mg/L-1), Ni (5.21 mg/L-1), (Hg 0.014 mg/L-1) which were above the prescribed limit of environmental standard. The complexation of organic compounds with heavy metal restricts the bioavailability of metals to plants. But the metal analysis in various parts of the plant showed a significant amount of metal accumulation. Further, histological observations of root tissue through TEM showed apparent deposition of metal granules near the cell wall and vacuole as adoption features of plants. But the variable concentration of metal accumulation in different parts by various plants indicated the variable potential of tested plants with various metals. This also indicated their metal bio-availability and movement to plant tissue. Further, their bioconcentration factor (BCF) and translocation factor (TF) > 1.0 indicated the hyperaccumulation tendency of plants Mn was accumulated maximum in leaves C. album (69.38 mg/kg-1) followed by Cu (25.75 mg/kg -1), As (23.20 mg/kg -1), Fe (20.90 mg/kg -1) and Pb was maximum accumulated (22.41 mg/kg -1) in R. cummunis leaves. The result revealed that arsenic has been accumulated in higher amount root, shoot and leaves of all tested plants. The metal accumulator plants showed phytoremediation potential also by reducing various pollution parameters after growth on sludge. These potential plants may be used as biotechnological tools for the eco-restoration of polluted sites.

Response of rhizospheric and endophytic bacterial communities of white mustard (Sinapis alba) to bioaugmentation of soil with the Pseudomonas sp. H15 strain

A factor that may significantly increase the efficacy of phytoextraction is soil bioaugmentation with specific bacteria, which can alter the composition of rhizospheric and endophytic bacterial communities. The aim of this study was to compare the effect of soil treatment with living (bioaugmentation) and dead (control) cells of the plant growth-promoting metal-resistant endophytic strain Pseudomonas sp. H15 on the bacterial community composition in the rhizo- and endo-sphere of white mustard during enhanced phytoextraction. The bacterial communities in the rhizosphere were dominated (51.7-68.2%) by Proteobacteria, regardless of the soil treatment or sampling point. A temporary increase in the number of sequences belonging to Gammaproteobacteria (up to 37.3%) was only observed 24 h after the soil treatment with living Pseudomonas sp. H15 cells, whereas for the remaining samples, the relative abundance of this class did not exceed 7.1%. The relative abundance of Proteobacteria in the endosphere of the roots, stems, and leaves of white mustard was higher in the control than in bioaugmented plants. The most pronounced dominance of the Gammaproteobacteria sequences was observed in the stems and leaves of the control plants at the first sampling point, which strongly indicates the ability of the plants to rapidly uptake DNA from soil and translocate it to the aboveground parts of the plants. Additionally, the bioaugmentation of the soil caused a diverse shift in the bacterial communities in the rhizo- and endo-sphere of white mustard compared to control. The most distinct differences, which were dependent on the treatment, were observed in the endosphere of plants at the beginning of the experiment and decreased over time. These results indicate that the rhizo- and endo-biome of white mustard reacts to soil bioaugmentation and may influence the efficiency of bacterial-assisted phytoextraction.

Hydroponic approach to assess rhizodegradation by sudangrass (Sorghum x drummondii) reveals pH- and plant age-dependent variability in bacterial degradation of polycyclic aromatic hydrocarbons (PAHs)

Rhizodegradation of polycyclic aromatic hydrocarbons (PAHs) is a product of complex interactions between plant and bacteria. In this study, hydroponic culture of sudangrass was established in order to investigate the effects of the plant on PAHs degradation and vice versa through changes in rhizosphere bacterial community. Results showed a plant-induced variability in PAHs degradation dependent on a characteristic shift in bacterial community, with pH and plant age as driving factors. Moreover, bacterial communities with high diversity seemed to abate the phytotoxic effects of PAHs degradation as observed in the plant's gross health. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that regardless of plant age and culture conditions, the increase or decrease of Sphingobium sp. could dictate the PAHs degradation potential of the bacterial consortium. Overall, this study utilized hydroponic culture of sudangrass to show that plant even of same species can suppress, support, or enhance PAHs degradation of bacteria depending on specific factors.

Exploring the genetic potential of a fosmid metagenomic library from an oil-impacted mangrove sediment for metabolism of aromatic compounds

Aromatic hydrocarbons (AH) are widely distributed in nature, and many of them have been reported as relevant environmental pollutants and valuable carbon sources for different microorganisms. In this work, high-throughput sequencing of a metagenomic fosmid library was carried out to evaluate the functional and taxonomic diversity of genes involved in aromatic compounds degradation in oil-impacted mangrove sediments. In addition, activity-based approach and gas chromatography were used to assess the degradation potential of fosmid clones. Results indicated that AH degradation genes, such as monooxygenases and dioxygenases, were grouped into the following categories: anaerobic degradation of aromatic compounds (20.34%), metabolism of central aromatic intermediates (35.40%) and peripheral pathways for catabolism of aromatic compounds (22.56%). Taxonomic affiliation of genes related to aromatic compounds metabolism revealed the prevalence of the classes Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. Aromatic hydrocarbons (phenol, naphthalene, phenanthrene, pyrene and benzopyrene) were used as the only carbon source to screen clones with degradation potential. Of the 2500 clones tested, 48 showed some respiratory activity in at least one of the five carbon sources used. The hydrocarbon degradation ability of the top ten fosmid clones was confirmed by GC-MS. Further, annotation of assembled metagenomic fragments revealed ORFs corresponding to proteins and functional domains directly or indirectly involved in the aromatic compound metabolism, such as catechol 2,3-dioxygenase and ferredoxin oxidoreductase. Finally, these data suggest that the indigenous mangrove sediment microbiota developed essential mechanisms towards ecosystem remediation of petroleum hydrocarbon impact.

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

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

Rhizosphere response to nickel in a facultative hyperaccumulator

This study faces the characterization of the culturable microbiota of the facultative Ni-hyperaccumulator Alyssoides utriculata to obtain a collection of bacterial and fungal strains for potential applications in Ni phytoextraction. Rhizosphere soil samples and adjacent bare soil associated with A. utriculata from serpentine and non-serpentine sites were collected together with plant roots and shoots. Rhizobacteria and fungi were isolated and characterized genotypically and phenotypically. Plants and soils were analyzed for total element concentration using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Serpentine and non-serpentine sites differ in terms of elements concentration in soil, plant roots and shoots. Ni and Co are significantly higher on serpentine site, while Ca is more abundant in non-serpentine site. Bacteria and fungi were significantly more abundant in rhizosphere than in bare soil and were dominated by genera Arthrobacter, Bacillus and Streptomyces, Penicillium and Mucor. The genus Pseudomonas was only found in rhizospheric serpentine soils (<2% of total serpentine isolates) and with Streptomyces sp. showed highest Ni-tolerance up to 15 mM. The same occurred for Trichoderma strain, belonging to the harzianum group (<2% of the total microfungal count) and Penicillium ochrochloron (<10% of the total microfungal count, tolerance up to Ni 20 mM). Among serpentine bacterial isolates, 8 strains belonging to 5 genera showed at least one PGPR activity (1-Aminocyclopropane-1-Carboxylic Acid (ACC) deaminase activity, production of indole-3-acetic acid (IAA), siderophores and phosphate solubilizing capacity), especially genera Pantoea, Pseudomonas and Streptomyces. Those microorganisms might thus be promising candidates for employment in bioaugmentation trials.

Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils

Extended soil contamination by polychlorinated biphenyls (PCBs) represents a global environmental issue that can hardly be addressed with the conventional remediation treatments. Rhizoremediation is a sustainable alternative, exploiting plants to stimulate in situ the degradative bacterial communities naturally occurring in historically polluted areas. This approach can be enhanced by the use of bacterial strains that combine PCB degradation potential with the ability to promote plant and root development. With this aim, we established a collection of aerobic bacteria isolated from the soil of the highly PCB-polluted site “SIN Brescia-Caffaro” (Italy) biostimulated by the plant Phalaris arundinacea. The strains, selected on biphenyl and plant secondary metabolites provided as unique carbon source, were largely dominated by Actinobacteria and a significant number showed traits of interest for remediation, harbouring genes homologous to bphA, involved in the PCB oxidation pathway, and displaying 2,3-catechol dioxygenase activity and emulsification properties. Several strains also showed the potential to alleviate plant stress through 1-aminocyclopropane-1-carboxylate deaminase activity. In particular, we identified three Rhodococcus strains able to degrade in vitro several PCB congeners and to promote lateral root emergence in the model plant Arabidopsis thaliana in vivo. In addition, these strains showed the capacity to colonize the root system and to increase the plant biomass in PCB contaminated soil, making them ideal candidates to sustain microbial-assisted PCB rhizoremediation through a bioaugmentation approach.

Microbial diversity and bioremediation of rhizospheric soils from Trindade Island - Brazil

Pristine environments may harbor complex microbial communities with metabolic potential for use in bioremediation of organic pollutants. This study aimed to evaluate crude oil biodegradation by microbial communities present in rhizospheric soils of Bulbostylis nesiotis and Cyperus atlanticus on Trindade Island and the compositional structure of these communities. After 60 days under aerobic conditions, Total Petroleum Hydrocarbon biodegradation ranged from 66 to 75%, depending on the plant species and the origin of the soil samples. There was no response of petroleum biodegradation to fertilization with N:P:K (80:160:80 mg dm^-3). Soil contamination with crude oil did not necessarily reduce microbial diversity. The richness and diversity increased in contaminated soils in some specific situations. We conclude that microbial communities from pristine soils have the ability to remove hydrocarbons through biodegradation and that Bulbostylis nesiotis and Cyperus atlanticus inhabiting Trindade Island harbor rhizospheric microbial communities with potential for application in rhizoremediation.

Metal-tolerant endophytic bacteria associated with Silene vulgaris support the Cd and Zn phytoextraction in non-host plants

The aim of this study was to isolate and characterise metal-resistant endophytic bacteria from the tissues of Silene vulgaris collected within the vicinity of non-ferrous steelworks in Katowice, Upper Silesia, Southern Poland. Twenty-four strains of metal-resistant endophytic bacteria that belong to 15 genera were isolated from the stems and leaves of Silene vulgaris. Most of these strains showed multiple plant growth-promoting capabilities. The most promising strains, Proteus vulgaris H7, Pseudomonas sp. H15, and Pseudomonas helmanticensis H16, were used in a pot experiment, and their impact on the biomass of white mustard and Zn and Cd accumulation was examined. Soil inoculation with the tested strains resulted in a higher fresh biomass of shoots, which increased by 74.5% (Proteus vulgaris H7), 121.7% (Pseudomonas sp. H15), and 142.2% (P. helmanticensis H16) compared to the control plants. The highest phytoextraction enhancement was caused by P. helmanticensis H16, which increased Zn and Cd accumulation in the shoot tissues by 43.8% and 112.6%, respectively. All of the tested strains were detected in the soil at the last sampling points, but only Proteus vulgaris H7 and Pseudomonas sp. H15 were capable of temporary colonisation of the roots of white mustard. None of the inoculants were found in the stems and leaves of the plants during the experimental period. The plant growth-promoting features of the isolates combined with their resistance to heavy metals and high survival in soil after inoculation make these strains good candidates for the promotion of plant growth and increased phytoremediation efficiency.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.

Non-halophilic endophytes associated with the euhalophyte Arthrocnemum macrostachyum and their plant growth promoting activity potential

Numerous microbial taxa establish natural relations with plants, and especially endophytes can be relevant in the development and growth promotion of their host. In this work, we explore the diversity of non-halophilic microorganisms inhabiting the endosphere of the halophyte Arthrocnemum macrostachyum. A total of 1045 isolates were recovered using standard non-saline media, which clustered into 22 operational phylogenetic units (OPUs) including 7 putative new species and 13 OPUs not previously detected as endophytes. The more abundant isolates corresponded to close relatives of Kushneria indalinina/K. marisflavi, Providencia rettgeri, Pseudomonas zhaodongensis and Bacillus safensis, which made up to ∼ 62% of the total isolates. We also isolated OPUs not detected by the culture-independent approach reinforcing the need of culturing to reveal the microbial diversity associated with plants. Additionally, the plant growth promoting activity was evaluated by representative strains of the more abundant OPUs (total = 94 strains) including also some previously isolated halophiles from the same plants. Under both saline and non-saline conditions, some strains principally those affiliated to Paenibacillus borealis, Staphylococcus equorum, Salinicola halophilus and Marinococcus tarijensis, presented growth promoting activity in Arabidopsis thaliana, which was evaluated as an increment of weight and root length.

Compared the physiological response of two petroleum tolerant-contrasting plants to petroleum stress

Petroleum not only benefits the world economy but also contaminates the soil. In order to select the plants tolerant to petroleum, the physiological response of two petroleum tolerant-contrasting plants, Mirabilis jalapa and Orychophragmus violace, were investigated in variation of petroleum-contaminated soils (0, 5, 10, 20, and 40 g petroleum per kg soil) for 120 d. Petroleum degradation rate, seeds germination rate, free proline, and superoxide dismutase and peroxidase activities of M. jalapa were higher than that of O. violace under petroleum stress. However, the decrease rate of soluble protein, plant height, chlorophyll, and root fresh weight was greater in O. violace as compared to M. jalapa. Pearson correlation coefficient analysis was conducted, which indicated that the higher tolerance of M. jalapa was correlated with the higher level of free proline and antioxidative enzyme activities. Besides, the 10 g petroleum per kg soil may be appropriate for petroleum-tolerant plants selection, in which petroleum significantly restrain growth in O. violace but not in M. jalapa.

Advances and perspective in bioremediation of polychlorinated biphenyl-contaminated soils

In recent years, microbial degradation and bioremediation approaches of polychlorinated biphenyls (PCBs) have been studied extensively considering their toxicity, carcinogenicity and persistency potential in the environment. In this direction, different catabolic enzymes have been identified and reported for biodegradation of different PCB congeners along with optimization of biological processes. A genome analysis of PCB-degrading bacteria has led in an improved understanding of their metabolic potential and adaptation to stressful conditions. However, many stones in this area are left unturned. For example, the role and diversity of uncultivable microbes in PCB degradation are still not fully understood. Improved knowledge and understanding on this front will open up new avenues for improved bioremediation technologies which will bring economic, environmental and societal benefits. This article highlights on recent advances in bioremediation of PCBs in soil. It is demonstrated that bioremediation is the most effective and innovative technology which includes biostimulation, bioaugmentation, phytoremediation and rhizoremediation and acts as a model solution for pollution abatement. More recently, transgenic plants and genetically modified microorganisms have proved to be revolutionary in the bioremediation of PCBs. Additionally, other important aspects such as pretreatment using chemical/physical agents for enhanced biodegradation are also addressed. Efforts have been made to identify challenges, research gaps and necessary approaches which in future, can be harnessed for successful use of bioremediation under field conditions. Emphases have been given on the quality/efficiency of bioremediation technology and its related cost which determines its ultimate acceptability.

Environmental parameters altered by climate change affect the activity of soil microorganisms involved in bioremediation

Bioremediation, based on the use of microorganisms to break down pollutants, can be very effective at reducing soil pollution. But the climate change we are now experiencing is bound to have an impact on bioremediation performance, since the activity and degrading abilities of soil microorganisms are dependent on a series of environmental parameters that are themselves being altered by climate change, such as soil temperature, moisture, amount of root exudates, etc. Many climate-induced effects on soil microorganisms occur indirectly through changes in plant growth and physiology derived from increased atmospheric CO2 concentrations and temperatures, the alteration of precipitation patterns, etc., with a concomitant effect on rhizoremediation performance (i.e. the plant-assisted microbial degradation of pollutants in the rhizosphere). But these effects are extremely complex and mediated by processes such as acclimation and adaptation. Besides, soil microorganisms form complex networks of interactions with a myriad of organisms from many taxonomic groups that will also be affected by climate change, further complicating data interpretation.

Rhizoremediation of cadmium-contaminated soil associated with hydroxamate siderophores isolated from Cd-resistant plant growth-promoting Dietzia maris and Lysinibacillus strains

In search of multitrait plant growth-promoting (PGP) inoculants, we introduced two cadmium-resistant bacterial strains, C4 (PG), C5 (WB), and their consortium C6 (PG × WB) isolated from metal-contaminated industrial waste-fed canal near West Bengal. The test isolates were biochemically characterized and screened in vitro for siderophore production. The infrared spectra revealed the hydroxamate nature of the siderophore produced. Further in green house, siderophore-based seed inoculation with selected PGP isolates exhibited stimulatory effects on seed germination (up to 85.4%), chlorophyll index (22.9 spad unit), shoot and root length (70% and 62.7%), tiller numbers (38.82%), spikelet numbers (52.2%), straw yield (62.2%), grain yield (76.1%), total dry matter of root and shoot (55.56% and 64.4%, respectively), and grain yields (76.1%) of tested wheat cultivars. The 16S rRNA sequencing identified strain PG and WB as Dietzia maris and Lysinibacillus sp. strains. Furthermore, inoculation of C6 (consortium) in both cultivar UP-2565 and KS-227 showed maximum Cd sorption capacity in roots (38.3% and 67.1%) and shoots (68.4% and 67.5%), respectively. Both the strains and their consortium showed a great potential to increase the growth and yield of wheat cultivars, which can also be utilized for rhizoremediation process.

Biochemical and Molecular Mechanisms of Plant-Microbe-Metal Interactions: Relevance for Phytoremediation

Plants and microbes coexist or compete for survival and their cohesive interactions play a vital role in adapting to metalliferous environments, and can thus be explored to improve microbe-assisted phytoremediation. Plant root exudates are useful nutrient and energy sources for soil microorganisms, with whom they establish intricate communication systems. Some beneficial bacteria and fungi, acting as plant growth promoting microorganisms (PGPMs), may alleviate metal phytotoxicity and stimulate plant growth indirectly via the induction of defense mechanisms against phytopathogens, and/or directly through the solubilization of mineral nutrients (nitrogen, phosphate, potassium, iron, etc.), production of plant growth promoting substances (e.g., phytohormones), and secretion of specific enzymes (e.g., 1-aminocyclopropane-1-carboxylate deaminase). PGPM can also change metal bioavailability in soil through various mechanisms such as acidification, precipitation, chelation, complexation, and redox reactions. This review presents the recent advances and applications made hitherto in understanding the biochemical and molecular mechanisms of plant-microbe interactions and their role in the major processes involved in phytoremediation, such as heavy metal detoxification, mobilization, immobilization, transformation, transport, and distribution.

Rhizoremediation of petroleum hydrocarbon, prospects and future

Oil refineries generate several tones of oily waste which is dumped in an open pit within the vicinity of oil field.

Evaluation of removal efficiency of human antibiotics in wastewater treatment plants in Bangkok, Thailand

This study aimed to investigate the antibiotic concentration at each stage of treatment and to evaluate the removal efficiency of antibiotics in different types of secondary and advanced treatment, as well as the effects of the location of their discharge points on the occurrence of antibiotics in surface water. Eight target antibiotics and four hospital wastewater treatment plants in Bangkok with different conventional and advanced treatment options were investigated. Antibiotics were extracted by solid phase extraction and analysed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The antibiotic with the highest concentration at influent was cefazolin at 13,166 ng/L, while the antibiotic with the highest concentration at effluent was sulfamethoxazole at 1,499 ng/L. The removal efficiency of antibiotics from lowest to highest was sulfamethoxazole, piperacillin, clarithromycin, metronidazole, dicloxacillin, ciprofloxacin, cefazolin, and cefalexin. The adopted conventional treatment systems could not completely remove all antibiotics from wastewater. However, using advanced treatments or disinfection units such as chlorination and UV could increase the antibiotic removal efficiency. Chlorination was more effective than UV, ciprofloxacin and sulfamethoxazole concentration fluctuated during the treatment process, and sulfamethoxazole was the most difficult to remove. Both these antibiotics should be studied further regarding their contamination in sludge and suitable treatment options for their removal.

Diversity of alkane hydroxylase genes on the rhizoplane of grasses planted in petroleum-contaminated soils

The study investigated the diversity and genotypic features of alkane hydroxylase genes on rhizoplanes of grasses planted in artificial petroleum-contaminated soils to acquire new insights into the bacterial communities responsible for petroleum degradation in phytoremediation. Four types of grass (Cynodon dactylon, two phenotypes of Zoysia japonica, and Z. matrella) were used. The concentrations of total petroleum hydrocarbon effectively decreased in the grass-planted systems compared with the unplanted system. Among the representative alkane hydroxylase genes alkB, CYP153, almA and ladA, the first two were detected in this study, and the genotypes of both genes were apparently different among the systems studied. Their diversity was also higher on the rhizoplanes of the grasses than in unplanted oil-contaminated soils. Actinobacteria-related genes in particular were among the most diverse alkane hydroxylase genes on the rhizoplane in this study, indicating that they are one of the main contributors to degrading alkanes in oil-contaminated soils during phytoremediation. Actinobacteria-related alkB genes and CYP153 genes close to the genera Parvibaculum and Aeromicrobium were found in significant numbers on the rhizoplanes of grasses. These results suggest that the increase in diversity and genotype differences of the alkB and CYP153 genes are important factors affecting petroleum hydrocarbon-degrading ability during phytoremediation.

A rhizosphere-associated symbiont, Photobacterium spp. strain MELD1, and its targeted synergistic activity for phytoprotection against mercury

Though heavy metal such as mercury is toxic to plants and microorganisms, the synergistic activity between them may offer benefit for surviving. In this study, a mercury-reducing bacterium, Photobacterium spp. strain MELD1, with an MIC of 33 mg x kg(-1) mercury was isolated from a severely mercury and dioxin contaminated rhizosphere soil of reed (Phragmites australis). While the whole genome sequencing of MELD1 confirmed the presence of a mer operon, the mercury reductase MerA gene showed 99% sequence identity to Vibrio shilloni AK1 and implicates its route resulted from the event of horizontal gene transfer. The efficiency of MELD1 to vaporize mercury (25 mg x kg(-1), 24 h) and its tolerance to toxic metals and xenobiotics such as lead, cadmium, pentachlorophenol, pentachloroethylene, 3-chlorobenzoic acid, 2,3,7,8-tetrachlorodibenzo-p-dioxin and 1,2,3,7,8,9-hexachlorodibenzo-p-dioxin is promising. Combination of a long yard bean (Vigna unguiculata ssp. Sesquipedalis) and strain MELD1 proved beneficial in the phytoprotection of mercury in vivo. The effect of mercury (Hg) on growth, distribution and tolerance was examined in root, shoot, leaves and pod of yard long bean with and without the inoculation of strain MELD1. The model plant inoculated with MELD1 had significant increases in biomass, root length, seed number, and increased mercury uptake limited to roots. Biolog plate assay were used to assess the sole-carbon source utilization pattern of the isolate and Indole-3-acetic acid (IAA) productivity was analyzed to examine if the strain could contribute to plant growth. The results of this study suggest that, as a rhizosphere-associated symbiont, the synergistic activity between the plant and MELD1 can improve the efficiency for phytoprotection, phytostabilization and phytoremediation of mercury.

Field trial on removal of petroleum-hydrocarbon pollutants using a microbial consortium for bioremediation and rhizoremediation

Petroleum waste sludges are toxic and dangerous that is why environmental protection agencies have declared their treatment top priority. Physicochemical treatments are expensive and environmentally unfriendly, while alternative biological treatments are less costly but, in general, work at a slower pace. An in situ bioremediation and rhizoremediation field scale trial was performed in an area contaminated with oil refinery sludge under semiarid climate. The bioremediation and rhizoremediation treatments included the use of an artificial consortium made up of plant growth-promoting rhizobacteria and polycyclic aromatic hydrocarbon-degrading bacteria,and the combined use of the mentioned consortium along with pasture plants respectively. Rhizoremediation revealed that the development of vegetation favoured the evolution of indigenous microbiota with potential to remove petroleum wastes. This was inferred as the decline of total petroleum hydrocarbons 7 months after the biological treatment.

Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial

Forest fires pose a serious threat to countries in the Mediterranean basin, often razing large areas of land each year. After fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons produced during the combustion of cellulose and lignins. In this study, we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected Mediterranean ecosystem after a controlled fire. Our bioremediation strategy combined the use of Pseudomonas putida strains, indigenous culturable microbes and annual grasses. After 8 months of monitoring soil quality parameters, including the removal of monoaromatic and polycyclic aromatic hydrocarbons as well as vegetation cover, we found that the site had returned to pre-fire status. Microbial population analysis revealed that fires induced changes in the indigenous microbiota and that rhizoremediation favours the recovery of soil microbiota in time. The results obtained in this study indicate that the rhizoremediation strategy could be presented as a viable and cost-effective alternative for the treatment of ecosystems affected by fires.

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.

Rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils

Environmental pollutants have received considerable attention due to their serious effects on human health. There are physical, chemical, and biological means to remediate pollution; among them, bioremediation has become increasingly popular. The nitrogen-fixing rhizobia are widely distributed in the soil and root ecosystems and can increase legume growth and production by supplying nitrogen, resulting in the reduced need for fertilizer applications. Rhizobia also possess the biochemical and ecological capacity to degrade organic pollutants and are resistant to heavy metals, making them useful for rehabilitating contaminated soils. Moreover, rhizobia stimulate the survival and action of other biodegrading bacteria, thereby lowering the concentration of pollutants. The synergistic action of multiple rhizobial strains enhances both plant growth and the availability of pollutants ranging from heavy metals to persistent organic pollutants. Because phytoremediation has some restrictions, the beneficial interaction between plants and rhizobia provides a promising option for remediation. This review describes recent advances in the exploitation of rhizobia for the rehabilitation of contaminated soil and the biochemical and molecular mechanisms involved, thereby promoting further development of this novel bioremediation strategy into a widely accepted technique.

Enhanced phytoremediation of toxic metals by inoculating endophytic Enterobacter sp. CBSB1 expressing bifunctional glutathione synthase

To engineer plant-bacteria symbionts for remediating complex sites contaminated with multiple metals, the bifunctional glutathione (GSH) synthase gene gcsgs was introduced into endophytic Enterobacter sp. CBSB1 to improve phytoremediation efficiency of host plant Brassica juncea. The GSH contents of shoots inoculated with CBSB1 is 0.4μMg(-1) fresh weight. However, the GSH concentration of shoots with engineered CBSB1-GCSGS increased to 0.7μMg(-1) fresh weight. The shoot length, fresh weight and dry weight of seedlings inoculated with CBSB1-GCSGS increased 67%, 123%, and 160%, compared with seedlings without inoculation, respectively. The Cd and Pb concentration in shoots with CBSB1-GCSGS increased 48% and 59% compared with seedlings without inoculation, respectively. The inoculation of CBSB1 and CBSB1-GCSGS could increase the Cd and Pb extraction amounts of seedlings significantly compared with those without inoculation (P<0.05), the seedlings inoculated with CBSB1-GCSGS showed the highest Cd and Pb extraction amounts. It was concluded that the gcsgs gene introduced into Enterobacter sp. CBSB1 upgraded the phytoremediation efficacy of B. juncea. So the engineered Enterobacter sp. CBSB1-GCSGS showed potentials in remediation sites contaminated with complex contaminants by inoculating into remediating plants.

Rhizoremediation of diesel-contaminated soil with two rapeseed varieties and petroleum degraders reveals different responses of the plant defense mechanisms

Plant-assisted bioremediation (rhizoremediation) stands out as a potential tool to inactivate or completely remove xenobiotics from the polluted environment. Therefore, it is of key importance to find an adequate combination of plant species and microorganisms that together enhance the clean-up process. To understand the response of plants upon bioaugmentation, the antioxidative and detoxification system was analyzed in high and low erucic acid rapeseed varieties (HEAR and LEAR, respectively), after 8 weeks of their treatment with petroleum degraders and 6000 mg diesel oil/kg dry soil. The oxidative stress was enhanced in LEAR being exposed to sole diesel oil, in comparison with HEAR. However, when LEAR plants were additionally inoculated with bacteria, suppression of total catalase (CAT) and ascorbate peroxidase (APX) activity were observed. Interestingly, glutathione transferase (GST) activity was found in these plants at a much higher level than in HEAR, which correlated with a more efficient diesel removal performed by LEAR in the polluted soil and upon bioaugmentation. A distinct profile of polycyclic aromatic hydrocarbons (PAH) was detected in leaves of these plants. Neither LEAR nor HEAR experienced any changes in the photosynthetic capacity upon diesel pollution and presence of petroleum degraders, which supports the usefulness of rhizoremediation with rapeseed.

Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome

Pseudomonas putida DOT-T1E is an organic solvent tolerant strain capable of degrading aromatic hydrocarbons. Here we report the DOT-T1E genomic sequence (6 394 153 bp) and its metabolic atlas based on the classification of enzyme activities. The genome encodes for at least 1751 enzymatic reactions that account for the known pattern of C, N, P and S utilization by this strain. Based on the potential of this strain to thrive in the presence of organic solvents and the subclasses of enzymes encoded in the genome, its metabolic map can be drawn and a number of potential biotransformation reactions can be deduced. This information may prove useful for adapting desired reactions to create value-added products. This bioengineering potential may be realized via direct transformation of substrates, or may require genetic engineering to block an existing pathway, or to re-organize operons and genes, as well as possibly requiring the recruitment of enzymes from other sources to achieve the desired transformation.

Funding Information Work in our laboratory was supported by Fondo Social Europeo and Fondos FEDER from the European Union, through several projects (BIO2010-17227, Consolider-Ingenio CSD2007-00005, Excelencia 2007 CVI-3010, Excelencia 2011 CVI-7391 and EXPLORA BIO2011-12776-E).

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.

Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the Southern Gulf of Mexico

Chemosynthetic life was recently discovered at Chapopote, an asphalt hydrocarbon seep in the southern Gulf of Mexico. Preliminary morphological analyses indicated that one tubeworm and two mussel species colonize Chapopote. Our molecular analyses identified the tubeworm as Escarpia sp., and the mussels as Bathymodiolus heckerae and B. brooksi. Comparative 16S rRNA analysis and FISH showed that all three species harbour intracellular sulfur-oxidizing symbionts highly similar or identical to those found in the same host species from northern Gulf of Mexico (nGoM). The mussels also harbour methane-oxidizing symbionts, and these shared highly similar to identical 16S rRNA sequences to their nGoM conspecifics. We discovered a novel symbiont in B. heckerae, which is closely related to hydrocarbon-degrading bacteria of the genus Cycloclasticus. In B. heckerae, we found key genes for the use of aromatic compounds, and its stable carbon isotope values were consistently higher than B. brooksi, indicating that the novel symbiont might use isotopically heavy aromatic hydrocarbons from the asphalt seep. This discovery is particularly intriguing because until now only methane and reduced sulfur compounds have been shown to power cold-seep chemosynthetic symbioses. The abundant hydrocarbons available at Chapopote would provide these mussel symbioses with a rich source of nutrition.

Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1

Pseudomonas putida BIRD-1 is a plant growth-promoting rhizobacterium whose genome size is 5.7 Mbp. It adheres to plant roots and colonizes the rhizosphere to high cell densities even in soils with low moisture. This property is linked to its ability to synthesize trehalose, since a mutant deficient in the synthesis of trehalose exhibited less tolerance to desiccation than the parental strain. The genome of BIRD-1 encodes a wide range of proteins that help it to deal with reactive oxygen stress generated in the plant rhizosphere. BIRD-1 plant growth-promoting rhizobacteria properties derive from its ability to enhance phosphorous and iron solubilization and to produce phytohormones. BIRD-1 is capable of solubilizing insoluble inorganic phosphate forms through acid production. The genome of BIRD-1 encodes at least five phosphatases related to phosphorous solubilization, one of them being a phytase that facilitates the utilization of phytic acid, the main storage form of phosphorous in plants. Pyoverdine is the siderophore produced by this strain, a mutant that in the FvpD siderophore synthase failed to grow on medium without supplementary iron, but the mutant was as competitive as the parental strain in soils because it captures the siderophores produced by other microbes. BIRD-1 overproduces indole-3-acetic acid through convergent pathways.

Enhanced remediation of chlorpyrifos from soil using ryegrass (Lollium multiflorum) and chlorpyrifos-degrading bacterium Bacillus pumilus C2A1

The combined use of plants and associated microorganisms has great potential for remediating soil contaminated with organic compounds such as pesticides. The objective of this study was to determine whether the bacterial inoculation influences plant growth promotion and chlorpyrifos (CP) degradation and accumulation in different parts of the plant. Ryegrass was grown in soil spiked with CP and inoculated with a pesticide degrading bacterial strain Bacillus pumilus C2A1. Inoculation generally had a beneficial effect on CP degradation and plant biomass production, highest CP degradation (97%) was observed after 45 days of inoculation. Furthermore, inoculated strain efficiently colonized in the rhizosphere of inoculated plant and enhanced CP and its primary metabolite 3,5,6-trichloro-2-pyridinol (TCP) degradation. There was significantly less CP accumulation in roots and shoots of inoculated plants as compared to uninoculated plants. The results show the effectiveness of inoculated exogenous bacteria to boost the remediation of CP contaminated sites and decrease levels of toxic pesticide residues in crop plants.

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.

Cyanobacteria-mediated phenylpropanoids and phytohormones in rice (Oryza sativa) enhance plant growth and stress tolerance

Phenylpropanoids, flavonoids and plant growth regulators in rice (Oryza sativa) variety (UPR 1823) inoculated with different cyanobacterial strains namely Anabaena oryzae, Anabaena doliolum, Phormidium fragile, Calothrix geitonos, Hapalosiphon intricatus, Aulosira fertilissima, Tolypothrix tenuis, Oscillatoria acuta and Plectonema boryanum were quantified using HPLC in pot conditions after 15 and 30 days. Qualitative analysis of the induced compounds using reverse phase HPLC and further confirmation with LC-MS/MS showed consistent accumulation of phenolic acids (gallic, gentisic, caffeic, chlorogenic and ferulic acids), flavonoids (rutin and quercetin) and phytohormones (indole acetic acid and indole butyric acid) in rice leaves. Plant growth promotion (shoot, root length and biomass) was positively correlated with total protein and chlorophyll content of leaves. Enzyme activity of peroxidase and phenylalanine ammonia lyase and total phenolic content was fairly high in rice leaves inoculated with O. acuta and P. boryanum after 30 days. Differential systemic accumulation of phenylpropanoids in plant leaves led us to conclude that cyanobacterial inoculation correlates positively with plant growth promotion and stress tolerance in rice. Furthermore, the study helped in deciphering possible mechanisms underlying plant growth promotion and stress tolerance in rice following cyanobacterial inoculation and indicated the less explored avenue of cyanobacterial colonization in stress tolerance against abiotic stress.

Streptomyces lividans inhibits the proliferation of the fungus Verticillium dahliae on seeds and roots of Arabidopsis thaliana

Verticillium wilt, a vascular disease in more than 200 dicotyledonous plants, is due to the ascomycete fungus Verticillium dahliae. As documented by video-microscopy, the soil bacterium Streptomyces lividans strongly reduces the germination of V. dahliae conidia, and the subsequent growth of hyphae. Quantification by the use of DNA-intercalating dyes and Calcofluor-staining revealed that during prolonged co-cultivation, bacterial hyphae proliferate to a dense network, provoke a poor development of V. dahliae vegetative hyphae and lead to an enormous reduction of conidia and microsclerotia. Upon individual application to seeds of the model plant Arabidopsis thaliana, either the bacterial spores or the fungal conidia germinate at or within the mucilage, including its volcano-shaped structures. The extension of hyphae from each individual strain correlates with the reduction of the pectin-containing mucilage-layer. Proliferating hyphae then spread to roots of the emerging seedlings. Plants, which arise in the presence of V. dahliae within agar or soil, have damaged root cells, an atrophied stem and root, as well as poorly developed leaves with chlorosis symptoms. In contrast, S. lividans hyphae settle in bunches preferentially at the outer layer near tips and alongside roots. Resulting plants have a healthy appearance including an intact root system. Arabidopsis thaliana seeds, which are co-inoculated with V. dahliae and S. lividans, have preferentially proliferating bacterial hyphae within the mucilage, and at roots of the outgrowing seedlings. As a result, plants have considerably reduced disease symptoms. As spores of the beneficial S. lividans strain are obtainable in large quantity, its application is highly attractive.