Bioremediation of Artificial Diesel-Contaminated Soil Using Bacterial Consortium Immobilized to Plasma-Pretreated Wood Waste

Response of bacterial ecological and functional properties to anthropogenic interventions during maturation of mine sand soil

Soil formation is a complex process that starts from the biological development. The ecological principles and biological function in soil are of great importance, whereas their response to anthropogenic intervention has been poorly understood. In this study, a 150-day microcosmic experiment was conducted with the addition of sludge and/or fermented wood chips (FWC) to promote the soil maturation. The results showed that, compared to the control (natural development without anthropogenic intervention), sludge, FWC, and their combination increased the availability of carbon, nitrogen, and potassium, and promoted the soil aggregation. They also enhanced the cellulase activity, microbial biomass carbon (MBC) and bacterial diversity, indicating that anthropogenic interventions promoted the maturation of sand soil. Molecular ecology network and functional analyses indicated that soil maturation was accomplished with the enhancement of ecosystem functionality and stability. Specifically, sludge promoted a transition in bacterial community function from denitrification to nitrification, facilitated the degradation of easily degradable organic matter, and enhanced the autotrophic nutritional mode. FWC facilitated the transition of bacterial function from denitrification to ammonification, promoted the degradation of recalcitrant organic matter, and simultaneously enhanced both autotrophic and heterotrophic nutritional modes. Although both sludge and FWC promoted the soil functionality, they showed distinct mechanistic actions, with sludge enhancing the physical structure, and FWC altering chemical composition. It is also worth emphasizing that sludge and FWC exhibited a synergistic effect in promoting biological development and ecosystem stability, thereby providing an effective avenue for soil maturation.

Characterization of Diesel Degrading Indigenous Bacterial Strains, Acinetobacter pittii and Pseudomonas aeruginosa, Isolated from Oil Contaminated Soils

In this study, 13 diesel degrading bacteria were isolated from the oil contaminated soils and the promising strains identified as Acinetobacter pittii ED1 and Pseudomonas aeruginosa BN were evaluated for their diesel degrading capabilities. These strains degraded the diesel optimally at 30 °C, pH 7.0 and 1% diesel concentration. Both the strains produced biofilm at 1% diesel concentration indicating their ability to tolerate diesel induced abiotic stress. Gravimetric analysis of the spent medium after 7 days of incubation showed that A. pittii ED1 and P. aeruginosa BN degraded 68.61% and 76% diesel, respectively, while biodegradation reached more than 90% after 21 days. Fourier Transform Infrared (FTIR) analysis of the degraded diesel showed 1636.67 cm-1 (C=C stretch, N-H bond) peak corresponding to alkenes and primary amines, while GC-TOF-MS analysis showed decline in hydrocarbon intensities after 7 days of incubation. The present study revealed that newly isolated A. pittii ED1 and P. aeruginosa BN were able to degrade diesel hydrocarbons (C11-C18, and C19-C24) efficiently and have potential for bioremediation of the oil-contaminated sites.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01317-3.

Delignified porous wood as biofilm support for 1,4-dioxane-degrading bacterial consortium

Delignified porous wood samples were used as carriers for biofilm formation of a bacterial consortium with the ability to degrade 1,4-dioxane (DX). The delignification treatment of the natural wood resulted in higher porosity, formation of macropores, increase in surface roughness and hydrophilicity of the treated wood pieces. These superior properties of two types of treated carriers (respectively, A and B) compared to the untreated wood resulted in 2.19 ± 0.52- and 2.66 ± 0.23-fold higher growth of biofilm. Moreover, analysis of the fatty acid profiles indicated an increase in proportion of the saturated fatty acids during the biofilm formation, characterising an enhancement in rigidity and hydrophobicity of the biofilms. DX initial concentration of 100 mg/L was completely degraded (detection limit 0.01 mg/L) in 24 and 32 h using the treated A and B woods, while only 25.84 ± 5.95% was removed after 32 h using the untreated wood. However, fitting the DX biodegradation data to the Monod model showed a lower maximum specific growth rate for biofilm (0.0276 ± 0.0018 1/h) versus planktonic (0.0382 ± 0.0024 1/h), because of gradual accumulation of inactive cells in the biofilm. Findings of this study can contribute to the knowledge of biofilm formation regarding the physical/chemical properties of biofilm carriers and be helpful to the ongoing research on bioremediation of DX.

Newly isolated halotolerant Aspergillus sp. showed high diesel degradation efficiency under high salinity environment aided with hematite

The contamination of saline soil with hazardous petroleum hydrocarbons is a common problem across coastal areas globally. Bioaugmentation combined with chemical treatment is an emerging remediation technique, but it currently shows low efficiency under high saline environments. In this study, we screened and used a novel halotolerant lipolytic fungal consortium (HLFC) combined with hematite (Fe₂O₃) for the bioremediation of diesel contaminated saline soils. The changes in total petroleum hydrocarbons (TPH) concentrations, enzyme activity, and microbial diversity were compared among different treatments (HLFC, hematite, hematite-HLFC, and control). The results showed that TPH degradation was significantly (P < 0.05) enhanced in hematite-HLFC (47.59-88.01%) and HLFC (24.26-72.04%) amended microcosms across all salinity levels, compared to the treatments of hematite (23.71-66.26%) and control (6.39-55.20%). TPH degradation was positively correlated with lipase and laccase enzyme activities, electrical conductivity, and the water holding capacity of the soil. Analyses of the microbial community structure showed that microbial richness decreased, while evenness increased in HLFC and hematite-HLFC treatments. The relative abundances of Alicyclobacillus, Sediminibacillus, Alcanivorax, Penicillium, Aspergillus, and Candida genera were significantly high in hematite-HLFC and HLFC amended microcosms. Our findings provide a promising new microbial-based technique, which can degrade TPH efficiently in saline soil.

Microbial biofilms: Recent advances and progress in environmental bioremediation

Microbial biofilms are formed by adherence of the bacteria through their secreted polymer matrices. The major constituents of the polymer matrices are extracellular DNAs, proteins, polysaccharides. Biofilms have exhibited a promising role in the area of bioremediation. These activities can be further improved by tuning the parameters like quorum sensing, characteristics of the adhesion surface, and other environmental factors. Organic pollutants have created a global concern because of their long-term toxicity on human, marine, and animal life. These contaminants are not easily degradable and continue to prevail in the environment for an extended period. Biofilms are being used for the remediation of different pollutants, among which organic pollutants have been of significance. The bioremediation of organic contaminants using biofilms is an eco-friendly, cheap, and green process. However, the development of this technology demands knowledge on the mechanism of action of the microbes to form the biofilm, types of specific bacteria or fungi responsible for the degradation of a particular organic compound, and the mechanistic role of the biofilm in the degradation of the pollutants. This review puts forth a comprehensive summary of the role of microbial biofilms in the bioremediation of different environment-threatening organic pollutants.

Geothermal heating: Is it a boon or a bane for bioremediation?

There has been a worldwide interest in renewable energy technologies, as a means of decreasing reliance on fossil fuels, minimizing climate change effects, and reducing greenhouse emissions. One such technology is geothermal heating where the constant subsurface temperature is used to cool or heat building interiors via heat pumps. In Canada, the use of geothermal heating has become a popular option for heating and cooling buildings, and it is anticipated that, in the near term, most large buildings will include geothermal heating as part of their climate control strategy. However, little is known about the environmental impacts of geothermal heating on the subsurface environment. The present review will examine the effect of geothermal heating on groundwater flow and remediation efforts, whereby the heat generated by geothermal systems may help with urban pollution. "Geothermal Remediation" could leverage the subsurface heating resulting from geothermal systems to accelerate biodegradation of certain petroleum-based pollutants at brown-field sites, while providing building(s) with sustainable heating and cooling. This idea coincides with the rising momentum towards sustainable and green remediation in Europe and the United States. To ensure that Geothermal Remediation is achievable, the effect of heat on bioremediation needs to be examined. This review provides an insight into what we know about heat effects on bioremediation activities and subsurface transport.

Bibliometric Analysis of Hydrocarbon Bioremediation in Cold Regions and a Review on Enhanced Soil Bioremediation

Simple Summary

Anthropogenic activities in cold regions require petroleum oils to support various purposes. With the increased demand of petroleum, accidental oil spills are generated during transportation or refuelling processes. Soil is one of the major victims in petroleum pollution, hence studies have been devoted to find solutions to remove these petroleum hydrocarbons. However, the remote and low-temperature conditions in cold regions hindered the implementation of physical and chemical removal treatments. On the other hand, biological treatments in general have been proposed as an innovative approach to attenuate these hydrocarbon pollutants in soils. To understand the relevancy of biological treatments for cold regions specifically, bibliometric analysis has been applied to systematically analyse studies focused on hydrocarbon removal treatment in a biological way. To expedite the understanding of this analysis, we have summarised these biological treatments and suggested other biological applications in the context of cold conditions.

Abstract

The increased usage of petroleum oils in cold regions has led to widespread oil pollutants in soils. The harsh environmental conditions in cold environments allow the persistence of these oil pollutants in soils for more than 20 years, raising adverse threats to the ecosystem. Microbial bioremediation was proposed and employed as a cost-effective tool to remediate petroleum hydrocarbons present in soils without significantly posing harmful side effects. However, the conventional hydrocarbon bioremediation requires a longer time to achieve the clean-up standard due to various environmental factors in cold regions. Recent biotechnological improvements using biostimulation and/or bioaugmentation strategies are reported and implemented to enhance the hydrocarbon removal efficiency under cold conditions. Thus, this review focuses on the enhanced bioremediation for hydrocarbon-polluted soils in cold regions, highlighting in situ and ex situ approaches and few potential enhancements via the exploitation of molecular and microbial technology in response to the cold condition. The bibliometric analysis of the hydrocarbon bioremediation research in cold regions is also presented.

Diesel-born organosulfur compounds stimulate community re-structuring in a diesel-biodesulfurizing consortium

We enriched and characterized a biodesulfurizing consortium (designated as MG1). The MG1 consortium reduced the total sulfur of diesel by 25 % and utilized each of the diesel-born compounds dibenzothiophene (DBT), benzothiophene (BT), 4-methyldibenzothiophene (4-MDBT) and 4, 6-dimethyldibenzothiophene (4, 6-DMDBT) as a sole sulfur source. MiSeq analysis revealed compositional shifts in the MG1 community according to the type of the sulfur source. A DBT-grown MG1 culture had Klebsiella, Pseudomonas, Rhodococcus and Sphingomonas as the most abundant genera. When diesel or 4, 6-DMDBT was provided as a sole sulfur source, Klebsiella and Pseudomonas spp. were the most abundant. In the BT culture, Rhodococcus spp. were the key biodesulfurizers, while Klebsiella, Pseudomonas and Sphingomonas spp. dominated the 4-MDBT-grown consortium. MG1 also utilized 2-hydroxybiphenyl (the product of the 4S biodesulfurization pathway) where Pseudomonas spp. uniquely dominated the consortium. The data improves our understanding of the sulfur source-driven structural adaptability of biodesulfurizing consortia.

Pseudomonas fluorescens: A Bioaugmentation Strategy for Oil-Contaminated and Nutrient-Poor Soil

Bioremediation technology is one of the most profitable and sustainable strategies for remediating soils contaminated with hydrocarbons. This study focuses on assessing the influence of biostimulation and bioaugmentation with Pseudomonas fluorescens to contribute to the removal of total petroleum hydrocarbons (TPHs) of a soil. Laboratory studies were carried out (measurements of emitted CO₂, surface tension, and residual TPH) to select the best bioaugmentation and biostimulation treatment. The sources of C, N, and P were glucose–yeast extract, NH₄Cl–NaNO₃, and K₂HPO₄–K₃PO₄, respectively. The effect of culture conditions on the reduction of TPH and respiratory activity was evaluated through a factorial design, 2³, in a solid culture system. After 80 days of incubation, it was observed that treatments of yeast extract–NH₄Cl–K₂HPO₄ (Y4) and glucose–NaNO₃–K₃PO₄ (Y5) presented a higher level of TPH removal (20.91% and 20.00% degradation of TPH, respectively). Biostimulation favors the production of biosurfactants, indirectly measured by the change in surface tension in the soil extracts. The treatments Y4 and Y5 showed a lower change value of the surface tension (23.15 and 23.30 mN·m⁻¹ at 25 °C). A positive correlation was determined between the change in surface tension and the removal of TPH; hence there was a contribution of the biosurfactants produced to the removal of hydrocarbons.

New Insights into Modelling Bacterial Growth with Reference to the Fish Pathogen Flavobacterium psychrophilum

Simple Summary

Flavobacteriumpsychrophilum is a cold-water bacterium responsible for cold water disease and rainbow trout fry syndrome which has significant impacts on fish health and, by extension, negative economic impacts on aquaculture operations. Models can be applied to bacterial growth curves yielding parameter estimates describing rates of bacterial growth and the time it takes for a bacterium to reach its exponential phase of growth (lag time). These parameter estimates can be used to establish the relationship between microbial growth and environmental variables such as pH, temperature and effect of anti-microbial treatments. Two novel models are derived and their potential to describe bacterial growth assessed through their ability to mimic the growth of Flavobacteriumpsychrophilum on liquid media. Due to their mechanistic derivation, the proposed models result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. Based upon statistical measures of goodness-of-fit and cross-validation, the purposed models were able to describe satisfactorily the growth of Flavobacteriumpsychrophilum on various media. Furthermore, the proposed models also provide insight into underlying mechanisms that are driving microbial growth and how the current environment affects bacterial rate of growth.

Abstract

Two new models, based upon the principles promulgated by Baranyi and co-workers are presented and resulting growth functions evaluated based upon their ability to mimic bacterial growth of the fish pathogen Flavobacterium psychrophilum. These growth functions make use of a dampening function to suppress potential growth, represented by a logistic, and are derived from rate:state differential equations. Dampening effects are represented by a rectangular hyperbola or a simple exponential, incorporated into a logistic differential equation and solved analytically resulting in two newly derived growth equations, viz. logistic × hyperbola (log × hyp) and logistic × exponential (log × exp). These characteristics result in flexible and robust growth functions that can be expressed as equations with biologically meaningful parameters. The newly derived functions (log × hyp and log × exp), along with the Baranyi (BAR), simple logistic (LOG) and its modified form (MLOG) were evaluated based upon examination of residuals and measures of goodness-of-fit and cross-validation. Using these criteria, log × hyp, log × exp and BAR performed better than, or at least equally well as, LOG and MLOG. In contrast with log × exp and BAR, log × hyp can be easily manipulated mathematically allowing for simple algebraic expressions for time and microbial biomass at inflexion point, in addition to maximum and scaled maximum growth rates.

High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments

Estuaries and coastal environments are often regarded as a critical resource for the bioremediation of organic pollutants such as azo dyes due to their high abundance and diversity of extremophiles. Bioremediation through the activities of azoreductase, laccase, and other associated enzymes plays a critical role in the removal of azo dyes in built and natural environments. However, little is known about the biodegradation genes and azo dye degradation genes residing in sediments from coastal and estuarine environments. In this study, high-throughput sequencing (16S rRNA) of sediment DNA was used to explore the distribution of azo-dye degrading bacteria and their functional genes in estuaries and coastal environments. Unlike laccase genes, azoreductase (azoR), and naphthalene degrading genes were ubiquitous in the coastal and estuarine environments. The relative abundances of most functional genes were higher in the summer compared to winter at locations proximal to the mouths of the Hanjiang River and its distributaries. These results suggested inland river discharges influenced the occurrence and abundance of azo dye degrading genes in the nearshore environments. Furthermore, the azoR genes had a significant negative relationship with total organic carbon, Hg, and Cr (p < 0.05). This study provides critical insights into the biodegradation potential of indigenous microbial communities in nearshore environments and the influence of environmental factors on microbial structure, composition, and function which is essential for the development of technologies for bioremediation in azo dye contaminated sites.

Hydrocarbon Removal by Two Differently Developed Microbial Inoculants and Comparing Their Actions with Biostimulation Treatment

Bioremediation of soils polluted with petroleum compounds is a widely accepted environmental technology. We compared the effects of biostimulation and bioaugmentation of soil historically contaminated with aliphatic and polycyclic aromatic hydrocarbons. The studied bioaugmentation treatments comprised of the introduction of differently developed microbial inoculants, namely: an isolated hydrocarbon-degrading community C1 (undefined-consisting of randomly chosen degraders) and a mixed culture C2 (consisting of seven strains with well-characterized enhanced hydrocarbon-degrading capabilities). Sixty days of remedial treatments resulted in a substantial decrease in total aliphatic hydrocarbon content; however, the action of both inoculants gave a significantly better effect than nutrient amendments (a 69.7% decrease for C1 and 86.8% for C2 vs. 34.9% for biostimulation). The bioaugmentation resulted also in PAH removal, and, again, C2 degraded contaminants more efficiently than C1 (reductions of 85.2% and 64.5%, respectively), while biostimulation itself gave no significant results. Various bioassays applying different organisms (the bacterium Vibrio fischeri, the plants Sorghum saccharatum, Lepidium sativum, and Sinapis alba, and the ostracod Heterocypris incongruens) and Ames test were used to assess, respectively, potential toxicity and mutagenicity risk after bioremediation. Each treatment improved soil quality, however only bioaugmentation with the C2 treatment decreased both toxicity and mutagenicity most efficiently. Illumina high-throughput sequencing revealed the lack of (C1) or limited (C2) ability of the introduced degraders to sustain competition from indigenous microbiota after a 60-day bioremediation process. Thus, bioaugmentation with the bacterial mixed culture C2, made up of identified, hydrocarbon-degrading strains, is clearly a better option for bioremediation purposes when compared to other treatments.