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

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.

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.

Providing octane degradation capability to Pseudomonas putida KT2440 through the horizontal acquisition of oct genes located on an integrative and conjugative element

The extensive use of petrochemicals has produced serious environmental pollution problems; fortunately, bioremediation is considered an efficient way to fight against pollution. In line with Synthetic Biology is that robust microbial chassis with an expanded ability to remove environmental pollutants are desirable. Pseudomonas putida KT2440 is a robust lab microbe that has preserved the ability to survive in the environment and is the natural host for the self-transmissible TOL plasmid, which allows metabolism of toluene and xylenes to central metabolism. We show that the P. putida KT2440 (pWW0) acquired the ability to use octane as the sole C-source after acquisition of an almost 62-kb ICE from a microbial community that harbours an incomplete set of octane metabolism genes. The ICE bears genes for an alkane monooxygenase, a PQQ-dependent alcohol dehydrogenase and aldehyde dehydrogenase but lacks the electron donor enzymes required for the monooxygenase to operate. Host rubredoxin and rubredoxin reductase allow metabolism of octane to octanol. Proteomic assays and mutants unable to grow on octane or octanoic acid revealed that metabolism of octane is mediated by redundant host and ICE enzymes. Octane is oxidized to octanol, octanal and octanoic acid, the latter is subsequently acylated and oxidized to yield acetyl-CoA that is assimilated via the glyoxylate shunt; in fact, a knockout mutant in the aceA gene, encoding isocitrate lyase was unable to grow on octane or octanoic acid.

Methyl Orange Biodegradation by Immobilized Consortium Microspheres: Experimental Design Approach, Toxicity Study and Bioaugmentation Potential

Methyl orange (MO) is categorized among the recalcitrant and refractory xenobiotics, representing a significant burden in the ecosystem. To clean-up the surrounding environment, advances in microbial degradation have been made. The main objective of this study was to investigate the extent to which an autochthonous consortium immobilized in alginate beads can promote an efficient biodegradation of MO. By employing response surface methodology (RSM), a parametric model explained the interaction of immobilized consortium (Raoultella planticola, Ochrobactrum thiophenivorans, Bacillus flexus and Staphylococcus xylosus) to assimilate 200 mg/L of MO in the presence of 40 g/L of NaCl within 120 h. Physicochemical analysis, including UV-Vis spectroscopy and FTIR, and monitoring of the degrading enzymes (azoreductase, DCIP reductase, NADH reductase, laccase, LiP, MnP, nitrate reductase and tyrosinase) were used to evaluate MO degradation. In addition, the toxicity of MO-degradation products was investigated by means of phytotoxicity and cytotoxicity. Chlorella vulgaris retained its photosynthetic performance (>78%), as shown by the contents of chlorophyll-a, chlorophyll-b and carotenoids. The viability of normal lung and kidney cell lines was recorded to be 90.63% and 99.23%, respectively, upon exposure to MO-metabolic outcomes. These results reflect the non-toxicity of treated samples, implying their utilization in ferti-irrigation applications and industrial cooling systems. Moreover, the immobilized consortium was employed in the bioremediation of MO from artificially contaminated agricultural and industrial effluents, in augmented and non-augmented systems. Bacterial consortium remediated MO by 155 and 128.5 mg/L in augmented systems of agricultural and industrial effluents, respectively, within 144 h, revealing its mutual synergistic interaction with both indigenous microbiotas despite differences in their chemical, physical and microbial contents. These promising results encourage the application of immobilized consortium in bioaugmentation studies using different resources.

Enhanced remediation of pollutants by microorganisms-plant combination

The pollutants have become ubiquitous in the total environment (water, soil and air) due to human activities and they are hazardous to all forms of life on the earth. This problem has made scientists focus on mitigating or complete reduction in pollutants by several means. Microorganism and plants are known to scavenge pollutants. Both are studied enormously in reducing, refining, and removing pollutants from the environment successfully. But, their slow process for removal is disadvantage. However, according to recent advancements in the abatement of pollutants, a combined system of both microorganisms and plant has shown to enhance the remediation of pollutants to an efficient level. In a nutrient-depleted pollutant-rich environment, when suitable plant and microorganisms are introduced, the plant interacts with the rhizosphere and root associate with microorganisms to survive in toxic conditions. The chemicals released by plants signal the microorganisms for interactions. This interaction leads in higher germination efficiency and enhanced root elongation which results in enhanced degradation of pollutants in both rhizosphere and phyllosphere. In this background, the current review article provides an overview of the recent advancement in microorganisms plant combined systems in enhanced removal of several recalcitrant pollutants. The conclusion highlights the challenges and future perspectives in this area of research.

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.

Phosphate solubilizing rhizobacteria isolated from jujube ziziphus lotus plant stimulate wheat germination rate and seedlings growth

Jujube plant (Ziziphus lotus (L.) Desf.) can survive in arid climates and tolerates both biotic and abiotic stresses. Here, we isolated, for the first time in Morocco, nine phosphate solubilizing bacteria strains from jujube rhizosphere, designated J10 to J13, J15, & J153 to J156. Genotypic identification based on 16S rDNA sequencing, revealed six strains that belong to Pseudomonas (J10, J12, J13, J15, J153 and J154), two to Bacillus (J11 and J156), and one to Paenibacillus J155. Siderophores were produced by all strains. Proteases activity was missing in Pseudomonas sp. J153 & J154, whereas cellulase was restricted only to Pseudomonas sp. J10, Paenibacillus xylanexedens J155 and Bacillus cereus J156. Indole-3- acetic acid and ammonia were also produced by all strains, with a maxima of 204.28 µg mL⁻¹ in Bacillus megaterium J11 and 0.33 µmol mL⁻¹ in Pseudomonas sp. J153, respectively. Pseudomonas sp. J10 and B. cereus J156 grew on plates containing 1,500 µg mL⁻¹ of nickel nitrate, while Pseudomonas sp. J153 withstood 1,500 µg mL⁻¹ of either copper sulfate or cadmium sulfate. Phenotypic analysis of the potential of the isolates to promote early plant growth showed that wheat seeds inoculated with either P. moraviensis J12 or B. cereus J156 remarkably increased germination rate and seedlings growth. Lastly, antibiotic resistance profiling revealed that except for Pseudomonas sp. J11 and B. cereus J156, remaining strains displayed resistance at least to one of tested antibiotics. Collectively, Pseudomonas sp. J10, P. moraviensis J12, Pseudomonas sp. J153 and B. cereus J156, represent potential biofertilizers suitable for soils that are poor in P, and/or heavy metals contaminated.

Phytotoxicity of petroleum hydrocarbons: Sources, impacts and remediation strategies

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

Combination of plant-growth-promoting and fluoranthene-degrading microbes enhances phytoremediation efficiency in the ryegrass rhizosphere

Plant- and/or microbe-based systems can provide a cost-effective, sustainable means to remove contaminants from soil. Microbe-assisted phytoremediation has potential utility for polycyclic aromatic hydrocarbons such as fluoranthene (Flu) removal from soils; however, the efficiency varies with the plant and microbes used. This study evaluated the Flu removal efficiency in a system with ryegrass (Lolium multiflorum), an IAA-producing Arthrobacter pascens strain (ZZ21), and/or a Flu-degrading Bacillus cereus strain (Z21). Strain ZZ21 significantly enhanced the growth of ryegrass. Ryegrass in combination with both strains (FIP) was the most effective method for Flu removal. By day 60, 74.9% of the Flu was depleted in the FIP treatment, compared with 21.1% in the control (CK), 63.7% with ryegrass alone (P), 69.0% for ryegrass with ZZ21 (IP), and 72.6% for ryegrass with Z21 (FP). FIP treatment promoted ryegrass growth, accelerated Flu accumulation in plants, and increased soil microbial counts. Microbial carbon utilization was significantly higher in soil in the FIP than with the CK treatment. Principal component analysis of the distribution of carbon substrate utilization showed that microbial functional profiles diverged among treatments, and this divergence became more profound at day 60 than day 30. Microbial inoculation significantly enhanced microbial utilization of phenols. Microbes in the FIP soil dominantly utilized amines/amides and phenols at day 30 but shifted to carbohydrates by day 60. Together, the combination of IAA-producing microbes and Flu-degrading microbes could promote plant growth, facilitate Flu degradation, and change soil microbial functional structure.

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.

Diagnosing bioremediation of crude oil-contaminated soil and related geochemical processes at the field scale through microbial community and functional genes

Purpose

Bioremediation is widely considered the most desirable procedure for remediation of oil-contaminated soil. Few studies have focused on the relationships among microbial community, functional genes of biodegradation, and geochemical processes during field bioremediation, which provide crucial information for bioremediation.

Methods

In the current study, the microbial community and functional genes related to hydrocarbon and nitrogen metabolism, combined with the soil physico-chemical properties, were used to diagnose a set of bioremediation experiments, including bioaugmentation, biostimulation, and phytoremediation, at the field scale.

Result

The results showed that the added nutrients stimulated a variety of microorganisms, including hydrocarbon degradation bacteria and nitrogen metabolism microorganisms. The functional genes reflected the possibility of aerobic denitrification in the field, which may be helpful in biodegradation. Biostimulation was found to be the most suitable of the studied bioremediation methods in the field.

Conclusion

We offer a feasible approach to obtain useful bioremediation information and assist with the development of appropriate remediation procedures. The findings improve our knowledge of the interactions between microorganisms and edaphic parameters.

Differentiation between physical and chemical effects of oil presence in freshly spiked soil during rhizoremediation trial

Petroleum contamination and its remediation via plant-based solutions have got increasing attention by environmental scientists and engineers. In the current study, the physiological and growth responses of two diesel-tolerant plant species (tolerance limit: 1500-2000 mg/kg), Italian ryegrass (Lolium multiflorum) and Birdsfoot trefoil (Lotus corniculatus), have been investigated in vegetable oil- and diesel oil-amended soils. A long-term (147-day) greenhouse pot experiment was conducted to differentiate the main focus of the study: physical and chemical effects of oil (vegetable and diesel) in freshly spiked soils via evaluating the plant performance and hydrocarbon degradation. Moreover, plant performance was evaluated in terms of seed germination, plant shoot biomass, physiological parameters, and root biomass. Addition of both diesel oil and vegetable oil in freshly spiked soils showed deleterious effects on seedling emergence, root/shoot biomass, and chlorophyll content of grass and legume plants. Italian ryegrass showed more sensitivity in terms of germination rate to both vegetable and diesel oil as compared to non-contaminated soils while Birdsfoot trefoil reduced the germination rate only in diesel oil-impacted soils. The results of the current study suggest that both physical and chemical effects of oil pose negative effects of plant growth and root development. This observation may explain the phenomenon of reduced plant growth in aged/weathered contaminated soils during rhizoremediation experiments.

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

Phytoremediation is a green and sustainable alternative to physico-chemical methods for contaminated soil remediation. One of the flavours of phytoremediation is rhizoremediation, where plant roots stimulate soil microbes to degrade organic contaminants. This approach is particularly interesting as it takes advantage of naturally evolved interaction mechanisms between plant and microorganisms and often results in a complete mineralization of the contaminants (i.e. transformation to water and CO2 ). However, many biotic and abiotic factors influence the outcome of this interaction, resulting in variable efficiency of the remediation process. The difficulty to predict precisely the timeframe associated with rhizoremediation leads to low adoption rates of this green technology. Here, we review recent literature related to rhizoremediation, with a particular focus on soil organisms. We then expand on the potential of rhizoremediation to be a model plant-microbe interaction system for microbiome manipulation studies.

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams

Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key, although still not fully understood, player that must be considered to assess the toxicity of environmental contaminants. Bacteria-dependent metabolism of xenobiotics may indeed modulate the host toxicity. Conversely, environmental variables (including pollution) may alter the microbial community and/or its metabolic activity leading to host physiological alterations that may contribute to their toxicity. Here, 16s rRNA gene amplicon sequencing has been applied to characterize the hepatopancreas microbiota composition of the Manila clam, Ruditapes philippinarum. The animals were collected in the Venice lagoon area, which is subject to different anthropogenic pressures, mainly represented by the industrial activities of Porto Marghera (PM). Seasonal and geographic differences in clam microbiotas were explored and linked to host response to chemical stress identified in a previous study at the transcriptome level, establishing potential interactions among hosts, microbes, and environmental parameters. The obtained results showed the recurrent presence of putatively detoxifying bacterial taxa in PM clams during winter and over-representation of several metabolic pathways involved in xenobiotic degradation, which suggested the potential for host-microbial synergistic detoxifying actions. Strong interaction between seasonal and chemically-induced responses was also observed, which partially obscured such potentially synergistic actions. Seasonal variables and exposure to toxicants were therefore shown to interact and substantially affect clam microbiota, which appeared to mirror host response to environmental variation. It is clear that understanding how animals respond to chemical stress cannot ignore a key component of such response, the microbiota.

Hydrocarbon degraders establish at the costs of microbial richness, abundance and keystone taxa after crude oil contamination in permafrost environments

Oil spills from pipeline ruptures are a major source of terrestrial petroleum pollution in cold regions. However, our knowledge of the bacterial response to crude oil contamination in cold regions remains to be further expanded, especially in terms of community shifts and potential development of hydrocarbon degraders. In this study we investigated changes of microbial diversity, population size and keystone taxa in permafrost soils at four different sites along the China-Russia crude oil pipeline prior to and after perturbation with crude oil. We found that crude oil caused a decrease of cell numbers together with a reduction of the species richness and shifts in the dominant phylotypes, while bacterial community diversity was highly site-specific after exposure to crude oil, reflecting different environmental conditions. Keystone taxa that strongly co-occurred were found to form networks based on trophic interactions, that is co-metabolism regarding degradation of hydrocarbons (in contaminated samples) or syntrophic carbon cycling (in uncontaminated samples). With this study we demonstrate that after severe crude oil contamination a rapid establishment of endemic hydrocarbon degrading communities takes place under favorable temperature conditions. Therefore, both endemism and trophic correlations of bacterial degraders need to be considered in order to develop effective cleanup strategies.

Engineering Pseudomonas putida KT2440 for simultaneous degradation of carbofuran and chlorpyrifos

Currently, chlorpyrifos (CP) and carbofuran are often applied together to control major agricultural pests in many developing countries, in most cases, they are simultaneously detected in agricultural soils. Some cost‐effective techniques are required for the remediation of combined pollution caused by multiple pesticides. In this work, we aim at constructing a detectable recombinant microorganism with the capacity to simultaneously degrade CP and carbofuran. To achieve this purpose, CP/carbofuran hydrolase genes and gfp were integrated into the chromosome of a biosafety strain Pseudomonas putida KT2440 using a chromosomal scarless modification strategy with upp as a counter‐selectable marker. The toxicity of the hydrolysis products was significantly lower compared with the parent compounds. The recombinant strain could utilize CP or carbofuran as the sole source of carbon for growth. The inoculation of the recombinant strain to soils treated with carbofuran and CP resulted in a higher degradation rate than in noninoculated soils. Introduced green fluorescent protein can be employed as a biomarker to track the recombinant strain during bioremediation. Therefore, the recombinant strain has potential to be applied for in situ bioremediation of soil co‐contaminated with carbofuran and CP.

The ecological and physiological responses of the microbial community from a semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment

The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in semiarid soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted semiarid soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.