Biostimulation of petroleum-hydrocarbon-contaminated marine sediment with co-substrate: involved metabolic process and microbial community

Effect of luminescent materials on the biochemistry, ultrastructure, and rhizobial microbiota of Spirodela polyrhiza

Fluorescent materials and technologies have become widely used in scientific research, and due to the ability to convert light wavelengths, their application to photosynthetic organisms can affect their development by altering light quality. However, the impacts of fluorescent materials on aquatic plants and their environmental risks remain unclear. To assess the effects of luminescent materials on floating aquatic macrophytes and their rhizosphere microorganisms, 4-(di-p-tolylamino)benzaldehyde-A (DTB-A) and 4-(di-p-tolylamino)benzaldehyde-M (DTB-M) (emitting blue-green and orange-red light, respectively) were added individually and jointly to Spirodela polyrhiza cultures and set at different concentrations (1, 10, and 100 μM). Both DTB-A and DTB-M exhibited phytotoxicity, which increased with concentration under separate treatment. Moreover, the combined group exhibited obvious stress relief at 10 μM compared to the individually treated group. Fluorescence imaging showed that DTB-A and DTB-M were able to enter the cell matrix and organelles of plant leaves and roots. Peroxidation induced cellular damage, contributing to a decrease in superoxide dismutase (SOD) and peroxidase (POD) activities and malondialdehyde (MDA) accumulation. Decomposition of organelle structures, starch accumulation in chloroplasts, and plasmolysis were observed under the ultrastructure, disrupting photosynthetic pigment content and photosynthesis. DTB-A and DTB-M exposure resulted in growth inhibition, dry weight loss, and leaf yellowing in S. polyrhiza. A total of 3519 Operational Taxonomic Units (OTUs) were identified in the rhizosphere microbiome. The microbial communities were dominated by Alphaproteobacteria, Oxyphotobacteria, and Gammaproteobacteria, with the abundance and diversity varied significantly among treatment groups according to Shannon, Simpson, and Chao1 indices. This study revealed the stress defense response of S. polyrhiza to DTB-A and DTB-M exposures, which provides a broader perspective for the bioremediation of pollutants using aquatic plants and supports the further development of fluorescent materials for applications.

Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments

Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.

Microbial electrochemical system: an emerging technology for remediation of polycyclic aromatic hydrocarbons from soil and sediments

Worldwide industrialization and other human activities have led to a frightening stage of release of hazardous, highly persistent, toxic, insoluble, strongly adsorbed to the soil and high molecular weight ubiquitous polycyclic aromatic hydrocarbons (PAHs) in soils and sediments. The various conventional remediation methods are being used to remediate PAHs with certain drawbacks. Time taking process, high expenditure, excessive quantities of sludge generation, and various chemical requirements do not only make these methods outdated but produce yet much resistant and toxic intermediate metabolites. These disadvantages may be overcome by using a microbial electrochemical system (MES), a booming technology in the field of bioremediation. MES is a green remediation approach that is regulated by electrochemically active microorganisms at the electrode in the system. The key advantage of the system over the conventional methods is it does not involve any additional chemicals, takes less time, and generates minimal sludge or waste during the remediation of PAHs in soils. However, a comprehensive review of the MES towards bioremediation of PAHs adsorbed in soil and sediment is still lacking. Therefore, the present review intended to summarize the recent information on PAHs bioremediation, application, risks, benefits, and challenges based on sediment microbial fuel cell and microbial fuel cell to remediate mount-up industrial sludge, soil, and sediment rich in PAHs. Additionally, bio-electrochemically active microbes, mechanisms, and future perspectives of MES have been discussed.

Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach

Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.

Mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX mixed contaminants in soil by native microbial consortium

Despite the co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) in the field, to date, knowledge on the bioremediation of benzene and benzo[a]pyrene (BaP) mixed contaminants is limited. In this study, the mechanisms underlying the biodegradation of benzene and BaP under individual and co-contaminated conditions followed by the enhanced biodegradation using methanol, ethanol, and vegetable oil as biostimulants were investigated. The results demonstrated that the benzene biodegradation was highly reduced under the co-contaminated condition compared to the individual benzene contamination, whereas the BaP biodegradation was slightly enhanced with the co-contamination of benzene. Moreover, biostimulation significantly improved the biodegradation of both contaminants under co-contaminated conditions. A trend of significant reduction in the bioavailable BaP contents was observed in all biostimulant-enhanced groups, implying that the bioavailable BaP was the preferred biodegradable BaP fraction. Furthermore, the enzymatic activity analysis revealed a significant increase in lipase and dehydrogenase (DHA) activities, as well as a reduction in the catalase and polyphenol oxidase, suggesting that the increased hydrolysis of fats and proton transfer, as well as the reduced oxidative stress, contributed to the enhanced benzene and BaP biodegradation in the vegetable oil treatment. In addition, the microbial composition analysis results demonstrated that the enriched functional genera contributed to the increased biodegradation efficiency, and the functional genera in the microbial consortium responded differently to different biostimulants, and competitive growth was observed in the biostimulant-enhanced treatments. In addition, the enrichment of Pseudomonas and Rhodococcus species was noticed during the biostimulation of benzene and BaP co-contamination soil, and was positively correlated with the DHA enzyme activities, indicating that these species encode DHA genes which contributed to the higher biodegradation. In conclusion, multiple lines of evidence were provided to shed light on the mechanisms of biostimulant-enhanced biodegradation of PAHs and BTEX co-contamination with native microbial consortiums.

Effect of terminal electron acceptors on the anaerobic biodegradation of PAHs in marine sediments

The existing polycyclic aromatic hydrocarbons (PAHs) in marine sediment has become a critical threat to biological security. Terminal electron acceptor (TEA) amendment has been applied as a potential strategy to accelerate bioremediation in sediment. HCO₃^-, NO₃^-, and SO₄^2- were separately added to anaerobic sediment system containing five kinds of PAH, namely, phenanthrene, anthracene, fluoranthene, pyrene and benzo(a)pyrene. PAH concentration, PAH metabolites, TEA concentration, and electron transport system (ETS) activity were investigated. The HCO₃^- amendment group achieved the max PAH degradation efficiency of 84.98 %. SO₄^2- group led to the highest benzo(a)pyrene removal rate of 69.26 %. NO₃^- had the lowest PAH degradation rate of 76.16 %. ETS activity test showed that NO₃^- significantly inhibited electron transport activity in the sediment. The identified PAH metabolites were the same in each group, including 4,5-dimethylphenanthrene, 3-acetylphenanthrene, 9,10-anthracenedione, pyrene-7-hydroxy-8-carboxylic acid, anthrone, and dibenzothiophene. After 126 d's anaerobic degradation at 25 °C, the utilization of HCO₃^- and SO₄^2- as selected TEAs promoted the PAH biodegradation performance better than the utilization of NO₃^-.

Enhanced bioremediation of sediment contaminated with polycyclic aromatic hydrocarbons by combined stimulation with sodium acetate/phthalic acid

In this study, four groups of laboratory scale experiments were performed by adding sodium acetate (SA), phthalic acid (PA), and SA-PA to river sediment to observe the microbial response and biodegradation efficiency of polycyclic aromatic hydrocarbons (PAHs). The results showed that the amount of total organic carbon consumed and the amount of sulfate reduction were both positively correlated (p < 0.01) with the biodegradation efficiency of the sum (∑) PAHs (∼40.5%). The lower the number of rings, the more PAHs were biodegraded, with an efficiency of 63.0% for ∑ (2 + 3) ring PAHs. Based on high-throughput sequencing and molecular ecological network analysis, it was found that the combined stimulation of SA and PA not only increased the relative abundance of PAHs-degrading bacterial (eg., Proteobacteria, Desulfobacterota, Campilobacterota and Firmicutes), but also had a strengthening effect on microbes in sediments. The altered microbial structure caused a variation in metabolic functions, which increased the amino acid metabolism to 12.2%, thus increasing the positive correlations among genera and improving the connectivity of the microbial network (p < 0.01). These changes may be responsible for the enhanced biodegradation of PAHs under SA-PA dosing in comparison to SA or PA dosing alone. This study revealed that the microbial community was stimulated by the combined addition of SA and PA, and indicated its role in enhancing biodegradation of PAHs in contaminated river sediments.

Removal of Petroleum Contaminants Through Bioremediation with Integrated Concepts of Resource Recovery: A Review

There is an upsurge in industrial production to meet the rising demands of the rapidly growing population globally. The enormous energy demand of the growing economies still depends upon petroleum. It has also resulted in environmental pollution due to the release of petroleum origin pollutants. Soil and aquifers, especially in the direct impact zones of petroleum refineries, are the worst hit. The integrated concept of bioremediation and resource recovery offers a sustainable solution to mitigate environmental pollution. It involves biodegradation, a benign utilization of toxic wastes, and the recycling of natural resources. Bioremediation is considered an integral contributor to the emerging concepts of bio-economy and sustainable development goals. This review article aims to provide an updated overview of bioremediation involving petroleum-based contaminants. Microbial degradation is discussed as a promising strategy for petroleum refinery effluent and sludge treatment. The review also provides an insight into resource reuse and recovery as a holistic approach towards sustainable refinery waste treatment. Furthermore, the integrated technologies that deserve in-depth exploration for future study in the refinery sector are highlighted in the present study.

Enhanced bioelectrochemical treatment of petroleum refinery wastewater with Labaneh whey as co-substrate

Petroleum refinery wastewater (PRW) that contains recalcitrant components as the major portion of constituents is difficult to treat by conventional biological processes. Microbial fuel cells (MFCs) which also produce renewable energy were found to be promising for the treatment of PRW. However, due to the high total dissolved solids and low organic matter content, the efficiency of the process is limited. Labaneh whey (LW) wastewater, having higher biodegradability and high organic matter was evaluated as co-substrate along with PRW in standard dual chambered MFC to achieve improved power generation and treatment efficiency. Among several concentrations of LW as co-substrate in the range of 5–30% (v/v) with PRW, 85:15 (PRW:LW) showed to have the highest power generation (power density (PD), 832 mW/m²), which is two times higher than the control with PRW as sole substrate (PD, 420 mW/m²). On the contrary, a maximum substrate degradation rate of 0.420 kg COD/m³-day (ξCOD, 63.10%), was registered with 80:20 feed. Higher LW ratios in PRW lead to the production of VFA which in turn gradually decreased the anolyte pH to below 4.5 (70:30 feed). This resulted in a drop in the performance of MFC with respect to power generation (274 mW/m², 70:30 feed) and substrate degradation (ξCOD, 17.84%).

The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design

Polycyclic aromatic hydrocarbons (PAHs), especially high molecular weight PAHs, are carcinogenic and mutagenic organic compounds that are difficult to degrade. Microbial remediation is a popular method for the PAH removal in diverse environments and yet it is limited by the lack of electron acceptors. An emerging solution is to use the microbial electrochemical system, in which the solid anode is used as an inexhaustible electron acceptor and the microbial activity is stimulated by biocurrent in situ to ensure the PAH removal and avoid the defects of bioremediation. Based on the extensive investigation of recent literatures, this paper summarizes and comments on the research progress of PAH removal by the microbial electrochemical system of diversified design, enhanced measures and functional microorganisms. First, the bioelectrochemical degradation of PAHs is reviewed in separate and mixed PAH degradation, and the removal performance of PAHs in different system configurations is compared with the anode modification, the enhancement of substrate and electron transfer, the addition of chemical reagents, and the combination with phytoremediation. Second, the key functional microbiota including PAH degrading microbes and exoelectrogens are overviewed as well as the reduced microbes without competitive advantage. Finally, the typical representations of electrochemical activity especially the internal resistance, power density and current density of systems and influence factors are reviewed with the correlation analysis between PAH removal and energy generation. Presently, most studies focused on the anode modification in the bioelectrochemical degradation of PAHs and actually more attentions need to be paid to enhance the mass transfer and thus larger remediation radius, and other smart designs are also proposed, especially that the combined use of phytoremediation could be an eco-friendly and sustainable approach. Additionally, exoelectrogens and PAH degraders are partially overlapping, but the exact functional mechanisms of interaction network are still elusive, which could be revealed with the aid of advanced bioinformatics technology. In order to optimize the efficacy of functional community, more advanced techniques such as omics technology, photoelectrocatalysis and nanotechnology should be considered in the future research to improve the energy generation and PAH biodegradation rate simultaneously.

Comparing performances, costs and energy balance of ex situ remediation processes for PAH-contaminated marine sediments

This study proposes a comparison of different ex situ technologies aimed at the removal of polycyclic aromatic hydrocarbons from marine sediments in terms of performances, costs and energy balance. In accordance with the principles of water-energy nexus, anaerobic bioremediation, soil washing and thermal desorption were investigated under low liquid phase and temperature conditions using phenanthrene (PHE) as model compound. After 42 days of anaerobic bioremediation, the highest PHE biodegradation of 68 and 64% was observed under denitrifying and methanogenic conditions, respectively, accompanied by N₂ and CH₄ production and volatile fatty acid accumulation. During soil washing, more than 97% of PHE was removed after 60 min using a solid-to-liquid ratio of 1:3. Along the same treatment time, low-temperature thermal desorption (LTTD) allowed a PHE removal of 88% at 200 °C. The economic analysis indicated that LTTD resulted in a higher cost (i.e. 1782 € m^-3) than bioremediation and soil washing (228 and 371 € m^-3, respectively). The energy balance also suggested that bioremediation and soil washing are more sustainable technologies as a lower required energy (i.e. 16 and 14 kWh m^-3, respectively) than LTTD (i.e. 417 kWh m^-3) is needed.

Effects of cellulose on polycyclic aromatic hydrocarbons removal and microbial community structure variation during anaerobic digestion of sewage sludge

Waste-activated sludge (WAS) with trace organic pollutants, e.g., polycyclic aromatic hydrocarbons (PAHs), has become an environmental concern. Anaerobic technology is a feasible option for WAS treatment due to its advantages of low-energy consumption and high-energy recovery compared to aerobic technology, but it still has many shortcomings, such as low biogas production and a low organic pollutant removal efficiency. Thus, this study investigated the effects of cellulose on PAHs degradation and microbial community structure variation during anaerobic digestion of sewage sludge. Four semicontinuous experiments were set by adding cellulose to sewage sludge based on the volatile solids (VS) concentration. The proportions of sludge VS to cellulose VS were 1:0 (CK), 1:0.2, 1:0.5 and 1:1. The results showed the following: (1) The biodegradation of 2-ring, 3-ring and 4-ring PAHs was enhanced by cellulose addition, with total PAHs removal efficiencies of 14.82%, 20.75% and 19.35%, respectively. (2) The abundance of bacteria that could degrade PAHs, such as Chloroflexi, Bacteroidetes, Aminicenantes, Planctomycetes and Spirochaeta, was obviously increased by cellulose addition. (3) The abundance of Methanosaeta during sludge anaerobic digestion was apparently increased by cellulose addition. Methanobacterium and Methanolinea appeared after cellulose addition, while they were not observed in the blank experiment.

Biodegradation of petroleum hydrocarbons and changes in microbial community structure in sediment under nitrate-, ferric-, sulfate-reducing and methanogenic conditions

In the present study, the biodegradation behaviors of petroleum hydrocarbons under various reducing conditions were investigated. n-Alkanes and polycyclic aromatic hydrocarbons (PAHs) were degraded with NO₃^-, Fe³⁺, SO₄^2-, or HCO₃^- as terminal electron acceptors (TEAs), which link to four typical reducing conditions (i.e., nitrate-reducing, ferric-reducing, sulfate-reducing and methanogenic conditions, respectively) in sediment. The fastest degradation rates were achieved under sulfate-reducing conditions with half-lives of 49.51 days for n-alkanes and 58.74 days for PAHs. For short-chain n-alkanes and low-molecular weight (LMW) PAHs, relatively higher removal efficiencies were achieved under nitrate- and ferric-reducing conditions. The degradation of long-chain n-alkanes and high-molecular weight (HMW) PAHs coupled to methanogenesis was the most favored as compared with other reducing conditions. Carboxylation was found to be the principle mechanism for regulating n-alkane degradation coupled to denitrification, while the activation of n-alkanes by the addition of fumarate was the principle mechanism for the n-alkane degradation under sulfate-reducing conditions. The anaerobic metabolism of n-alkanes may not proceed via fumarate addition or carboxylation under ferric-reducing and methanogenic conditions. Illumina HiSeq sequencing revealed dissimilar structures of the microbial communities under various reducing conditions. It is hypothesized that the utilization of different TEAs for n-alkane and PAH degradation resulted in distinct microbial community structures, which were highly correlated with the varied degradation behaviors of petroleum hydrocarbons in sediment. The current results may provide reference value on better understanding the biodegradation behaviors of n-alkanes and PAHs in association with the induced microbial communities in sedimentary environments under the four typical reducing conditions.

Biostimulation of in situ microbial degradation processes in organically-enriched sediments mitigates the impact of aquaculture

Fish farm deposition, resulting in organic matter accumulation on bottom sediments, has been identified as among the main phenomena causing negative environmental impacts in aquaculture. An in situ bioremediation treatment was carried out in order to reduce the organic matter accumulation in the fish farm sediments by promoting the natural microbial biodegradation processes. To assess the effect of the treatment, the concentration of organic matter in the sediment and its microbial degradation, as well as the response of the benthic prokaryotic community, were investigated. The results showed a significant effect of the treatment in stimulating microbial degradation rates, and the consequent decrease in the concentration of biochemical components beneath the cages during the treatment. During the bioremediation process, the prokaryotic community in the fish farm sediment responded to the overall improvement of the sediment conditions by showing the decrease of certain anaerobic taxa (e.g. Clostridiales, Acidaminobacteraceae and Caldilinaceae). This suggested that the bioactivator was effective in promoting a shift from an anaerobic to an aerobic metabolism in the prokaryotic community. However, the larger importance of Lachnospiraceae (members of the gut and faecal microbiota of the farmed fishes) in treated compared to non-treated sediments suggested that the bioactivator was not efficient in reducing the accumulation of faecal bacteria from the farmed fishes. Our results indicate that bioremediation is a promising tool to mitigate the aquaculture impact in fish farm sediments, and that further research needs to be oriented to identifying more successful interventions able to specifically target also fish-faeces related microbes.

Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment

AIM

To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment.

METHODS AND RESULTS

A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC-MS and 16S rRNA high-throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C₂₂ -C₃₀ alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon-contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities' response to additional contamination.

CONCLUSION

This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.

Laboratory and field microcosms as useful experimental systems to study the bioaugmentation treatment of tannery effluents

Tannery effluents require effective treatment prior to their final disposal, and the use of native bacterial consortia could be an appropriate strategy for this purpose. In the present work, consortium SFC 500-1 was found to be highly tolerant to different metals, metalloids and aromatic compounds like phenols. It was also able to remove the black dye commonly used in tanneries. Moreover, it promoted a significant reduction in chemical oxygen demand and exhibited high capability for the simultaneous removal of Cr(VI) and phenol. However, the effectiveness of the remediation processes markedly varied from one experimental system (Erlenmeyer flasks) to another (field microcosm system), highlighting the importance of moving from a small-scale study system to one involving more realistic environmental scenarios. In addition, we found a decrease in the toxicity of the effluent treated with consortium SFC 500-1. Taken together, our results indicate that this consortium possesses great potential for the treatment of tannery effluents. We conclude that for the development of a bioremediation strategy, it is necessary to develop experiments at a larger scale under conditions similar to those of the original system, in order to complete the scenario first created by in vitro approaches.

Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes

The intense pollution of urban river sediments with rapid urbanization has attracted considerable attention. Complex contaminated sediments urgently need to be remediated to conserve the ecological functions of impacted rivers. This study investigated the effect of using methanol as a co-substrate on the stimulation of the indigenous microbial consortium to enhance the bioremediation of petroleum hydrocarbons (PHs) and polycyclic aromatic hydrocarbons (PAHs) in an urban river sediment. After 65 days of treatment, the PAHs degradation efficiencies in the sediment adding methanol were 4.87%-40.3% higher than the control. The removal rate constant of C31 was 0.0749 d^-1 with 100 mM of supplied methanol, while the corresponding rate was 0.0399 d^-1 in the control. Four-ring PAHs were effectively removed at a degradation efficiency of 65%-69.8%, increased by 43.3% compared with the control. Sulfate reduction and methanogenesis activity were detected, and methane-producing archaea (such as Methanomethylovorans, with a relative abundance of 25.87%-58.53%) and the sulfate-reducing bacteria (SRB, such as Desulfobulbus and Desulfobacca) were enriched. In addition, the chemolithoautotrophic sulfur-oxidizing bacteria (SOB, such as Sulfuricurvum, with a relative abundance of 34%-39.2%) were predominant after the depletion of total organic carbon (TOC), and markedly positively correlated with the PHs and PAHs degradation efficiencies (P < 0.01). The SRB and SOB populations participated in the sulfur cycle, which was associated with PHs and PAHs degradation. Other potential functional bacteria (such as Dechloromonas) were also obviously enriched and significantly positively correlated with the TOC concentration after methanol injection (P < 0.001). This study provides a new insight into the succession of the indigenous microbial community with methanol as a co-substrate for the enhanced bioremediation of complexly contaminated urban river sediments.

Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations

Background

Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation.

Results

All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members.

Conclusion

Refinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1275-8) contains supplementary material, which is available to authorized users.

Diversity and Niche of Archaea in Bioremediation

Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.

Variation in electrode redox potential selects for different microorganisms under cathodic current flow from electrodes in marine sediments

Extracellular electron transport (EET) is a microbial process that allows microorganisms to transport electrons to and from insoluble substrates outside of the cell. Although progress has been made in understanding how microbes transfer electrons to insoluble substrates, the process of receiving electrons has largely remained unexplored. We investigated redox potentials favourable for donating electrons to dissolved and insoluble components in Catalina Harbor marine sediment by combining electrochemical techniques with geochemistry and molecular methods. Working electrodes buried in sediment microcosms were poised at seven redox potentials between -300 and -750 mV versus Ag/AgCl using a three-electrode system. In electrode biofilms recovered after 2-month incubations, overall community diversity increased with more negative redox potentials. Abundances of known EET-capable groups (e.g., Alteromonadales and Desulfuromonadales) varied with redox potential. Motility and chemotaxis genes were found in greater abundance in electrode communities, suggesting a possible selective advantage of these pathways for colonization and utilization of the electrode. Our enrichments demonstrated the validity of this approach in capturing groups known, as well as novel groups (e.g., Campylobacterales) that perform EET. The diverse nature of the enriched cathode communities suggest that insoluble substrate oxidation may be a critical, although poorly described microbial metabolic process in marine sediment.

Enhancement of methane production from 1-hexadecene by additional electron donors

1-Hexadecene-contaminated wastewater is produced in oil refineries and can be treated in methanogenic bioreactors, although generally at low conversion rates. In this study, a microbial culture able to degrade 1-hexadecene was enriched, and different stimulation strategies were tested for enhancing 1-hexadecene conversion to methane. Seven and three times faster methane production was obtained in cultures stimulated with yeast extract or lactate, respectively, while cultures amended with crotonate lost the ability to degrade 1-hexadecene. Methane production from 1-hexadecene was not enhanced by the addition of extra hydrogenotrophic methanogens. Bacteria closely related to Syntrophus and Smithella were detected in 1-hexadecene-degrading cultures, but not in the ones amended with crotonate, which suggests the involvement of these bacteria in 1-hexadecene degradation. Genes coding for alkylsuccinate synthase alpha-subunit were detected in cultures degrading 1-hexadecene, indicating that hydrocarbon activation may occur by fumarate addition. These findings are novel and show that methane production from 1-hexadecene is improved by the addition of yeast extract or lactate. These extra electron donors may be considered as a potential bioremediation strategy of oil-contaminated sites with bioenergy generation through methane production.

Biodegradation of Poly(3-hydroxybutyrate- co-3-hydroxyhexanoate) Plastic under Anaerobic Sludge and Aerobic Seawater Conditions: Gas Evolution and Microbial Diversity

Poly(3-hydroxybutyrate- co-3-hydroxyhexanoate) (poly(3HB- co-3HHx)) thermoplastics are a promising biodegradable alternative to traditional plastics for many consumer applications. Biodegradation measured by gaseous carbon loss of several types of poly(3HB- co-3HHx) plastic was investigated under anaerobic conditions and aerobic seawater environments. Under anaerobic conditions, the biodegradation levels of a manufactured sheet of poly(3HB- co-3HHx) and cellulose powder were not significantly different from one another over 85 days with 77.1 ± 6.1 and 62.9 ± 19.7% of the carbon converted to gas, respectively. However, the sheet of poly(3HB- co-3HHx) had significantly higher methane yield ( p ≤ 0.05), 483.8 ± 35.2 mL·g^-1 volatile solid (VS), compared to cellulose controls, 290.1 ± 92.7 mL·g^-1 VS, which is attributed to a greater total carbon content. Under aerobic seawater conditions (148-195 days at room temperature), poly(3HB- co-3HHx) sheets were statistically similar to cellulose for biodegradation as gaseous carbon loss (up to 83% loss in about 6 months), although the degradation rate was lower than that for cellulose. The microbial diversity was investigated in both experiments to explore the dominant bacteria associated with biodegradation of poly(3HB- co-3HHx) plastic. For poly(3HB- co-3HHx) treatments, Cloacamonales and Thermotogales were enriched under anaerobic sludge conditions, while Clostridiales, Gemmatales, Phycisphaerales, and Chlamydiales were the most enriched under aerobic seawater conditions.

Enhanced bioelectroremediation of a complexly contaminated river sediment through stimulating electroactive degraders with methanol supply

Bioelectroremediation is an efficient, sustainable, and environment-friendly remediation technology for the complexly contaminated sediments. Although various recalcitrant pollutants could be degraded in the electrode district, the degradation efficiency was generally confined by the low total organic carbon (TOC) content in the sediment. How to enhance the electroactive degraders' activity and efficiency remain poorly understood. Here we investigated the bioeletroremediation of a complexly contaminated river sediment with low TOC in a cylindric sediment microbial fuel cell stimulated by methanol. After 200 days treatment, the degradation efficiencies of total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAH), and cycloalkenes (CYE) in the electrode district with methanol stimulation were 1.45-4.38 times higher compared with those in the non-electrode district without methanol stimulation. The overall electrode district communities were significantly positively correlated with the variables of the enhanced TPH, PAH, CYE and TOC degradation efficiencies (p < .01). The joint electrical and exogenous methanol stimulation selectively enriched electroactive degraders (Geobacter and Desulfobulbus) in the anode biofilms, and their proportion was markedly positively correlated with the characteristic and total pollutants degradation efficiencies (p < .001). This study offers a new insight into the response of key electroactive degraders to the joint stimulation process.

Biodegradation of di-n-butyl phthalate (DBP) by a novel endophytic Bacillus megaterium strain YJB3

Phthalic acid esters (PAEs) are a group of recalcitrant and hazardous organic compounds that pose a great threat to both ecosystem and human beings. A novel endophytic strain YJB3 that could utilize a wide range of PAEs as the sole carbon and energy sources for cell growth was isolated from Canna indica root tissue. It was identified as Bacillus megaterium based on morphological characteristics and 16S rDNA sequence homology analysis. The degradation capability of the strain YJB3 was investigated by incubation in mineral salt medium containing di-n-butyl-phthalate (DBP), one of important PAEs under different environmental conditions, showing 82.5% of the DBP removal in 5days of incubation under the optimum conditions (acetate 1.2g·L^-1, inocula 1.8%, and temperature 34.2°C) achieved by two-step sequential optimization technologies. The DBP metabolites including mono-butyl phthalate (MBP), phthalic acid (PA), protocatechuic acid (PCA), etc. were determined by GC-MS. The PCA catabolic genes responsible for the aromatic ring cleavage of PCA in the strain YJB3 were excavated by whole-genome sequencing. Thus, a degradation pathway of DBP by the strain YJB3 was proposed that MBP was formed, followed by PA, and then the intermediates were further utilized till complete degradation. To our knowledge, this is the first study to show the biodegradation of PAEs using endophyte. The results in the present study suggest that the strain YJB3 is greatly promising to act as a competent inoculum in removal of PAEs in both soils and crops.

Biodegradation of polycyclic aromatic hydrocarbons: Using microbial bioelectrochemical systems to overcome an impasse

Polycyclic aromatic hydrocarbons (PAHs) are hardly biodegradable carcinogenic organic compounds. Bioremediation is a commonly used method for treating PAH contaminated environments such as soils, sediment, water bodies and wastewater. However, bioremediation has various drawbacks including the low abundance, diversity and activity of indigenous hydrocarbon degrading bacteria, their slow growth rates and especially a limited bioavailability of PAHs in the aqueous phase. Addition of nutrients, electron acceptors or co-substrates to enhance indigenous microbial activity is costly and added chemicals often diffuse away from the target compound, thus pointing out an impasse for the bioremediation of PAHs. A promising solution is the adoption of bioelectrochemical systems. They guarantee a permanent electron supply and withdrawal for microorganisms, thereby circumventing the traditional shortcomings of bioremediation. These systems combine biological treatment with electrochemical oxidation/reduction by supplying an anode and a cathode that serve as an electron exchange facility for the biocatalyst. Here, recent achievements in polycyclic aromatic hydrocarbon removal using bioelectrochemical systems have been reviewed. This also concerns PAH precursors: total petroleum hydrocarbons and diesel. Removal performances of PAH biodegradation in bioelectrochemical systems are discussed, focussing on configurational parameters such as anode and cathode designs as well as environmental parameters like porosity, salinity, adsorption and conductivity of soil and sediment that affect PAH biodegradation in BESs. The still scarcely available information on microbiological aspects of bioelectrochemical PAH removal is summarised here. This comprehensive review offers a better understanding of the parameters that affect the removal of PAHs within bioelectrochemical systems. In addition, future experimental setups are proposed in order to study syntrophic relationships between PAH degraders and exoelectrogens. This synopsis can help as guide for researchers in their choices for future experimental designs aiming at increasing the power densities and PAH biodegradation rates using microbial bioelectrochemistry.

Bioremediation of PAHs contaminated river sediment by an integrated approach with sequential injection of co-substrate and electron acceptor: Lab-scale study

In this study, the feasibility of employing an integrated bioremediation approach in contaminated river sediment was evaluated. Sequential addition of co-substrate (acetate) and electron acceptor (NO₃^-) in a two-phase treatment was capable of effectively removing polycyclic aromatic hydrocarbons (PAHs) in river sediment. The residual concentration of total PAHs decreased to far below effect range low (ERL) value within 91 days of incubation, at which concentration it could rarely pose biological impairment. The biodegradation of high molecular weight PAHs were found to be mainly occurred in the sediment treated with co-substrates (i.e. acetate or methanol), in which acetate was found to be more suitable for PAHs degradation. The role of co-substrates in influencing PAHs biodegradation was tentatively discussed herein. Additionally, the sediment odorous problem and blackish appearance were intensively addressed by NO₃^- injection. The results of this study demonstrated that integrating two or more approaches/processes would be a helpful option in sediment remediation. It can lead to a more effective remediation performance, handle multiple contamination issues, as well as mitigate environmental risks caused by one of the single methods.

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge

Nutrient deficiency severely impairs the catabolic activity of indigenous microorganisms in hydrocarbon rich environments (HREs) and limits the rate of intrinsic bioremediation. The present study aimed to characterize the microbial community in refinery waste and evaluate the scope for biostimulation based in situ bioremediation. Samples recovered from the wastewater lagoon of Guwahati refinery revealed a hydrocarbon enriched [high total petroleum hydrocarbon (TPH)], oxygen-, moisture-limited, reducing environment. Intrinsic biodegradation ability of the indigenous microorganisms was enhanced significantly (>80% reduction in TPH by 90 days) with nitrate amendment. Preferred utilization of both higher- (>C30) and middle- chain (C20-30) length hydrocarbons were evident from GC-MS analysis. Denaturing gradient gel electrophoresis and community level physiological profiling analyses indicated distinct shift in community’s composition and metabolic abilities following nitrogen (N) amendment. High throughput deep sequencing of 16S rRNA gene showed that the native community was mainly composed of hydrocarbon degrading, syntrophic, methanogenic, nitrate/iron/sulfur reducing facultative anaerobic bacteria and archaebacteria, affiliated to γ- and δ-Proteobacteria and Euryarchaeota respectively. Genes for aerobic and anaerobic alkane metabolism (alkB and bssA), methanogenesis (mcrA), denitrification (nirS and narG) and N₂ fixation (nifH) were detected. Concomitant to hydrocarbon degradation, lowering of dissolve O₂ and increase in oxidation-reduction potential (ORP) marked with an enrichment of N₂ fixing, nitrate reducing aerobic/facultative anaerobic members [e.g., Azovibrio, Pseudoxanthomonas and Comamonadaceae members] was evident in N amended microcosm. This study highlighted that indigenous community of refinery sludge was intrinsically diverse, yet appreciable rate of in situ bioremediation could be achieved by supplying adequate N sources.

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing

This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (p<0.05). Despite explaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation.

Biodegradation of antibiotic ciprofloxacin: pathways, influential factors, and bacterial community structure

Antibiotic ciprofloxacin is ubiquitous in the environment. However, little is known about ciprofloxacin dissipation by microbial community. The present study investigated the biodegradation potential of ciprofloxacin by mixed culture and the influential factors and depicted the structure of ciprofloxacin-degrading microbial community. Both the original microbiota from drinking water biofilter and the microbiota previously acclimated to high levels of ciprofloxacin could utilize ciprofloxacin as sole carbon and nitrogen sources, while the acclimated microbiota had a much stronger removal capacity. Temperature rise and the presence of carbon or nitrogen sources favored ciprofloxacin biodegradation. Many novel biotransformation products were identified, and four different metabolic pathways for ciprofloxacin were proposed. Bacterial community structure illustrated a profound shift with ciprofloxacin biodegradation. The ciprofloxacin-degrading bacterial community was mainly composed of classes Gammaproteobacteria, Bacteroidia, and Betaproteobacteria. Microorganisms from genera Pseudoxanthomonas, Stenotrophomonas, Phenylobacterium, and Leucobacter might have links with the dissipation of ciprofloxacin. This work can provide some new insights towards ciprofloxacin biodegradation.

Induced metal redistribution and bioavailability enhancement in contaminated river sediment during in situ biogeochemical remediation

In situ sediment remediation using Ca(NO3)2 or CaO2 for odor mitigation and acid volatile sulfide (AVS) and organic pollutant (such as TPH and PAHs) removal was reported in many studies and fieldwork. Yet, the associated effects on metal mobilization and potential distortion in bioavailability were not well documented. In this study, contaminated river sediment was treated by Ca(NO3)2 and CaO2 in bench studies. Through the investigation of AVS removal, organic matter removal, the changes in sediment oxidation-reduction potential (ORP), microbial activity, and other indigenous parameters, the effects on metal bioavailability, bioaccessibility, and fraction redistribution in sediment were evaluated. The major mechanisms for sediment treated by Ca(NO3)2 and CaO2 are biostimulation with indigenous denitrifying bacteria and chemical oxidation, respectively. After applying Ca(NO3)2 and CaO2, the decreases of metal concentrations in the treated sediment were insignificant within a 35-day incubation period. However, the [SEMtot-AVS]/f OC increased near to the effective boundary of toxicity (100 μmol g(-1) organic carbon (OC)), indicating that both bioavailability and bioaccessibility of metals (Cu, Zn, and Ni) to benthic organisms are enhanced after remediation. Metals were found redistributed from relatively stable fractions (oxidizable and residual fractions) to weakly bound fractions (exchangeable and reducible fractions), and the results are in line with the enhanced metal bioavailability. Compared with Ca(NO3)2, CaO2 led to higher enhancement in metal bioavailability and bioaccessibility, and more significant metal redistribution, probably due to its stronger chemical reactive capacity to AVS and sediment organic matter. The reactions in CaO2-treated sediment would probably shift from physicochemical to biochemical heterotrophic oxidation for sediment organic matter degradation. Therefore, further investigation on the long-term metal redistribution and associated mobility as well as bioavailability is recommended.

An integrated bioremediation process for petroleum hydrocarbons removal and odor mitigation from contaminated marine sediment

This study developed a novel integrated bioremediation process for the removal of petroleum hydrocarbons and the mitigation of odor induced by reduced sulfur from contaminated marine sediment. The bioremediation process consisted of two phases. In Phase I, acetate was dosed into the sediment as co-substrate to facilitate the sulfate reduction process. Meanwhile, akaganeite (β-FeOOH) was dosed in the surface layer of the sediment to prevent S(2-) release into the overlying seawater. In Phase II, NO3(-) was injected into the sediment as an electron acceptor to facilitate the denitrification process. After 20 weeks of treatment, the sequential integration of the sulfate reduction and denitrification processes led to effective biodegradation of total petroleum hydrocarbons (TPH), in which about 72% of TPH was removed. In Phase I, the release of S(2-) was effectively controlled by the addition of akaganeite. The oxidation of S(2-) by Fe(3+) and the precipitation of S(2-) by Fe(2+) were the main mechanisms for S(2-) removal. In Phase II, the injection of NO3(-) completely inhibited the sulfate reduction process. Most of residual AVS and S(0) were removed within 4 weeks after NO3(-) injection. The 16S rRNA clone library-based analysis revealed a distinct shift of bacterial community structure in the sediment over different treatment phases. The clones affiliated with Desulfobacterales and Desulfuromonadales were the most abundant in Phase I, while the clones related to Thioalkalivibrio sulfidophilus, Thiohalomonas nitratireducens and Sulfurimonas denitrificans predominated in Phase II.