Survival and activity of individual bioaugmentation strains

Systematic degradation process of petroleum hydrocarbons by an integrated bacterial consortium under bottom seawater and surface seawater environments

Dealing with oil spills is urgent, and bioaugmentation is a low-cost and environmentally friendly method. However, little research has been done on the remediation effect of bioaugmentation in oil-polluted environments with bottom seawater microorganisms. This work constructed the bottom seawater (S) group and surface seawater environment (T) group to study the oil degradation ability and the microbial community successions tendency with the function of integrated bacterial consortium. After 50 days of bioaugmentation, the oil degradation rates of the S and T groups were 53.33% and 43.72%, which were 26.98% and 25.82% higher than that of natural restoration, respectively. Furthermore, the microbial community structure succeeded in the same direction under different environments after oil pollution and bioaugmentation, and the main classes were Gammaproteobacteria, Alphaproteobacteria. Precisely, Alcanivorax and Cycloclasticus played the primary roles in oil degradation under two different initial environments, and they were mainly affected by natural restoration and bioaugmentation, respectively. This work can contribute to a better base for bioaugmentation strategy development in the bottom seawater environment.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Critical analysis on the transformation and upgrading strategy of Chinese municipal wastewater treatment plants: Towards sustainable water remediation and zero carbon emissions

In the light of circular economy aspects, processing of large-scale municipal wastewater treatment plants (WWTPs) needs reconsideration to limit the overuse of energy, implement of non-green technologies and emit abundant greenhouse gas. Along with the huge increase in the worldwide population and agro-industrial activities, global environmental organizations have issued several recent roles to boost scientific and industrial communities towards sustainable development. Over recent years, China has imposed national and regional standards to control and manage the discharged liquid and solid waste, as well as to achieve carbon peaking and carbon neutrality. The aim of this report is to analyze the current state of Chinese WWTPs routing and related issues such as climate change and air pollution. The used strategies in Chinese WWTPs and upgrading trends were critically discussed. Several points were addressed including the performance, environmental impact, and energy demand of bio-enhanced technologies, including hydrolytic acidification pretreatment, efficient (toxic) strain treatment, and anaerobic ammonia oxidation denitrification technology, as well as advanced treatment technologies composed of physical and chemical treatment technologies, biological treatment technology and combined treatment technology. Discussion and critical analysis based on the current data and national policies were provided and employed to develop the future development trend of municipal WWTPs in China from the construction of sustainable and "Zero carbon" WWTPs.

Microbial degradation as a powerful weapon in the removal of sulfonylurea herbicides

Sulfonylurea herbicides have been widely used worldwide and play a significant role in modern agricultural production. However, these herbicides have adverse biological effects that can damage the ecosystems and harm human health. As such, rapid and effective techniques that remove sulfonylurea residues from the environment are urgently required. Attempts have been made to remove sulfonylurea residues from environment using various techniques such as incineration, adsorption, photolysis, ozonation, and microbial degradation. Among them, biodegradation is regarded as a practical and environmentally responsible way to eliminate pesticide residues. Microbial strains such as Talaromyces flavus LZM1, Methylopila sp. SD-1, Ochrobactrum sp. ZWS16, Staphylococcus cohnii ZWS13, Enterobacter ludwigii sp. CE-1, Phlebia sp. 606, and Bacillus subtilis LXL-7 can almost completely degrade sulfonylureas. The degradation mechanism of the strains is such that sulfonylureas can be catalyzed by bridge hydrolysis to produce sulfonamides and heterocyclic compounds, which deactivate sulfonylureas. The molecular mechanisms associated with microbial degradation of sulfonylureas are relatively poorly studied, with hydrolase, oxidase, dehydrogenase and esterase currently known to play a pivotal role in the catabolic pathways of sulfonylureas. Till date, there are no reports specifically on the microbial degrading species and biochemical mechanisms of sulfonylureas. Hence, in this article, the degradation strains, metabolic pathways, and biochemical mechanisms of sulfonylurea biodegradation, along with its toxic effects on aquatic and terrestrial animals, are discussed in depth in order to provide new ideas for remediation of soil and sediments polluted by sulfonylurea herbicides.

Enhanced treatment of synthetic wastewater by bioaugmentation with a constructed consortium

Bioaugmentation by adding well-functioning mixed microorganism consortia represents a potentially useful approach to improve contaminant removal in wastewater treatment plants (WWTPs). However, unfavorable environmental conditions (i.e., low temperatures) can severely inhibit microbial activity, drawing our attention to constructing cold-tolerant microorganism preparations and investigating their availability in practical applications. Here we screened four in situ functional isolates from the activated sludge of secondary sedimentation tanks in WWTPs to construct a psychrophilic microbial consortium, which was used to perform bioaugmentation for enhanced removal of nitrogen and phosphorus under low temperatures. The consortium was established by cocultivation of four isolates, characterized by 16 S rRNA as the COD-degrading bacterium Aeromonas sp. Z3, aerobic denitrifying bacterium Acinetobacter sp. HF9, nitrifying bacterium Klebsiella sp. X8, and polyphosphate-accumulating bacterium Pseudomonas sp. PC5 respectively. The microorganism preparation was composed of Z3, HF9, X8, and PC5 under the ratio of 1: 1: 3: 1, which can exert optimal pollutant removal under the conditions of 12 °C, 6.0-9.0 pH, 120-200 r‧min-1, and a dosage of 5% (V/V). A 30-day continuous operation of the bioaugmented and control sequencing batch reactors (SBRs) was investigated, and the bioaugmented SBR showed a shorter start-up stage and a more stable operating situation. Compared to the control SBR, the COD, NH4+-N, TN, and TP removal efficiency of the bioaugmented SBR increased by an average of 7.95%, 9.05%, 9.54%, and 7.45% respectively. The analysis of the microbial community revealed that the introduced isolates were dominant in the activated sludge and that functional taxa such as Proteobacteria, Bacteroidota, and Actinobacteria were further enriched after a period of bioaugmentation. The study provides some basis and guidance for the practical application of how to strengthen the stable operation of WWTPs under low temperatures.

Full-scale activated sludge transplantation reveals a highly resilient community structure

Well-functioning and stable microbial communities are critical for the operation of activated sludge (AS) wastewater treatment plants (WWTPs). Bioaugmentation represents a potentially useful approach to recover deteriorated systems or to support specific AS processes, but its application in full-scale WWTPs is generally problematic. We conducted a massive transplantation (in one day) exchanging AS from a donor to a recipient full-scale WWTP with similar process type (biological removal of nitrogen and phosphorus) and performance, but with differences in microbial community structure. The treatment performance in the recipient plant was not compromised and the effluent quality remained stable. The AS community structure of the recipient plant was initially very similar to the donor AS, but it almost completely restored the pre-transplantation structure approximately 40 days after transplantation, corresponding to 3 times the solid retention time. Most of the unique species of donor AS added to recipient AS disappeared quickly, although some disappeared more slowly the following months, indicating some survival and potentially a time limited function in the recipient plant. Moreover, the addition in higher abundance of most species already present in the recipient AS (e.g., the polyphosphate accumulating organisms) or the reduction of the abundance of unwanted bacteria (e.g., filamentous bacteria) in the recipient plant was not successful. Moreover, we observed similar abundance patterns after transplantation for species belonging to different functional guilds, so we did not observe an increase of the functional redundancy. Investigations of the microbial community structure in influent wastewater revealed that for some species the abundance trends in the recipient plant were closely correlated to their abundance in the influent. We showed that a very resilient microbial community was responsible for the outcome of the transplantation of AS at full-scale WWTP, potentially as a consequence of mass-immigration from influent wastewater. The overall results imply that massive transplantation of AS across different WWTPs is not a promising strategy to permanently solve operational problems. However, by choosing a compatible AS donor, short term mitigation of serious operational problems may be possible.

Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation

Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.

Microbial associations for bioremediation. What does "microbial consortia" mean?

Microbial associations arise as useful tools in several biotechnological processes. Among them, bioremediation of contaminated environments usually takes advantage of these microbial associations. Despite being frequently used, these associations are indicated using a variety of expressions, showing a lack of consensus by specialists in the field. The main idea of this work is to analyze the variety of microbial associations referred to as "microbial consortia" (MC) in the context of pollutants biodegradation and bioremediation. To do that, we summarize the origin of the term pointing out the features that an MC is expected to meet, according to the opinion of several authors. An analysis of related bibliography was done seeking criteria to rationalize and classify MC in the context of bioremediation. We identify that the microbe's origin and the level of human intervention are usually considered as a category to classify them as natural microbial consortia (NMC), artificial microbial consortia (AMC), and synthetic microbial consortia (SMC). In this sense, NMC are those associations composed by microorganisms obtained from a single source while AMC members come from different sources. SMC are a class of AMC in which microbial composition is defined to accomplish a certain specific task. We propose that the effective or potential existence of the interaction among MC members in the source material should be considered as a category in the classification as well, in combination with the origin of the source and level of intervention. Cross-kingdom MC and new developments were also considered. Finally, the existence of grey zones in the limits between each proposed microbial consortia category is addressed. KEY POINTS: • Microbial consortia for bioremediation can be obtained through different methods. • The use of the term "microbial consortia" is unclear in the specialized literature. • We propose a simplified classification for microbial consortia for bioremediation.

Field Test of In Situ Groundwater Treatment Applying Oxygen Diffusion and Bioaugmentation Methods in an Area with Sustained Total Petroleum Hydrocarbon (TPH) Contaminant Flow

Contamination of groundwater by petroleum hydrocarbons is a widespread environmental problem in many regions. Contamination of unsaturated and saturated zones could also pose a significant risk to human health. The main purpose of the study was to assess the efficiency of biodegradation of total petroleum hydrocarbon (TPH) in situ, in an area with loam and sandy loam soils, and to identify features and characteristics related to groundwater treatment in an area with a persistent flow of pollutants. We used methods of biostimulation (oxygen as stimulatory supplement) and bioaugmentation to improve water quality. Oxygen was added to the groundwater by diffusion through silicone tubing. The efficiency of groundwater treatment was determined by detailed monitoring. Implementation of the applied measure resulted in an average reduction in TPH concentration of 73.1% compared with the initial average concentration (4.33 mg/L), and in the local area, TPH content was reduced by 95.5%. The authors hope that this paper will contribute to a better understanding of the topic of groundwater treatment by in situ biodegradation of TPH. Further studies on this topic are particularly needed to provide more data and details on the efficiency of groundwater treatment under adverse geological conditions.

Enhanced methane production and hydrocarbon removal from petroleum refinery sludge after Pseudomonas putida pretreatment and process scale-up

The influence of Pseudomonas putida 7525 strain on the pretreatment of petroleum refinery sludge was optimized at different dosages to maximize solubilization for improved biodegradability. Laccase-producing P. putida strain at a dosage of 10⁸ CFU/mL resulted in 249% and 121.57% increments in soluble chemical oxygen demand and volatile fatty acids production respectively as compared to untreated within 6 days of incubation. 1L biochemical methane potential test conducted for optimization of different inoculum and pretreated substrate ratios (0.3, 0.4, 0.5, 0.7 and 1.0) revealed maximum methane augmentation (62%) and volatile solids degradation (66.7%) at ratio 0.5. Scaled-up study (20L) for ratio 0.5 resulted in 57.07% total petroleum hydrocarbon, 62.98% oil and grease and 91.9% phenol removal within 50 days of digestion of pretreated PS. Kinetic modelling of cumulative methane yield indicated that modified Gompertz model showed the best fit thereby, evincing the potency of bacterial species for bioremediation of PS.

Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants

Over the past two decades, various eco-friendly approaches utilizing microbial species to clean up contaminated environments have surfaced. In this aspect, actinobacteria have demonstrated their potential in contaminant degradation. The members of actinobacteria phylum exhibits a cosmopolitan distribution, which means that they can be found widely in both aquatic and terrestrial ecosystems. Actinobacteria play important ecological roles in the environment, such as degrading complex polymers, recycling compounds, and producing bioactive molecules. Hence, using actinobacteria to clean up contaminants is an attractive method in the field of biotechnology. This can be achieved through the green technology of bioaugmentation, whereby the degradative capacity of contaminated areas can be greatly improved through the introduction of specific microorganisms. This review describes actinobacteria as an eco-friendly and a promising technology for the bioaugmentation of contaminants, with focus on pesticides and heavy metals.

Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean)

Deep-sea sediments (DSS) are one of the largest biotopes on Earth and host a surprisingly diverse microbial community. The harsh conditions of this cold environment lower the rate of natural attenuation, allowing the petroleum pollutants to persist for a long time in deep marine sediments raising problematic environmental concerns. The present work aims to contribute to the study of DSS microbial resources as biotechnological tools for bioremediation of petroleum hydrocarbon polluted environments. Four deep-sea sediment samples were collected in the Mid-Atlantic Ridge, south of the Azores (North Atlantic Ocean). Their autochthonous microbial diversity was investigated by 16S rRNA metabarcoding analysis. In addition, a total of 26 deep-sea bacteria strains with the ability to utilize crude oil as their sole carbon and energy source were isolated from the DSS samples. Eight of them were selected for a novel hydrocarbonoclastic-bacterial consortium and their potential to degrade petroleum hydrocarbons was tested in a bioremediation experiment. Bioaugmentation treatments (with inoculum pre-grown either in sodium acetate or petroleum) showed an increase in degradation of the hydrocarbons comparatively to natural attenuation. Our results provide new insights into deep-ocean oil spill bioremediation by applying DSS hydrocarbon-degrading consortium in lab-scale microcosm to simulate an oil spill in natural seawater.

A Pseudomonas monteilii unilateral inguinofemoral granulomatous lymphadenitis in a two-year-old girl. A case report

Introduction: Pseudomonas monteilii is an environmental contaminant and is considered as an emerging human pathogen. We report the case of a Pseudomonas monteilii granulomatous lymphadenitis in a two-year-old girl.Clinical Presentation and Intervention: A two-year-old, previously healthy, Caucasian girl developed a unilateral inguinofemoral granulomatous lymphadenitis with Pseudomonas monteilii. The protracted course, the violaceous discoloration of the overlying skin, the mild tenderness without constitutional signs, the reactive tuberculin skin test with a negative interferon gamma release assay (IGRA) and the negative Bartonella henselae serology ranked non-tuberculous mycobacterial lymphadenitis high in our differential diagnosis. The ultrasonography showed signs of abcedation. We decided for surgical excision of the nodes. A P.monteilii granulomatous lymphadenitis was revealed. Treatment with an oral course of 2 weeks ciprofloxacin was prescribed. The course after treatment was uneventful and after one year of follow-up, the child is still doing well.Conclusions: Unusual clinical presentation should raise suspicion of uncommon pathogens and uncommon pathogens should raise suspicion of an underlying problem such as immunodeficiency, which was not the case in our patient.

Construction of biotreatment platforms for aromatic hydrocarbons and their future perspectives

Aromatic hydrocarbons (AHCs) are one of the major environmental pollutants introduced from both natural and anthropogenic sources. Many AHCs are well known for their toxic, carcinogenic, and mutagenic impact on human health and ecological systems. Biodegradation is an eco-friendly and cost-effective option as microorganisms (e.g., bacteria, fungi, and algae) can efficiently breakdown or transform such pollutants into less harmful and simple metabolites (e.g., carbon dioxide (aerobic), methane (anaerobic), water, and inorganic salts). This paper is organized to offer a state-of-the-art review on the biodegradation of AHCs (monocyclic aromatic hydrocarbons (MAHs) and polycyclic aromatic hydrocarbons (PAHs)) and associated mechanisms. The recent progress in biological treatment using suspended and attached growth bioreactors for the biodegradation of AHCs is also discussed. In addition, various substrate growth and inhibition models are introduced along with the key factors governing their biodegradation kinetics. The growth and inhibition models have helped gain a better understanding of substrate inhibition in biodegradation. Techno-economic analysis (TEA) and life cycle assessment (LCA) aspects are also described to assess the technical, economical, and environmental impacts of the biological treatment system.

Worms eat oil: Alcanivorax borkumensis hydrocarbonoclastic bacteria colonise Caenorhabditis elegans nematodes intestines as a first step towards oil spills zooremediation

The environmental hazards of oil spills cannot be underestimated. Bioremediation holds promise among various approaches to tackle oil spills in soils and sediments. In particular, using oil-degrading bacteria is an efficient and self-regulating way to remove oil spills. Using animals for oil spills remediation is in its infancy, mostly due to the lack of efficient oil-degrading capabilities in eukaryotes. Here we show that Caenorhabditis elegans nematodes survive for extended periods (up to 22 days) on pure crude oil diet. Moreover, we report for the first time the use of Alcanivorax borkumensis hydrocarbonoclastic bacteria for colonisation of C. elegans intestines, which allows for effective digestion of crude oil by the nematodes. The worms fed and colonised by A. borkumensis demonstrated the similar or even better longevity, resistance against oxidative and thermal stress and reproductivity as those animals fed with Escherichia coli bacteria (normal food). Importantly, A. borkumensis-carrying nematodes were able to accumulate oil droplet from oil-contaminated soils. Artificial colonisation of soil invertebrates with oil-degrading bacteria will be an efficient way to distribute microorganisms in polluted soil, thus opening new avenues for oil spills zooremediation.

Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.

Highly Contaminated Marine Sediments Can Host Rare Bacterial Taxa Potentially Useful for Bioremediation

Coastal areas impacted by high anthropogenic pressures typically display sediment contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). Microbial-based bioremediation represents a promising strategy for sediment reclamation, yet it frequently fails due to poor knowledge of the diversity and dynamics of the autochthonous microbial assemblages and to the inhibition of the target microbes in the contaminated matrix. In the present study, we used an integrated approach including a detailed environmental characterization, high-throughput sequencing and culturing to identify autochthonous bacteria with bioremediation potential in the sediments of Bagnoli-Coroglio (Gulf of Naples, Mediterranean Sea), a coastal area highly contaminated by PAHs, aliphatic hydrocarbons and HMs. The analysis of the benthic prokaryotic diversity showed that the distribution of the dominant taxon (Gammaproteobacteria) was mainly influenced by PAHs, As, and Cd concentrations. The other abundant taxa (including Alphaproteobacteria, Deltaproteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, NB1-j, Desulfobacterota, and Myxococcota) were mainly driven by sediment grain size and by Cu and Cr concentrations, while the rare taxa (i.e., each contributing <1%) by As and aliphatic hydrocarbons concentrations and by sediment redox potential. These results suggest a differential response of bacterial taxa to environmental features and chemical contamination and those different bacterial groups may be inhibited or promoted by different contaminants. This hypothesis was confirmed by culturing and isolating 80 bacterial strains using media highly enriched in PAHs, only nine of which were contextually resistant to high HM concentrations. Such resistant isolates represented novel Gammaproteobacteria strains affiliated to Vibrio, Pseudoalteromonas, and Agarivorans, which were only scarcely represented in their original assemblages. These findings suggest that rare but culturable bacterial strains resistant/tolerant to high levels of mixed contaminants can be promising candidates useful for the reclamation by bioaugmentation strategies of marine sediments that are highly contaminated with PAHs and HMs.

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.

Enhancing Salix viminalis L.-mediated phytoremediation of polycyclic aromatic hydrocarbon-contaminated soil by inoculation with Crucibulum laeve (white-rot fungus)

Although plant-white-rot fungi (WRF) remediation is considered efficient in improving polycyclic aromatic hydrocarbon (PAH)-contaminated soil, the prospects for using it remain poorly known. Therefore, we evaluated whether the WRF Crucibulum laeve could improve the phytoremediation of PAH-contaminated soil by Salix viminalis L. A 60-day pot experiment was conducted to investigate the effects of C. laeve inoculation (using two inoculation treatments and a non-inoculated control) on the phytoremediation potential, growth, and antioxidant metabolism of S. viminalis cultivated in PAH-contaminated soil. The S. viminalis-C. laeve association synergistically caused the highest PAH removal rate. Under the S. viminalis-C. laeve treatment, 80% of the biological concentration and translocation factors for all tissues of S. viminalis were > 1, whereas only 20% of these factors were > 1 when S. viminalis was used alone. C. laeve inoculation remarkably enhanced phytoremediation by promoting S. viminalis-based phytoextraction of PAHs from soils. Furthermore, although C. laeve inoculation altered the antioxidant metabolism of S. viminalis by inducing oxidative stress, thereby inhibiting plant growth, the plant's hardiness enabled it to survive and grow normally for 60 days after treatment. Therefore, phytoremediation using S. viminalis inoculated with C. laeve can be considered a feasible approach for the phytoremediation of PAH-contaminated soil.

Analysis of the Bioaugmentation Potential of Pseudomonas putida OR45a and Pseudomonas putida KB3 in the Sequencing Batch Reactors Fed with the Phenolic Landfill Leachate

The treatment of landfill leachate could be challenging for the biological wastewater treatment systems due to its high toxicity and the presence of poorly biodegradable contaminants. In this study, the bioaugmentation technology was successfully applied in sequencing batch reactors (SBRs) fed with the phenolic landfill leachate by inoculation of the activated sludge (AS) with two phenol-degrading Pseudomonas putida OR45a and Pseudomonas putida KB3 strains. According to the results, the SBRs bioaugmented with Pseudomonas strains withstood the increasing concentrations of the leachate. This resulted in the higher removal efficiency of the chemical oxygen demand (COD) of 79–86%, ammonia nitrogen of 87–88% and phenolic compounds of 85–96% as compared to 45%, 64%, and 50% for the noninoculated SBR. Simultaneously, the bioaugmentation of the AS allowed to maintain the high enzymatic activity of dehydrogenases, nonspecific esterases, and catalase in this ecosystem, which contributed to the higher functional capacity of indigenous microorganisms than in the noninoculated AS. Herein, the stress level experienced by the microorganisms in the SBRs fed with the leachate computed based on the cellular ATP measurements showed that the abundance of exogenous Pseudomonas strains in the bioreactors contributed to the reduction in effluent toxicity, which was reflected by a decrease in the stress biomass index to 32–45% as compared to the nonbioaugmented AS (76%).

Comparative Study on Different Remediation Strategies Applied in Petroleum-Contaminated Soils

Due to the increasing pollution by petroleum hydrocarbons (PHs), it is an important task to develop eco-friendly and highly efficient methods for remediating petroleum-contaminated soils. In this study, bioremediation technology was applied to remediate PHs contaminated soils, and the bacterial community structure and physicochemical characteristics of the soil treated using different bioremediation regimens were analyzed. Compared with the control condition (S0), the PHs removal efficiency of biostimulation (S2) and bioaugmentation (S3) was increased significantly. Combined biostimulation with bioaugmentation (S4) had the highest PHs removal efficiency, up to 60.14 ± 4.12%. Among all the selected remediation strategies (S1-S4, S1: soil moisture content: 25-30%), the bacterial alpha-diversity was higher than in S0. The genera Acinetobacter, Escherichia-Shigella, Bacteroides, Microbacterium, and Parabacteroides were found to greatly contribute to PHs' degradation. In the group S4, the PH-degraders and soil enzyme activity were higher than in the other remediation regimens, and these indices gradually decreased in the mid-to-later periods of all remediation tests. Additionally, the abundance of alkB and nah genes was increased by improving the environmental condition of the microorganism communities. Redundancy analysis (RDA) revealed that the total nitrogen (TN) and total phosphorus (TP) had a positive correlation with total PHs degradation. This study offers insights into the microbial community response to environmental factors during bioremediation, which shows a promoting effect in enhancing the efficiency of PHs remediation.

Ecological role of Acinetobacter calcoaceticus GSN3 in natural biofilm formation and its advantages in bioremediation

This study assessed the role of a new Acinetobacter calcoaceticus strain, GSN3, with biofilm-forming and phenol-degrading abilities. Three biofilm reactors were spiked with activated sludge (R1), green fluorescent plasmid (GFP) tagged GSN3 (R2), and their combination (R3). More than 99% phenol removal was achieved during four weeks in R3 while this efficiency was reached after two and four further operational weeks in R2 and R1, respectively. Confocal scanning electron microscopy revealed that GSN3-gfp strains appeared mostly in the deeper layers of the biofilm in R3. After four weeks, almost 7.07 × 10⁷ more attached sludge cells were counted per carrier in R3 in comparison to R1. Additionally, the higher numbers of GSN3-gfp in R2 were unable to increase the efficiency as much as measured in R3. The presence of GSN3-gfp in R3 conveyed advantages, including enhancement of cell immobilization, population diversity, metabolic cooperation and ultimately treatment efficiency.

Molecular and Microbiological Insights on the Enrichment Procedures for the Isolation of Petroleum Degrading Bacteria and Fungi

Autochthonous bioaugmentation, by exploiting the indigenous microorganisms of the contaminated environment to be treated, can represent a successful bioremediation strategy. In this perspective, we have assessed by molecular methods the evolution of bacterial and fungal communities during the selective enrichment on different pollutants of a soil strongly polluted by mixtures of aliphatic and polycyclic hydrocarbons. Three consecutive enrichments were carried out on soil samples from different soil depths (0-1, 1-2, 2-3 m), and analyzed at each step by means of high-throughput sequencing of bacterial and fungal amplicons biomarkers. At the end of the enrichments, bacterial and fungal contaminants degrading strains were isolated and identified in order to (i) compare the composition of enriched communities by culture-dependent and culture-independent molecular methods and to (ii) obtain a collection of hydrocarbon degrading microorganisms potentially exploitable for soil bioremediation. Molecular results highlighted that for both bacteria and fungi the pollutant had a partial shaping effect on the enriched communities, with paraffin creating distinct enriched bacterial community from oil, and polycyclic aromatic hydrocarbons generally overlapping; interestingly neither the soil depth or the enrichment step had significant effects on the composition of the final enriched communities. Molecular analyses well-agreed with culture-dependent analyses in terms of most abundant microbial genera. A total of 95 bacterial and 94 fungal strains were isolated after selective enrichment procedure on different pollutants. On the whole, isolated bacteria where manly ascribed to Pseudomonas genus followed by Sphingobacterium, Bacillus, Stenothrophomonas, Achromobacter, and Serratia. As for fungi, Fusarium was the most abundant genus followed by Trichoderma and Aspergillus. The species comprising more isolates, such as Pseudomonas putida, Achromobacter xylosoxidans and Ochromobactrum anthropi for bacteria, Fusarium oxysporum and Fusarium solani for fungi, were also the dominant OTUs assessed in Illumina.

Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge

Scope for developing an engineered bioremediation strategy for the treatment of hydrocarbon-rich petroleum refinery waste was investigated through biostimulation and bioaugmentation approaches. Enhanced (46-55%) total petroleum hydrocarbon (TPH) attenuation was achieved through phosphate, nitrate or nitrate+phosphate amendment in the sludge with increased (upto 12%) abundance of fermentative, hydrocarbon degrading, sulfate-reducing, CO₂-assimilating and methanogenic microorganisms (Bacillus, Coprothermobacter, Rhodobacter, Pseudomonas, Achromobacter, Desulfitobacter, Desulfosporosinus, T78, Methanobacterium, Methanosaeta, etc). Together with nutrients, bioaugmentation with biosurfactant producing and hydrocarbon utilizing indigenous Bacillus strains resulted in 57-75% TPH reduction. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed enhanced gene allocation for transporters (0.45-3.07%), ABC transporters (0.38-2.07%), methane (0.16-1.06%), fatty acid (0.018-0.15%), nitrogen (0.07-0.17%), butanoate (0.06-0.35%), propanoate (0.004-0.26%) metabolism and some xenobiotics (0.007-0.13%) degradation. This study indicated that nutrient-induced community dynamics of native microorganisms and their metabolic interplay within oil refinery sludge could be a driving force behind accelerated bioremediation.

Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review

Petroleum is currently the world's main energy source, and its demand is expected to increase in coming years. Its intense exploitation can lead to an increase in the number of environmental accidents, such as spills and leaks, and an increase in the generation of environmental liabilities resulting from refining. Due to its hydrophobic characteristics and slow process of biodegradation, petroleum can remain in the environment for a long time and its toxicity can cause a negative impact on both terrestrial and aquatic ecosystems, with the main negative effects related to its carcinogenic potential for both animals and humans. The objective of the present review is to discuss environmental contamination by oil, conventional treatment techniques and bioremediation an alternative tool for recovery petroleum-contaminated soils, focusing on the rhizodegradation process, plant growth-promoting rhizobacteria (PGPR), a phytoremediation strategy in which the microorganisms that colonize the roots of phytoremediatior plants are responsible for the biodegradation of petroleum. These microorganisms can be selected and tested individually or in the form of consortia to evaluate their potential for oil degradation, or even to measure the use of biosurfactants produced by them to constitute tools for the development of environmental recovery strategies and biotechnological application.

Pyrimidine nucleotide synthesis in the emerging pathogen Pseudomonas monteilii

Regulation of pyrimidine biosynthesis by pyrimidines in the emerging, opportunistic human pathogen Pseudomonas monteilii ATCC 700476 was evident. When wild-type cells were grown on succinate in the presence of uracil or orotic acid, the activities of all 5 pyrimidine biosynthetic enzymes were depressed while the activities of 3 of the enzymes decreased in glucose-grown cells supplemented with uracil or orotic acid compared with unsupplemented cells. Pyrimidine limitation of succinate- or glucose-grown pyrimidine auxotrophic cells lacking orotate phosphoribosyltransferase activity resulted in more than a doubling of the pyrimidine biosynthetic enzyme activities relative to their activities in uracil-grown cells. Independent of carbon source, pyrimidine-limited cells of the pyrimidine auxotrophic cells deficient for dihydroorotase activity generally resulted in a slight elevation or depression of the pyrimidine biosynthetic enzyme activities compared with their activities in cells grown under saturating uracil conditions. Aspartate transcarbamoylase activity in P. monteilii was regulated at the enzyme activity level, since the enzyme was strongly inhibited by CTP, UMP, GMP, GDP, ADP, and UTP. In summary, the regulation of pyrimidine biosynthesis in P. monteilii could be used to control its growth or to differentiate it biochemically from other related species of Pseudomonas.

A comparative study to evaluate natural attenuation, mycoaugmentation, phytoremediation, and microbial-assisted phytoremediation strategies for the bioremediation of an aged PAH-polluted soil

Biological treatments are considered an environmentally option to clean-up polluted soil with polycyclic aromatic hydrocarbons (PAHs). A pot experiment was conducted to comparatively evaluate four different strategies, including natural attenuation (NA), mycoaugmentation (M) by using Crucibulum leave, phytoremediation (P) using maize plants, and microbial-assisted phytoremediation (MAP) for the bioremediation of an aged PAH-polluted soil at 180 days. The P treatment had higher affinity degrading 2-3 and 4 ring compounds than NA and M treatments, respectively. However, M and P treatments were more efficient in regards to naphthalene, indeno[l,2,3-c,d]pyrene and benzo[g,h,i]perylene degradation respect to NA. However, 4, 5-6 rings undergo a strong decline during the microbe-assisted phytoremediation, being the treatment which determined the highest rates of PAHs degradation. Sixteen PAH compounds, except fluorene and dibenzo[a,h]anthracene, were found in maize roots, whereas the naphthalene, phenanthrene, anthracene, fluoranthene, and pyrene were accumulated in the shoots, in both P and MAP treatments. However, higher PAH content in maize biomass was achieved during the MAP treatment respect to P treatment. The bioconversion and translocation factors were less than 1, indicating that phystabilization/phytodegradation processes occurred rather than phytoextraction. The microbial biomass, activity and ergosterol content were significantly boosted in the MAP treatment respect to the other treatments at 180 days. Ours results demonstrated that maize-C. laeve association was the most profitable technique for the treatment of an aged PAH-polluted soil when compared to other bioremediation approaches.

Enrichment and characterization of hydrocarbon-degrading bacteria from petroleum refinery waste as potent bioaugmentation agent for in situ bioremediation

Intrinsic biodegradation potential of bacteria from petroleum refinery waste was investigated through isolation of cultivable strains and their characterization. Pseudomonas and Bacillus spp. populated the normal cultivable taxa while prolonged enrichment with hydrocarbons and crude oil yielded hydrocarbonoclastic bacteria of genera Burkholderia, Enterobacter, Kocuria, Pandoraea, etc. Strains isolated through enrichment showed assemblages of superior metabolic properties: utilization of aliphatic (C6-C22) and polyaromatic compounds, anaerobic growth with multiple terminal electron acceptors and higher biosurfactant production. Biodegradation of dodecane was studied thoroughly by GC-MS along with detection of gene encoding alkane hydroxylase (alkB). Microcosms bioaugmented with Enterobacter, Pandoraea and Burkholderia strains showed efficient biodegradation (98% TPH removal) well fitted in first order kinetic model with low rate constants and decreased half-life. This study proves that catabolically efficient bacteria resides naturally in complex petroleum refinery wastes and those can be useful for bioaugmentation based bioremediation.

Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms

The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.

Bioaugmentation as a strategy for the remediation of pesticide-polluted soil: A review

Bioaugmentation, a green technology, is defined as the improvement of the degradative capacity of contaminated areas by introducing specific microorganisms, has emerged as the most advantageous method for cleaning-up soil contaminated with pesticides. The present review discusses the selection of pesticide-utilising microorganisms from various sources, their potential for the degradation of pesticides from different chemical classes in liquid media as well as soil-related case studies in a laboratory, a greenhouse and field conditions. The paper is focused on the microbial degradation of the most common pesticides that have been used for many years such as organochlorinated and organophosphorus pesticides, triazines, pyrethroids, carbamate, chloroacetamide, benzimidazole and derivatives of phenoxyacetic acid. Special attention is paid to bacterial strains from the genera Alcaligenes, Arthrobacter, Bacillus, Brucella, Burkholderia, Catellibacterium, Pichia, Pseudomonas, Rhodococcus, Serratia, Sphingomonas, Stenotrophomonas, Streptomyces and Verticillum, which have potential applications in the bioremediation of pesticide-contaminated soils using bioaugmentation technology. Since many factors strongly influence the success of bioaugmentation, selected abiotic and biotic factors such as pH, temperature, type of soil, pesticide concentration, content of water and organic matter, additional carbon and nitrogen sources, inoculum size, interactions between the introduced strains and autochthonous microorganisms as well as the survival of inoculants were presented.

Metagenomic insight into the bioaugmentation mechanism of Phanerochaete chrysosporium in an activated sludge system treating coking wastewater

Phanerochaete chrysosporium was seeded to a sequencing batch reactor treating phenol wastewater. Compared to the contrast reactor (R1), the bioaugmented reactor (R2) exhibits better performance in sludge settling ability, as well as biomass and phenol removal, even though the added fungus is not persistently surviving in the reactor. Bioaugmentation improved bacterial population, growing up to 10,000 times higher than that of eukaryotes. Metagenomic sequencing results show the bioaugmentation finally increases bacterial and eukaryotic richness, but reduces their community diversity. In contrast to R1, bacterial distribution in R2 is more concentrated in Proteobacteria. The relative abundances of filamentous fungi, yeast and microalgae in R2 are all higher than those in R1 at different treatment phases, and two reactors are finally dominated by different protozoan and metazoan. In conclusion, P. chrysosporium improves reactor performances by influencing microbial community structure, and this phenomenon might be attributed to the ecological competition in sludge and toxicity reduction of phenol wastewater. The novelty of this study emphasizes why a species which is not persistently active in bioreactor still plays a crucial role in enhancing reactor performance. Results obtained here impact the conventional criteria for selection of bioaugmentation microbes used in activated sludge systems.

Efficient remediation of PAH-metal co-contaminated soil using microbial-plant combination: A greenhouse study

A 2-year greenhouse study was conducted to remediate an actual wastewater-irrigated soil co-contaminated with polycyclic aromatic hydrocarbons (PAHs) and heavy metals (Cd and Zn). The remediation methods included microbial remediation, phytoremediation, and microbe-assisted phytoremediation. The maximum PAH removal (96.4%), PAH mineralization, and metal phytoextraction (36.1% Cd and 12.7% Zn) were obtained by interplanting ryegrass with Seduce alfredii with regular re-inoculation with Microbacterium sp. KL5 and Candida tropicalis C10 in the co-contaminated soil. The plants shoots were harvested at a 4-month interval. After 2 years, the concentrations of 16 individual PAHs were reduced to below the limit of Chinese soil quality standard for agricultural use (grade II, pH 6.5-7.5), and the metal concentrations in ryegrass shoots were below the Chinese national limit for animal feeds (GB13078-2001). The exogenous microbes gradually disappeared with time, and thus a 2-month re-inoculation interval was applied for a purpose to maintain high cell density and activity of the inoculants. KL5 introduction increased soil enzyme activity, plant growth, PAH removal and metal phytoextraction, while C10 promoted soil enzyme activity and removal of high-molecular-weight PAHs. Interplanting with S. alfredii reduced metal concentrations in ryegrass tissues. Ryegrass showed stronger rhizosphere effects than S. alfredii did.