Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

Enhanced anaerobic bioremediation of oil-contaminated intertidal sediment with a combination of anaerobically-synthesized rhamnolipids and sulfate

Oil pollution in intertidal sediments is a serious environmental issue. The anoxic environment of the sediment hinders the decomposition of hydrophobic organic pollutants. Conventional bioremediation methods, such as the sole addition of electron acceptors, have struggled to achieve high efficiencies because of the low solubility of oil pollutants. Herein, the combination of anaerobically-synthesized rhamnolipids and electron acceptor was evaluated for the bioremediation of oil-polluted sediments. Meanwhile, the key genes involved in CNPS cycling were detected to understand the biogeochemical processes and the complex interactions between microbial metabolism, nutrient availability, and pollutant degradation. After the bioremediation, the combination of rhamnolipids and sulfate significantly enhanced the removal of polycyclic aromatic hydrocarbons (74.8 ± 1.4%). On day 270, the polyphenol oxidase activity of rhamnolipids and sulfate with rhamnolipids treatments reached 20870.1 ± 1988.7 mg/(kg·h) and 22373.8 ± 970.1 mg/(kg·h), respectively, which was significantly higher (P < 0.05) than other treatments. The sulfate consumption rate in the treatment with both sulfate and rhamnolipids consistently exceeded that of treatment with sulfate alone. Moreover, on day 60, the abundances of functional genes mediating sulfur oxidation (yedZ and soxY) were significantly higher in the combined treatment than in the sulfate group. The results revealed that the addition of rhamnolipids favored the growth of microorganisms and promoted S cycling, and the combination with sulfate dramatically enhanced the removal of polycyclic aromatic hydrocarbons. This study demonstrated that the combination of sulfate and rhamnolipids exhibited great potential on the anaerobic bioremediation of oil-contaminated intertidal zones.

Transformation and environmental fate of 6-OH-BDE-47 and 6-MeO-BDE-47 in oxic and anoxic sediments

Pollutants often exhibit different environmental behaviors at varying redox potentials, and the fate and microbial response of 6-OH-BDE-47 and 6-MeO-BDE-47 under these conditions remain unclear. Herein, 14C-labeled 6-OH-BDE-47 and 6-MeO-BDE-47 were used to investigate their fate in water-sediment systems at different redox potentials. For 6-OH-BDE-47, aerobic microorganisms and nitrate electron acceptors promoted nonextractable residues (NERs) formation and anaerobic microorganisms facilitated their release and was highest formed in the O2-containing group. For 6-MeO-BDE-47, aerobic microorganisms, electron acceptors, and anaerobic microorganisms promoted NER formation, and was highest formed in the nitrate group. Microorganisms markedly promoted 6-OH/MeO-BDE-47 transformation. For 6-OH-BDE-47, the degradation followed the order nitrate group (29.6 %) > O2-containing group (6.5 %) > sulfate group (1.45 %) > anaerobic group (0 %), while for 6-MeO-BDE-47, the order was O2-containing group (8.8 %) > nitrate group = sulfate group = anaerobic group (0 %). The complexity of the 6-OH-BDE-47 and 6-MeO-BDE-47 microbial community network was consistent with the results of redox potentials, where microbial networks connectivity linking were more complex under O2-containing and nitrate conditions. Overall, our study comprehensively revealed the fate of 6-OH-BDE-47 and 6-MeO-BDE-47 under different redox conditions, showing that electron acceptors can alter microbial community structure and regulating interactions. It provided guidelines for selecting electron acceptors in the remediation of 6-OH-BDE-47 and 6-MeO-BDE-47.

Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils

This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.

Disentangling the microbial genomic traits associated with aromatic hydrocarbon degradation in a jet fuel-contaminated aquifer

Spills of petroleum or its derivatives in the environment lead to an enrichment of microorganisms able to degrade such compounds. The interactions taking place in such microbial communities are complex and poorly understood, since they depend on multiple factors, including diversity and metabolic potential of the microorganisms and a broad range of fluctuating environmental conditions. In our previous study, a complete characterization, based on high-throughput sequencing, was performed in a jet-fuel plume using soil samples and in in-situ microcosms amended with hydrocarbons and exposed for 120 days. Herein, we propose a metabolic model to describe the monoaromatic hydrocarbon degradation process that takes place in such jet-fuel-contaminated sites, by combining genome-centered analysis, functional predictions, and flux balance analysis (FBA). In total, twenty high/medium quality MAGs were recovered; three of them assigned to anaerobic bacteria (Thermincolales, Geobacter and Pelotomaculaceace) and one affiliated to the aerobic bacterium Acinetobacter radioresistens, potentially the main players of hydrocarbon degradation in jet-fuel plumes. Taxonomic assignment of the genes indicated that a putative new species of Geobacteria has the potential for anaerobic degradation pathway, while the Pelotomaculaceae and Thermincolales members probably act via syntrophy oxidizing acetate and hydrogen (fermentation products of oil degradation) via sulfate and/or nitrate reduction.

Insights into the characteristics of changes in dissolved organic matter fluorescence components on the natural attenuation process of toluene

Natural attenuation (NA) is of great significance for the remediation of contaminated groundwater, and how to identify NA patterns of toluene in aquifers more quickly and effectively poses an urgent challenge. In this study, the NA of toluene in two typical soils was conducted by means of soil column experiment. Based on column experiments, dissolved organic matter (DOM) was rapidly identified using fluorescence spectroscopy, and the relationship between DOM and the NA of toluene was established through structural equation modeling analysis. The adsorption rates of toluene in clay and sandy soil were 39 % and 26 %, respectively. The adsorption capacity and total NA capacity of silty clay were large. The occurrence of fluorescence peaks of protein-like components and specific products indicated the occurrence of biodegradation. Arenimonas, Acidovorax and Brevundimonas were the main degrading bacteria identified in Column A, while Pseudomonas, Azotobacter and Mycobacterium were the main ones identified in Column B. The pH, ORP, and Fe(II) were the most important factors affecting the composition of microbial communities, which in turn affected the NA of toluene. These results provide a new way to quickly identify NA of toluene.

Analyzing atmospheric plasma's potential for diesel soil remediation: Insightful mechanisms

The remediation of diesel-contaminated soil is a critical environmental concern, driving the need for effective solutions. Recently, the methodology of Non-thermal Atmospheric Plasma (NTAP) technology, which is equipped with a Dielectric Barrier Discharge (DBD) electrode and has become a feasible approach, was proven to be viable. The reactive species from the plasma were exposed to the contaminated soil in this investigation using the NTAP technique. The reacted soil was then extracted using dichloromethane, and the amount of Total Petroleum Hydrocarbon (TPH) removed was assessed. Investigation into varying power levels, treatment durations, and hydrogen peroxide integration revealed significant findings. With an initial concentration of 3086 mg of diesel/kg of soil and a pH of 5.0, 83% of the diesel was removed from the soil at 150 W in under 20 min. Extended exposure to NTAP further improved removal rates, highlighting the importance of treatment duration optimization. Additionally, combining hydrogen peroxide (H2O2) with NTAP enhanced removal efficiency by facilitating diesel breakdown. This synergy offers a promising avenue for comprehensive soil decontamination. Further analysis considered the impact of soil characteristics on removal efficacy. Mechanistically, NTAP generates reactive species that degrade diesel into less harmful compounds, aiding subsequent removal. Overall, NTAP advances environmental restoration efforts by offering a quick, economical, and environmentally benign method of remediating diesel-contaminated soil especially when used in tandem with hydrogen peroxide.

New perspectives on the anaerobic degradation of BTEX: Mechanisms, pathways, and intermediates

Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.

Spatial distribution of volatile organic compounds in contaminated soil and distinct microbial effect driven by aerobic and anaerobic conditions

The vertical distribution of 35 volatile organic compounds (VOCs) was investigated in soil columns from two obsolete industrial sites in Eastern China. The total concentrations of ΣVOCs in surface soils (0-20 cm) were 134-1664 ng g-1. Contamination of VOCs in surface soil exhibited remarkable variability, closely related to previous production activities at the sampling sites. Additionally, the concentrations of ΣVOCs varied with increasing soil depth from 0 to 10 m. Soils at depth of 2 m showed ΣVOCs concentrations of 127-47,389 ng g-1. Among the studied VOCs, xylene was the predominant contaminant in subsoils (2 m), with concentrations ranging from n.d. to 45,400 ng g-1. Chlorinated alkanes and olefins demonstrated a greater downward migration ability compared to monoaromatic hydrocarbons, likely due to their lower hydrophobicity. As a result, this vertical distribution of VOCs led to a high ecological risk in both the surface and deep soil. Notably, the risk quotient (RQ) of xylene in subsoil (2 m, RQ up to 319) was much higher than that in surface soil. Furthermore, distinct effects of VOCs on soil microbes were observed under aerobic and anaerobic conditions. Specifically, after the 30-d incubation of xylene-contaminated soil, Ilumatobacter was enriched under aerobic condition, whereas Anaerolineaceae was enriched under anaerobic condition. Moreover, xylene contamination significantly affected methylotrophy and methanol oxidation functions for aerobic soil (t-test, p < 0.05). However, aromatic compound degradation and ammonification were significantly enhanced by xylene in anaerobic soil (t-test, p < 0.05). These findings suggest that specific VOC compound has distinct microbial ecological effects under different oxygen content conditions in soil. Therefore, when conducting soil risk assessments of VOCs, it is crucial to consider their ecological effects at different soil depths.

Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Improved microalgae growth and lipid production in anaerobic digestate with ultraviolet radiation pretreatment

Inappropriate sterilization strategies inhibit microalgal growth when culturing microalgae with anaerobic digestate. This study aimed to scientifically select a low-cost disinfection pretreatment of anaerobic digestate for large-scale microalgae cultivations. In this work, three different methods, including autoclaving, ultraviolet or NaClO treatments, were employed to sterilize the municipal anaerobic digestate. Scenedesmus quadricauda was then cultured in diluted liquid digestate for the simultaneous lipid production and nutrient removal. The results indicated that the growth of S. quadricauda was inhibited after NaClO treatment due to the residual free chlorine. The 15-min ultraviolet effectively mitigated microbial contamination and increasing nutrient availability, enhancing the electron transport of microalgal photosynthesis. After 6-days cultivation, the microalgal biomass concentration of the ultraviolet group was 1.09 g/L, comparable to that of the autoclaving group (1.15 g/L). High nutrient removal efficiency was observed: COD (93.30 %), NH4+-N (92.56 %), TN (85.82 %) and TP (95.12 %). Moreover, S. quadricauda outcompeted the indigenous microorganisms, contributing to its dominance in the culture system of ultraviolet group. The facultative anaerobe Comamonadaceae and aerobes Moraxellaceae, rather than strict anaerobe Paludibacteraceae and Bacteroidetes_vadinHA17, played vital roles in synergistic removal of contaminants by bacteria and algae. The potential competition for nitrogen and phosphorus by bacteria contributed to the ultraviolet group having the greatest lipid content (48.19 %). Therefore, this work suggested using 15-min ultraviolet treatment for anaerobic digestate in large-scale microalgae cultivation.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Thermal plasma potential to remediate soil contaminated with diesel

Petroleum hydrocarbons (PHCs) are recognized as one of the major soil contaminants causing negative environmental impact. Thereby, PHCs remediation from the soil is essential. Hence, this experimental study aimed to assess the potential of thermal water vapor and air plasmas to remediate soil contaminated with habitually used PHCs - diesel. The impact of contaminant content in the soil on the remediation process also was estimated. The results of this research demonstrated that 99.9% contaminant removal efficiency was received proceeding diesel contaminated soil remediation in the environment of the thermal plasma in defiance of whether water vapor or air was employed as a plasma-forming gas. Moreover, the soil's contaminant content (80-160 g/kg) did not influence its' removal efficiency. The soil de-pollution process also caused the decomposition of the soils' natural carbon reserves since carbon content decreased from an initial 9.8 wt% in the clean soil to 3-6 wt% in the remediated soil. Furthermore, PHCs - diesel was decomposed into producer gas mainly consisting of H₂, CO (also known as synthesis gas) and CO₂. Thus, the thermal plasma offers a way not only to de-pollute the soil but also to reuse the PHCs present in the soil by breaking it down into gaseous products that can further be used to meet human needs.

Electron acceptors determine the BTEX degradation capacity of anaerobic microbiota via regulating the microbial community

Anaerobic degradation is the major pathway for microbial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) under electron acceptor lacking conditions. However, how exogenous electron acceptors modulate BTEX degradation through shaping the microbial community structure remains poorly understood. Here, we investigated the effect of various exogenous electron acceptors on BTEX degradation as well as methane production in anaerobic microbiota, which were enriched from the same contaminated soil. It was found that the BTEX degradation capacities of the anaerobic microbiota gradually increased along with the increasing redox potentials of the exogenous electron acceptors supplemented (WE: Without exogenous electron acceptors < SS: Sulfate supplement < FS: Ferric iron supplement < NS: Nitrate supplement), while the complexity of the co-occurring networks (e.g., avgK and links) of the microbiota gradually decreased, showing that microbiota supplemented with higher redox potential electron acceptors were less dependent on the formation of complex microbial interactions to perform BTEX degradation. Microbiota NS showed the highest degrading capacity and the broadest substrate-spectrum for BTEX, and it could metabolize BTEX through multiple modules which not only contained fewer species but also different key microbial taxa (eg. Petrimonas, Achromobacter and Comamonas). Microbiota WE and FS, with the highest methanogenic capacities, shared common core species such as Sedimentibacter, Acetobacterium, Methanobacterium and Smithella/Syntrophus, which cooperated with Geobacter (microbiota WE) or Desulfoprunum (microbiota FS) to perform BTEX degradation and methane production. This study demonstrates that electron acceptors may alter microbial function by reshaping microbial community structure and regulating microbial interactions and provides guidelines for electron acceptor selection for bioremediation of aromatic pollutant-contaminated anaerobic sites.

Coupled effect of porous network and water content on the natural attenuation of diesel in unsaturated soils

The natural attenuation potential of a vadose zone against diesel is critical for optimizing remedial actions and determining groundwater vulnerability to contamination. Here, diesel attenuation in unsaturated soils was systematically examined to develop a qualitative relationship between physical soil properties and the natural attenuation capacity of a vadose zone against diesel. The uniformity coefficient (C_u) and water saturation (S_w, %) were considered as the proxies reflecting the degree of effects by porous network and water content in different soils, respectively. These, in turn, are related to the primary diesel attenuation mechanisms of volatilization and biodegradation. The volatilization of diesel was inversely proportional to C_u and S_w, which could be attributed to effective pore channels facilitating gas transport. Conversely, biodegradation was highly proportional to C_u under unsaturated conditions (S_w = 35-71%), owing to nutrients typically associated with fine soil particles. The microbial community in unsaturated soils was affected by S_w rather than C_u. The overall diesel attenuation including volatilization and biodegradation was optimized at S_w = 35% for all tested soils.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water

Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO₄^2-/rCl^-), coefficient of sodium and chloride (rNa⁺/rCl^-), and coefficient of magnesium and chloride (rMg²⁺/rCl^-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO₃^-, Fe³⁺, and SO₄^2-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.

Culture-Independent Survey of Thermophilic Microbial Communities of the North Caucasus

Simple Summary

The Republic of North Ossetia-Alania, located in the southern part of the North Caucasus, possess a number of hydrothermal habitats, including both subterranean thermal reservoirs and terrestrial hot springs. At the same time, reports on microbiology of numerous geothermal sites are rather scarce for the whole North Caucasus region. In this paper, we report on the first culture-independent metabarcoding study of thermal habitats in the North Caucasus, coupled with a chemical analysis of the elemental composition of water. The results of this work include the conclusions regarding key metabolic characteristics of these habitats as well as detection of few but abundant deep lineages of uncultivated microorganisms which could be regarded as endemic. This study may represent a first step in closing the knowledge gap in extremophilic microbial communities of the North Caucasus.

Abstract

The Greater Caucasus is a part of seismically active Alpine–Himalayan orogenic belt and has been a center of significant volcanic activity during the Quaternary period. That led to the formation of the number of hydrothermal habitats, including subterranean thermal aquifers and surface hot springs. However, there are only a limited number of scientific works reporting on the microbial communities of these habitats. Moreover, all these reports concern only studies of specific microbial taxa, carried out using classical cultivation approaches. In this work, we present first culture-independent study of hydrotherms in the Republic of North Ossetia-Alania, located in the southern part of the North Caucasus. Using 16S metabarcoding, we analyzed the composition of the microbial communities of two subterranean thermal aquifers and terrestrial hot springs of the Karmadon valley. Analysis of correlations between the chemical composition of water and the representation of key taxa allowed us to identify the key factors determining the formation of microbial communities. In addition, we were able to identify a significant number of highly abundant deep phylogenetic lineages. Our study represents a first glance on the thermophilic microbial communities of the North Caucasus and may serve as a basis for further microbiological studies of the extreme habitats of this region.

Degradation of organic contaminants in marine sediments by peroxymonosulfate over LaFeO3 nanoparticles supported on water caltrop shell-derived biochar and the associated microbial community responses

Sediment is an important final repository of persistent organic pollutants such as polycyclic aromatic hydrocarbons (PAHs). Herein, a novel catalyst of LaFeO₃ nanoparticles supported on biochar was synthesized from water caltrop shell by chemical precipitation. The composite (LFBC) was used as peroxymonosulfate (PMS) activator to oxidize PAHs in real marine sediments. Systematic surface characterization confirmed the immobilization of well crystalline nano LaFeO₃ particles onto the biochar surface. Under optimal conditions, i.e., [PMS] = 3 × 10^-4 M, [LFBC] = 0.75 g/L, pH 6.0, and seawater, the total PAH degradation efficiency was 90%, while that of 2-, 3-, 4-, 5-, and 6-ring PAHs was 52%, 61%, 66%, 56%, and 29%, respectively, in 24 h. The Langmuir-Hinshelwood equation better predicted the PAHs degradation kinetics over LFBC by PMS. Interactions between surface oxygen species at LaFeO₃ defective sites and the graphitized biochar network facilitated the PAHs degradation. Furthermore, changes in the bacterial community during the LFBC/PMS treatment were highlighted to assess the sustainable development of the sediment ecosystem. The LFBC/PMS process enhanced the biological richness and diversity of sediment eco-systems. The major phylum was Proteobacteria initially, while Hyphomonas was the genera after LFBC/PMS treatment of the sediment.

Anaerobic-petroleum degrading bacteria: Diversity and biotechnological applications for improving coastal soil

Due to the industrial emissions and accidental spills, the critical material for modern industrial society petroleum pollution causes severe ecological damage. The prosperous oil exploitation and transportation causes the recalcitrant, hazardous, and carcinogenic sludge widespread in the coastal wetlands. The costly physicochemical-based remediation remains the secondary and inadequate treatment for the derivatives along with the tailings. Anaerobic microbial petroleum degrading biotechnology has received extensive attention for its cost acceptable, eco-friendly, and fewer health hazards. As a result of the advances in biotechnology and microbiology, the anaerobic oil-degrading bacteria have been well developing to achieve the same remediation effects with lower operating costs. This review summarizes the advantages and potential scenarios of the anaerobic degrading bacteria, such as sulfate-reducing bacteria, denitrifying bacteria, and metal-reducing bacteria in the coastal area decomposing the alkanes, alkenes, aromatic hydrocarbons, polycyclic aromatic, and related derivatives. In the future, a complete theoretical basis of microbiological biotechnology, molecular biology, and electrochemistry is necessary to make efficient and environmental-friendly use of anaerobic degradation bacteria to mineralize oil sludge organic wastes.

Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities

Global environmental contamination with a complex mixture of xenobiotics has become a major environmental issue worldwide. Many xenobiotic compounds severely impact the environment due to their high toxicity, prolonged persistence, and limited biodegradability. Microbial-assisted degradation of xenobiotic compounds is considered to be the most effective and beneficial approach. Microorganisms have remarkable catabolic potential, with genes, enzymes, and degradation pathways implicated in the process of biodegradation. A number of microbes, including Alcaligenes, Cellulosimicrobium, Microbacterium, Micrococcus, Methanospirillum, Aeromonas, Sphingobium, Flavobacterium, Rhodococcus, Aspergillus, Penecillium, Trichoderma, Streptomyces, Rhodotorula, Candida, and Aureobasidium, have been isolated and characterized, and have shown exceptional biodegradation potential for a variety of xenobiotic contaminants from soil/water environments. Microorganisms potentially utilize xenobiotic contaminants as carbon or nitrogen sources to sustain their growth and metabolic activities. Diverse microbial populations survive in harsh contaminated environments, exhibiting a significant biodegradation potential to degrade and transform pollutants. However, the study of such microbial populations requires a more advanced and multifaceted approach. Currently, multiple advanced approaches, including metagenomics, proteomics, transcriptomics, and metabolomics, are successfully employed for the characterization of pollutant-degrading microorganisms, their metabolic machinery, novel proteins, and catabolic genes involved in the degradation process. These technologies are highly sophisticated, and efficient for obtaining information about the genetic diversity and community structures of microorganisms. Advanced molecular technologies used for the characterization of complex microbial communities give an in-depth understanding of their structural and functional aspects, and help to resolve issues related to the biodegradation potential of microorganisms. This review article discusses the biodegradation potential of microorganisms and provides insights into recent advances and omics approaches employed for the specific characterization of xenobiotic-degrading microorganisms from contaminated environments.

Effects of biochar on catalysis treatment of 4-nonylphenol in estuarine sediment and associated microbial community structure

The effect of pyrolysis temperature on the generation of polycyclic aromatic hydrocarbons (PAHs) in sewage sludge biochar (SSB) and the removal of hazardous chemicals from esturine sediments by SSB and sodium percarbonate (SPC), exemplified by 4-nonylphenol (4-NP) were studied. SSB synthesized at 500 °C (SSB500) achieved the highest 4-NP degradation efficiency of 73%, at pH₀ 9.0 in 12 h of reaction time. The enhanced 4-NP degradation was attributed to the SSB500 activation activation of SPC that produced sufficient •OH and CO₃^-• due to electron-transfer interaction on the Fe-Mn redox pairs. The microbial community diversity and composition of the treated sediment were compared using high-throughput sequencing. Results showed SSB/SPC treatment increased the microbial diversity and richness in the sediments. Proteobacteria were the keystone phylum, while Thioalkalispira genera were responsible for 4-NP degradation in the SSB/SPC treatment. Over all, results revealed the change in the bacterial community during the environmental applications of SSB, which provided essential information for better understanding of the monitoring and improvement of sustainable sediment ecosystems.

Dissipation of Sulfonamides in Soil Emphasizing Taxonomy and Function of Microbiomes by Metagenomic Analysis

Sulfonamides (SAs) are widespread in soils, and their dissipation behavior is important for their fate, risk assessment, and pollution control. In this work, we investigated the dissipation behavior of different SAs in a soil under aerobic condition, focusing on revealing the relationship between overall dissipation (without sterilization and in dark) and individual abiotic (sorption, hydrolysis)/biotic (with sterilization and in dark) factors and taxonomy/function of microbiomes. The results showed that dissipation of all SAs in the soil followed the pseudo-first-order kinetic model with dissipation time at 50% removal (DT₅₀) of 2.16-15.27 days. Based on, experimentally, abiotic/biotic processes and, theoretically, partial least-squares modeling, a relationship between overall dissipation and individual abiotic/biotic factors was developed with microbial degradation as the dominant contributor. Metagenomic analysis showed that taxonomic genera like Bradyrhizobium/Sphingomonas/Methyloferula and functions like CAZy family GT51/GH23/GT2, eggNOG category S, KEGG pathway ko02024/ko02010, and KEGG ortholog K01999/K03088 are putatively involved in SA microbial degradation in soil. Spearman correlation suggests abundant genera being multifunctional. This study provides some new insights into SA dissipation and can be applied to other antibiotics/soils in the future.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Distinct bacterial communities in tropical island aquifers

The groundwater biome is a poorly characterized habitat hypothesized to harbor uniquely diverse bacterial communities; the degree to which these communities differ from associated soils is a central question in environmental microbiology. We characterized the Bacterial community composition in 37 aquifer and 32 surface soil samples across the island of O‘ahu, Hawaiʻi. Several bacterial phyla (Acetothermia, Omnitrophica, Parcubacteria, Peregrinibacteria) relatively abundant in the aquifer samples were rare to absent in the soils. Immense bacterial diversity detected in the deep aquifers indicates that these environments are not as homogenous as expected, but provide various niches and energy sources for wide variety of bacteria. A small proportion of OTUs were widespread in all the basal (0.63%) and all the dike aquifer (0.31%) samples. However, these core bacteria comprised an average of 31.8% (ranging 16.2%-62.0%) and 15.4% (0.1%-31.5%) of all sequences isolated from the basal and dike aquifers respectively. Bacterial community composition correlated significantly with the sodium, sulfate, potassium, total dissolved solids, nitrate, conductivity, and pH in the basal aquifers, while phosphate and bicarbonate levels were also highly important when dike water samples were included in the analyses. This was consistent with high relative abundance of putative chemolithoautoroph taxa in the aquifer communities relative to soils. Targeted molecular and culture-based fecal indicator microbial analyses indicated good water quality of aquifers. The dominance of unique, deeply branching lineages in tropical aquifers emphasizes a large adaptive potential in O‘ahu’s aquifers; variability among groundwater samples suggests that aquifer habitats are surprisingly variable potentially harboring a variety of chemolithotrophic energy sources. Although parallel analyses of conventional and alternative indicators indicated good groundwater quality, this study calls for groundwater monitoring programs which would consider public as well as ecosystem health.

A Screening Model to Predict Entrapped LNAPL Depletion

Accidental leakage of hydrocarbons is a common subsurface contamination scenario. Once released, the hydrocarbons migrate until they reach the vicinity of the uppermost portion of the saturated zone, where it accumulates. Whenever the amplitude of the water table fluctuation is high, the light non-aqueous phase liquid (LNAPL) may be completely entrapped in the saturated zone. The entrapped LNAPL, comprised of multicomponent products (e.g., gasoline, jet fuel, diesel), is responsible for the release of benzene, toluene, ethylbenzene, and xylenes (BTEX) into the water, thus generating the dissolved phase plumes of these compounds. In order to estimate the time required for source-zone depletion, we developed an algorithm that calculates the mass loss of BTEX compounds in LNAPL over time. The simulations performed with our algorithm provided results akin to those observed in the field and demonstrated that the depletion rate will be more pronounced in regions with high LNAPL saturation. Further, the LNAPL depletion rate is mostly controlled by flow rate and is less sensible to the biodegradation rate in the aqueous phase.