Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

Fate of dissolved organics in oil sands process water during long-term storage: Mechanistic insights into toxicity removal and microbial processes

Refining oil sand process water (OSPW), a byproduct of bitumen extraction from oil sands in Canada, presents significant environmental challenges due to its complex makeup. This complexity is mainly due to the presence of naphthenic acids (NAs), which play a substantial role in contributing to the toxicity of OSPW. Although various treatment technologies have been explored, the long-term behaviour of OSPW dissolved organics under different storage conditions has not been studied extensively. This study is the first to delve deeply into the natural attenuation of OSPW under diverse controlled conditions, focusing on the effects of temperature, dissolved oxygen, and ozone pretreatment on water quality, NAs degradation, toxicity, and bioavailability. Our results revealed the critical role of temperature in OSPW characteristics, with long-term storage at 4 °C demonstrating minimal degradation of dissolved organics, providing the first empirical support for current OSPW storage practices. In contrast, at 20 °C, ozoned OSPW exhibited maximum reduction in the following parameters: total NAs, 72.6 %; chemical oxygen demand, 25.3 %; acute toxicity towards A. fischeri by 60.7 %; and bioavailability of organics by 35.2 %. This suggests that ozone pretreatment facilitates the biodegradation process by breaking down NAs into more readily metabolized compounds, which are further degraded by microbial activity over time. Furthermore, the study identified evolving microbial communities during OSPW storage, highlighting the presence of Bacillus and Fontimonas genera, which may play a role in organics degradation but require further investigation into their specific functions. These findings provide critical insights into the long-term dynamics of organics in OSPW and provide a foundation for optimizing management strategies.

Dynamic interplay of immune response, metabolome, and microbiota in cows during high-grain feeding: insights from multi-omics analysis

This study explores the dynamics of immune gene expression, ruminal metabolome, and gut microbiota in cows due to the duration of high-grain feeding, shedding light on host response and microbial dynamics in parallel. Cows consumed forage for a week, then gradually transitioned to a high-grain diet, which they consumed for 4 weeks. Immune response was evaluated in ruminal papillae by expression of genes related to the nuclear factor-kappaB (NFkB) pathway and correlated with the microbiota. Rumen metabolome was evaluated with high-performance liquid chromatography coupled with mass spectrometry and anion-exchange chromatography. Rumen and fecal microbiota were evaluated with 16S rRNA gene amplicon sequencing. In the rumen, expression of inflammation-associated genes increased with the duration on high grain, indicating activation of pro-inflammatory cascades; microbial diversity decreased with a high-grain diet but stabilized after week 3 on high grain. Changes in microbial relative abundance and metabolite enrichment were observed throughout the 4 weeks on high grain, with increments in propionogenic taxa (i.e., Succinivibrionaceae). Metabolite enrichment analysis showed that at the start of high-grain feeding, simple carbohydrates were enriched; then, these were substituted by their fermentation products. There were correlations between certain ruminal bacterial taxa (i.e., Ruminococcaceae UCG-005) and expression of genes of the NFkB pathway, suggesting the influence of these taxa on host immune response. In feces, microbial diversity and several Ruminococcaceae members initially declined but recovered by weeks 3 and 4. Overall, despite the stabilization of microbial diversity, changes in microbial relative abundance and proinflammatory genes were observed throughout high-grain feeding, suggesting that cows need more than 4 weeks to fully adjust once consuming a high-grain diet.IMPORTANCEDespite the stepwise diet transition typically assumed to serve for animal adaptation, expression of signaling receptors, mediators, and downstream targets of nuclear factor-kappaB pathway were found throughout the 4 weeks on high grain, which correlated with changes in the rumen microbial profile. In addition, although microbial diversity recovered in the feces and stabilized in the rumen in week 3 on high grain, we observed changes in microbial relative abundance throughout the 4 weeks on high grain, suggesting that cows need more than 4 weeks to adjust once consuming this diet. Findings are particularly important to consider when planning experiments involving dietary changes.

Enhanced removal of phenanthrene and nutrients in wetland sediment with metallic biochar: Performance and mechanisms

Polycyclic aromatic hydrocarbon (PAHs) are persistent organic pollutants and pose high risk in aquatic environment. The utilization of biochar is a strategy for PAHs-contaminated remediation but is challenging due to the adsorption saturation and reoccurrence of PAHs desorbed back into water. In this study, iron (Fe) and manganese (Mn) were provided as electron acceptors for biochar modification to enhance anaerobic biodegradation of phenanthrene (Phe). Results revealed that, the Mn(Ⅳ) and Fe(Ⅲ) modification improved the removal of Phe by 24.2% and 31.4% than that of biochar, respectively. Additionally, nitrate removal was improved by 19.5% with Fe(Ⅲ) amendment. The Mn-and Fe-biochar decreased Phe contents by 8.7% and 17.4% in sediment, 10.3% and 13.8% in biochar than that of biochar. Much higher DOC contents were observed with Mn- and Fe-biochar, which provided bioavailable carbon source for microbes and contributed to microbial degradation of Phe. The greater degree of humification, higher proportions of humic and fulvic acid like components in metallic biochar participated in electron transport and further enhancing the degradation of PAHs. Microbial analysis proved the high abundance of Phe-degrading bacteria (e.g. PAH-RHD_α, Flavobacterium and Vibrio), nitrogen removal microbes (e.g. amoA, nxrA, and nir), Fe and Mn bioreduction or oxidation (e. g. Bacillus, Thermomonas, Deferribacter) with metallic biochar. Based on the results, the Fe and Mn modification, especially Fe-modified biochar provided well performance for PAHs removal in aquatic sediment.

Keystone microbial taxa organize micropollutant-related modules shaping the microbial community structure in estuarine sediments

The fluctuation of environmental conditions drives the structure of microbial communities in estuaries, highly dynamic ecosystems. Microorganisms inhabiting estuarine sediments play a key role in ecosystem functioning. They are well adapted to the changing conditions, also threatened by the presence of pollutants. In order to determine the environmental characteristics driving the organization of the microbial assemblages, we conducted a seasonal survey along the Adour Estuary (Bay of Biscay, France) using 16S rRNA gene Illumina sequencing. Microbial diversity data were combined with a set of chemical analyses targeting metals and pharmaceuticals. Microbial communities were largely dominated by Proteobacteria (41 %) and Bacteroidota (32 %), showing a strong organization according to season, with an important shift in winter. The composition of microbial communities showed spatial distribution according to three main areas (upstream, middle, and downstream estuary) revealing the influence of the Adour River. Further analyses indicated that the microbial community was influenced by biogeochemical parameters (C_org/N_org and δ¹³C) and micropollutants, including metals (As, Cu, Mn, Sn, Ti, and Zn) and pharmaceuticals (norfloxacin, oxolinic acid and trimethoprim). Network analysis revealed specific modules, organized around keystone taxa, linked to a pollutant type, providing information of paramount importance to understand the microbial ecology in estuarine ecosystems.

Surfactant-enhanced mobilization of persistent organic pollutants: Potential for soil and sediment remediation and unintended consequences

This review aims to provide an overview of the sources and reactions of persistent organic pollutants (POPs) and surfactants in soil and sediments, the surfactant-enhanced solubilisation of POPs, and the unintended consequences of surfactant-induced remediation of soil and sediments contaminated with POPs. POPs include chemical compounds that are recalcitrant to natural degradation through photolytic, chemical, and biological processes in the environment. POPs are potentially toxic compounds mainly used in pesticides, solvents, pharmaceuticals, or industrial applications and pose a significant and persistent risk to the ecosystem and human health. Surfactants can serve as detergents, wetting and foaming compounds, emulsifiers, or dispersants, and have been used extensively to promote the solubilization of POPs and their subsequent removal from environmental matrices, including solid wastes, soil, and sediments. However, improper use of surfactants for remediation of POPs may lead to unintended consequences that include toxicity of surfactants to soil microorganisms and plants, and leaching of POPs, thereby resulting in groundwater contamination.

Allochthonous arbuscular mycorrhizal fungi promote Salix viminalis L.-mediated phytoremediation of polycyclic aromatic hydrocarbons characterized by increasing the release of organic acids and enzymes in soils

Polycyclic aromatic hydrocarbons (PAHs) are well known persistent organic pollutants that have carcinogenic, teratogenic, and mutagenic effects on humans and animals. Arbuscular mycorrhizal fungi (AMF) that can infest plant hosts and form symbioses may help plants to enhance potential rhizosphere effects, thus contributing to the rhizodegradation of PAH-contaminated soils. The present study aimed to assess the effectiveness of AMF on enhancing Salix viminalis-mediated phytoremediation of PAH-polluted soil and clarify the plant enzymatic and organic acid mechanisms induced by AMF. Natural attenuation (NA), phytoremediation (P, Salix viminalis), S. viminalis-AMF combined remediation using willow inoculated with Funneliformis mosseae (PM), Laroideoglomus etunicatum (PE), and Rhizophagus intraradices (PI) were used as strategies for the remediation of PAH-polluted soils. The results showed that AMF inoculation contributed to the dissipation of the high-molecular-weight PAH benzo (α) pyrene that had concentrations in PM, PE, and PI treatments of 40.1 %, 24.49 %, and 36.28 % of the level in the NA treatment, and 62.32 %, 38.05 %, and 56.38 % of the level in the P treatment after 90 days. The mycorrhizal treatment also improved the removal efficiency of phenanthrene and pyrene, as their concentrations were sharply decreased after 30 days compared to the NA and P treatments. The research further clarified the changes in rhizosphere substances induced by AMF. Organic acids including arachidonic acid, octadecanedioic acid, α-linolenic acid, 10,12,14-octadecarachidonic acid and 5-methoxysalicylic acid that can act as co-metabolic substrates for certain microbial species to metabolize PAHs were significantly increased in AMF-inoculated treatments. AMF inoculation also elevated the levels of polyphenol oxidase, laccase, and dehydrogenase, that played crucial roles in PAHs biodegradation. These findings provide an effective strategy for using AMF-assisted S. viminalis to remediate PAH-polluted soils, and the results have confirmed the key roles of organic acids and soil enzymes in plant-AMF combined remediation of PAHs.

Impact of lignocellulosic waste-immobilised white-rot fungi on enhancing the development of 14C-phenanthrene catabolism in soil

In this study, an investigation was carried out to explore the the impact of white-rot fungi (WRF) on enhancing the development of phenanthrene catabolism in soil over time (1, 25, 50, 75 and 100 d). The WRF were immobilised on spent brewery grains (SBG) prior to inoculation to the soil. The results showed that SBG-immobilised WRF-amended soils reduced the lag phases and increased the extents of ¹⁴C-phenanthrene mineralisation. Greater reductions in the lag phases and increases in the rates of mineralisation were observed in immobilised Trametes versicolor-amended soil compared to the other WRF-amendments. However, the presence of Pleurotus ostreatus and Phanerochaete chrysosporium influenced biodegradation more strongly than the other fungal species. In addition, fungal enzyme activities increased in the amended soils and positively correlated with the extents of ¹⁴C-phenanthrene mineralisation in all soil amendments. Maximum ligninolytic enzyme activities were observed in P. ostreatus-amended soil. Microbial populations increased in all amended soils while PAH-degrading fungal numbers increased with increased soil-PAH contact time and strongly positively correlated with fastest rates of mineralisation. The findings presented in this study demonstrate that inoculating the soil with these immobilised WRFs generally enhanced the mineralisation of the ¹⁴C-phenanthrene in soil. This has the potential to be used to stimulate or enhance PAH catabolism in field-contaminated soils.

A rhamnolipid biosurfactant increased bacterial population size but hindered hydrocarbon biodegradation in weathered contaminated soils

Surfactants are used to enhance the bioavailability of recalcitrant residual petroleum contamination during bioremediation. However, surfactants in some cases inhibit biodegradation, which is often attributed to their toxicity. Herein, we show that a rhamnolipid biosurfactant likely served as a carbon source and exhibited physiological inhibition on petroleum biodegradation. The addition of biosurfactants in mixed, batch, slurry bioreactors with soils from a petroleum-contaminated site led to a dose-dependent shift in the microbial community with a decrease in diversity and increase in population size and delayed biodegradation. Microbial community analysis indicated the enrichment of Alphaproteobacteria affiliated taxa such as Sphingomonadaceae in systems amended with biosurfactant. The diversity was significantly lower in systems with higher doses of biosurfactants compared to systems without biosurfactant. Droplet Digital PCR indicated a 30-90 fold increase in 16S rRNA copy numbers in systems with higher doses of biosurfactant than control systems without surfactant and nutrients, whereas the nutrient amendment alone led to a two-fold increase in population size. Total petroleum hydrocarbon analysis showed that the biodegradation extent was negatively impacted by rhamnolipid at the highest dose compared to lower doses (23% vs. 40%) or without the biosurfactant. Indigenous isolates cultivated from the oil-amended soil exhibited growth on rhamnolipid as a sole carbon source. A novel insight gained is how dose-dependent responses of microbial communities to biosurfactants alter the biodegradation time profile of hydrocarbons. The study highlights the significance of microbial assessment prior to surfactant-mediated bioremediation practices.

Root exudates enhance the PAH degradation and degrading gene abundance in soils

Root exudates could influence the bioavailability of polycyclic aromatic hydrocarbons (PAHs), provide nutrients for soil microorganisms, and affect PAH biodegradation. However, it remains unclear how a bacterial community and its PAH-degrading genes play crucial roles in PAH biodegradation and respond to root exudates. In this study, a 32-day soil microcosm study was conducted to explore the impacts of artificial and actual root exudates on PAH degradation, degrading genes, and bacterial community structure. The results showed that 10-100 mg DOC/kg artificial and actual root exudates promoted the degradation of naphthalene, phenanthrene, and pyrene in soils, and their percent removal increased initially and then decreased with the increasing root exudates. Quantitative polymerase chain reaction analysis and 16S rRNA gene high-throughput sequencing suggested that the artificial root exudates significantly promoted the Nocardioides and Arthrobacter genera, which may harbor the nidA gene (the representative PAH-degrading gene from Gram-positive bacteria). In contrast, actual root exudates significantly stimulated the Pseudomonas genus that may harbor the nahAc gene (the representative PAH-degrading gene from Gram-negative bacteria). The correlation analysis further indicated that the absolute abundance of PAH degraders and degrading genes had strong correlations with PAH degradation efficiency. Therefore, these findings suggest that root exudates enhanced PAH biodegradation probably due to increases in abundance of both PAH-degraders and their degrading genes.

Bioaugmentation of Native Fungi, an Efficient Strategy for the Bioremediation of an Aged Industrially Polluted Soil With Heavy Hydrocarbons

The concurrence of structurally complex petroleum-associated contaminants at relatively high concentrations, with diverse climatic conditions and textural soil characteristics, hinders conventional bioremediation processes. Recalcitrant compounds such as high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) and heavy alkanes commonly remain after standard soil bioremediation at concentrations above regulatory limits. The present study assessed the potential of native fungal bioaugmentation as a strategy to promote the bioremediation of an aged industrially polluted soil enriched with heavy hydrocarbon fractions. Microcosms assays were performed by means of biostimulation and bioaugmentation, by inoculating a defined consortium of six potentially hydrocarbonoclastic fungi belonging to the genera Penicillium, Ulocladium, Aspergillus, and Fusarium, which were isolated previously from the polluted soil. The biodegradation performance of fungal bioaugmentation was compared with soil biostimulation (water and nutrient addition) and with untreated soil as a control. Fungal bioaugmentation resulted in a higher biodegradation of total petroleum hydrocarbons (TPH) and of HMW-PAHs than with biostimulation. TPH (C14-C35) decreased by a 39.90 ± 1.99% in bioaugmented microcosms vs. a 24.17 ± 1.31% in biostimulated microcosms. As for the effect of fungal bioaugmentation on HMW-PAHs, the 5-ringed benzo(a)fluoranthene and benzo(a)pyrene were reduced by a 36% and 46%, respectively, while the 6-ringed benzoperylene decreased by a 28%, after 120 days of treatment. Biostimulated microcosm exhibited a significantly lower reduction of 5- and 6-ringed PAHs (8% and 5% respectively). Higher TPH and HMW-PAHs biodegradation levels in bioaugmented microcosms were also associated to a significant decrease in acute ecotoxicity (EC50) by Vibrio fischeri bioluminiscence inhibition assays. Molecular profiling and counting of viable hydrocarbon-degrading bacteria from soil microcosms revealed that fungal bioaugmentation promoted the growth of autochthonous active hydrocarbon-degrading bacteria. The implementation of such an approach to enhance hydrocarbon biodegradation should be considered as a novel bioremediation strategy for the treatment of the most recalcitrant and highly genotoxic hydrocarbons in aged industrially polluted soils.

Diversity and structure of phenanthrene degrading bacterial communities associated with fungal bioremediation in petroleum contaminated soil

Fungal bioremediation is a promising technique for the cleanup of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). However, due to limited understanding of the composition and dynamics of the native PAH-degrading microorganisms in contaminated sites, its application has been difficult. In the present study, DNA stable-isotope probing was performed to identify indigenous phenanthrene (PHE)-degrading bacteria and determine their diversity during the fungal bioremediation process. The results showed a total of 14 operational taxonomic units (OTUs) enriched in the heavy DNA fractions, which were related to seven genera (Sphingomonas, Sphingobacterium, Acidovorax, Massilia, Flavobacterium, Cupriavidus, Aeromicrobium, and unclassified Chitinophagaceae). Along with enhanced efficiency of PHE removal, the number and diversity of indigenous PHE-degrading bacteria in soil bioaugmented with fungi were significantly increased. Furthermore, based on the results of linear model analysis, we found that PHE degraders affiliated with the genus Sphingomonas were significantly enriched during fungal bioremediation. Moreover, fungal bioaugmentation promoted indigenous functional Proteobacteria involved in PAH degradation through co-metabolism, suggesting that PAH biodegradation was attributable to cooperative metabolism by fungi and indigenous bacteria. Our findings provide new insights into the diversity of PHE-degrading communities and support a more comprehensive view of the fungal bioremediation process.

Enhanced Benzofluoranthrene Removal in Surface Flow Constructed Wetlands with the Addition of Carbon

Polycyclic aromatic hydrocarbons (PAHs), as hazardous pollutants, could be removed by constructed wetlands (CWs). While the traditional substrate of CWs has a weak adsorption capacity for PAHs, in this study, the carbonous fillers-activated carbon (AC) and biochar-were added into the substrate of surface flow CWs to improve the removal performance of benzofluoranthrene (BbFA), a typical PAH. The results showed that the BbFA removal efficiencies in CWs with the addition of AC and biochar were 11.8 and 1.2% higher than those in the Control group, respectively. Simultaneously, the removal efficiencies of NO₃ ^--N were 42.8 and 68.4% in these two CWs, while the BbFA content in the substrate and plants with the addition of carbon was lower than that in the Control group. The addition of carbonous filler reduced the absorption of PAHs by plants in CWs and enhanced microbial degradation. The microbial community results showed that the relative abundance of Proteobacteria, especially γ-proteobacteria, was higher with the addition of fillers, which related to PAH degradation.

Degradation and effect of 6:2 fluorotelomer alcohol in aerobic composting of sludge

Perfluoroalkyl carboxylates (PFCAs) is toxic to the environment and human health. However, the degradation characteristics of fluorotelomer alcohols (FTOHs), precursors of PFACAs biodegradation, in the sludge during aerobic composting remain unclear. In this study, the degradation characteristics of 6:2 FTOH in sewage sludge by composting were researched and the influences of 6:2 FTOH on the composting process and microbial communities of the sludge were evaluated. After 52 days of composting, 6:2 FTOH retained only 0.73% of its original concentration, and its half-life was less than 1 d; 6:2 FTOH was degraded finally to perfluorohex unsaturated acid, perfluoropentanoic acid, 5:3 polyfluorinated acid (FTCA), 4:3 FTCA, and perfluorobutanoic acid through two pathways; and 6:2 FTCA and 6:2 fluorotel unsaturated acid were the intermediate products. Notably, dosing with 6:2 FTOH affected the composting process of sewage sludge. Additionally, 50 mg/kg 6:2 FTOH resulted in a decrease in the microbial richness and diversity of sludge compost. When compared with the compost without 6:2 FTOH, the proportion of Proteobacteria had increased, and the proportion of Firmicutes had decreased as the concentration of 6:2 FTOH increased. The negative effect of a dosage of 50 mg/kg 6:2 FTOH was more obvious than the effect of other treatments. This study expanded our understanding of the risk of sludge contaminated by 6:2 FTOH being used as a fertilizer after composting.

Comparative transcriptome analysis unveils the adaptative mechanisms of Scedosporium apiospermum to the microenvironment encountered in the lungs of patients with cystic fibrosis

Scedosporium species rank second among the filamentous fungi colonizing the lungs of patients with cystic fibrosis (CF). Apart from the context of immunodeficiency (lung transplantation), the colonization of the CF airways by these fungi usually remains asymptomatic. Why the colonization of the lower airways by Scedosporium species is fairly tolerated by CF patients while these fungi are able to induce a marked inflammatory reaction in other clinical contexts remains questionable. In this regards, we were interested here in exploring the transcriptional reprogramming that accompanies the adaptation of these fungi to the particular microenvironment encountered in the airways of CF patients. Cultivation of Scedosporium apiospermum in conditions mimicking the microenvironment in the CF lungs was shown to induce marked transcriptional changes. This includes notably the down-regulation of enzymes involved in the synthesis of some major components of the plasma membrane which may reflect the ability of the fungus to evade the host immune response by lowering the biosynthesis of some major antigenic determinants or inhibiting their targeting to the cell surface through alterations of the membrane fluidity. In addition, this analysis revealed that some genes encoding enzymes involved in the biosynthesis of some mycotoxins were down-regulated suggesting that, during the colonization process, S. apiospermum reduces the production of some toxic secondary metabolites to prevent exacerbation of the immune system response. Finally, a strong up-regulation of many genes encoding enzymes involved in the degradation of aromatic compounds was observed, suggesting that these catabolic properties would predispose the fungus to particular patterns of human pathogenicity. Together these data provide new insights into the adaptative mechanisms developed by S. apiospermum in the CF lungs, which should be considered for identification of potential targets for drug development, but also for the experimental conditions to be used in in vitro susceptibility testing of clinical isolates to current antifungals.

Removal pathways of benzofluoranthene in a constructed wetland amended with metallic ions embedded carbon

The limited adsorption capacity of the substrate and the concentration of dissolved oxygen in constructed wetlands (CWs) have inhibited their ability to efficiently remove polycyclic aromatic hydrocarbons (PAHs) from wastewater. Presently, biochar and activated carbon modified with Fe³⁺ and Mn⁴⁺ were used as effective sorbents in the removal of benzofluoranthene (BbFA), a typical PAH, in CW microcosms. The addition of metallic ions embedded carbon increased NO₃-N accumulation by the reduction of Fe³⁺ and Mn⁴⁺, which led to improved BbFA degradation. Additionally, plant adsorption in root and stem sections were observed separately. The abundance of PAH-degrading microbes in the rhizosphere substrate was higher with the metallic ions embedded carbon than control group. The Fe³⁺, Mn⁴⁺ and NO₃-N served as electron acceptors increased BbFA microbial degradation. The removal pathways of BbFA in the modified CWs were proposed which involved settlement in the substrate, plant absorption, and microbial degradation.

Impact of necrophytoremediation on petroleum hydrocarbon degradation, ecotoxicity and soil bacterial community composition in diesel-contaminated soil

Hydrocarbon degradation is usually measured in laboratories under controlled conditions to establish the likely efficacy of a bioremediation process in the field. The present study used greenhouse-based bioremediation to investigate the effects of natural attenuation (NA) and necrophytoremediation (addition of pea straw (PS)) on hydrocarbon degradation, toxicity and the associated bacterial community structure and composition in diesel-contaminated soil. A significant reduction in total petroleum hydrocarbon (TPH) concentration was detected in both treatments; however, PS-treated soil showed more rapid degradation (87%) after 5 months together with a significant reduction in soil toxicity (EC50 = 91 mg diesel/kg). Quantitative PCR analysis revealed an increase in the number of 16S rRNA and alkB genes in the PS-amended soil. Substantial shifts in soil bacterial community were observed during the bioremediation, including an increased abundance of numerous hydrocarbon-degrading bacteria. The bacterial community shifted from dominance by Alphaproteobacteria and Gammaproteobacteria in the original soil to Actinobacteria during bioremediation. The dominance of two genera of bacteria, Sphingobacteria and Betaproteobacteria, in both NA- and PS-treated soil demonstrated changes occurring within the soil bacterial community through the incubation period. Additionally, pea straw itself was found to harbour a diverse hydrocarbonoclastic community including Luteimonas, Achromobacter, Sphingomonas, Rhodococcus and Microbacterium. At the end of the experiment, PS-amended soil exhibited reduced ecotoxicity and increased bacterial diversity as compared with the NA-treated soil. These findings suggest the rapid growth of species stimulated by the bioremediation treatment and strong selection for bacteria capable of degrading petroleum hydrocarbons during necrophytoremediation. Graphical abstract.

Investigating the mycobiome of the Holcomb Creosote Superfund Site

Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.

Evaluation of fecal fermentation profile and bacterial community in organically fed dairy cows consuming forage-rich diets with different particle sizes

Organic cattle farming encourages the use of forage-rich diets, and the reduction of particle size has been suggested as an approach to improve forage utilization and enhance nutrient intake of cows. However, reducing forage particle size increases passage rate, as well as the flow of potentially fermentable nutrients out of the rumen, and the consequences for hindgut fermentation have not been evaluated yet. This study evaluated the effects of decreasing dietary forage particle size on the fecal short-chain fatty acid (SCFA) profile and the bacterial community structure of dairy cows fed forage-based rations. Twenty-one organically fed lactating Holstein cows (4 primiparous and 17 multiparous; mean and standard deviation 703 ± 65 kg body weight, 135 ± 104 days in milk) were divided into 2 groups and fed 1 of 2 diets for 34 d. Diets contained 20% concentrate and 80% forage (dry matter basis), and were fed either as a control with a forage geometric mean particle size of 52 mm (CON; 11 cows) or as a diet with the forage particle size reduced to a geometric mean size of 7 mm (RED; 10 cows). Fecal samples were collected at the end of the experiment, and samples were immediately frozen at -20°C. Samples were analyzed for SCFA, and the fecal bacterial community was evaluated using 16S rRNA sequencing. Data showed that the concentration of total SCFA was not affected by treatment, but the proportion of propionate, a key glucogenic precursor in cattle, tended to be greater for RED (13.3 and 13.8 ± 0.1%, respectively). The predominant bacterial phyla, including Firmicutes (58.0 ± 0.7%), Bacteroidetes (26.9 ± 0.4%), and Verrucomicrobia (4.0 ± 0.4%), were not affected by forage particle size. Family Lachnospiraceae increased in relative abundance when the RED diet was fed (12.1 and 13.9 ± 0.5% for CON and RED, respectively), and genera Acetitomaculum (1.1 and 1.8 ± 0.2%), Turicibacter (0.7 and 0.9 ± 0.1%), and Ruminobacter (0.1 and 0.4 ± 0.1%) increased in relative abundance when RED was fed. In addition, relative abundance of some fecal bacterial taxa was correlated with major fecal SCFA and pH. Reducing the particle size of forages, from 52 to 7 mm geometric mean particle size, maintained fecal concentration of total SCFA and tended to enhance propionate concentration, without risk of dysbiosis. Thus, results suggest that reduction of forage particle size represents an effective approach to optimizing forage utilization while maintaining hindgut fermentation and fecal bacterial diversity in dairy cows fed forage-rich diets.

Enhanced anaerobic digestion performance by two artificially constructed microbial consortia capable of woody biomass degradation and chlorophenols detoxification

Catalpa sawdust (CSW) is a promising biomass-based biofuel. However, the complex lignocellulosic structure limits its efficient utilization in biorefinery applications. It is even more so when chlorophenols (CPs), highly toxic organic substances widely used as wood preservatives, are present. Hence, it is crucial to develop effective and eco-friendly approaches to attain deconstruction of lignocellulose and chlorophenols simultaneously as well as to improve methane (CH4) production efficiently. This study might be the first to explore the performance of the novel constructed microbial consortia CS-5 and BC-4 on woody biomass degradation and CPs detoxification simultaneously with CH4 production. After the degradation of CSW and CPs for 15 days by C5-5 or BC-4, significant reduction in lignocellulosic components and CPs mixture was realized with a total weight loss of 69.2 and 56.3 % and CPs degradation of 89 and 95 %, respectively. The toxicity of individual or mixed CPs after 15 days of degradation was reduced by approximately 90 %. The synergistic action of CS-5 and BC-4 enhanced biogas and CH4 yields over 76 and 64 % respectively, higher than control. Furthermore, CH4 production increased by 113.7 % at the peak phase of AD process. Methanosataceae represented 45.1 % of the methanogenic Archaea in digester G-III.

Fire Phoenix facilitates phytoremediation of PAH-Cd co-contaminated soil through promotion of beneficial rhizosphere bacterial communities

Pot experiments were conducted in a growth chamber to evaluate the phytoremediation efficiency and rhizosphere regulation mechanism of Fire Phoenix (a mixture of Festuca L.) in polycyclic aromatic hydrocarbon-cadmium (PAH-Cd) co-contaminated soils. Plant biomass, removal rates of PAHs and Cd, soil enzyme activity, and soil bacterial community were determined. After 150 days of planting, the removal rates of the total 4 PAHs and Cd reached 64.57% and 40.93% in co-contaminated soils with low-PAH (104.79-144.87 mg·kg^-1), and 68.29% and 25.40% in co-contaminated soils with high-PAH (169.17-197.44 mg·kg^-1), respectively. The polyphenol oxidase (PPO) activity decreased in soils having Fire Phoenix, while the dehydrogenase (DHO) activity increased as the changes of DHO activity had a strong positive correlation with the removal rates of PAHs and Cd in the low-PAH soils (r = 0.862 (P < 0.006) and 0.913 (P < 0.002), respectively). Meanwhile, successional changes in the bacterial communities were detected using high-throughput 454 Gs-FLX pyrosequencing of the 16S rRNA, and these changes were especially apparent for the co-contaminated soils with the low PAH concentration. The Fire Phoenix could promote the growth of Mycobacterium, Dokdonella, Gordonia and Kaistobacter, which played important roles in PAHs degradation or Cd dissipation. These results indicated that Fire Phoenix could effectively motivate the soil enzyme and bacterial community and enhance the potential for phytoremediation of PAH-Cd co-contaminated soils.

Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia

Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.

Soil bacterial community dynamics following surfactant addition and bioaugmentation in pyrene-contaminated soils

Because of their toxic properties, polycyclic aromatic hydrocarbons (PAHs) are designated as priority pollutants. The low solubility and strong sorption of PAHs in soil often limits bioremediation. To increase PAH bioavailability and enhance microbial degradation, surfactants are often added to contaminated soils. However, the effects of surfactants on the PAH degradation capacities of soil microbes are generally neglected. In this study, 16S rRNA gene high-throughput sequencing was used to evaluate changes in the soil microbial community after the application of rhamnolipid biosurfactant or Brij-35 surfactant and Mycobacterium vanbaalenii PYR-1 bioaugmentation over a 50-d mineralization study in two soils contaminated with pyrene at 10 mg kg^-1. The introduction of pyrene in both soils resulted in an increase in Firmicutes and a decrease in microbial richness and Shannon diversity index. Amendment of rhamnolipid at 1,400 μg g^-1 to the native clay soil resulted in a decrease in Bacillus from 48% to 2%, which was accompanied with an increase in Mycoplana that accounted for 67% of the total genera relative abundance. Phylogenetic investigation of communities by reconstruction of unobserved states was used to predict the activity of functional genes involved in the PAH degradation KEGG pathway and determined that M. vanbaalenii PYR-1 bioaugmentation resulted in an increased number of functional genes utilized in PAH biodegradation. Results of this study provide a better understanding of the soil microbial dynamics in response to surfactant amendments in addition to bioaugmentation of a PAH-degrading microbe. This knowledge contributes to successful and efficient surfactant-enhanced bioremediation of PAH-contaminated soils.

Stimulation of earthworms (Eisenia fetida) on soil microbial communities to promote metolachlor degradation

Degradation of metolachlor in surface soil is extremely important to its potential mobility and overall persistence. In this study, the effects of earthworms (Eisenia fetida) on the degradation of metolachlor at two concentration levels (5 and 20 mg kg^-1) in soil were investigated via the column experiment. The degradation kinetics of metolachlor indicate that addition of earthworms enhances metolachlor degradation significantly (P < 0.05), with the enhanced degradation rate of 30% and 63% in the low and high concentration treatments at the 15th day, respectively. Fungi rather than bacteria are primarily responsible for metolachlor degradation in soil, and earthworms stimulate metolachlor degradation mainly by stimulating the metolachlor-degrading functional microorganisms and improving fungal community structure. Earthworms prefer to promote the possible fungal degraders like order Sordariales, Microascales, Hypocreales and Mortierellales and the possible bacteria genus Rubritalea and strengthen the relationships between these primary fungi. Two metabolites metolachlor oxanilic (MOXA) and moetolachlor ethanesulfonic acid (MESA) are detected in soil and earthworms in the high concentration treatments. Earthworms stimulate the formation of MOXA and yet inhibit the formation of MESA in soil. Another metabolite metolachlor-2-hydroxy (M2H) is also detected in earthworms, which is reported firstly. The study provides an important information for the remediation of metolachlor-polluted soil.

Natural and assisted dissipation of polycyclic aromatic hydrocarbons in a long-term co-contaminated soil with creosote and potentially toxic elements

An enhanced bioremediation strategy was applied to an industrial soil co-contaminated with Polycyclic Aromatic Hydrocarbons (PAHs) and Potentially Toxic Elements (PTEs). Hydroxypropyl-β-cyclodextrin (HPBCD) and a natural mixture of two rhamnolipids (RL) were added to increase PAHs bioavailability, and combined with a microbial consortium (MC) to biodegrade soil PAHs. Bioavailability of only six PAHs (3-, 4-ring PAHs) increased when using HPBCD, with a maximum increase about 2.8-fold higher. The highest dose of HPBCD (5%) enhanced PAH degradation, with the best results for 4-ring PAHs with treatments of HPBCD + MC (up to 48% degradation for pyrene and 43% for fluoranthene), whereas dissipation for 5-ring PAHs was very low and for 6-ring was negligible. The use of RL increased the bioavailability of 13 of the 16 PAHs studied, reaching up to 60-fold higher values for phenanthrene or 18-fold higher for acenaphtene. RL addition did not show degradation improvement in any situation, and even inhibited the scarce degradation observed in the control treatment. The high increase in availability of both PAHs and mainly PTEs when using RL as amendment could make them toxic for microorganisms. In fact, Microtox Acute Toxicity test using Aliivibrio fischeri and the absence of colony forming units (CFUs) of indigenous bacteria demonstrated the extremely high levels of toxicity in RL treated soil.

Aerobic co-composting degradation of highly PCDD/F-contaminated field soil. A study of bacterial community

This study investigated bacterial communities during aerobic food waste co-composting degradation of highly PCDD/F-contaminated field soil. The total initial toxic equivalent quantity (TEQ) of the soil was 16,004 ng-TEQ kg^-1 dry weight. After 42-day composting and bioactivity-enhanced monitored natural attenuation (MNA), the final compost product's TEQ reduced to 1916 ng-TEQ kg^-1 dry weight (approximately 75% degradation) with a degradation rate of 136.33 ng-TEQ kg^-1 day^-1. Variations in bacterial communities and PCDD/F degraders were identified by next-generation sequencing (NGS). Thermophilic conditions of the co-composting process resulted in fewer observed bacteria and PCDD/F concentrations. Numerous organic compound degraders were identified by NGS, supporting the conclusion that PCDD/Fs were degraded during food waste co-composting. Bacterial communities of the composting process were defined by four phyla (Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes). At the genus level, Bacillus (Firmicutes) emerged as the most dominant phylotype. Further studies on specific roles of these bacterial strains are needed, especially for the thermophiles which contributed to the high degradation rate of the co-co-composting treatment's first 14 days.

Linking initial soil bacterial diversity and polycyclic aromatic hydrocarbons (PAHs) degradation potential

The aim of this study was to understand the role of indigenous soil microbial communities on the biodegradation of polycyclic aromatic hydrocarbons (PAHs) and to determine whether PAHs degradation potential in soils may be evaluated by analysis of bacterial diversity and potential metabolisms using a metagenomics approach. Five different soils were artificially contaminated with seven selected PAHs and the most abundant bacterial taxa were assessed by sequencing the 16S rRNA gene, and linking them to PAH biodegradation efficiencies. A PICRUSt approach was then led to estimate the degradation potentials by metagenomics inference. Although the role of bacteria in PAHs degradation is not directly established here, the presence of a large number of bacteria belonging to the Betaproteobacteria class correlated to a higher degradation of LMW PAHs. A link with specific bacterial taxa was more difficult to establish concerning HMW PAHs, which seemed to require more complex mechanisms as shown by PICRUSt.

Efficiency of surfactant-enhanced bioremediation of aged polycyclic aromatic hydrocarbon-contaminated soil: Link with bioavailability and the dynamics of the bacterial community

Shifts in the bacterial-community dynamics, bioavailability, and biodegradation of polycyclic aromatic hydrocarbons (PAHs) of chronically contaminated soil were analyzed in Triton X-100-treated microcosms at the critical micelle concentration (T-CMC) and at two sub-CMC doses. Only the sub-CMC-dose microcosms reached sorbed-PAH concentrations significantly lower than the control: 166±32 and 135±4mgkg^-1 dry soil versus 266±51mgkg^-1; consequently an increase in high- and low-molecular-weight PAHs biodegradation was observed. After 63days of incubation pyrosequencing data evidenced differences in diversity and composition between the surfactant-modified microcosms and the control, with those with sub-CMC doses containing a predominance of the orders Sphingomonadales, Acidobacteriales, and Gemmatimonadales (groups of known PAHs-degrading capability). The T-CMC microcosm exhibited a lower richness and diversity index with a marked predominance of the order Xanthomonadales, mainly represented by the Stenotrophomonas genus, a PAHs- and Triton X-100-degrading bacterium. In the T-CMC microcosm, whereas the initial surface tension was 35mNm^-1, after 63days of incubation an increase up to 40mNm^-1 was registered. The previous observation and the gas-chromatography data indicated that the surfactant may have been degraded at the CMC by a highly selective bacterial community with a consequent negative impact on PAHs biodegradation. This work obtained strong evidence for the involvement of physicochemical and biologic influences determining the different behaviors of the studied microcosms. The results reported here contribute significantly to an optimization of, surfactant-enhanced bioremediation strategies for chronically contaminated soil since the application of doses below the CMC would reduce the overall costs.

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas?

Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic “adverse toxin effect” paradigm and our novel “altered environmental microbiome” hypothesis.

Surfactant-enhanced remediation of polycyclic aromatic hydrocarbons: A review

Polycyclic aromatic hydrocarbons (PAHs) are toxic, mutagenic and carcinogenic organic compounds that are widely present in the environment. The bioremediation of PAHs is an economical and environmentally friendly remediation technique, but it is limited because PAHs have low water solubility and fewer bioavailable properties. The solubility and bioavailability of PAHs can be increased by using surfactants to reduce surface tension and interfacial tension; this method is called surfactant-enhanced remediation (SER). The SER of PAHs is influenced by many factors such as the type and concentration of surfactants, PAH hydrophobicity, temperature, pH, salinity, dissolved organic matter and microbial community. Furthermore, as mixed micelles have a synergistic effect on PAH solubilisation, selecting the optimum ratio of mixed surfactants leads to effective PAH remediation. Although the use of surfactants inhibits microbial activities in some cases, this could be avoided by choosing an optimum combination of surfactants and a proper microbial community for the targeted PAH(s), resulting in up to 99.99% PAH removal. This article reviews the literature on SER of PAHs, including surfactant types, the synergistic effect of mixed micelles on PAH removal, the impact of surfactants on the PAH biodegradation process, factors affecting the SER process, and the mechanisms of surfactant-enhanced solubilisation of PAHs.

Drivers and applications of integrated clean-up technologies for surfactant-enhanced remediation of environments contaminated with polycyclic aromatic hydrocarbons (PAHs)

Surfactant-enhanced remediation (SER) is considered as a promising and efficient remediation approach. This review summarizes and discusses main drivers on the application of SER in removing polycyclic aromatic hydrocarbons (PAHs) from contaminated soil and water. The effect of PAH-PAH interactions on SER efficiency is, for the first time, illustrated in an SER review. Interactions between mixed PAHs could enhance, decrease, or have no impact on surfactants' solubilization power towards PAHs, thus affecting the optimal usage of surfactants for SER. Although SER can transfer PAHs from soil/non-aqueous phase liquids to the aqueous phase, the harmful impact of PAHs still exists. To decrease the level of PAHs in SER solutions, a series of SER-based integrated cleanup technologies have been developed including surfactant-enhanced bioremediation (SEBR), surfactant-enhanced phytoremediation (SEPR) and SER-advanced oxidation processes (SER-AOPs). In this review, the general considerations and corresponding applications of the integrated cleanup technologies are summarized and discussed. Compared with SER-AOPs, SEBR and SEPR need less operation cost, yet require more treatment time. To successfully achieve the field application of surfactant-based technologies, massive production of the cost-effective green surfactants (i.e. biosurfactants) and comprehensive evaluation of the drivers and the global cost of SER-based cleanup technologies need to be performed in the future.

Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis

This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg^-1 of each PAH), and acenaphthene (600 mg kg^-1). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.

The microbial degradation of 2,4,6-tribromophenol (TBP) in water/sediments interface: Investigating bioaugmentation using Bacillus sp. GZT

The substance 2,4,6-Tribromophenol (TBP) is used as a flame retardant in electronic and electric devices, and is a replacement for pentachlorophenol in wood preservation. TBP is a contaminant in different environmental matrices, at levels where treatment is required. This study examined the relationship between the bioaugmention of TBP degradation and the evolution of the microbial community in river water/sediment microcosms. When compared with unamended controls, bioaugmentation with Bacillus sp. GZT effectively enhanced TBP biodegradation, with approximately 40.7% of the TBP removal after a 7-week incubation period, without a lag phase (p<0.01). Amendments with 2-bromophenol, 2,6-dibromophenol, and 2,4-dibromophenol did not promote TBP biodegradation in river water/sediments (p>0.05). However, TBP biodegradation was enhanced by adding other additives, including NaCl, humic acid, sodium lactate, and sodium propionate alone, especially glucose and yeast extract. A metagenomics analysis of the total 16S rRNA genes from the treatment system with bioaugmentation showed that four microbial phyla were dominant: Proteobacteria (52.08-66.22%), Actinobacteria (20.03-5.47%), Bacteroidetes (6.68-13.68%), and Firmicutes (4.53-20.83%). This study highlights the possible benefits using bioaugmentation with GZT to remediate TBP-polluted water and sediments.

Comparative Investigation of Bacterial, Fungal, and Archaeal Community Structures in Soils in a Typical Oilfield in Jianghan, China

Agricultural soils in oilfields have high risk for polycyclic aromatic hydrocarbon (PAH) pollution. In this study, from the Jianghan Oilfield (Hubei Province, China) with a history of >50 years, 7 soil samples (OS-1 to OS-7) were collected. Subsequently, the bacterial, archaeal, and fungal community structures were investigated by Illumina MiSeq sequencing, and the relationship between microbial community structure and soil PAH content was analyzed. The results indicated that bacterial and archaeal Chao 1 indices showed a significantly negative relationship with soil PAH content, and only the bacterial Shannon index had a significantly negative relationship with soil PAH content. Moreover, the community structure of bacteria (r ² = 0.9001, p = 0.013) showed a stronger correlation with PAH content than that of fungi (r ² = 0.7357, p = 0.045), and no significant relationship was found between archaeal community structure (r ² = 0.4553, p = 0.262) and soil PAH content. In addition, the relative greater abundances of some bacterial genus belonging to Actinobacteria (Mycobacterium and Micromonospora) and Proteobacteria (Pseudomonas, Lysobacter, Idiomarina, Oxalobacteraceae, and Massilia), fungal genus belonging to Ascomycota (Sordariales and Pleosporales), and archaeal phylum (Euryarchaeota) were detected in the soil samples (OS-3 and OS-5) with greater PAH content. In summary, soil PAHs showed an obvious influence and selectivity on the soil microbiota. Furthermore, compared with fungi and archaea, bacteria was more sensitive to soil PAH pollution, and the diversity indices and community structure of bacteria both might be suitable indicators for assessment of soil PAH stress on the soil ecosystem.

Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil

Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the primary process of removing PAHs from environments. The metabolic pathway of PAHs in pure cultures has been intensively studied, but cooperative metabolisms at community-level remained to be explored. In this study, we determined the dynamic composition of a microbial community and its metabolic intermediates during fluoranthene degradation using high-throughput metagenomics and gas chromatography-mass spectrometry (GC-MS), respectively. Subsequently, a cooperative metabolic network for fluoranthene degradation was constructed. The network shows that Mycobacterium contributed the majority of ring-hydroxylating and -cleavage dioxygenases, while Diaphorobacter contributed most of the dehydrogenases. Hyphomicrobium, Agrobacterium, and Sphingopyxis contributed to genes encoding enzymes involved in downstream reactions of fluoranthene degradation. The contributions of various microbial groups were calculated with the PICRUSt program. The contributions of Hyphomicrobium to alcohol dehydrogenases were 62.4% in stage 1 (i.e., when fluoranthene was rapidly removed) and 76.8% in stage 3 (i.e., when fluoranthene was not detectable), respectively; the contribution of Pseudomonas were 6.6% in stage 1 and decreased to 1.2% in subsequent stages. To the best of the author's knowledge, this report describes the first cooperative metabolic network to predict the contributions of various microbial groups during PAH-degradation at community-level.

Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment

Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.

Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method - the observation of DNAemia

Blood is considered to be a sterile microenvironment, in which bacteria appear only periodically. Previously used methods allowed only for the detection of either viable bacteria with low sensitivity or selected species of bacteria. The Next-Generation Sequencing method (NGS) enables the identification of all bacteria in the sample with their taxonomic classification. We used NGS for the analysis of blood samples from healthy volunteers (n = 23) and patients with sepsis (n = 62) to check whether any bacterial DNA exists in the blood of healthy people and to identify bacterial taxonomic profile in the blood of septic patients. The presence of bacterial DNA was found both in septic and healthy subjects; however, bacterial diversity was significantly different (P = 0.002) between the studied groups. Among healthy volunteers, a significant predominance of anaerobic bacteria (76.2 %), of which most were bacteria of the order Bifidobacteriales (73.0 %), was observed. In sepsis, the majority of detected taxa belonged to aerobic or microaerophilic microorganisms (75.1 %). The most striking difference was seen in the case of Actinobacteria phyla, the abundance of which was decreased in sepsis (P < 0.001) and Proteobacteria phyla which was decreased in the healthy volunteers (P < 0.001). Our research shows that bacterial DNA can be detected in the blood of healthy people and that its taxonomic composition is different from the one seen in septic patients. Detection of bacterial DNA in the blood of healthy people may suggest that bacteria continuously translocate into the blood, but not always cause sepsis; this observation can be called DNAemia.

Exploring the potential of fungi isolated from PAH-polluted soil as a source of xenobiotics-degrading fungi

The aim of this study was to find polycyclic aromatic hydrocarbon (PAH)-degrading fungi adapted to polluted environments for further application in bioremediation processes. In this study, a total of 23 fungal species were isolated from a historically pyrogenic PAH-polluted soil in Spain and taxonomically identified. The dominant groups in these samples were the ones associated with fungi belonging to the Ascomycota phylum and two isolates belonging to the Mucoromycotina subphylum and Basiodiomycota phylum. We tested their ability to convert the three-ring PAH anthracene in a 42-day time course and analysed their ability to secrete extracellular oxidoreductase enzymes. Among the 23 fungal species screened, 12 were able to oxidize anthracene, leading to the formation of 9,10-anthraquinone as the main metabolite, a less toxic one than the parent compound. The complete removal of anthracene was achieved by three fungal species. In the case of Scopulariopsis brevicaulis, extracellular enzyme independent degradation of the initial 100 μM anthracene occurred, whilst in the case of the ligninolytic fungus Fomes (Basidiomycota), the same result was obtained with extracellular enzyme-dependent transformation. The yield of accumulated 9,10-anthraquinone was 80 and 91 %, respectively, and Fomes sp. could slowly deplete it from the growth medium when offered alone. These results are indicative for the effectiveness of these fungi for pollutant removal. Graphical abstract ᅟ.

Surfactant-induced bacterial community changes correlated with increased polycyclic aromatic hydrocarbon degradation in contaminated soil

Bioremediation as a method for removing polycyclic aromatic hydrocarbons (PAHs) from contaminated environments has been criticized for poor removal of potentially carcinogenic but less bioavailable high molecular weight (HMW) compounds. As a partial remedy to this constraint, we studied surfactant addition at sub-micellar concentrations to contaminated soil to enhance the biodegradation of PAHs remaining after conventional aerobic bioremediation. We demonstrated increased removal of four- and five-ring PAHs using two nonionic surfactants, polyoxyethylene(4)lauryl ether (Brij 30) and polyoxyethylene sorbitol hexaoleate (POESH), and analyzed bacterial community shifts associated with those conditions. Eight groups of abundant bacteria were implicated as potentially being involved in increased HMW PAH removal. A group of unclassified Alphaproteobacteria and members of the Phenylobacterium genus in particular showed significantly increased relative abundance in the two conditions exhibiting increased PAH removal. Other implicated groups included members of the Sediminibacterium, Terrimonas, Acidovorax, and Luteimonas genera, as well as uncharacterized organisms within the families Chitinophagaceae and Bradyrhizobiaceae. Targeted isolation identified a subset of the community likely using the surfactants as a growth substrate, but few of the isolates exhibited PAH-degradation capability. Isolates recovered from the Acidovorax and uncharacterized Bradyrhizobiaceae groups suggest the abundance of those groups may have been attributable to growth on surfactants. Understanding the specific bacteria responsible for HMW PAH removal in natural and engineered systems and their response to stimuli such as surfactant amendment may improve bioremediation efficacy during treatment of contaminated environmental media.

Shifts in microbial community structure during in situ surfactant-enhanced bioremediation of polycyclic aromatic hydrocarbon-contaminated soil

This study aims to reveal the microbial mechanism of in situ surfactant-enhanced bioremediation (SEBR). Various concentrations of rhamnolipids, Tween 80, and sodium dodecyl benzenesulfonate (SDBS) were separately sprayed onto soils contaminated with polycyclic aromatic hydrocarbons (PAHs) for years. Within 90 days, the highest level of degradation (95 %) was observed in the soil treated with rhamnolipids (10 mg/kg), followed by 92 % degradation with Tween 80 (50 mg/kg) and 90 % degradation with SDBS (50 mg/kg). The results of the microbial phospholipid fatty acids (PLFAs) suggest that bacteria dominated the enhanced PAH biodegradation (94 % of the maximum contribution). The shift of bacterial community structure during the surfactant treatment was analyzed by using the 16S rRNA gene high-throughput sequencing. In the presence of surfactants, the number of the operational taxonomic units (OTUs) associated with Bacillus, Pseudomonas, and Sphingomonas increased from 2-3 to 15-30 % at the end of the experiment (two to three times of control). Gene prediction with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) shows that the PAH-degrading genes, such as 1-hydroxy-2-naphthoate dioxygenase and PAH dioxygenase large subunit, significantly increased after the surfactant applications (p < 0.05). The findings of this study provide insights into the surfactant-induced shifts of microbial community, as well as critical factors for efficient bioremediation.

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing

The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales, Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.

Effects of CO2 leakage on soil bacterial communities from simulated CO2-EOR areas

CO2-EOR (enhanced oil recovery) has been proposed as a viable option for flooding oil and reducing anthropogenic CO2 contribution to the atmospheric pool. However, the potential risk of CO2 leakage from the process poses a threat to the ecological system. High-throughput sequencing was used to investigate the effects of CO2 emission on the composition and structure of soil bacterial communities. The diversity of bacterial communities notably decreased with increasing CO2 flux. The composition of bacterial communities varied along the CO2 flux, with increasing CO2 flux accompanied by increases in the relative abundance of Bacteroidetes and Firmicutes phyla, but decreases in the relative abundance of Acidobacteria and Chloroflexi phyla. Within the Firmicutes phylum, the genus Lactobacillus increased sharply when the CO2 flux was at its highest point. Alpha and beta diversity analysis revealed that differences in bacterial communities were best explained by CO2 flux. The redundancy analysis (RDA) revealed that differences in bacterial communities were best explained by soil pH values which related to CO2 flux. These results could be useful for evaluating the risk of potential CO2 leakages on the ecosystems associated with CO2-EOR processes.

Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil

Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO₂ and by using gas chromatography–mass spectrometry (GC–MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2–3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO₂, given the high respiration activities of the soybean meal alone. GC–MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7–1.8 fold increase in the degraded C₁₄ to C₃₀ alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C₁₄ to C₃₀ alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5–86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95–98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.

Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood

The feasibility of decontaminating creosote-treated wood (CTW) by co-composting with agricultural wastes was investigated using two bulking agents, grass cuttings (GC) and broiler litter (BL), each employed at a 1:1 ratio with the matrix. The initial concentration of total polycyclic aromatic hydrocarbons (PAHs) in CTW (26,500 mg kg(-1)) was reduced to 3 and 19% after 240 d in GC and BL compost, respectively. PAH degradation exceeded the predicted bioaccesible threshold, estimated through sequential supercritical CO2 extraction, together with significant detoxification, assessed by contact tests using Vibrio fisheri and Hordeum vulgare. GC composting was characterized by high microbial biomass growth in the early phases, as suggested by phospholipid fatty acid analyses. Based on the 454-pyrosequencing results, fungi (mostly Saccharomycetales) constituted an important portion of the microbial community, and bacteria were characterized by rapid shifts (from Firmicutes (Bacilli) and Actinobacteria to Proteobacteria). However, during BL composting, larger amounts of prokaryotic and eukaryotic PLFA markers were observed during the cooling and maturation phases, which were dominated by Proteobacteria and fungi belonging to the Ascomycota and those putatively related to the Glomeromycota. This work reports the first in-depth analysis of the chemical and microbiological processes that occur during the co-composting of a PAH-contaminated matrix.

Pesticides in Ichkeul Lake-Bizerta Lagoon Watershed in Tunisia: use, occurrence, and effects on bacteria and free-living marine nematodes

This study aimed to identify the most commonly used agricultural pesticides around Ichkeul Lake-Bizerta Lagoon watershed. First survey of pesticide use on agricultural watershed was performed with farmers, Regional Commissioner for Agricultural Development, and pesticide dealers. Then, sediment contamination by pesticides and response of benthic communities (bacteria and free-living marine nematode) were investigated. The analysis of 22 active organochlorine pesticides in sediments was performed according to quick, easy, cheap, effective, rugged, and safe (QuEChERS) method, biodiversity of indigenous bacterial community sediment was determined by terminal restriction fragment length polymorphism (T-RFLP), and free-living marine nematodes were counted. The results of the field survey showed that iodosulfuron, mesosulfuron, 2,4-dichlorophenoxyacetic acid (2,4 D), glyphosate, and fenoxaprops were the most used herbicides, tebuconazole and epoxiconazole the most used fungicides, and deltamethrin the most used insecticide. Sixteen organochlorine pesticide compounds among the 22 examined were detected in sediments up to 2 ppm in Ichkeul Lake, endrin, dieldrin, and hexachlorocyclohexane being the most detected molecules. The most pesticide-contaminated site in the lake presented the higher density of nematode, but when considering all sites, no clear correlation with organochlorine pesticide (OCP) content could be established. The bacterial community structure in the most contaminated site in the lake was characterized by the terminal restriction fragments (T-RFs) 97, 146, 258, 285, and 335 while the most contaminated site in the lagoon was characterized by the T-RFs 54, 263, 315, 403, and 428. Interestingly, T-RFs 38 and 143 were found in the most contaminated sites of both lake and lagoon ecosystems, indicating that they were resistant to OCPs and able to cope with environmental fluctuation of salinity. In contrast, the T-RFs 63, 100, 118, and 381 in the lake and the T-RFs 40, 60, 80, 158, 300, 321, and 357 in the lagoon were sensitive to OCPs. This study highlighted that the intensive use of pesticides in agriculture, through transfer to aquatic ecosystem, may disturb the benthic ecosystem functioning of the protected area. The free-living marine nematodes and bacterial communities represent useful proxy to follow the ecosystem health and its capacity of resilience.

Chemical and microbiological characterization of an aged PCB-contaminated soil

This study was aimed at complex characterization of three soil samples (bulk soil, topsoil and rhizosphere soil) from a site historically contaminated with polychlorinated biphenyls (PCB). The bulk soil was the most highly contaminated, with a PCB concentration of 705.95 mg kg(-1), while the rhizosphere soil was the least contaminated (169.36 mg kg(-1)). PCB degradation intermediates, namely chlorobenzoic acids (CBAs), were detected in all the soil samples, suggesting the occurrence of microbial transformation processes over time. The higher content of organic carbon in the topsoil and rhizosphere soil than in the bulk soil could be linked to the reduced bioaccessibility (bioavailability) of these chlorinated pollutants. However, different proportions of the PCB congener contents and different bioaccessibility of the PCB homologues indicate microbial biotransformation of the compounds. The higher content of organic carbon probably also promoted the growth of microorganisms, as revealed by phospholipid fatty acid (PFLA) quantification. Tag-encoded pyrosequencing analysis showed that the bacterial community structure was significantly similar among the three soils and was predominated by Proteobacteria (44-48%) in all cases. Moreover, analysis at lower taxonomic levels pointed to the presence of genera (Sphingomonas, Bulkholderia, Arthrobacter, Bacillus) including members with reported PCB removal abilities. The fungal community was mostly represented by Basidiomycota and Ascomycota, which accounted for >80% of all the sequences detected in the three soils. Fungal taxa with biodegradation potential (Paxillus, Cryptococcus, Phoma, Mortierella) were also found. These results highlight the potential of the indigenous consortia present at the site as a starting point for PCB bioremediation processes.

Operational, design and microbial aspects related to power production with microbial fuel cells implemented in constructed wetlands

This work aimed at determining the amount of energy that can be harvested by implementing microbial fuel cells (MFC) in horizontal subsurface constructed wetlands (HSSF CWs) during the treatment of real domestic wastewater. To this aim, MFC were implemented in a pilot plant based on two HSSF CW, one fed with primary settled wastewater (Settler line) and the other fed with the effluent of a hydrolytic up-flow sludge blanket reactor (HUSB line). The eubacterial and archaeal community was profiled on wetland gravel, MFC electrodes and primary treated wastewater by means of 16S rRNA gene-based 454-pyrosequencing and qPCR of 16S rRNA and mcrA genes. Maximum current (219 mA/m(2)) and power (36 mW/m(2)) densities were obtained for the HUSB line. Power production pattern correlated well with water level fluctuations within the wetlands, whereas the type of primary treatment implemented had a significant impact on the diversity and relative abundance of eubacteria communities colonizing MFC. It is worth noticing the high predominance (13-16% of relative abundance) of one OTU belonging to Geobacter on active MFC of the HUSB line that was absent for the settler line MFC. Hence, MFC show promise for power production in constructed wetlands receiving the effluent of a HUSB reactor.