Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor

Assessing Microbial Activity and Rhizoremediation in Hydrocarbon and Heavy Metal-Impacted Soil

Rhizodegradation enhances pollutant degradation through plant-microbe interactions in the rhizosphere. Plant roots provide a colonisation surface and root exudates that promote microbial abundance and activity, facilitating organic pollutant breakdown via direct microbial degradation and co-metabolism. This study assessed the rhizodegradation of weathered petroleum hydrocarbons (PHCs) in heavy metal co-contaminated soil in a microcosm-scale pot trial. Treatments included Sinapis alba, Lolium perenne, a L. perenne + Trifolium repens mix, and Cichorium intybus, alongside a non-planted control. After 14 weeks, PHC concentrations were analysed via gas chromatography, and rhizosphere microbial communities were characterised through sequencing. Sinapis alba achieved the highest PHC degradation (68%), significantly exceeding the non-planted control (p < 0.05, Kruskal-Wallis test). Hydrocarbon-degrading bacteria, including KCM-B-112, C1-B045, Hydrogenophaga, unclassified Saccharimonadales sp., and Pedobacter, were enriched in the rhizosphere, with the uncultured clade mle1-27 potentially contributing indirectly. Metals analysis of plant tissues showed that mustard could accumulate copper more than lead and zinc, despite higher concentrations of zinc and lead in the soil. These results highlight the potential of S. alba for rhizoremediation in PHC-heavy metal co-contaminated soils.

Depletion of crude oil and fuel in the Arctic. Summer and winter field studies with immobilized oil in seawater at Svalbard

Seasonal dynamics can vastly influence the natural depletion of oil spilled into the ocean and the Arctic regions are characterized by large seasonal changes, especially in temperature and daylight. To determine the influences of seasonal variation on natural oil depletion processes like dissolution, photooxidation and biodegradation, we deployed thin films of three oils in natural seawater during the Arctic summer and winter in Svalbard, Norway. The extent of oil depletion varied with season and the type of the oil, however, considerable depletion of n-alkanes and polycyclic aromatic compounds were observed during both summer and winter. The influence of temperature on depletion of components was not consistent between the three oils and only small effects of photooxidation were found during the summer. We further found variations in the composition of bacterial communities associated with the oil films between the seasons with an apparently delayed succession during the winter. The bacterial communities generally contained high abundances of previously reported oil degrading taxa which displayed distinct seasonal patterns in their relative abundance. Oleispira and Oleibacter were dominantly found during the summer and Colwellia during the winter, while Cycloclasticus and C1-B045 were highly abundant during both seasons. While the environmental factors were likely the cause for variations in oil depletion between the seasons and oils, the seasonal differences in the bacterial community composition did not seem to affect their biodegradation potential.

Compositional change of bacterial communities in oil-polluted seawater amid varying degrees of nanoplankton bacterivory

Petroleum hydrocarbons are being released into the marine environment continuously. They will undergo weathering and may eventually be biodegraded by bacteria and other microbes. While nanoplankton (2-20 μm) are the major consumers of marine bacteria, their effect on the process of biodegradation of oil hydrocarbons is still debated. A 14-day microcosm experiment was conducted to investigate the effects of crude oil hydrocarbons on nanoplankton bacterivory and bacterial community in coastal waters. The coefficients of population growth (0.56-1.80 d-1 for all treatments considered) and grazing mortality (0.38-1.65 d-1 for all treatment considered) of bacteria estimated with the dilution method did not differ among the treatments of control (Ctrl), low dose chemically dispersed oil (LDOil, 2 μL L-1 of crude oil), and high dose chemically dispersed oil (HDOil, 8 μL L-1 of crude oil). Bacterial abundance ranged between 0.21-0.86 × 106 cells mL-1 on average for all treatments. The lack of drastic increases in the cell density of bacterial cells in the oil-loaded treatments was observed throughout the experiment period. Sequencing analysis of the 16S rRNA gene revealed the progressive changes in the community compositions of bacteria in all treatments. The relatively high abundance of oil-degrading bacteria, including Cycloclasticus and Alcanivorax on Days 3-14 of the experiment reflected the presence of biodegradation of oil in the LDOil and HDOil treatments. Throughout the 14 days, the community composition of bacteria in the LDOil and HDOil treatments became more similar and they both differed from that in the Ctrl treatment. This study concluded that, in oil-polluted seawater, the changes in the bacterial community composition were mainly resulting from the addition of chemically dispersed crude oil.

A seawater field study of crude and fuel oil depletion in Northern Norway at two different seasons - Chemistry and bacterial communities

After marine oil spills, natural processes like photooxidation and biodegradation can remove the oil from the environment. However, these processes are strongly influenced by environmental conditions. To achieve a greater understanding of how seasonal variations in temperature, light exposure and the bacterial community affect oil depletion in the marine environment, we performed two field experiments during the spring and autumn. Field systems equipped with a thin oil film of Statfjord, Grane or ULSFO were deployed in northern Norway. Depletion of the total extractable matter was faster during the spring than during the autumn. Statfjord showed faster depletion of n-alkanes during spring, while depletion of polycyclic aromatic hydrocarbons varied between the seasons based on the degree of alkyl-substitutions. ULSFO displayed the overall slowest depletion. Biodegradation of the oils was associated with high abundances of unassigned bacteria during the spring but was governed by Alcanivorax, Cycloclasticus, Oleibacter and Oleispira during the autumn.

Genomic analysis of the class Phycisphaerae reveals a versatile group of complex carbon-degrading bacteria

Bacteria of the phylum Planctomycetota have received much attention over the years due to their unique cell biology and potential for biotechnological application. Within the phylum, bacteria of the class Phycisphaerae have been found in a multitude of environmental datasets. However, only a few species have been brought into culture so far and even enrichments are scarce. Therefore, very little is known about their lifestyle, which has hindered efforts to estimate their environmental relevance. Here, we analysed all medium- and high-quality Phycisphaerae genomes represented in the genome taxonomy database to learn more about their physiology. We combined automatic and manual annotation efforts to provide a bird's eye view of their diverse energy metabolisms. Contrasting previous reports, we did not find indications for the presence of genes for anaerobic ammonium oxidation in any Phycisphaerae genome. Instead, we found that many members of this class are adapted to a facultative anaerobic or strictly fermentative lifestyle and may be specialized in the breakdown of carbon compounds produced by other organisms. Based on these findings, we provide a practical overview of organic carbon substrates predicted to be utilized by Phycisphaerae families.

Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms

This study assessed the bacterioplankton community and its relationship with environmental variables, including total petroleum hydrocarbon (TPH) concentration, in the Yucatan shelf area of the Southern Gulf of Mexico. Beta diversity analyses based on 16S rRNA sequences indicated variations in the bacterioplankton community structure among sampling sites. PERMANOVA indicated that these variations could be mainly related to changes in depth (5 to 180 m), dissolved oxygen concentration (2.06 to 5.93 mg L-1), and chlorophyll-a concentration (0.184 to 7.65 mg m3). Moreover, SIMPER and one-way ANOVA analyses showed that the shifts in the relative abundances of Synechococcus and Prochlorococcus were related to changes in microbial community composition and chlorophyll-a values. Despite the low TPH content measured in the studied sites (0.01 to 0.86 μL L-1), putative hydrocarbon-degrading bacteria such as Alteromonas, Acinetobacter, Balneola, Erythrobacter, Oleibacter, Roseibacillus, and the MWH-UniP1 aquatic group were detected. The relatively high copy number of the alkB gene detected in the water column by qPCR and the enrichment of hydrocarbon-degrading bacteria obtained during lab crude oil tests exhibited the potential of bacterioplankton communities from the Yucatan shelf to respond to potential hydrocarbon impacts in this important area of the Gulf Mexico.

Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas

The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways

Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.

Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes

Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.

Dynamic changes in the microbial community in the surface seawater of Jiaozhou Bay after crude oil spills: An in situ microcosm study

The changes in the composition and structure of microbial communities in Jiaozhou Bay are strongly affected by marine oil pollution, but the outcomes of the microbial responses and effects of dispersant application remain unclear. Herein, we performed an in situ microcosm study to investigate the response of the indigenous microbial community under crude oil alone and combined oil and dispersant treatment in the surface seawater of a semi-enclosed marine area of Jiaozhou Bay. The dynamics of the bacterial classification based on 16s rDNA sequencing were used to assess the changes with the crude oil concentration, dispersant use, and time. The crude oil resulted in a high abundance of the genera Pseudohongiella, Cycloclasticus, Marivita, and C1-B045 from the Gammaproteobacteria and Alphaproteobacteria classes, suggesting for hydrocarbon degradation. However, the dispersant treatment was more advantageous for Pacificibacter, Marivita, and Loktanella. Besides accelerating the rate of bacterial community succession, the dispersants had significantly stronger effects on the structure of the bacterial community and the degradation functions than the oil. A higher dose of oil exposure corresponded to fewer dominant species with a high relative abundance. Our study provides information for screening potential degradation bacteria and assessing the risks that oil spills pose to marine ecosystems.

Best available technique for the recovery of marine benthic communities in a gravel shore after the oil spill: A mesocosm-based sediment triad assessment

Ecotoxicological effects of spilled oils are well documented, but study of recovery of marine benthic communities is limited. Long-term recovery of hard bottom communities during physical and biological remediations after a spill was monitored. A 60-day experiment was conducted using a mesocosm with monitoring of eight endpoints by use of the sediment quality triad (SQT). First, physical treatment of hot water + high pressure flushing maximally removed residual oils (max=93%), showing the greatest recovery among SQT variables (mean=72%). Physical cleanup generally involved adverse effects such as depression of the microphytobenthic community during the initial period. Next, biological treatments, such as fertilizer, emulsifier, enzyme and augmentation of the microbes, all facilitated removal of oil (max=66%) enhancing ecological recovery. Analysis of the microbiome confirmed that oil-degrading bacteria, such as Dietzia sp. and Rosevarius sp. were present. A mixed bioremediation, including fertilizer + multi-enzyme + microbes (FMeM) maximized efficacy of remediation as indicated by SQT parameters (mean=47%). Natural attenuation with "no treatment" showed comparable recovery to other remediations. Considering economic availability, environmental performance, and technical applicability, of currently available techniques, combined treatments of physical removal via hand wiping followed by FMeM could be most effective for recovery of the rocky shore benthic community.

Assessing the Effect of Chemical Dispersant Nokomis 3-F4 on the Degradation of a Heavy Crude Oil in Water by a Marine Microbial Consortium

Degradation efficiency of a heavy crude oil by a marine microbial consortium was evaluated in this study, with and without the addition of a chemical dispersant (Nokomis 3-F4). 15.50% of total petroleum hydrocarbons (TPH) were removed after 15 days of incubation without dispersant, with a degradation rate of 2.39 ± 0.22 mg L^-1 day^-1. In contrast, the addition of Nokomis 3-F4 increased TPH degradation up to 30.81% with a degradation rate of 5.07 ± 0.37 mg L^-1 day^-1. 16S rRNA gene sequencing indicated a dominance of the consortium by Achromobacter and Alcanivorax. Nonetheless, significant increases in the relative abundance of Martelella and Ochrobactrum were observed with the addition of Nokomis 3-F4. These results will contribute to further environmental studies of the Gulf of Mexico, where Nokomis 3-F4 can be used as chemical dispersant.

Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants

Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg^-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.

Molecular biological methods in environmental engineering

Microbes are sensitive to environmental changes and can respond in a short time. Genomics, proteomics, transcriptomics, metabolomics, and multigroup association are used to characterize the composition, function, and metabolism of microorganisms, and to evaluate the environment according to the changes in microorganisms, which has important reference and guiding significance of environmental monitoring, management, and repair. In this paper, the application of molecular biological methods to study environmental microorganisms in the fields of wastewater treatment, pollution control, soil improvement, and environmental monitoring in 2019 is reviewed.

Enhancing the degradation of mixed polycyclic aromatic hydrocarbon and medium-chain-length polyhydroxyalkanoate production by mixed bacterial cultures using modified repeated batch fermentation

AIMS

To increase the biodegradation of phenanthrene (PHE), pyrene (PYR) and fluoranthene (FLU) through mixed cultures of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria, using modified repeated batch fermentation.

METHODS AND RESULTS

Novel bacterial strains of Pseudomonas putida, Pseudomonas sp. and Ralstonia eutropha were cultivated and the biodegradation and conversion of mixed PAH to medium-chain-length polyhydroxyalkanoates (MCL-PHA) was determined. The highest degradation of PAH (100%) and PHA production (50·0%) was obtained in medium containing 30 mmol l^-1 of mixed PAH after three cycles of repeated batch fermentation. The concentration of PAH in the reactor was increased from 30 to 90 mmol l^-1 with repeated additions of PAH, and bacteria were able to produce PHA at 40% of cell dry mass. The MCL-PHA were identified by gas chromatography/mass spectroscopy, with the 3-hydroxydecanoate (3-HD) monomer higher than 75 mol.%.

CONCLUSIONS

This study demonstrated that the biodegradation of PHE, PYR and FLU was enhanced by modified repeated batch fermentation using a mixed culture of bacteria. In addition, this fermentation strategy also increased the production of PHA, with an increase in monomer composition.

SIGNIFICANCE AND IMPACT OF THE STUDY

This was the first study to describe the enhancement of the degradation of mixed solutions of PHE, PYR and FLU, and PHA production, using novel mixed bacterial cultures and modified repeated batch fermentation. The MCL-PHA formed had uniquely high 3-HD content.

Time- and compound-dependent microbial community compositions and oil hydrocarbon degrading activities in seawater near the Chinese Zhoushan Archipelago

Marine microorganisms play an irreplaceable role in removing spilled oil. Zhoushan archipelago has one of the busiest ports and oil stockpiles in China. However, little is known about which and how fast oil-degrading microorganisms could biodegrade spilled oil here. By combining ¹⁴C-/³H-based radiotracer assays and MiSeq sequencing, we report the successive pattern of microbial oil-degrading activities and community compositions. The biodegradation rates of alkanes and PAHs (Polycyclic Aromatic Hydrocarbons) were significantly stimulated by oil addition, and reached their maximum after incubation for 3 and 7 days, respectively. Meanwhile, the abundances of alkB and phnAc genes increased and the bacterial communities continuously shifted. Potential oil-degrading bacteria Alcanivorax, Erythrobacter were the dominant degraders by day 3, whereas the dominant degraders shifted to C1-B045, Alteromonas, Pseudohongiella in the later period. These results provide valuable insights into the cooperative system of the versatile oil-degrading bacteria in successively biodegrading complex oil hydrocarbons in oil spills.

A succession of marine bacterial communities in batch reactor experiments during the degradation of five different petroleum types

Marine microbial communities might be subjected to accidental petroleum spills; however, some bacteria can degrade it, making these specific bacteria valuable for bioremediation from petroleum contamination. Thus, characterizing the microbial communities exposed to varying types of petroleum is essential. We evaluated five enriched microbial communities from the northwest Gulf of Mexico (four from the water column and one from sediments). Enrichments were performed using five types of petroleum (extra light, light, medium, heavy and extra heavy), to reveal the microbial succession using a 16S rDNA amplicon approach. Four communities were capable of degrading from extra light to heavy petroleum. However, only the community from sediment was able to degrade the extra heavy petroleum. Successional changes in the microbial communities' structures were specific for each type of petroleum where genus Dietzia, Gordonia, Microvirga, Rhizobium, Paracoccus, Thalassobaculum, Sphingomonas, Moheibacter, Acinetobacter, Pseudohongiella, Porticoccus, Pseudoalteromonas, Pseudomonas, Shewanella, and Planctomyces presented differential abundance between the treatments.

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r² = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r² = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.