Rhizoremediation of petroleum hydrocarbons: a model system for plant microbiome manipulation

Diversity of hydrocarbon-degrading bacteria in mangroves rhizosphere as an indicator of oil-pollution bioremediation in mangrove forests

Mangrove ecosystems, characterized by high levels of productivity, are susceptible to anthropogenic activities, notably oil pollution arising from diverse origins including spills, transportation, and industrial effluents. Owing to their role in climate regulation and economic significance, there is a growing interest in developing mangrove conservation strategies. In the Arabian Gulf, mangroves stand as the sole naturally occurring green vegetation due to the region's hot and arid climate. However, they have faced persistent oil pollution for decades. This review focuses on global mangrove distribution, with a specific emphasis on Qatar's mangroves. It highlights the ongoing challenges faced by mangroves, particularly in relation to the oil industry, and the impact of oil pollution on these vital ecosystems. It outlines major oil spill incidents worldwide and the diverse hydrocarbon-degrading bacterial communities within polluted areas, elucidating their potential for bioremediation. The use of symbiotic interactions between mangrove plants and bacteria offers a more sustainable, cost-effective and environmentally friendly alternative. However, the success of these bioremediation strategies depends on a deep understanding of the dynamics of bacterial communities, environmental factors and specific nature of the pollutants.

Mechanistic and future prospects in rhizospheric engineering for agricultural contaminants removal, soil health restoration, and management of climate change stress

Climate change, food insecurity, and agricultural pollution are all serious challenges in the twenty-first century, impacting plant growth, soil quality, and food security. Innovative techniques are required to mitigate these negative outcomes. Toxic heavy metals (THMs), organic pollutants (OPs), and emerging contaminants (ECs), as well as other biotic and abiotic stressors, can all affect nutrient availability, plant metabolic pathways, agricultural productivity, and soil-fertility. Comprehending the interactions between root exudates, microorganisms, and modified biochar can aid in the fight against environmental problems such as the accumulation of pollutants and the stressful effects of climate change. Microbes can inhibit THMs uptake, degrade organic pollutants, releases biomolecules that regulate crop development under drought, salinity, pathogenic attack and other stresses. However, these microbial abilities are primarily demonstrated in research facilities rather than in contaminated or stressed habitats. Despite not being a perfect solution, biochar can remove THMs, OPs, and ECs from contaminated areas and reduce the impact of climate change on plants. We hypothesized that combining microorganisms with biochar to address the problems of contaminated soil and climate change stress would be effective in the field. Despite the fact that root exudates have the potential to attract selected microorganisms and biochar, there has been little attention paid to these areas, considering that this work addresses a critical knowledge gap of rhizospheric engineering mediated root exudates to foster microbial and biochar adaptation. Reducing the detrimental impacts of THMs, OPs, ECs, as well as abiotic and biotic stress, requires identifying the best root-associated microbes and biochar adaptation mechanisms.

How to deal with xenobiotic compounds through environment friendly approach?

Every year, a huge amount of lethal compounds, such as synthetic dyes, pesticides, pharmaceuticals, hydrocarbons, etc. are mass produced worldwide, which negatively affect soil, air, and water quality. At present, pesticides are used very frequently to meet the requirements of modernized agriculture. The Food and Agriculture Organization of the United Nations (FAO) estimates that food production will increase by 80% by 2050 to keep up with the growing population, consequently pesticides will continue to play a role in agriculture. However, improper handling of these highly persistent chemicals leads to pollution of the environment and accumulation in food chain. These effects necessitate the development of technologies to eliminate or degrade these pollutants. Degradation of these compounds by physical and chemical processes is expensive and usually results in secondary compounds with higher toxicity. The biological strategies proposed for the degradation of these compounds are both cost-effective and eco-friendly. Microbes play an imperative role in the degradation of xenobiotic compounds that have toxic effects on the environment. This review on the fate of xenobiotic compounds in the environment presents cutting-edge insights and novel contributions in different fields. Microbial community dynamics in water bodies, genetic modification for enhanced pesticide degradation and the use of fungi for pharmaceutical removal, white-rot fungi's versatile ligninolytic enzymes and biodegradation potential are highlighted. Here we emphasize the factors influencing bioremediation, such as microbial interactions and carbon catabolism repression, along with a nuanced view of challenges and limitations. Overall, this review provides a comprehensive perspective on the bioremediation strategies.

Interactions between plants and bacterial communities for phytoremediation of petroleum-contaminated soil

Plants can stimulate the microbes to degrade ubiquitous petroleum hydrocarbons (PHCs), which has prompted a novel view on rhizoremediation. In the present study, the degradation rate of PHCs was investigated and 16S rRNA gene analysis was performed to investigate the PHC-degrading bacteria in petroleum-contaminated soil with different plants. Mirabilis jalapa (M. jalapa) has a higher PHC degradation rate than Lolium perenne (L. perenne) under petroleum contamination. The bacterial diversity in rhizospheric soil was decreased but the relative abundance of Actinobacteriota, Proteobacteria, and Candidatus Saccharibacteria were significant increased on 45 days petroleum-contaminated rhizospheric soil. In addition, the relative expression of PHC degradation-related genes, the content of malic acid and citric acid of the root exudates in the two plants was significantly increased in response to petroleum stress. The content of citric acid increased 11.9 times in M. jalapa and 3.4 times in L. perenne, respectively, in response to petroleum stress. These results indicate that M. jalapa changes the hydrocarbon-degrading microbial community to enhance the degradation of PHCs by root exudates and phytostimulation.

A combined landfarming-phytoremediation method to enhance remediation of mixed persistent contaminants

Contamination of soil and water with petroleum hydrocarbons and metals can pose a significant threat to the environment and human health. This study aimed to investigate the establishment and growth of tall fescue and agropyron in two petroleum-contaminated soils (soil S1 and soil S2) with previous landfarming treatments, and to assess the phytoremediation potential for heavy metal removal from these polluted soils. The results showed that the presence of petroleum hydrocarbons significantly (P < 0.05) reduced plant growth, but plant development was facilitated in soils with prior landfarming treatments. Urease activity in the rhizosphere of agropyron for soil S1 was about 47% higher than the unplanted control soil. The rhizosphere of agropyron and tall fescue eliminated more than 40% and 20% of total hydrocarbon amounts in soil S1, respectively, compared to the unplanted soil. Moreover, the plants grown in the landfarming treatment exhibited higher concentrations of metals (Fe, Zn, Mn, Cu, and Ni) than the control. Based on the findings, the combination of landfarming and phytoremediation techniques can provide an optimal solution for removing mixed pollutants, including petroleum hydrocarbons and metals, from the environment.

Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400

Introduction

Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.

Methods

By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.

Results

Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.

Discussions

This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.

Microbes-assisted phytoremediation of lead and petroleum hydrocarbons contaminated water by water hyacinth

An experiment was carried out to explore the impact of petroleum hydrocarbons (PHs)-degrading microbial consortium (MC) on phytoremediation ability and growth of water hyacinth (WH) plants in water contaminated with lead (Pb) and PHs. Buckets (12-L capacity) were filled with water and WH plants, PHs (2,400 mg L-1) and Pb (10 mg L-1) in respective buckets. Plants were harvested after 30 days of transplanting and results showed that PHs and Pb substantially reduced the agronomic (up to 62%) and physiological (up to 49%) attributes of WH plants. However, the application of MC resulted in a substantial increase in growth (38%) and physiology (22%) of WH plants over uninoculated contaminated control. The WH + MC were able to accumulate 93% Pb and degrade/accumulate 72% of PHs as compared to initial concentration. Furthermore, combined use of WH plants and MC in co-contamination of PHs and Pb, reduced Pb and PHs contents in water by 74% and 68%, respectively, than that of initially applied concentration. Our findings suggest that the WH in combination with PHs-degrading MC could be a suitable nature-based water remediation technology for organic and inorganic contaminants and in future it can be used for decontamination of mix pollutants from water bodies.

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.

Biological remediation treatments improve the health of a mixed contaminated soil before significantly reducing contaminant levels

The remediation of mixed contaminated soil is challenging as it often requires actions to minimize metal-induced risks while degrading organic contaminants. Here, the effectiveness of different bioremediation strategies, namely, rhizoremediation with native plant species, mycoremediation with Pleurotus ostreatus spent mushroom substrate, and biostimulation with organic by-products (i.e., composted sewage sludge and spent mushroom substrate), for the recovery of a mixed contaminated soil from an abandoned gravel pit was studied. The combination of biostimulation and rhizoremediation led to the most significant increase in soil health, according to microbial indicator values. The application of composted sewage sludge led to the highest reduction in anthracene and polychlorinated biphenyls concentrations. None of the strategies managed to decrease contamination levels below regulatory limits, but they did enhance soil health. It was concluded that the biological remediation treatments improved soil functioning in a short time, before the concentration of soil contaminants was significantly reduced.

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

A diverse microbial community and common core microbiota associated with the gonad of female Parascaris spp

The microbiome plays an important role in health, where changes in microbiota composition can have significant downstream effects within the host, and host-microbiota relationships can be exploited to affect health outcomes. Parasitic helminths affect animals globally, but an exploration of their microbiota has been limited, despite the development of anti-Wolbachia drugs to help control infections with some filarial nematodes. The equine ascarids, Parascaris spp., are considered the most pathogenic nematodes affecting juvenile horses and are also the only ascarid parasite to have developed widespread anthelmintic resistance. The aim of this study was to characterize the microbiota of this helminth, focusing on the female gonad, determine a core microbiota for this organ, identify bacterial species, and show bacterial localization to the female gonad via in situ hybridization (ISH). A total of 22 gonads were isolated from female Parascaris spp. collected from three foals, and 9 female parasites were formalin-fixed and paraffin-embedded for ISH. Next-generation sequencing was performed using V3-V4 primers as well as the Swift Amplicon™ 16S+ ITS Panel. Overall, ten genera were identified as members of the Parascaris spp. female gonad and twelve bacterial species were identified. The most prevalent genus was Mycoplasma, followed by Reyranella, and there were no differences in alpha diversity between parasites from different horses. Specific eubacteria staining was identified in both the intestine and within the gonad using ISH. Overall, this study provided in-depth information regarding the female Parascaris spp. microbiota and was the first to identify the core microbiota within a specific parasite organ.

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.

Soil fauna-microbial interactions shifts fungal and bacterial communities under a contamination disturbance

The aim of this study was to determine whether the soil faunal-microbial interaction complexity (SFMIC) is a significant factor influencing the soil microbial communities and the willow growth in the context of PAH contamination. The SFMIC treatment had eight levels: just the microbial community, or the microbial community with nematodes, springtails, earthworms and all the possible combinations. SFMIC affected the height and biomass of willows after eight weeks or growth. SFMIC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFMIC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many polycyclic aromatic hydrocarbons (PAH) degraders. These SFMIC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFMIC treatments. Over 95% of PAH was degraded in all pots at the end of the experiment. Overall, our results suggest that, under our experimental conditions, SFMIC changes willow phytoremediation outcomes.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Metabolic engineering of Escherichia coli for 2,4-dinitrotoluene degradation

2,4-Dinitrotoluene (2,4-DNT) as a common industrial waste has been massively discharged into the environment with industrial wastewater. Due to its refractory degradation, high toxicity, and bioaccumulation, 2,4-DNT pollution has become increasingly serious. Compared with the currently available physical and chemical methods, in situ bioremediation is considered as an economical and environmentally friendly approach to remove toxic compounds from contaminated environment. In this study, we relocated a complete degradation pathway of 2,4-DNT into Escherichia coli to degrade 2,4-DNT completely. Eight genes from Burkholderia sp. strain were re-synthesized by PCR-based two-step DNA synthesis method and introduced into E. coli. Degradation experiments revealed that the transformant was able to degrade 2,4-DNT completely in 12 h when the 2,4-DNT concentration reached 3 mM. The organic acids in the tricarboxylic acid cycle were detected to prove the degradation of 2,4-DNT through the artificial degradation pathway. The results proved that 2,4-DNT could be completely degraded by the engineered bacteria. In this study, the complete degradation pathway of 2,4-DNT was constructed in E. coli for the first time using synthetic biology techniques. This research provides theoretical and experimental bases for the actual treatment of 2,4-DNT, and lays a technical foundation for the bioremediation of organic pollutants.

The effect of petroleum levels on some soil biological properties under phytoremediation and bioaugmentation

With the development of industries and excessive use of petroleum compounds, petroleum pollution has become a serious threat to the environment. The aim of this study was to the effect of petroleum levels on the biological activities of soil affected by phytoremediation and bioaugmentation. A surface soil sample was collected from the polluted areas around Bandar Abbas Oil Refinery Company, and the petroleum-degrading bacteria were isolated. M. yunnanensis (native) was selected among the isolated colonies for further experiment. The used soil in this study was a surface soil collected from Baghu region of Bandar Abbas, Sothern Iran, and treatments were added to soil samples. To evaluate removal of petroleum levels (0, 4, and 8%) from the soil by phytoremediation (control, sorghum, barley, and bermudagrass) and bioaugmentation (control, A. brasilense (non-native) and M. yunnanensis) and bioaugmented phytoremediation, a factorial pot experiment with completely randomized design and three replications was performed. The results demonstrated that sorghum and bermudagrass were more resistant than barley to the toxic effects of petroleum. Positive effect of bacteria on dry weight in polluted soil was greater than in the non-polluted soil. The degradation of petroleum reaches 77% in sorghum + M. yunanesis + 4% petroleum. Plants had stronger ability to degrade total petroleum hydrocarbon (TPH), while bacteria could better degrade polyaromatic hydrocarbons (PAHs). Application of bacteria and plants stimulated soil biological characteristics (dehydrogenase, arylsulfatase, lipase, bacterial population, and respiration) in polluted soil. Among measured enzymes, dehydrogenase exhibited a stronger response to petroleum levels. Four-percent level had greater irritating effect on soil biological properties. Plants and bacteria rely on differences in biological properties to attain synergy in petroleum degradation. Results indicated that M. yunnanensis has a high ability to remove petroleum from soil, and plants enhance the efficiency of this bacterium.

Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons

Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

Bioelimination of Phytotoxic Hydrocarbons by Biostimulation and Phytoremediation of Soil Polluted by Waste Motor Oil

Soils contaminated by waste motor oil (WMO) affect their fertility, so it is necessary to recover them by means of an efficient and safe bioremediation technique for agricultural production. The objectives were: (a) to biostimulate the soil impacted by WMO by applying crude fungal extract (CFE) and Cicer arietinum as a green manure (GM), and (b) phytoremediation using Sorghum vulgare with Rhizophagus irregularis and/or Rhizobium etli to reduce the WMO below the maximum value according to NOM-138 SEMARNAT/SS or the naturally detected one. Soil impacted by WMO was biostimulated with CFE and GM and then phytoremediated by S. vulgare with R. irregularis and R. etli. The initial and final concentrations of WMO were analyzed. The phenology of S. vulgare and colonization of S. vulgaris roots by R. irregularis were measured. The results were statistically analyzed by ANOVA/Tukey's HSD test. The WMO in soil that was biostimulated with CFE and GM, after 60 days, was reduced from 34,500 to 2066 ppm, and the mineralization of hydrocarbons from 12 to 27 carbons was detected. Subsequently, phytoremediation with S. vulgare and R. irregularis reduced the WMO to 86.9 ppm after 120 days, which is a concentration that guarantees the restoration of soil fertility for safe agricultural production for human and animal consumption.

Microbial communities in the rhizosphere of maize and cowpea respond differently to chromium contamination

Chromium (Cr) contamination can affect microorganisms in the soil, but the response of the microbial community in the rhizosphere of plants grown in Cr-contaminated soils is poorly understood. Therefore, this study assessed the microbial community, by amplicon sequencing, in the rhizosphere of maize and cowpea growing in uncontaminated (∼6.0 mg kg^-1 Cr) and Cr-contaminated soils (∼250 mg kg^-1 Cr). Comparing Cr-contaminated and uncontaminated soils, the microbial community in the maize rhizosphere clustered separately, while the microbial community in the cowpea rhizosphere did not present clear clustering. The microbial richness ranged from ∼5000 (rhizosphere in Cr-contaminated soil) to ∼8000 OTUs (in uncontaminated soil). In the comparison of specific bacterial groups in the rhizosphere of maize, Firmicutes were enriched in Cr-contaminated soil, including Bacilli, Bacillales, and Paenibacillus. Cowpea rhizosphere showed a higher abundance of six microbial groups in Cr-contaminated soil, highlighting Rhizobiales, Pedomicrobium, and Gemmatimonadetes. The microbial community in both rhizospheres presented a similar proportion of specialists comparing uncontaminated (2.2 and 3.4% in the rhizosphere of maize and cowpea, respectively) and Cr-contaminated soils (1.8 and 3.2% in the rhizosphere of maize and cowpea, respectively). This study showed that each plant species drove differently the microbial community in the rhizosphere, with an important effect of Cr-contamination on the microbial community assembly.

Effect of partially hydrolyzed polyacrylamide (HPAM) on the bacterial communities of wetland rhizosphere soils and their efficiency in HPAM and alkane degradation

The effect of partially hydrolyzed polyacrylamide (HPAM) on structure and function of rhizosphere soil bacterial communities in constructed wetlands has been largely underinvestigated. In this study, we compare the effect of 250, 500, and 1000 mg/L of HPAM on bacterial community composition of Phragmites australis associated rhizosphere soils in an experimental wetland using MiSeq amplicon sequencing. Rhizosphere soils from the HPAM-free and the 500-mg/L-exposed treatments were used for laboratory experiments to further investigate the effect of HPAM on the soil's degradation and respiration activities. Soils treated with HPAM showed differences in bacterial communities with the dominance of Proteobacteria and the enrichment of potential hydrocarbon and HPAM-degrading bacteria. CO₂ generation was higher in the HPAM-free soils than in the HPAM pre-exposed soil, with a noticeable increase in both soils when oil was added. The addition of HPAM at different concentrations had a more pronounced effect on CO₂ evolution in the HPAM-pre-exposed soil. Soils were able to degrade between 37 ± 18.0 and 66 ± 6.7% of C₁₀ to C₃₀ alkanes after 28 days, except in the case of HPAM-pre-exposed soil treated with 500 mg/L where degradation reached 92 ± 4.3%. Both soils reduced HPAM concentration by 60 ± 15% of the initial amount in the 500 mg/L treatment, but by only ≤ 21 ± 7% in the 250-mg/L and 1000-mg/L treatments. In conclusion, the rhizosphere soils demonstrated the ability to adapt and retain their ability to degrade hydrocarbon in the presence of HPAM.

Regional distribution, properties, treatment technologies, and resource utilization of oil-based drilling cuttings: A review

Oil-based drilling cuttings (OBDC) are hazardous wastes produced during the extensive use of oil-based drilling mud in oil and gas exploration and development. They have strong mutagenic, carcinogenic, and teratogenic effects and need to be properly disposed of to avoid damaging the natural environment. This paper reviews the recent research progress on the regional distribution, properties, treatment technologies, and resource utilization of OBDC. The advantages and disadvantages of different technologies for removing petroleum pollutants from OBDC were comprehensively analyzed, and required future developments in treatment technologies were proposed.

The co-application of biochar with bioremediation for the removal of petroleum hydrocarbons from contaminated soil

Soil pollution from petroleum hydrocarbon is a global environmental problem that could contribute to the non-actualisation of the United Nations Sustainable Development Goals. Several techniques have been used to remediate petroleum hydrocarbon-contaminated soils; however, there are technical and economical limitations to existing methods. As such, the development of new approaches and the improvement of existing techniques are imperative. Biochar, a low-cost carbonaceous product of the thermal decomposition of waste biomass has gained relevance in soil remediation. Biochar has been applied to remediate hydrocarbon-contaminated soils, with positive and negative results reported. Consequently, attempts have been made to improve the performance of biochar in the hydrocarbon-based remediation process through the co-application of biochar with other bioremediation techniques as well as modifying biochar properties before use. Despite the progress made in this domain, there is a lack of a detailed single review consolidating the critical findings, new developments, and challenges in biochar-based remediation of petroleum hydrocarbon-contaminated soil. This review assessed the potential of biochar co-application with other well-known bioremediation techniques such as bioaugmentation, phytoremediation, and biostimulation. Additionally, the benefits of modification in enhancing biochar suitability for bioremediation were examined. It was concluded that biochar co-application generally resulted in higher hydrocarbon removal than sole biochar treatment, with up to a 4-fold higher removal observed in some cases. However, most of the biochar co-applied treatments did not result in hydrocarbon removal that was greater than the additive effects of individual treatment. Overall, compared to their complementary treatments, biochar co-application with bioaugmentation was more beneficial in hydrocarbon removal than biochar co-application with either phytoremediation or biostimulation. Future studies should integrate the ecotoxicological and cost implications of biochar co-application for a viable remediation process. Lastly, improving the synergistic interactions of co-treatment on hydrocarbon removal is critical to capturing the full potential of biochar-based remediation.

Emerging bio-dispersant and bioremediation technologies as environmentally friendly management responses toward marine oil spill: A comprehensive review

Marine oil spills emanating from wells, pipelines, freighters, tankers, and storage facilities draw public attention and necessitate quick and environmentally friendly response measures. It is sometimes feasible to contain the oil with booms and collect it with skimmers or burn it, but this is impracticable in many circumstances, and all that can be done without causing further environmental damage is adopting natural attenuation, particularly through microbial biodegradation. Biodegradation can be aided by carefully supplying biologically accessible nitrogen and phosphorus to alleviate some of the microbial growth constraints at the shoreline. This review discussed the characteristics of oil spills, origin, ecotoxicology, health impact of marine oils spills, and responses, including the variety of remedies and responses to oil spills using biological techniques. The different bioremediation and bio-dispersant treatment technologies are then described, with a focus on the use of green surfactants and their advances, benefits/drawbacks. These technologies were thoroughly explained, with a timeline of research and recent studies. Finally, the hurdles that persist as a result of spills are explored, as well as the measures that must be taken and the potential for the development of existing treatment technologies, all of which must be linked to the application of integrated procedures.

The microbial community associated with Parascaris spp. infecting juvenile horses

Background

Parasitic nematodes, including large roundworms colloquially known as ascarids, affect the health and well-being of livestock animals worldwide. The equine ascarids, Parascaris spp., are important parasites of juvenile horses and the first ascarids to develop widespread anthelmintic resistance. The microbiota has been shown to be an important factor in the fitness of many organisms, including parasitic nematodes, where endosymbiotic Wolbachia have been exploited for treatment of filariasis in humans.

Methods

This study used short-read 16S rRNA sequences and Illumina sequencing to characterize and compare microbiota of whole worm small intestinal stages and microbiota of male and female intestines and gonads. Diversity metrics including alpha and beta diversity, and the differential abundance analyses DESeq2, ANCOM-BC, corncob, and metagenomeSeq were used for comparisons.

Results

Alpha and beta diversity of whole worm microbiota did not differ significantly between groups, but Simpson alpha diversity was significantly different between female intestine (FI) and male gonad (MG) (P= 0.0018), and Shannon alpha diversity was significantly different between female and male gonads (P = 0.0130), FI and horse jejunum (HJ) (P = 0.0383), and FI and MG (P= 0.0001). Beta diversity (Fig. 2B) was significantly different between female and male gonads (P = 0.0006), male intestine (MI) and FG (P = 0.0093), and MG and FI (P = 0.0041). When comparing organs, Veillonella was differentially abundant for DESeq2 and ANCOM-BC (p < 0.0001), corncob (P = 0.0008), and metagenomeSeq (P = 0.0118), and Sarcina was differentially abundant across four methods (P < 0.0001). Finally, the microbiota of all individual Parascaris spp. specimens were compared to establish shared microbiota between groups.

Conclusions

Overall, this study provided important information regarding the Parascaris spp. microbiota and provides a first step towards determining whether the microbiota may be a viable target for future parasite control options.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05533-y.

Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere

Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.

Biochar application strategies for polycyclic aromatic hydrocarbons removal from soils

Polycyclic aromatic hydrocarbons (PAHs) are known as a hazardous group of pollutants in the soil which causes many challenges to the environment. In this study, the potential of biochar (BC), as a carbonaceous material, is evaluated for the immobilization of PAHs in soils. For this purpose, various bonding mechanisms of BC and PAHs, and the strength of bonds are firstly described. Also, the effect of impressive criteria including BC physicochemical properties (such as surface area, porosity, particle size, polarity, aromaticity, functional group, etc., which are mostly the function of pyrolysis temperature), number of rings in PAHs, incubation time, and soil properties, on the extent and rate of PAHs immobilization by BC are explained. Then, the utilization of BC in collaboration with biological tools which simplifies further dissipation of PAHs in the soil is described considering detailed interactions among BC, microbes, and plants in the soil matrix. The co-effect of BC and biological remediation has been authenticated by previous studies. Moreover, recent technologies and challenges related to the application of BC in soil remediation are explained. The implementation of a combined BC-biological remediation method would provide excellent prospects for PAHs-contaminated soils.

Eco-physiological response and genotoxicity induced by crude petroleum oil in the potential phytoremediator Vinca rosea L

Background

Phytoremediation is determined as an emerging green technology suitable for the safe remediation and restoration of polluted terrestrial and aquatic environments. In this study, the assessment of an ornamental plant, Vinca rosea L., as a phytoremediator of crude oil in polluted soils was conducted. In an open greenhouse experiment, plants were raised in sandy-clayey soils treated with 1, 3, 5, and 7% oil by weight. The experiment was conducted over 5 months.

Results

Total petroleum hydrocarbon (TPH) degradation percentage by V. rosea after a 5-month growth period ranged from 86.83 ± 0.44% to 59.05% ± 0.45% in soil treated with 1 and 7%, respectively. Plants raised in polluted soils demonstrated a dramatic reduction in germination rates, in addition to growth inhibition outcomes shown from decreased plant height. An increase in branching was observed with an increase in oil pollution percentages. Moreover, the phytomass allocated to the leaves was higher, while the phytomass witnessed lower values for fine roots, flowering and fruiting when compared to the controls. Apart from the apparent morphological changes, there was a decrease in chlorophyll a/b ratio, which was inversely proportional to the oil pollution level. The contents of carotenoids, tannins, phenolics, flavonoids, and antioxidant capacity were elevated directly with an increase in oil pollution level. The start codon-targeted (SCoT) polymorphisms and inter-simple sequence repeat (ISSR) primers showed the molecular variations between the control and plants raised in polluted soils. The genetic similarity and genomic DNA stability were negatively affected by increased levels of crude oil pollution.

Conclusions

The ability of V. rosea to degrade TPH and balance the increased or decreased plant functional traits at the macro and micro levels of plant structure in response to crude oil pollution supports the use of the species for phytoremediation of crude oil-polluted sites. The genotoxic effects of crude oil on V. rosea still require further investigation. Further studies are required to demonstrate the mechanism of phenolic, flavonoid, and antioxidant compounds in the protection of plants against crude oil pollution stress. Testing different molecular markers and studying the differentially expressed genes will help understand the behavior of genetic polymorphism and stress-resistant genes in response to crude oil pollution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00412-6.

Indigenous bacterial consortium-mediated cypermethrin degradation in the presence of organic amendments and Zea mays plants

Cypermethrin is a toxic pyrethroid insecticide that is widely used in agricultural and household activities. One of the most serious issues is its persistence in the environment, because it is easily transported to the soil and aquatic ecosystem. The biodegradation of cypermethrin is emerging as an environmentally friendly method for large-scale treatment. This study examined the application of a novel binary bacterial combination-based (Bacillus thuringiensis strain SG4 and Bacillus sp. strain SG2) approach used for the enhanced degradation of cypermethrin from the environment. The bacterial strains degraded cypermethrin (80% and 85%) in the presence of external nitrogen sources (KNO₃ and NaNO₃). Furthermore, when immobilized in agar disc beads, the co-culture degraded cypermethrin (91.3%) with a half-life (t_1/2) of 4.3 days compared to 4.9 days using sodium alginate beads. Cereal straw, farmyard manure, press mud compost, fresh cow dung, and gypsum were used as organic amendments in the soil to stimulate cypermethrin degradation. Cereal straw promoted the fastest cypermethrin degradation among the different organic amendments tested, with a t_1/2 of 4.4 days. The impact of cypermethrin-degrading bacterial consortium on cypermethrin rhizoremediation was also investigated. Bacterial inoculums exhibited beneficial effects on plant biomass. Moreover, Zea mays and the bacterial partnership substantially enhanced cypermethrin degradation in soil. Six intermediate metabolites were detected during the degradation of cypermethrin, indicating that cypermethrin could be degraded first by the hydrolysis of its carboxyl ester bond, followed by the cleavage of the diaryl linkage and subsequent metabolism. Our findings highlight the promising potential and advantages of the bacterial consortium for the bioremediation of a cypermethrin-contaminated environment.

Nature-Based Solutions for Restoring an Agricultural Area Contaminated by an Oil Spill

A feasibility study is presented for a bioremediation intervention to restore agricultural activity in a field hit by a diesel oil spill from an oil pipeline. The analysis of the real contaminated soil was conducted following two approaches. The first concerned the assessment of the biodegradative capacity of the indigenous microbial community through laboratory-scale experimentation with different treatments (natural attenuation, landfarming, landfarming + bioaugmentation). The second consisted of testing the effectiveness of phytoremediation with three plant species: Zea mays (corn), Lupinus albus (lupine) and Medicago sativa (alfalfa). With the first approach, after 180 days, the different treatments led to biodegradation percentages between 83 and 96% for linear hydrocarbons and between 76 and 83% for branched ones. In case of contamination by petroleum products, the main action of plants is to favor the degradation of hydrocarbons in the soil by stimulating microbial activity thanks to root exudates. The results obtained in this experiment confirm that the presence of plants favors a decrease in the hydrocarbon content, resulting in an improved degradation of up to 18% compared with non-vegetated soils. The addition of plant growth-promoting bacteria (PGPB) isolated from the contaminated soil also promoted the growth of the tested plants. In particular, an increase in biomass of over 50% was found for lupine. Finally, the metagenomic analysis of the contaminated soil allowed for evaluating the evolution of the composition of the microbial communities during the experimentation, with a focus on hydrocarbon- oxidizing bacteria.

Understanding Willow Transcriptional Response in the Context of Oil Sands Tailings Reclamation

One of the reclamation objectives for treated oil sands tailings (OST) is to establish boreal forest communities that can integrate with the surrounding area. Hence, selection of appropriate soil reclamation cover designs and plant species for revegetation are important aspects of tailings landform reclamation and closure. Research and monitoring of the long term and immediate impacts of capped OST on the growth and survival of native boreal plant species are currently underway. However, plant responses to OST-associated toxicity are not well known at the molecular level. Using RNA sequencing, we examined the effects of three types of OST on the willow transcriptome under different capping strategies. The transcriptomic data showed that some genes respond universally and others in a specific manner to different types of OST. Among the dominant and shared upregulated genes, we found some encoding protein detoxification (PD), Cytochrome P450 (CYPs), glutathione S-transferase regulatory process (GST), UDP-glycosyltransferase (UGT), and ABC transporter and regulatory process associated proteins. Moreover, genes encoding several stress-responsive transcription factors (bZIP, BHLH, ERF, MYB, NAC, WRKY) were upregulated with OST-exposure, while high numbers of transcripts related to photosynthetic activity and chloroplast structure and function were downregulated. Overall, the expression of 40 genes was found consistent across all tailings types and capping strategies. The qPCR analysis of a subset of these shared genes suggested that they could reliably distinguish plants exposed to different OST associated stress. Our results indicated that it is possible to develop OST stress exposure biosensors merely based on changes in the level of expression of a relatively small set of genes. The outcomes of this study will further guide optimization of OST capping and revegetation technology by using knowledge based plant stress adaptation strategies.

Toward understanding submersed macrophyte Vallisneria natans-microbe partnerships to improve remediation potential for PAH-contaminated sediment

Rhizodegradation using submersed macrophytes Vallisneria natans (V. natans) is a promising biotechnology with the potential to restore polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. However, how different sediment types influence the rhizoremediation outcome and the characterization of microbial community along the sediment-V. natans continuum is poorly understood. Here, we collect V. natans, sediments and overlying water from two types of vegetation zones with different levels of PAHs pollutions and set up sediment microcosms for phytoremediation tests. V. natans presence was particularly useful for PAHs remediation in the highly contaminated sites and had a significant effect on PAHs rhizodegradation and microbial communities, especially rhizosphere sediments. The structural composition of microbial communities along the sediment-plant continuum was shaped predominantly by compartment niche of V. natans. Moreover, selective enrichment of specific microbial taxa like Herbaspirillum (relative abundance = 94.80%) in endosphere of V. natans was observed. Herbaspirillum could use PAH as carbon source and promote the growth of plants. In the highly contaminated sediment, V. natans could recruit these bacteria for toxicant degradation into the root interior. Thus, understanding the complex V. natans-microbe interactions could help set up novel decontamination strategies based on the rhizosphere and root interior interactions between plants and their microbial associates.

Enhancing rhizoremediation of petroleum hydrocarbons through bioaugmentation with a plant growth-promoting bacterial consortium

The slow rate of natural attenuation of organic pollutants, together with unwanted environmental impacts of traditional remediation strategies, has necessitated the exploration of plant-microbe systems for enhanced bioremediation applications. The identification of microorganisms capable of promoting rhizoremediation through both plant growth-promoting and hydrocarbon-degrading processes is crucial to the success and adoption of plant-based remediation techniques. In this study, through successive enrichments of soil samples from a historic oil-contaminated site in Wietze, Germany, we isolated a plant growth-promoting and hydrocarbon-degrading bacterial consortium dominated by Alphaproteobacteria. In microcosm experiments involving Medicago sativa L. and the isolated bacterial consortium, we examined the ability of the consortium to enhance rhizoremediation of petroleum hydrocarbons. The inoculation of M. sativa with the consortium resulted in 66% increase in plant biomass, and achieved a 91% reduction in diesel fuel hydrocarbon concentrations in the soil within 60 days. Metagenome analysis led to the identification of genes and taxa putatively involved in these processes. The majority of the coding DNA sequences associated with plant growth promotion and hydrocarbon degradation in this study were affiliated to Acidocella aminolytica and Acidobacterium capsulatum indicating their potential for biotechnological applications in the rhizoremediation of sites contaminated by petroleum-derived organic pollutants.

The Role of Plant Growth-Promoting Rhizobacteria (PGPR) in Mitigating Plant’s Environmental Stresses

Phytoremediation is a cost-effective and sustainable technology used to clean up pollutants from soils and waters through the use of plant species. Indeed, plants are naturally capable of absorbing metals and degrading organic molecules. However, in several cases, the presence of contaminants causes plant suffering and limited growth. In such situations, thanks to the production of specific root exudates, plants can engage the most suitable bacteria able to support their growth according to the particular environmental stress. These plant growth-promoting rhizobacteria (PGPR) may facilitate plant growth and development with several beneficial effects, even more evident when plants are grown in critical environmental conditions, such as the presence of toxic contaminants. For instance, PGPR may alleviate metal phytotoxicity by altering metal bioavailability in soil and increasing metal translocation within the plant. Since many of the PGPR are also hydrocarbon oxidizers, they are also able to support and enhance plant biodegradation activity. Besides, PGPR in agriculture can be an excellent support to counter the devastating effects of abiotic stress, such as excessive salinity and drought, replacing expensive inorganic fertilizers that hurt the environment. A better and in-depth understanding of the function and interactions of plants and associated microorganisms directly in the matrix of interest, especially in the presence of persistent contamination, could provide new opportunities for phytoremediation.

Development of an Autochthonous Microbial Consortium for Enhanced Bioremediation of PAH-Contaminated Soil

The main objectives of this study were to isolate bacteria from soil chronically contaminated with polycyclic aromatic hydrocarbons (PAHs), develop an autochthonous microbial consortium, and evaluate its ability to degrade PAHs in their native contaminated soil. Strains with the best bioremediation potential were selected during the multi-stage isolation process. Moreover, to choose bacteria with the highest bioremediation potential, the presence of PAH-degrading genes (pahE) was confirmed and the following tests were performed: tolerance to heavy metals, antagonistic behavior, phytotoxicity, and antimicrobial susceptibility. In vitro degradation of hydrocarbons led to the reduction of the total PAH content by 93.5% after the first day of incubation and by 99.22% after the eighth day. Bioremediation experiment conducted in situ in the contaminated area resulted in the average reduction of the total PAH concentration by 33.3% after 5 months and by over 72% after 13 months, compared to the concentration recorded before the intervention. Therefore, this study implicates that the development of an autochthonous microbial consortium isolated from long-term PAH-contaminated soil has the potential to enhance the bioremediation process.

Detection of naphthenic acid uptake into root and shoot tissues indicates a direct role for plants in the remediation of oil sands process-affected water

Bitumen extraction from surface-mined oil sands deposits results in the accumulation of large volumes of oil sands process-affected water (OSPW). Naphthenic acids (NAs) are primary contributors to OSPW toxicity and have been a focal point for the development of OSPW remediation strategies. Phytoremediation is an approach that utilizes plants and their associated microbes to remediate contaminants from soil and groundwater. While previous evidence has indicated a role for phytoremediation in OSPW treatment through the transformation and degradation of NAs, there are no reports that demonstrate the direct uptake of NAs into plant tissue. Using NAs labelled with ¹⁴C radioisotopes (¹⁴C-NAs) paired with whole-plant autoradiography, we show that NAs representing aliphatic (linear), single-ring, and diamondoid compounds were effectively removed from hydroponic solution and OSPW-treated soil by sandbar willow (Salix interior) and slender wheatgrass (Elymus trachycaulus) and their associated microbiomes. The NA-derived ¹⁴C label accumulated in root and shoot tissues of both plant species and was concentrated in vascular tissue and rapidly growing sink tissues, indicating that ¹⁴C-NAs or their metabolic derivatives were incorporated into physiological processes within the plants. Slender wheatgrass seedlings grown under axenic (sterile) hydroponic and soil conditions also effectively removed all ¹⁴C-NAs, including a highly stable diamondoid NA, demonstrating that plants can directly take up simple and complex NAs without the assistance of microbes. Furthermore, root and shoot tissue fractionation into major biomolecule groups suggests that NA-derived carbon is allocated toward biomolecule synthesis rapidly after NA treatment. These findings provide evidence of plant-mediated uptake of NAs and support a direct role for plants and their associated microbes in the development of future large-scale OSPW phytoremediation strategies.

Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties

Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.

The remediation potential for PAHs of Verbascum sinuatum L. combined with an enhanced rhizosphere landscape: A full-scale mesocosm experiment

A full-scale mesocosm study was conducted to depict how integrated biological systems interact to adapt to contaminant stress and improve remediation of polycyclic aromatic hydrocarbons (PAHs)contaminated soils. The combination of Verbascum sinuatum L. and microbial consortium (fungi and bacteria) was employed along with three differently contaminated soils. After 240 days the highest PAHs removal (up to 68 %) and 6-rings compounds decrease was found in soil with lower pollution and cation exchange capacity. V. sinuatum showed a significant adaptability over time in terms of redox biology. Soil enzyme activities and microscopic evidences proved a rising plant-microorganisms association and a successful mycorrhization, arising from the inoculation of our consortia. In addition, an enhanced richness of PAHs degrading genes was achieved. Microbial co-metabolism, helped by the establishment of complex relationships with hosting plant, demonstrated to be suitable for the degradation of high molecular weight PAHs and represents a biotechnology with great prospects.

Mitigation of petroleum-hydrocarbon-contaminated hazardous soils using organic amendments: A review

The term "Total petroleum hydrocarbons" (TPH) is used to describe a complex mixture of petroleum-based hydrocarbons primarily derived from crude oil. Those compounds are considered as persistent organic pollutants in the terrestrial environment. A wide array of organic amendments is increasingly used for the remediation of TPH-contaminated soils. Organic amendments not only supply a source of carbon and nutrients but also add exogenous beneficial microorganisms to enhance the TPH degradation rate, thereby improving the soil health. Two fundamental approaches can be contemplated within the context of remediation of TPH-contaminated soils using organic amendments: (i) enhanced TPH sorption to the exogenous organic matter (immobilization) as it reduces the bioavailability of the contaminants, and (ii) increasing the solubility of the contaminants by supplying desorbing agents (mobilization) for enhancing the subsequent biodegradation. Net immobilization and mobilization of TPH have both been observed following the application of organic amendments to contaminated soils. This review examines the mechanisms for the enhanced remediation of TPH-contaminated soils by organic amendments and discusses the influencing factors in relation to sequestration, bioavailability, and subsequent biodegradation of TPH in soils. The uncertainty of mechanisms for various organic amendments in TPH remediation processes remains a critical area of future research.

Clover Root Exudates Favor Novosphingobium sp. HR1a Establishment in the Rhizosphere and Promote Phenanthrene Rhizoremediation

Rhizoremediation is based on the ability of microorganisms to metabolize nutrients from plant root exudates and, thereby, to cometabolize or even mineralize toxic environmental contaminants. Novosphingobium sp. HR1a is a bacterial strain able to degrade a wide variety of polycyclic aromatic hydrocarbons (PAHs). Here, we have demonstrated that the number of CFU in microcosms vegetated with clover was almost 2 orders of magnitude higher than that in nonvegetated microcosms or microcosms vegetated with rye-grass or grass. Strain HR1a was able to eliminate 92% of the phenanthrene in the microcosms with clover after 9 days. We have studied the molecular basis of the interaction between strain HR1a and clover by phenomic, metabolomic, and transcriptomic analyses. By measuring the relative concentrations of several metabolites exudated by clover both in the presence and in the absence of the bacteria, we identified some compounds that were probably consumed in the rhizosphere; the transcriptomic analyses confirmed the expression of genes involved in the catabolism of these compounds. By using a transcriptional fusion of the green fluorescent protein (GFP) to the promoter of the gene encoding the dioxygenase involved in the degradation of PAHs, we have demonstrated that this gene is induced at higher levels in clover microcosms than in nonvegetated microcosms. Therefore, the positive interaction between clover and Novosphingobium sp. HR1a during rhizoremediation is a result of the bacterial utilization of different carbon and nitrogen sources released during seedling development and the capacity of clover exudates to induce the PAH degradation pathway. IMPORTANCE The success of an eco-friendly and cost-effective strategy for soil decontamination is conditioned by the understanding of the ecology of plant-microorganism interactions. Although many studies have been published about the bacterial metabolic capacities in the rhizosphere and about rhizoremediation of contaminants, there are fewer studies dealing with the integration of bacterial metabolic capacities in the rhizosphere during PAH bioremediation, and some aspects still remain controversial. Some authors have postulated that the presence of easily metabolizable carbon sources in root exudates might repress the expression of genes required for contaminant degradation, while others found that specific rhizosphere compounds can induce such genes. Novosphingobium sp. HR1a, which is our model organism, has two characteristics desirable in bacteria for use in remediation: its ubiquity and the capacity to degrade a wide variety of contaminants. We have demonstrated that this bacterium consumes several rhizospheric compounds without repression of the genes required for the mineralization of PAHs. In fact, some compounds even induced their expression.

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

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

Soil Buffering Capacity Can Be Used To Optimize Biostimulation of Psychrotrophic Hydrocarbon Remediation

Effective bioremediation of hydrocarbons requires innovative approaches to minimize phosphate precipitation in soils of different buffering capacities. Understanding the mechanisms underlying sustained stimulation of bacterial activity remains a key challenge for optimizing bioremediation-particularly in northern regions. Positron emission tomography (PET) can trace microbial activity within the naturally occurring soil structure of intact soils. Here, we use PET to test two hypotheses: (1) optimizing phosphate bioavailability in soil will outperform a generic biostimulatory solution in promoting hydrocarbon remediation and (2) oligotrophic biostimulation will be more effective than eutrophic approaches. In so doing, we highlight the key bacterial taxa that underlie aerobic and anaerobic hydrocarbon degradation in subarctic soils. In particular, we showed that (i) optimized phosphate bioavailability outperformed generic biostimulatory solutions in promoting hydrocarbon degradation, (ii) oligotrophic biostimulation is more effective than eutrophic approaches, and (iii) optimized biostimulatory solutions stimulated specific soil regions and bacterial consortia. The knowledge gleaned from this study will be crucial in developing field-scale biodegradation treatments for sustained stimulation of bacterial activity in northern regions.

In situ microbial and phytoremediation of crude oil contaminated soil by Cynodon sp

Crude oil contamination of land and water leads to their abandonment after heavy oil recovery processes. Analogous to bioremediation, phytoremediation has provided an efficient solution towards land reclamation through enhancement of flora. The present work manifests significance of phytoremediation via reclamation of crude oil contaminated soil collected from Kalol, India. The collected soil was analyzed for pH, oxidation-reduction potential, electrical conductivity (EC), bulk density, particle size, moisture. The experimental work consists three batch units; pot A, pot B and pot C with crude oil contaminated soil, fresh soil and control respectively. While observing plant growth for 120 days, Total Petroleum Hydrocarbon (TPH) was measured at determined intervals for estimation of percentage degradation. After 90 days of pot observation, contaminated soil was inoculated with rhizospheric bacterial inoculum developed from pot A which forms new batch for microbial-remediation as an additional scope to this work. Gas chromatography mass spectroscopy (GC-MS-MS) was carried out for determination of naphthalene contamination. Crude oil degradation in pot A was estimated as 82.16% followed with the affirmation given by degradation kinetics whereas, 60.68% and 36.75% degradation was observed in pot C-control and new batch respectively. Cynodon sp. grown in pot A was confirmed by identification as reported.

Petroleum hydrocarbon rhizoremediation and soil microbial activity improvement via cluster root formation by wild proteaceae plant species

Rhizoremediation potential of different wild plant species for total (aliphatic) petroleum hydrocarbon (TPH)-contaminated soils was investigated. Three-week-old seedlings of Acacia inaequilatera, Acacia pyrifolia, Acacia stellaticeps, Banksia seminuda, Chloris truncata, Hakea prostrata, Hardenbergia violacea, and Triodia wiseana were transplanted in a soil contaminated with diesel and engine oil as TPH at pollution levels of 4,370 (TPH1) and 7,500 (TPH2) mg kg^-1, and an uncontaminated control (TPH0). After 150 days, the presence of TPH negatively affected the plant growth, but the growth inhibition effect varied between the plant species. Plant growth and associated root biomass influenced the activity of rhizo-microbiome. The presence of B. seminuda, C. truncata, and H. prostrata significantly increased the TPH removal rate (up to 30% compared to the unplanted treatment) due to the stimulation of rhizosphere microorganisms. No significant difference was observed between TPH1 and TPH2 regarding the plant tolerance and rhizoremediation potentials of the three plant species. The presence of TPH stimulated cluster root formation in B. seminuda and H. prostrata which was associated with enhanced TPH remediation of these two members of Proteaceae family. These results indicated that B. seminuda, C. truncata, and H. prostrata wild plant species could be suitable candidates for the rhizoremediation of TPH-contaminated soil.

Effects of Association of Barley Plants with Hydrocarbon-Degrading Bacteria on the Content of Soluble Organic Compounds in Clean and Oil-Contaminated Sand

Plant-bacteria consortia are more effective in bioremediation of petroleum contaminated soil than when either organism is used individually. The reason for this is that plant root exudates promote growth and activity of oil degrading bacteria. However, insufficient attention has been paid to the ability of bacteria to influence root exudation. Therefore, the influence of barley plants and/or bacterial inoculation (Pseudomonas hunanensis IB C7 and Enterobacter sp. UOM 3) on the content of organic acids, sugars and plant hormones in the eluate from clean and oil-polluted sand was studied separately or in combination. These strains are capable of oxidizing hydrocarbons and synthesizing auxins. Concentrations of organic acids and sugars were determined using capillary electrophoresis, and hormones by enzyme-linked immunosorbent assays. In the absence of plants, no sugars were detected in the sand, confirming that root exudates are their main source. Introducing bacteria into the sand increased total contents of organic compounds both in the presence and absence of oil. This increase could be related to the increase in auxin amounts in the sand eluate, as well as in plants. The results indicate that bacteria are able to increase the level of root exudation. Since auxins can promote root exudation, bacterial production of this hormone is likely responsible for increased concentrations of soluble organic compounds in the sand. Bacterial mediation of root exudation by affecting plant hormonal status should be considered when choosing microorganisms for phytoremediation.

Phenanthrene contamination and ploidy level affect the rhizosphere bacterial communities of Spartina spp

Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These events have resulted in a heightened tolerance to hydrocarbon contaminants, but the effects of this phenomenon on the rhizosphere microbial communities are unknown. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene was amplified and sequenced, whereas the abundances of the genes encoding for the PAH (polycyclic aromatic hydrocarbon) ring-hydroxylating dioxygenase (RHD) of Gram-negative and Gram-positive bacteria were quantified by real-time PCR. Both the contamination and the plant genotype significantly affected the bacterial communities. In particular, the allopolyploid S. anglica harbored a more diverse bacterial community in its rhizosphere. The interspecific hybrid and the allopolyploid also harbored significantly more copies of the PAH-RHD gene of Gram-negative bacteria in their rhizosphere than the parental species, irrespective of the contamination treatments. Overall, our results are showing that the recent polyploidization events in the Spartina affected its rhizosphere bacterial communities, both under normal and contaminated conditions, possibly increasing its phytoremediation potential.

Response of three native grass species on dry tailings reclamation substrate amended with petroleum coke

Surface mining around the world has produced large quantities of waste materials with ecological impacts. Oil sands mining in Canada generates large volumes of petroleum coke and tailings every year, which are stockpiled in the mining areas and must be reclaimed through capping or used in reclamation substrates. A greenhouse study was conducted to determine whether substrates of various mixes of dry tailings (DT), tailings sand (TS), and peat mineral mix (PMM) with coke amendment would support emergence and growth of three grass species commonly used in land reclamation. After 16 wk in the greenhouse, plant performance varied with substrate and amendment. Treatment with DT/TS/PMM (50:25:25) with 40% coke had greatest cover, biomass, and density and the best plant health. Plant growth was inhibited in treatments with DT (100%) and coke (100%) due to high concentrations of hydrocarbons, undesirable exchangeable ions, and salinity that restricted soil water retention (gravimetric water content, hydraulic conductivity) relative to treatments with PMM. Agrostis scabra Willd. and Festuca saximontana. showed poor growth or did not survive on DT and DT/TS with coke. Elymus trachycaulus (Link) Gould ex Shinners performed better in all DT mixes and performed the best in DT/TS/PMM with 40% coke. Results from this study indicate that mixing with PMM could improve the reclamation potential of DT and coke.

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.

Soil Characteristics Constrain the Response of Microbial Communities and Associated Hydrocarbon Degradation Genes during Phytoremediation

Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg^-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.

Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing

Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.

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.