Exploitation of Endophytic Bacteria to Enhance the Phytoremediation Potential of the Wetland Helophyte Juncus acutus

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater

Introduction

Constructed wetlands (CWs) are nature-based solutions for wastewater treatment where the root system microbiome plays a key role in terms of nutrient and pollutant removal. Nonetheless, little is known on plant-microbe interactions and bacterial population selection in CWs, which are mostly characterized in terms of engineering aspects.

Methods

Here, cultivation-independent and cultivation-based analyses were applied to study the bacterial communities associated to the root systems of Phragmites australis and Typha domingensis co-occurring in the same cell of a CW receiving primary treated wastewaters.

Results and discussion

Two endophytic bacteria collections (n = 156) were established aiming to find novel strains for microbial-assisted phytodepuration, however basing on their taxonomy the possible use of these strains was limited by their low degrading potential and/or for risks related to the One-Health concept. A sharp differentiation arose between the P. australis and T. domingensis collections, mainly represented by lactic acid bacteria (98%) and Enterobacteriaceae (69%), respectively. Hence, 16S rRNA amplicon sequencing was used to disentangle the microbiome composition in the root system fractions collected at increasing distance from the root surface. Both the fraction type and the plant species were recognized as drivers of the bacterial community structure. Moreover, differential abundance analysis revealed that, in all fractions, several bacteria families were significantly and differentially enriched in P. australis or in T. domingensis. CWs have been also reported as interesting options for the removal of emerging contaminants (e.g, antibiotic resistance genes, ARGs). In this study, ARGs were mostly present in the rhizosphere of both plant species, compared to the other analyzed fractions. Notably, qPCR data showed that ARGs (i.e., ermB, bla TEM, tetA) and intl1 gene (integrase gene of the class 1 integrons) were significantly higher in Phragmites than Typha rhizospheres, suggesting that macrophyte species growing in CWs can display a different ability to remove ARGs from wastewater. Overall, the results suggest the importance to consider the plant-microbiome interactions, besides engineering aspects, to select the most suitable species when designing phytodepuration systems.

A cyclic dipeptide for salinity stress alleviation and the trophic flexibility of endophyte provide insights into saltmarsh plant-microbe interactions

In response to climate change, the nature of endophytes and their applications in sustainable agriculture have attracted the attention of academics and agro-industries. This work focused on the endophytic halophiles of the endangered Taiwanese salt marsh plant, Bolboschoenus planiculmis, and evaluated the functions of these isolates through in planta salinity stress alleviation assay using Arabidopsis. The endophytic strain Priestia megaterium BP01R2, which can promote plant growth and salinity tolerance, was further characterized through multi-omics approaches. The transcriptomics results suggested that BP01R2 could function by tuning hormone signal transduction, energy-producing metabolism, multiple stress responses, etc. In addition, the cyclodipeptide cyclo(L-Ala-Gly), which was identified by metabolomics analysis, was confirmed to contribute to the alleviation of salinity stress in stressed plants via exogenous supplementation. In this study, we used multi-omics approaches to investigate the genomics, metabolomics, and tropisms of endophytes, as well as the transcriptomics of plants in response to the endophyte. The results revealed the potential molecular mechanisms underlying the occurrence of biostimulant-based plant-endophyte symbioses with possible application in sustainable agriculture.

Differential interference of copper with endophytic bacterial inoculation: Atrazine decontamination in Acorus tatarinowii and culture solution

To clarify the interference effects of inorganic ions, Acorus tatarinowii and endophytic bacterium Herbaspirillum huttiense (Hh) were combined to decontaminate atrazine pollution under different copper levels. This study verified inoculation effects and revealed the complicated processes of atrazine transformation in solutions. 35.9% leaf biomass was promoted by Hh inoculation, and the value was lowered to 7.87% by high doses of copper. The changing trend of leaf N, K, and S contents, and tiller numbers were consistent with that of leaf biomass. Hh injection improved atrazine accumulation by 43.5% in roots, and under copper interference, this value lowered to 10.6%. Hh promoted atrazine deethylation in plants, which was copper-dose dependent in different plant organs. In solutions, atrazine was conjugated with small-molecule secretions at m/z 118, detoxicated into 2-hxydroatrazine and 2-hydroxy-4-acetamido-atrazine, then the triazine ring opened. Copper interference had a more significant impact on residual atrazine conversion products than Hh inoculation treatments. Hh treatment promoted the ring-opening degradation of atrazine in water. The addition of high doses of copper ions promoted the oxidative process of atrazine while inhibiting its ring-opening transformation process in water.

Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water

Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal. Recent advances in genomics and analytical chemistry have provided insights into a better understanding of the metabolic pathways and genes involved in NA degradation. Here, we discuss the ecology of microbial NA degradation with a focus on CWTS and summarize the current knowledge related to the metabolic pathways and genes used by microorganisms to degrade NAs. Evidence to date suggests that NAs are mostly degraded aerobically through ring cleavage via the beta-oxidation pathway, which can be combined with other steps such as aromatization, alpha-oxidation, omega-oxidation, or activation as coenzyme A (CoA) thioesters. Anaerobic NA degradation has also been reported via the production of benzoyl-CoA as an intermediate and/or through the involvement of methanogens or nitrate, sulfate, and iron reducers. Furthermore, we discuss how genomic, statistical, and modeling tools can assist in the development of improved bioremediation practices.

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

Current Scenario and Future Prospects of Endophytic Microbes: Promising Candidates for Abiotic and Biotic Stress Management for Agricultural and Environmental Sustainability

Globally, substantial research into endophytic microbes is being conducted to increase agricultural and environmental sustainability. Endophytic microbes such as bacteria, actinomycetes, and fungi inhabit ubiquitously within the tissues of all plant species without causing any harm or disease. Endophytes form symbiotic relationships with diverse plant species and can regulate numerous host functions, including resistance to abiotic and biotic stresses, growth and development, and stimulating immune systems. Moreover, plant endophytes play a dominant role in nutrient cycling, biodegradation, and bioremediation, and are widely used in many industries. Endophytes have a stronger predisposition for enhancing mineral and metal solubility by cells through the secretion of organic acids with low molecular weight and metal-specific ligands (such as siderophores) that alter soil pH and boost binding activity. Finally, endophytes synthesize various bioactive compounds with high competence that are promising candidates for new drugs, antibiotics, and medicines. Bioprospecting of endophytic novel secondary metabolites has given momentum to sustainable agriculture for combating environmental stresses. Biotechnological interventions with the aid of endophytes played a pivotal role in crop improvement to mitigate biotic and abiotic stress conditions like drought, salinity, xenobiotic compounds, and heavy metals. Identification of putative genes from endophytes conferring resistance and tolerance to crop diseases, apart from those involved in the accumulation and degradation of contaminants, could open new avenues in agricultural research and development. Furthermore, a detailed molecular and biochemical understanding of endophyte entry and colonization strategy in the host would better help in manipulating crop productivity under changing climatic conditions. Therefore, the present review highlights current research trends based on the SCOPUS database, potential biotechnological interventions of endophytic microorganisms in combating environmental stresses influencing crop productivity, future opportunities of endophytes in improving plant stress tolerance, and their contribution to sustainable remediation of hazardous environmental contaminants.

Plant-minerals-water interactions: An investigation on Juncus acutus exposed to different Zn sources

Juncus acutus has been proposed as a suitable species for the design of phytoremediation plans. This research aimed to investigate the role played by rhizosphere minerals and water composition on Zn transformations and dynamics in the rhizosphere-plant system of J. acutus exposed to different Zn sources. Rhizobox experiments were conducted using three different growing substrates (Zn from 137 to 20,400 mg/kg), and two irrigation lines (Zn 0.05 and 180 mg/l). The plant growth was affected by the substrate type, whereas the Zn content in the water did not significantly influence the plant height for a specific substrate. J. acutus accumulated Zn mainly in roots (up to 10,000 mg/kg dw); the metal supply by the water led to variable increases in the total Zn concentration in the vegetal organs, and different Zn distributions both controlled by the rhizosphere mineral composition. Different Zn complexation mechanisms were observed, mainly driven by cysteine and citrate compounds, whose amount increased linearly with Zn content in water, but differently for each of the investigated systems. Our study contributes to gain a more complete picture of the Zn pathway in the rhizosphere-plant system of J. acutus. We demonstrated that this vegetal species is not only capable of developing site-specific tolerance mechanisms, but it is also capable to differently modulate Zn transformation when Zn is additionally supplied by watering. These findings are necessary for predicting the fate of Zn during phytoremediation of sites characterized by specific mineralogical properties and subject to water chemical variations.

Phytoremediation as an Effective Remedy for Removing Trace Elements from Ecosystems

The pollution of soil by trace elements is a global problem. Conventional methods of soil remediation are often inapplicable, so it is necessary to search intensively for innovative and environment-friendly techniques for cleaning up ecosystems, such as phytoremediation. Basic research methods, their strengths and weaknesses, and the effects of microorganisms on metallophytes and plant endophytes resistant to trace elements (TEs) were summarised and described in this manuscript. Prospectively, bio-combined phytoremediation with microorganisms appears to be an ideal, economically viable and environmentally sound solution. The novelty of the work is the description of the potential of "green roofs" to contribute to the capture and accumulation of many metal-bearing and suspended dust and other toxic compounds resulting from anthropopressure. Attention was drawn to the great potential of using phytoremediation on less contaminated soils located along traffic routes and urban parks and green spaces. It also focused on the supportive treatments for phytoremediation using genetic engineering, sorbents, phytohormones, microbiota, microalgae or nanoparticles and highlighted the important role of energy crops in phytoremediation. Perceptions of phytoremediation on different continents are also presented, and new international perspectives are presented. Further development of phytoremediation requires much more funding and increased interdisciplinary research in this direction.

A Review on Microorganisms in Constructed Wetlands for Typical Pollutant Removal: Species, Function, and Diversity

Constructed wetlands (CWs) have been proven as a reliable alternative to traditional wastewater treatment technologies. Microorganisms in CWs, as an important component, play a key role in processes such as pollutant degradation and nutrient transformation. Therefore, an in-depth analysis of the community structure and diversity of microorganisms, especially for functional microorganisms, in CWs is important to understand its performance patterns and explore optimized strategies. With advances in molecular biotechnology, it is now possible to analyze and study microbial communities and species composition in complex environments. This review performed bibliometric analysis of microbial studies in CWs to evaluate research trends and identify the most studied pollutants. On this basis, the main functional microorganisms of CWs involved in the removal of these pollutants are summarized, and the effects of these pollutants on microbial diversity are investigated. The result showed that the main phylum involved in functional microorganisms in CWs include Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. These functional microorganisms can remove pollutants from CWs by catalyzing chemical reactions, biodegradation, biosorption, and supporting plant growth, etc. Regarding microbial alpha diversity, heavy metals and high concentrations of nitrogen and phosphorus significantly reduce microbial richness and diversity, whereas antibiotics can cause large fluctuations in alpha diversity. Overall, this review can provide new ideas and directions for the research of microorganisms in CWs.

Fluopyram removal from agricultural equipment rinsing water using HSF pilot-scale constructed wetlands

Fluopyram is a novel broad-spectrum fungicide with nematocidal activity, and as an extensively used pesticide, it could cause toxicity in nontarget organisms. The aim of this study was to explore the efficiency of five horizontal subsurface flow (HSF) constructed wetlands (CWs) to remove fluopyram from rinsing water produced during the cleaning of pesticide spraying equipment. Four CWs, namely WG-R, WG-R-P, WG-C, and WG-U, contained fine gravel as porous media. WG-R and WG-R-P were planted with Phragmites australis, WG-C with Typha latifolia, and WG-U was left unplanted. Bioaugmentation with plant growth-promoting rhizobacteria was conducted in WG-R-P unit. The fifth unit (WGZ-R) planted with Phragmites australis and contained gravel and zeolite as porous media. All of CWs were loaded on a daily basis from December 2019 to January 2021 with water fortified with fluopyram. The removal rate follows the pattern of WG-R-P (70.67%) > WGZ-R (62.06%) > WG-C (59.98%) > WG-R (36.10%) > WG-U (25.09%). The most important parameters affecting the fluopyram removal were bioaugmentation, zeolite presence in porous media, and plant species. The WG-R-P unit showed higher fluopyram removal in comparison to the WG-R (increase about 96%), the zeolite increased the fluopyram removal by 72%, and the WG-C unit showed 66% higher fluopyram removal than the WG-R unit.

Particularities of Fungicides and Factors Affecting Their Fate and Removal Efficacy: A Review

Systemic fungicide use has increased over the last decades, despite the susceptibility of resistance development and the side effects to human health and the environment. Although herbicides and insecticides are detected more frequently in environmental samples, there are many fungicides that have the ability to enter water bodies due to their physicochemical properties and their increasing use. Key factors affecting fungicide fate in the environment have been discussed, including the non-target effects of fungicides. For instance, fungicides are associated with the steep decline in bumblebee populations. Secondary actions of certain fungicides on plants have also been reported recently. In addition, the use of alternative eco-friendly disease management approaches has been described. Constructed Wetlands (CWs) comprise an environmentally friendly, low cost, and efficient fungicide remediation technique. Fungicide removal within CWs is dependent on plant uptake and metabolism, absorption in porous media and soil, hydrolysis, photodegradation, and biodegradation. Factors related to the efficacy of CWs on the removal of fungicides, such as the type of CW, plant species, and the physicochemical parameters of fungicides, are also discussed in this paper. There are low-environmental-risk fungicides, phytohormones and other compounds, which could improve the removal performance of CW vegetation. In addition, specific parameters such as the multiple modes of action of fungicides, side effects on substrate microbial communities and endophytes, and plant physiological response were also studied. Prospects and challenges for future research are suggested under the prism of reducing the risk related to fungicides and enhancing CW performance.

Differences in gene expression and endophytic bacterial diversity in Atractylodes macrocephala Koidz. rhizomes from different growth years

Atractylodes macrocephala Koidz. (AMK) is widely used owing to its pharmacological activity in traditional Chinese medicine (TCM). Here, we aimed to characterize the differentially expressed genes (DEGs) of one- and three-year growth (OYG and TYG) rhizomes of AMK combined with the endophytic bacterial diversity analysis using high-throughput RNA-sequencing. 114,572 unigenes were annotated in six public databases. 3570 DEGs revealed a clear difference, of which 936 and 2634 genes were up- and down-regulated, respectively. The results of KEGG pathway analysis indicated that DEGs corresponding to the terpenoid synthesis gene were downregulated in TYG rhizomes. 414,424 sequences corresponding to the 16S rRNA gene were divided into 1267 operational taxonomic units (OTUs). Moreover, the diversity of endophytic bacteria changed with species in OYG (773) and TYG (1201) rhizomes at OTU level, and Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. Comparison of species differences among different growth years revealed that some species were significantly different, such as Actinomycetes, Variovorax, Cloacibacterium, etc. Interestingly, the decrease in the function-related metabolism of terpenoids and polyketides was found to be correlated the low expression of terpene synthesis genes in TYG rhizomes assessed using PICRUSt2. These data provide a scientific basis for elucidating the mechanism underlying metabolite accumulation and endophytic bacterial diversity in relation to the growth years in AMK.

Heavy metal ATPase genes (HMAs) expression induced by endophytic bacteria, "AI001, and AI002" mediate cadmium translocation and phytoremediation

Contamination of heavy metals is a serious threat, which causes threats to the environment. Our study aimed to determine the role of endophytic bacteria in Cd phytoremediation and heavy metal ATPase gene expression. Cadmium (Cd) resistant endophytic bacteria were isolated from Solanum nigrum on LB agar plates, contaminated with 0-30 mg/L Cd. The phosphate solubilization and indole-3-acetic acid (IAA) production of endophytes were estimated by growing them on Pikovskaya agar medium and GC-MS analysis, respectively. An experiment in a pot was performed to evaluate the effects of bacteria on rice plants contaminated with 5-25 mg/L of Cd. Expression of Cd response genes was quantified through qRT-PCR and Cd translocation from one part to another part of the plant was measured through the ICP. BLAST alignment of 16 S-rDNA gene sequences confirmed the bacterial isolates as Serratia sp. AI001 and Klebsiella sp. Strain AI002. Both strains tolerated Cd up to 25 mg/L and produced 27-30 μg/mL of IAA. Inoculation of AI001 and AI002 improved plant growth dynamics (i.e., plant length, biomass, chlorophyll contents), relieved electrolyte leakage, and improved reduced glutathione significantly (P < 0.05). The inoculation of AI001 and AI002 significantly (P < 0.05) induced the expression of heavy metal ATPase genes ie., "HMA2, HMA3, and HMA4" and Cd translocation compared to uninoculated plants. Both AI001 and AI002 exhibited very prominent plant-growth-promoting and Cd phytoremediation properties. The results revealed that isolates also contributed a lot to the expression of rice plant heavy metal ATPase genes and in the Cd translocation in the plant.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.

A review on the role of plant in pharmaceuticals and personal care products (PPCPs) removal in constructed wetlands

Pharmaceuticals and personal care products (PPCPs) cause ongoing water pollution and consequently have attracted wide attention. Constructed wetlands (CWs) show good PPCP removal performance through combined processes of substrates, plants, and microorganisms; however, most published research focuses on the role of substrates and microorganisms. This review summarizes the direct and indirect roles of wetland plants in PPCP removal, respectively. These direct effects include PPCP precipitation on root surface iron plaque, and direct absorption and degradation by plants. Indirect effects, which appear more significant than direct effects, include enhancement of PPCP removal through improved rhizosphere microbial activities (more than twice as much as bulk soil) stimulated by radial oxygen loss and exudate secretions, and the formation of supramolecular ensembles from PPCPs and humic acids from decaying plant materials which improving PPCPs removal efficiency by up to four times. To clarify the internal mechanisms of PPCP removal by plants in CWs, factors affecting wetland plant performance were reviewed. Based on this review, future research needs have been identified.

Application of floating treatment wetlands for stormwater runoff: A critical review of the recent developments with emphasis on heavy metals and nutrient removal

Floating treatment wetlands (FTWs) are increasingly gaining popularity due to a set of valuable features like wastewater remediation under varied conditions, ecosystem quality preservation, landscape conservation, and aesthetic benefits. FTW is a phyto-technology in which macrophytes grow on a floating raft with their roots in permanent contact with water and remove pollutants via several physicochemical-biological processes. FTW is highly capable of overcoming technical and operational challenges that come way in stormwater treatment due to the erratic nature of hydrologic and input pollutant loads because this innovative buoyant hydroponic design can move up and down with fluctuating water levels in the stormwater pond and can treat highly variable flows. Plants and biofilms attached to the roots hanging beneath the floating mat play a pivotal role in FTWs. The present review encompasses the concept of FTWs, their structural designs, relevance in stormwater management, and mechanism of plant uptake for pollutant removal. The role of FTWs to remove heavy metals and nutrients is also critically analyzed. Understanding hydraulics and other parameters of FTW is vital to effective design. Hence, the role of vegetation coverage, vegetation type, sorption media, aeration frequency, and intensity, and plant density to enhance system efficiency is also highlighted. Due to their operational flexibility and environmentally friendly working with no additional burden on existing urban land use, FTWs entice broad international interest and offer a coherent solution for stormwater management. MAIN FINDINGS: The review delivers state-of-the-art analysis of the current understanding of hydraulics and other parameters of FTWs, and associated mechanisms to enhance the treatment efficiency of FTWs for nutrients and heavy metals removal.

Diazotroph Paenibacillus triticisoli BJ-18 Drives the Variation in Bacterial, Diazotrophic and Fungal Communities in the Rhizosphere and Root/Shoot Endosphere of Maize

Application of diazotrophs (N2-fixing microorganisms) can decrease the overuse of nitrogen (N) fertilizer. Until now, there are few studies on the effects of diazotroph application on microbial communities of major crops. In this study, the diazotrophic and endospore-forming Paenibacillus triticisoli BJ-18 was inoculated into maize soils containing different N levels. The effects of inoculation on the composition and abundance of the bacterial, diazotrophic and fungal communities in the rhizosphere and root/shoot endosphere of maize were evaluated by sequencing the 16S rRNA, nifH gene and ITS (Inter Transcribed Spacer) region. P. triticisoli BJ-18 survived and propagated in all the compartments of the maize rhizosphere, root and shoot. The abundances and diversities of the bacterial and diazotrophic communities in the rhizosphere were significantly higher than in both root and shoot endospheres. Each compartment of the rhizosphere, root and shoot had its specific bacterial and diazotrophic communities. Our results showed that inoculation reshaped the structures of the bacterial, diazotrophic and fungal communities in the maize rhizosphere and endosphere. Inoculation reduced the interactions of the bacteria and diazotrophs in the rhizosphere and endosphere, while it increased the fungal interactions. After inoculation, the abundances of Pseudomonas, Bacillus and Paenibacillus in all three compartments, Klebsiella in the rhizosphere and Paenibacillus in the root and shoot were significantly increased, while the abundances of Fusarium and Giberella were greatly reduced. Paenibacillus was significantly correlated with plant dry weight, nitrogenase, N2-fixing rate, P solubilization and other properties of the soil and plant.

Genomic and Physiological Investigation of Heavy Metal Resistance from Plant Endophytic Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum

Combretum erythrophyllum is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa. In hyperaccumulators, metal detoxification has also been linked or attributed to the activities of endophytes, and, in this regard, metal detoxification can be considered a form of endophytic behavior. Therefore, we report herein on the identification of proteins that confer heavy metal resistance, the in vitro characterization of heavy metal resistance, and the production of plant growth-promoting (PGP) volatiles by Methylobacterium radiotolerans MAMP 4754. Multigenome comparative analyses of M. radiotolerans MAMP 4754 against eight other endophytic strains led to the identification of zinc, copper, and nickel resistance proteins in the genome of this endophyte. The maximum tolerance concentration (MTC) of this strain towards these metals was also investigated. The metal-exposed cells were analyzed by transmission electron microscopy (TEM). The ethyl acetate and chloroform extracts (1:1 v/v) of heavy metal untreated M. radiotolerans MAMP 4754 were also screened for the production of PGP compounds by Gas Chromatography–Mass Spectroscopy (GC/MS). The MTC was recorded at 15 mM, 4 mM, and 12 mM for zinc, copper, and nickel, respectively. The TEM analysis showed the accumulation of metals in the intracellular environment of M. radiotolerans MAMP 4754, while the GC/MS analysis revealed several plant growth-promoting compounds, including alcohols, phthalate esters, alkenes, ketones, sulfide derivatives, phenols, and thiazoles. Our findings suggest that the genetic makeup of M. radiotolerans MAMP 4754 encodes heavy metal resistant proteins that indicate hyperaccumulator-specific endophytic behavior and the potential for application in bioremediation. The production of plant growth-promoting volatiles in pure culture by M. raditotolerans MAMP 4754 is a characteristic feature for plant growth-promoting bacteria.

Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

Characteristics and Diversity of Endophytic Bacteria in Endangered Chinese Herb Glehnia littoralis Based on Illumina Sequencing

Glehnia littoralis is an endangered medicinal plant growing in the coastal ecological environment and plays an important role in coastal ecosystems. The endophytes in the plant have a significant role in promoting plant growth and enhancing plant stress resistance. However, the endophytic bacterial structure associated with halophyte G. littoralis is still not revealed. In this project, the construction and diversity of endophytic bacterial consortium associated with different tissues of G. littoralis were illustrated with high throughput sequencing of the V3-V4 region of the bacterial 16S rRNA. The results resolved that the diversity and richness of endophytic bacteria were significantly higher in root than in leaf and stem. The operational taxonomic units (OTU) analysis demonstrated that the Actinobacteria and Proteobacteria were dominant in all the samples at the phylum level, and Pseudomonas, Bacillus, Rhizobium were the dominant genera. Our results unraveled that the bacterial communities differed among different tissues of G. littoralis. Endophytic bacterial communities in leaf and stem shared more similarity than that in the root. Furthermore, the difference of bacteria community and structure among different tissues were also detected by principal coordinate analysis. Taken altogether, we can conclude that the bacterial communities of different tissues are unique, which could facilitate understanding the diversity of endophytic bacteria in G. littoralis.

Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance

The genus Eucalyptus with over 747 species occurs in wide ecological range and is preferred for bioenergy plantations due to their short rotation, rapid growth and superior wood properties. They are planted in 22 million ha area and India is third largest planter of Eucalyptus. In the present study, the bacterial endophyte community in leaves of six Eucalyptus clones belonging to E. tereticornis and E. camaldulensis was assessed by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The clones were selected based on their response to progressive water stress. A total of 4947 operational taxonomic units (OTUs) were obtained and the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes. Escherichia coli was enriched in all samples at species level. Comparison of endophyte diversity was conducted between the two species and across the water stress tolerant and susceptible clones. The alpha-diversity analysis revealed that species richness and diversity was high in E. camaldulensis and water stress susceptible clones. LefSe analysis predicted 69 and 54 significantly enriched taxonomic biomarkers between species and stress response groups respectively. A maximum of 49 taxonomic biomarkers were recorded in susceptible group and the significantly enriched species were Bacteroides thetaiotaomicron and Turicibacter sanguinis, while the tolerant group documented 5 biomarkers including oscillibacter sp. The presence of functional biomarkers was also assessed in both the groups. The findings of the present study provides an insight into the diversity of bacterial endophyte in Eucalyptus leaves and to our knowledge this is the first report on documenting the endophyte abundance in water stress responsive Eucalyptus clones.

Enrichment of endophytic Actinobacteria in roots and rhizomes of Miscanthus × giganteus plants exposed to diclofenac and sulfamethoxazole

This study investigates how wastewater containing 2 mg l^-1 of sulfamethoxazole (SMX) and 2 mg l^-1 of diclofenac (DCF) affects the composition of bacterial communities present in the roots and rhizomes of Miscanthus × giganteus plants grown in laboratory-scale constructed wetlands. Bacterial communities in plant roots and rhizomes were identified in treated and control samples by 16S rRNA amplicon sequencing. Moreover, bacterial endophytes were isolated in R2A and 1/10 869 media and screened for their ability to metabolize SMX and DCF in liquid medium by HPLC. Our results show significant changes in the abundance of main genera, namely Sphingobium and Streptomyces between control and treated plants. Around 70% of the strains isolated from exposed plants belonged to the phylum Actinobacteria and were classified as Streptomyces, Microbacterium, and Glycomyces. In non-exposed plants, Proteobacteria represented 43.5% to 63.6% of the total. We identified 17 strains able to remove SMX and DCF in vitro. From those, 76% were isolated from exposed plants. Classified mainly as Streptomyces, they showed the highest SMX (33%) and DCF (41%) removal efficiency. These isolates, alone or in combination, might be used as bio-inoculants in constructed wetlands to enhance the phytoremediation of SMX and DCF during wastewater treatment.

Burkholderia phytofirmans PsJN and tree twigs derived biochar together retrieved Pb-induced growth, physiological and biochemical disturbances by minimizing its uptake and translocation in mung bean (Vigna radiata L.)

Anthropogenic activities like industrial mining, refining and smelting release substantial amounts of lead (Pb) into the soil causing potential ecological menaces to environment, soil productivity and food security. Present pot scale study was undertaken to investigate the effects of tree twigs-derived biochar and a bacterium Burkholderia phytofirmans PsJN on Pb accumulation, growth, physiological, biochemical and antioxidative defense responses of mung bean grown in Pb spiked soil. The original soil was spiked with Pb (600 mg kg^-1) and amended with biochar (1% w/w). Upon screening in laboratory, B. phytofirmans PsJN exhibited high Pb tolerance and was able to grow at high Pb concentrations. Surface-disinfected seeds of mung bean were inoculated with B. phytofirmans PsJN and sown in pots along with un-inoculated seeds. Data were collected for various growth, physiological and biochemical parameters from fully matured harvested plants. Application of biochar and B. phytofirmans PsJN ameliorated Pb induced negative impacts in mung bean both individually and in combination, but better growth, physiological and seed quality responses were observed with their combined use. Compared with respective controls, their combined use increased the following parameters in normal and Pb spiked soils, respectively: plant height (69% and 159%), root dry weight (97% and 130%), shoot dry weight (42% and 104%), number of pods (70% and 210%), grains weight (58% and 194%) and number of root nodules (71% and 255%). Moreover, combined use increased chlorophyll contents (27% and 37%), photosynthetic rate (93% and 204%), transpiration rate (42% and 132%), stomatal conductance (70% and 218%), sub-stomatal conductance (93% and 148%) and water use efficiency (35% and 43%). In addition, combined application of biochar and B. phytofirmans PsJN retarded Pb-induced oxidative stress by intensifying antioxidant enzyme activities and reducing activities of reactive oxygen species. Similarly, considerable reduction in Pb uptake, translocation and bioaccumulation in mung bean was noticed in Pb spiked soil due to applied amendments. Furthermore, their combined use resulted in considerable increase in grain quality parameters (protein, fat, ash) both in normal and Pb-spiked soils. Therefore, it can be inferred that interactive use of biochar and B. phytofirmans PsJN provides an efficient innovative strategy to repossess Pb induced growth, physiological, biochemical and oxidative disturbances in mung bean.

Microbial assisted phytodepuration for water reclamation: Environmental benefits and threats

Climate changes push for water reuse as a priority to counteract water scarcity and minimize water footprint especially in agriculture, one of the highest water consuming human activities. Phytodepuration is indicated as a promising technology for water reclamation, also in the light of its economic and ecological sustainability, and the use of specific bacterial inocula for microbial assisted phytodepuration has been proposed as a further advance for its implementation. Here we provided an overview on the selection and use of plant growth promoting bacteria in Constructed Wetland (CW) systems, showing their advantages in terms of plant growth support and pollutant degradation abilities. Moreover, CWs are also proposed for the removal of emerging organic pollutants like antibiotics from urban wastewaters. We focused on this issue, still debated in the literature, revealing the necessity to deepen the knowledge on the antibiotic resistance spread into the environment in relation to treated wastewater release and reuse. In addition, given the presence in the plant system of microhabitats (e.g. rhizosphere) that are hot spot for Horizontal Gene Transfer, we highlighted the importance of gene exchange to understand if these events can promote the diffusion of antibiotic resistance genes and antibiotic resistant bacteria, possibly entering in the food production chain when treated wastewater is used for irrigation. Ideally, this new knowledge will lead to improve the design of phytodepuration systems to maximize the quality and safety of the treated effluents in compliance with the 'One Health' concept.

Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species

Allium species are popular vegetables in China and possess antifungal and antibacterial activities. This study aimed to compare the endophytic bacterial community in the four crucial Allium species in China, Chinese leek (CL), garlic (GA), onion (ON,) and Welsh onion (WO), using sequences of the V3–V4 region of the bacterial 16S rRNA gene. A total of 1,036,637 high-quality sequences and 719 operational taxonomic units (OTUs) were obtained across all libraries. A total of 20 phyla, 50 classes, 80 orders, 134 families, and 234 genera were identified. Among them, 18 OTUs and 19 genera were shared among the four Allium species. Proteobacteria (42.68%) and Bacteroidetes (20.18%) were the dominant phyla in CL, while one unclassified (>70%) was the dominant phyla in the other three Allium species. The alpha-diversity analysis showed the bacterial richness and diversity in CL were significantly higher than those in the other three Allium species. Principal coordinate analysis (PCA) showed endophytic bacterial communities in GA, WO, and ON were more similar than those in CL. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed endophytic bacteria mostly enriched in Membrane Transport, Amino Acid Metabolism and Carbohydrate Metabolism pathway. 17 of the 23 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories and 159 of the 206 lower-level KEGG pathways in CL were significantly higher than those in the other three Allium species. Pearson’s correlation indicated that KEGG pathways with significant differences among the Allium species were closely related to the bacterial genera with significant differences between the Allium species. The findings of our study provided insight into the complex endophytic microbial communities in Allium species.

Metal accumulation from leachate by polyculture in crushed brick and steel slag using pilot-scale constructed wetland in the climate of Pakistan

The temperate climate of Pakistan has enhanced the performance of macrophytes grown in crushed brick and steel slag in constructed wetland for removal of heavy metals from leachate. Two pilot-scale constructed wetlands [constructed wetland 1 (CW1) and constructed wetland 2 (CW2)] were planted with a polyculture of Phragmites australis and Typha latifolia in crushed brick and steel slag, respectively. These wetlands were located in the National University of Sciences and Technology, Islamabad campus, and operated for 15 months for treatment of leachate with climatic variations of Islamabad. The metal accumulation in a polyculture of Phragmites australis and Typha latifolia and in substrates was analyzed in the laboratory of Institute of Environmental Sciences and Engineering located near wetland site. Despite the high temperature in summer season, removal of Cu, Zn, and Pb was efficient due to the synergistic combination of macrophytes and substrates in both wetlands. Substrates acted as a primary sink of metals and enhanced metal accumulation in the plant's roots which resulted in poor translocation of Cu, Zn, and Pb to shoots. Despite the variation in precipitation and temperature during summer and winter seasons, the average removal of copper, zinc, and lead was 95%, 91%, and 89% by polyculture in crushed brick in CW1 and 97%, 95%, and 91% in steel slag in CW2, respectively. A The variation in climate has a negligible effect on the sorption of metals by both substrates in CW1 and CW2. Furthermore, Phragmites australis with crushed brick in CW1 was efficient for removal of Zn and Typha latifolia was performing better with steel slag in CW2 for significantly high removal of Cu and Pb in the climate of Islamabad, Pakistan.

Root Bacteria Recruited by Phragmites australis in Constructed Wetlands Have the Potential to Enhance Azo-Dye Phytodepuration

The microbiome associated with plants used in phytodepuration systems can boost plant growth and services, especially in ecosystems dealing with recalcitrant compounds, hardly removed via traditional wastewater (WW) treatments, such as azo-dyes used in textile industry. In this context, we aimed to study the cultivable microbiome selected by Phragmites australis plants in a Constructed Wetland (CW) in Morocco, in order to obtain candidate inoculants for the phytodepuration of azo-dye contaminated WW. A collection of 152 rhizospheric and endophytic bacteria was established. The strains were phylogenetically identified and characterized for traits of interest in the phytodepuration context. All strains showed Plant Growth Promotion potential in vitro and 67% of them significantly improved the growth of a model plant in vivo compared to the non bacterized control plants. Moreover, most of the isolates were able to grow in presence of several model micropollutants typically found in WW, indicating their potential use in phytodepuration of a wide spectrum of effluents. The six most promising strains of the collection were tested in CW microcosms alone or as consortium: the consortium and two single inocula demonstrated to significantly increase the removal of the model azo-dye Reactive Black 5 compared to the non bacterized controls.

Metal Resistant Endophytic Bacteria Reduces Cadmium, Nickel Toxicity, and Enhances Expression of Metal Stress Related Genes with Improved Growth of Oryza Sativa, via Regulating Its Antioxidant Machinery and Endogenous Hormones

The tolerance of plant growth-promoting endophytes (PGPEs) against various concentrations of cadmium (Cd) and nickel (Ni) was investigated. Two glutathione-producing bacterial strains (Enterobacter ludwigii SAK5 and Exiguobacterium indicum SA22) were screened for Cd and Ni accumulation and tolerance in contaminated media, which showed resistance up to 1.0 mM. Both strains were further evaluated by inoculating specific plants with the bacteria for five days prior to heavy metal treatment (0.5 and 1.0 mM). The enhancement of biomass and growth attributes such as the root length, shoot length, root fresh weight, shoot fresh weight, and chlorophyll content were compared between treated inoculated plants and treated non-inoculated plants. Both strains significantly increased the accumulation of Cd and Ni in inoculated plants. The accumulation of both heavy metals was higher in the roots than in the shoots, however; Ni accumulation was greater than Cd. Heavy metal stress-responsive genes such as OsGST, OsMTP1, and OsPCS1 were significantly upregulated in treated non-inoculated plants compared with treated inoculated plants, suggesting that both strains reduced heavy metal stress. Similarly, abscisic acid (ABA) was increased with increased heavy metal concentration; however, it was reduced in inoculated plants compared with non-inoculated plants. Salicylic acid (SA) was found to exert synergistic effects with ABA. The application of suitable endophytic bacteria can protect against heavy metal hyperaccumulation by enhancing detoxification mechanisms.

Floating treatment wetlands as biological buoyant filters for wastewater reclamation

Floating treatment wetlands (FTWs) are an innovative product of ecological engineering that can play a promising role in wastewater treatment. It provides low-cost, eco-friendly, and sustainable solutions for the treatment of wastewater, particularly in regions with economic constraints. Generally, FTWs comprise rooted plants that grow on the surface of water with their roots extending down into the pelagic zone rather than being embedded into the sediments. This drooping structure helps develop (1) a hydraulic flow between the root network and the bottom of the treatment system and (2) a large biologically active surface area for the physical entrapment (filtration) of contaminants, as well as their biochemical transformation and degradation. Furthermore, the rooted network allows proliferation of microorganisms that form biofilms and enhance pollutant degradation while promoting plant growth. The augmentation of bacteria in FTWs has been proven to be the most effective approach for reclamation of wastewater. This article discusses the operational parameters of FTWs for maximal remediation of wastewater and highlights the importance of plant-bacteria partnerships in a typical FTW system for enhanced cleanup of wastewater. We propose that this technology is preferable over other methods that require high energy, costs, and area to install or operate machinery.

Endophytic bacteria isolated from Solanum nigrum L., alleviate cadmium (Cd) stress response by their antioxidant potentials, including SOD synthesis by sodA gene

Cadmium (Cd) is a toxic heavy metal and an abiotic stressor to plants; however, inoculation of endophytic bacteria can raise resistance in plants against Cd, as well as improve plant growth. In the present study, two endophytic bacterial strains were isolated from Solanum nigrum, identified as Serratia sp. IU01 and Enterobacter sp. IU02 by 16S DNA sequencing. Both IU01 and IU02 were tolerant up to 9.0 mM of Cd in culture broth and successive increase in Cd concentration from 0 mM to 9.0 mM, led to an increase in the SOD enzyme activity of the isolates. Both strains were capable of indole-3-acetic acid (IAA) synthesis and phosphate solubilization, detected through gas spectrometry-mass chromatography (GC-MS) and Pikovskaya agar medium respectively. Brassica juncea plants stressed with 0-25 mg/kg Cd showed retardation in all growth attributes, however, inoculation of strain IU01 and IU02 significantly promoted the plant growth attributes as compared to control. Moreover, antioxidant enzymes and metabolites against reactive oxygen species (ROS) including polyphenol oxidase (PPO), peroxidase (POD), catalase (CAT), superoxide dismutase (SOD), alcohol dehydrogenase (ADH), reduced glutathione (GSH), malondialdehyde (MDA), flavonoid and polyphenolic contents were also significantly relieved by inoculation of IU01 and IU02 in plant exposed to different concentration of Cd stress as compared to control plants. Phytohormone production, phosphate solubilization, and/or antioxidative support of IU01 and IU02 might be responsible for growth promotion and Cd resistance in the plant.

Isolation of Bacterial Endophytes from Phalaris arundinacea and their Potential in Diclofenac and Sulfamethoxazole Degradation

Diclofenac (DCF), a non-steroidal anti-inflammatory drug (NSAID) and sulfamethoxazole (SMX), an antimicrobial agent, are in common use and can be often detected in the environment. The constructed wetland systems (CWs) are one of the technologies to remove them from the aquatic environment. The final effect of the treatment processes depends on many factors, including the interaction between plants and the plant-associated microorganisms present in the system. Bacteria living inside the plant as endophytes are exposed to secondary metabolites in the tissues. Therefore, they can possess the potential to degrade aromatic structures, including residues of pharmaceuticals. The endophytic strain MG7 identified as Microbacterium sp., obtained from root tissues of Phalaris arundinacea exposed to DCF and SMX was tested for the ability to remove 2 mg/l of SMX and DCF in monosubstrate cultures and in the presence of phenol as an additional carbon source. The MG7 strain was able to remove approximately 15% of DCF and 9% of SMX after 20 days of monosubstrate culture. However, a decrease in the optical density of the MG7 strain cultures was observed, caused by an insufficient carbon source for bacterial growth and proliferation. The adsorption of pharmaceuticals onto autoclaved cells was negligible, which confirmed that the tested strain was directly involved in the removal of DCF and SMX. In the presence of phenol as the additional carbon source, the MG7 strain was able to remove approximately 35% of DCF and 61% of SMX, while an increase in the optical density of the cultures was noted. The higher removal efficiency can be explained by adaptive mechanisms in microorganisms exposed to phenol (i.e. changes in the composition of membrane lipids) and by a co-metabolic mechanism, where non-growth substrates can be transformed by non-specific enzymes. The presence of both DCF and SMX and the influence of the supply frequency of CWs with the contaminated wastewater on the diversity of whole endophytic bacterial communities were demonstrated. The results of this study suggest the capability of the MG7 strain to degrade DCF and SMX. This finding deserves further investigations to improve wastewater treatment in CWs with the possible use of pharmaceuticals-degrading endophytes.

A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

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Microbiota are important for plant growth, health and stress resilience.

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Inoculation with key microbiota members can improve plant traits.

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Tailored selection and delivery of microbial strains or consortia is required.

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Microbiome improvement may be achieved by appropriate agro-management practices.

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Plant breeding for improved interaction with microbiota will be of benefit.

Plants have evolved with a plethora of microorganisms having important roles for plant growth and health. A considerable amount of information is now available on the structure and dynamics of plant microbiota as well as on the functional capacities of isolated community members. Due to the interesting functional potential of plant microbiota as well as due to current challenges in crop production there is an urgent need to bring microbial innovations into practice. Different approaches for microbiome improvement exist. On the one hand microbial strains or strain combinations can be applied, however, field success is often variable and improvement is urgently required. Smart, knowledge-driven selection of microorganisms is needed as well as the use of suitable delivery approaches and formulations. On the other hand, farming practices or the plant genotype can influence plant microbiota and thus functioning. Therefore, selection of appropriate farming practices and plant breeding leading to improved plant-microbiome interactions are avenues to increase the benefit of plant microbiota. In conclusion, different avenues making use of a new generation of inoculants as well as the application of microbiome-based agro-management practices and improved plant lines could lead to a better use of the plant microbiome. This paper reviews the importance and functionalities of the bacterial plant microbiome and discusses challenges and concepts in regard to the application of plant-associated bacteria.

Responses of the Endophytic Bacterial Communities of Juncus acutus to Pollution With Metals, Emerging Organic Pollutants and to Bioaugmentation With Indigenous Strains

Plants and their associated bacteria play a crucial role in constructed wetlands. In this study, the impact of different levels of pollution and bioaugmentation with indigenous strains individually or in consortia was investigated on the composition of the endophytic microbial communities of Juncus acutus. Five treatments were examined and compared in where the wetland plant was exposed to increasing levels of metal pollution (Zn, Ni, Cd) and emerging pollutants (BPA, SMX, CIP), enriched with different combinations of single or mixed endophytic strains. High levels of mixed pollution had a negative effect on alpha diversity indices of the root communities; moreover, the diversity indices were negatively correlated with the increasing metal concentrations. It was demonstrated that the root communities were separated depending on the level of mixed pollution, while the family Sphingomonadaceae exhibited the higher relative abundance within the root endophytic communities from high and low polluted treatments. This study highlights the effects of pollution and inoculation on phytoremediation efficiency based on a better understanding of the plant microbiome community composition.

Poplar and diclofenac pollution: A focus on physiology, oxidative stress and uptake in plant organs

Poplar plants may have an important role in the removal of pharmaceuticals from contaminated waters. In this context, plant uptake of the non-steroidal anti-inflammatory drug diclofenac, as well as physiological response in terms of growth traits and stress enzymes activity was assessed in Populus alba Villafranca clone, in order to establish the effectiveness of this species against pharmaceutical active compounds pollution. This evaluation was conducted in mesocosms with 1 mg L^-1 of this pharmaceutical for a maximum period of 28 days. Root appears to be the organ with clear uptake of diclofenac (14.76 ± 2.42 ng g^-1 fresh weight after 1 day of treatment), and presence of products derived from its metabolism. Indeed, 4-OH-diclofenac metabolite was detected in root tissues, indicating diclofenac uptake and metabolism inside the plants, already after 1 day of treatment. Regarding enzyme activities, glutathione-S-transferases increased in roots after long-term exposure to diclofenac, while an increase in activity of ascorbate peroxidase and glutathione reductase was detected in short and medium-term exposure, as a result of abiotic stress caused by diclofenac. Results suggest the ability of poplar to actively participate in the removal of diclofenac from water when used for phytoremediation purpose.

Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review

Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.

Role of Burkholderia cepacia CS8 in Cd-stress alleviation and phytoremediation by Catharanthus roseus

The current study was performed to assess the effect of Burkholderia cepacia CS8 on the phytoremediation of cadmium (Cd) by Catharanthus roseus grown in Cd-contaminated soil. The plants cultivated in Cd amended soil showed reduced growth, dry mass, gas-exchange capacity, and chlorophyll contents. Furthermore, the plants exhibited elevated levels of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) under Cd stress. The bacterized plants showed higher shoot length, root length; fresh and dry weight. The improved stress tolerance in inoculated plants was attributed to the reduced quantity of MDA and H₂O₂, enhanced synthesis of protein, proline, phenols, flavonoids, and improved activity of antioxidant enzymes including peroxidase, superoxide dismutase, ascorbate peroxidase, and catalase. Similarly, the 1-aminocyclopropane-1-carboxylate deaminase activity, phosphate solubilization, auxin, and siderophore production capability of B. cepacia CS8 improved growth and stress alleviation in treated plants. The bacterial inoculation enhanced the amount of water extractable Cd from soil. Furthermore, the inoculated plants showed higher bioconcentration factor and translocation factor. The current study exhibits that B. cepacia CS8 improves stress alleviation and phytoextraction potential of C. roseus plants growing under Cd stress.

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica

Halophytes play important roles in coastal ecosystems. However, few reports have described bacterial communities related to halophytes, and the distribution patterns of these bacteria in different plant tissues have been rarely compared. This paper mainly studied the diversity and community structure of endophytic and rhizosphere (Rh) bacteria related to the halophyte Messerschmidia sibirica, a dominant species in the coastal zone of Shandong Peninsula, China. We collected leaf (Lf), stem (Sm), root (Rt), Rh, and bulk (Bl) control soil samples, and sequenced the V5–V7 region of the bacterial 16S rRNA gene using the Illumina HiSeq platform to identify bacterial communities originating from different plant habitats. We found that the bacterial richness and diversity in Rh were significantly higher than those in the leaves, Sm, and Rt, but lower than those of the Bl control soil. In total, 37 phyla and 438 genera were identified. Microbial-diversity analysis showed that Proteobacteria and Actinobacteria were the dominant phyla and that Pseudomonas, Bacillus, Sphingomonas, Streptomyces, Microbacterium, Rhizobium, and Nocardioides were the dominant genera. However, there were clear differences in community diversity and structure among the samples. Endophytic bacteria community in Lf, Sm, and Rt shared more similarity than those in Rh and Bl control soil. The numbers of operational taxonomic units exclusive to the Lf, stem, Rt, Rh, and Bl control soil samples were 51, 43, 122, 139, and 922, respectively, implying habitat-specific patterns. Principal coordinate analysis demonstrated differences were apparent in the bacterial communities associated with habitats. On the whole, M. sibirica affected bacterial diversity and structured the bacterial community. This study provides insight into the complex microbial compositions of coastal halophytes.

Rhizobial symbiosis alleviates polychlorinated biphenyls-induced systematic oxidative stress via brassinosteroids signaling in alfalfa

The role of symbiotic rhizobia in the alleviation of polychlorinated biphenyl (PCB)-induced phytotoxicity in alfalfa and the brassinosteroid (BR) hormone signaling involved were investigated during phytoremediation. The association between alfalfa and Sinorhizobium meliloti was adopted as a remediation model. Phytotoxicity due to PCB 77 (3,3',4,4'-tetrachlorobiphenyl) exerted adverse impacts on plant performance (biomass accumulation and photosynthesis) and elicited cellular oxidative stress (overproduction of reactive oxygen species, lipid peroxidation, and cell necrosis) which was largely attenuated by pre-inoculation with S. meliloti strain NM. The protective role may have been achieved as a result of strengthening of basic antioxidant defense before stress as evidenced by the augmented activity and gene expression of antioxidative enzymes (peroxidase, glutathione reductase, superoxide dismutase, catalase, and ascorbate peroxidase) of both leaves and roots. In nodulated seedlings peroxidase showed additive increased activity following PCB exposure but the activities of the other four enzymes tended to remain stable after stress. Furthermore, application of strain NM and brassinolide both triggered the accumulation of endogenous BRs and the antioxidant network, while pre-treatment of seedlings with a biosynthetic inhibitor of BRs, brassinazole, abolished the rhizobia-induced activation of detoxification responses towards PCB. These observations indicate that association with S. meliloti NM enhanced the systemic antioxidant defenses of alfalfa to detoxify PCB, at least in part, via BR-dependent signaling pathways. These results contribute to our knowledge of the 'logistic role' played by rhizobia in assisting the phytoremediation of PCB-contaminated soils and suggest an optimum manipulation strategy for bioremediation.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Effect of Pseudomonas fluorescens RB4 and Bacillus subtilis 189 on the phytoremediation potential of Catharanthus roseus (L.) in Cu and Pb-contaminated soils

The remediation of heavy metal-contaminated soils has become a critical issue due to toxic effects of these metals on living organisms. The current research was conducted to study the effect of Pseudomonas fluorescens RB4 and Bacillus subtilis 189 on the growth and phytoremediation potential of Catharanthus roseus in Cu- and Pb-contaminated soils. The bacterial strains exhibited significantly higher level of water-extractable Pb and Cu in Pb, Cu, and Cu+Pb-contaminated. The P. fluorescens RB4 inoculated plants, produced 102%, 48%, and 45% higher fresh weight (FW) in soils contaminated with Cu, Pb, and both elements, respectively, as compared to un-inoculated control plants. Similarly, B. subtilis 189 inoculated plants produced 108%, 43%, and 114% more FW in the presence of Cu, Pb, and both elements. The plants co-cultivated with both bacteria exhibited 121%, 102%, and 177% higher FW, in Cu, Pb, and both elements contaminated soils, as compared to respective un-inoculated control. Co-cultivation of P. fluorescens RB4, B. subtilis 189, and P. fluorescens RB4 + B. subtilis 189 resulted in higher accumulation of Cu and Pb in shoots of the C. roseus grown in contaminated soils as compared to un-inoculated control. Bacterial treatments also improved the translocation and metal bioconcentration factors. The growth and phytoextraction capability of C. roseus was improved by inoculation of P. fluorescens RB4 and B. subtilis 189.

Juncus spp.-The helophyte for all (phyto)remediation purposes?

Helophytic plants contribute significantly to the remediation of ecosystems through a wide range of physiological or biochemical mechanisms including the role of endophytic bacteria. This review highlights the services provided by Juncus spp. wetland plants, from phytoremediation of soils and groundwater with heavy metals and/or organics to municipal or industrial wastewater treatment in constructed wetlands. The data presented also provide information on the efficiency of specific Juncus spp. in response to various metals and organic compounds, in an effort to exploit the natural capabilities of autochthonous over exotic species in phytoremediation strategies. An overall successful direct (the plant itself) or indirect (through stimulation of elimination mechanisms) contribution of Juncus to remediation of the above contaminants is revealed. However, the specific characteristics of the species used, the type of the pollutant and the region, are issues that should be addressed for a successful outcome.

The Plant as Metaorganism and Research on Next-Generation Systemic Pesticides - Prospects and Challenges

Systemic pesticides (SPs) are usually recommended for soil treatments and as seed coating agents and are taken up from the soil by involving various plant-mediated processes, physiological, and morphological attributes of the root systems. Microscopic insights and next-generation sequencing combined with bioinformatics allow us now to identify new functions and interactions of plant-associated bacteria and perceive plants as meta-organisms. Host symbiotic, rhizo-epiphytic, endophytic microorganisms and their functions on plants have not been studied yet in accordance with uptake, tanslocation and action of pesticides. Root tips exudates mediated by rhizobacteria could modify the uptake of specific pesticides while bacterial ligands and enzymes can affect metabolism and fate of pesticide within plant. Over expression of specific proteins in cell membrane can also modify pesticide influx in roots. Moreover, proteins and other membrane compartments are usually involved in pesticide modes of action and resistance development. In this article it is discussed what is known of the physiological attributes including apoplastic, symplastic, and trans-membrane transport of SPs in accordance with the intercommunication dictated by plant-microbe, cell to cell and intracellular signaling. Prospects and challenges for uptake, translocation, storage, exudation, metabolism, and action of SPs are given through the prism of new insights of plant microbiome. Interactions of soil applied pesticides with physiological processes, plant root exudates and plant microbiome are summarized to scrutinize challenges for the next-generation pesticides.