Root exudates modify bacterial diversity of phenanthrene degraders in PAH-polluted soil but not phenanthrene degradation rates

Uptake, subcellular distribution, and fate of tetracycline in two wetland plants supplemented with microbial agents: Effect and mechanism

The use of wetland plants in the context of phytoremediation is effective in the removal of antibiotics from contaminated water. However, the effectiveness and efficiency of many of these plants in the removal of antibiotics remain undetermined. In this study, the effectiveness of two plants-Phragmites australis and Iris pseudacorus-in the removal of tetracycline (TC) in hydroponic systems was investigated. The uptake of TC at the roots of I. pseudacorus and P. australis occurred at concentrations of 588.78 and 106.70 μg/g, respectively, after 7-day exposure. The higher uptake of TC in the root of I. pseudacorus may be attributed to its higher secretion of root exudates, which facilitate conditions conducive to the reproduction of microorganisms. These rhizosphere-linked microorganisms then drove the TC uptake, which was higher than that in the roots of P. australis. By elucidating the mechanisms underlying these uptake-linked outcomes, we found that the uptake of TC for both plants was significantly suppressed by metabolic and aquaporin inhibition, suggesting uptake and transport of TC were active (energy-dependent) and passive (aquaporin-dominated) processes, respectively. The subcellular distribution patterns of I. pseudacorus and P. australis in the roots were different, as expressed by differences in organelles, cell wall concentration levels, and transport-related dynamics. Additionally, the microbe-driven enhancement of the remediation capacities of the plants was studied comprehensively via a combined microbial-phytoremediation hydroponic system. We confirmed that the microbial agents increased the secretion of root exudates, promoting the variation of TC chemical speciation and thus enhancing the active transport of TC. These results contribute toward the improved application of wetland plants in the context of antibiotic phytoremediation.

Interactions between plants and bacterial communities for phytoremediation of petroleum-contaminated soil

Plants can stimulate the microbes to degrade ubiquitous petroleum hydrocarbons (PHCs), which has prompted a novel view on rhizoremediation. In the present study, the degradation rate of PHCs was investigated and 16S rRNA gene analysis was performed to investigate the PHC-degrading bacteria in petroleum-contaminated soil with different plants. Mirabilis jalapa (M. jalapa) has a higher PHC degradation rate than Lolium perenne (L. perenne) under petroleum contamination. The bacterial diversity in rhizospheric soil was decreased but the relative abundance of Actinobacteriota, Proteobacteria, and Candidatus Saccharibacteria were significant increased on 45 days petroleum-contaminated rhizospheric soil. In addition, the relative expression of PHC degradation-related genes, the content of malic acid and citric acid of the root exudates in the two plants was significantly increased in response to petroleum stress. The content of citric acid increased 11.9 times in M. jalapa and 3.4 times in L. perenne, respectively, in response to petroleum stress. These results indicate that M. jalapa changes the hydrocarbon-degrading microbial community to enhance the degradation of PHCs by root exudates and phytostimulation.

Perfluoroalkyl acid precursors in agricultural soil-plant systems: Occurrence, uptake, and biotransformation

Perfluoroalkyl acid (PFAA) precursors have been used in various consumer and industrial products due to their hydrophobic and oleophobic properties. In recent years, PFAA precursors in agricultural soil-plant systems have received increasing attention as they are susceptible to biotransformation into metabolites with high biotoxicity risks to human health. In this review, we systematically assessed the occurrence of PFAA precursors in agricultural soils, taking into account their sources and biodegradation pathways. In addition, we summarized the findings of the relevant literature on the uptake and biotransformation of PFAA precursors by agricultural plants. The applications of biosolids/composts and pesticides are the main sources of PFAA precursors in agricultural soils. The physicochemical properties of PFAA precursors, soil organic carbon (SOC) contents, and plant species are the key factors influencing plant root uptakes of PFAA precursors from soils. This review revealed, through toxicity assessment, the potential of PFAA precursors to generate metabolites with higher toxicity than the parent precursors. The results of this paper provide a reference for future research on PFAA precursors and their metabolites in soil-plant systems.

Elucidating the significant roles of root exudates in organic pollutant biotransformation within the rhizosphere

Biotransformation of organic pollutants is crucial for the dissipation of environmental pollutants. While the roles of microorganisms have been extensively studied, the significant contribution of various root exudates are still not very well understood. Through plant growth experiment, coupled with gas and liquid chromatography-mass spectrometry methods, this study examined the effect of the presence of M. sativa on microbial-associated biochemical transformation of petroleum hydrocarbons. The results of this study revealed that the concentration of exudates within the soil matrix is a function of proximity to root surfaces. Similarly, biodegradation was found to correlate with distance from roots, ranging from ≥ 90% within the rhizosphere to < 50% in bulk soil and unplanted control soil. Most importantly, for the first time in a study of an entire petroleum distillate, this study revealed a statistically significant negative correlation between root exudate concentration and residual total petroleum hydrocarbons. While not all the compounds that may influence biodegradation are derived from roots, the results of this study show that the presence of plant can significantly influence biodegradation of hydrocarbon pollutants through such root exudation as organic acids, amino acids, soluble sugars and terpenoids. Therefore, root exudates, including secondary metabolites, offer great prospects for biotechnological applications in the remediation of organic pollutants, including recalcitrant ones.

Transfer and Degradation of PAHs in the Soil-Plant System: A Review

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, persistent organic pollutants that threaten ecosystems and human health. Consistent monitoring is essential to minimize the entry of PAHs into plants and reduce food chain contamination. PAHs infiltrate plants through multiple pathways, causing detrimental effects and triggering diverse plant responses, ultimately increasing either toxicity or tolerance. Primary plant detoxification processes include enzymatic transformation, conjugation, and accumulation of contaminants in cell walls/vacuoles. Plants also play a crucial role in stimulating microbial PAHs degradation by producing root exudates, enhancing bioavailability, supplying nutrients, and promoting soil microbial diversity and activity. Thus, synergistic plant-microbe interactions efficiently decrease PAHs uptake by plants and, thereby, their accumulation along the food chain. This review highlights PAHs uptake pathways and their overall fate as contaminants of emerging concern (CEC). Understanding plant uptake mechanisms, responses to contaminants, and interactions with rhizosphere microbiota is vital for addressing PAH pollution in soil and ensuring food safety and quality.

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

The role of microplastics in the process of laccase-assisted phytoremediation of phenanthrene-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic organic pollutants widely distributed in terrestrial environments and laccase was considered as an effective enzyme in PAHs bioremediation. However, laccase-assisted phytoremediation of PAHs-contaminated soil has not been reported. Moreover, the overuse of plastic films in agriculture greatly increased the risk of co-existence of PAHs and microplastics in soil. Microplastics can adsorb hydrophobic organics, thus altering the bioavailability of PAHs and ultimately affecting the removal of PAHs from soil. Therefore, this study aimed to evaluate the efficiency of laccase-assisted maize (Zea mays L.) in the remediation of phenanthrene (PHE)-contaminated soil and investigate the effect of microplastics on this remediation process. The results showed that the combined application of laccase and maize achieved a removal efficiency of 83.47 % for soil PHE, and laccase significantly reduced the accumulation of PHE in maize. However, microplastics significantly inhibited the removal of soil PHE (10.88 %) and reduced the translocation factor of PHE in maize (87.72 %), in comparison with PHE + L treatment. Moreover, microplastics reduced the laccase activity and the relative abundance of some PAHs-degrading bacteria in soil. This study provided an idea for evaluating the feasibility of the laccase-assisted plants in the remediation of PAHs-contaminated soil, paving the way for reducing the risk of secondary pollution in the process of phytoremediation.

Community pattern of potential phenanthrene (PHE) degrading bacteria in PHE contaminated soil revealed by 13C-DNA stable isotope probing

Quantification of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and identification of potential PAH degraders are essential for comprehending their environmental fate and conducting bioremediation. However, the microbial population responsible for the breakdown of phenanthrene (PHE) in polluted soil environments is frequently disregarded. In this study, via DNA-stable-isotope probing (DNA-SIP), we found that soil microbiota likely plays a crucial part in the PHE degradation. The PHE removal rates were 98% and 99%, in 13C-PHE and 12C-PHE microcosmic incubations, respectively. 13CO2 was produced along with the degradation of 13C-PHE. According to the analysis of 16S rRNA gene, there was a relatively higher presence of unidentified bacteria in the 'heavy' DNA fractions treated with 13C-PHE. Genus of Enterobacteriales, Acidobacteria, Alphaproteobacteria, Paenibacillaceae, Flavobacteriia, Chloroflexi, Cyanobacteria, Caldilineae, Latescibacteria, Armatimonadetes and Blastocatellia were succseesfully labeled during the degradation of 13C-PHE, indicating their capacity of utilizing PHE. Co-occurrence network of 13C-heavy fractions exhibited greater complexity compared with that of 12C-heavy fractions, revealling an enhancement of bacterial interspecies interactions. Collectivley, this study eluidated the soil microbes involed in the PHE degradation and offered fresh perspectives on the community pattern of potential PHE degrading bacteria.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP)

Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.

Biostimulation of Petroleum-Contaminated Soil Using Organic and Inorganic Amendments

The most common approaches for the in-situ bioremediation of contaminated sites worldwide are bioaugmentation and biostimulation. Biostimulation has often proved more effective for chronically contaminated sites. This study examined the effectiveness of optimized water hyacinth compost in comparison with other organic and inorganic amendments for the remediation of crude oil-polluted soils. Water hyacinth was found to be rich in nutrients necessary to stimulate microbial growth and activity. An organic geochemical analysis revealed that all amendments in this study increased total petroleum hydrocarbon (TPH) biodegradation by ≥75% within 56 days, with the greatest biodegradation (93%) occurring in sterilized soil inoculated with optimized water hyacinth compost. This was followed by polluted soil amended with a combination of spent mushroom and water hyacinth composts (SMC + WH), which recorded a TPH biodegradation of 89%. Soil amendment using the inorganic fertilizer NPK (20:10:10) resulted in 86% TPH biodegradation. On the other hand, control samples (natural attenuation) recorded only 4% degradation. A molecular analysis of residual polycyclic aromatic hydrocarbons (PAHs) showed that the 16 PAHs designated by the US EPA as priority pollutants were either completely or highly degraded in the combined treatment (SMC + WH), indicating the potential of this amendment for the environmental remediation of soils contaminated with recalcitrant organic pollutants.

New insights into microbial community coalescence in the land-sea continuum

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

Synergetic effects of microbial-phytoremediation reshape microbial communities and improve degradation of petroleum contaminants

Microbial-phytoremediation is an effective bioremediation technology that introduces petroleum-degrading bacteria and oil-tolerant plants into oil-contaminated soils in order to achieve effective degradation of total petroleum hydrocarbons (TPH). In this work, natural attenuation (NA), microbial remediation (MR, using Acinetobacter sp. Tust-DM21), phytoremediation (PR, using Suaeda glauca), and microbial-phytoremediation (MPR, using both species) were utilized to degrade petroleum hydrocarbons. We evaluated four different biological treatments, assessing TPH degradation rates, soil enzyme activities, and the structure of microbial community in the petroleum-contaminated soil. This finding revealed that the roots of Suaeda glauca adsorbed small amounts of polycyclic aromatic hydrocarbons, causing the structure of soil microbiota community to reshape. The abundance of petroleum-degrading bacteria and plant growth-promoting rhizobacteria (PGPR) has increased, as has microbial diversity. According to correlation research, these genera increased soil enzyme activity, boosted the number of degradation-functional genes in the petroleum hydrocarbon degradation pathway, and accelerated the dissipation and degradation of TPH in petroleum-contaminated soil. This evidence contributes to a better understanding of the mechanisms involved in the combined microbial-phytoremediation strategies for contaminated soil, specifically the interaction between microflora and plants in co-remediation and the effects on the structural reshaping of rhizosphere microbial communities.

Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps

Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.

Assessment of dynamic microbial community structure and rhizosphere interactions during bioaugmented phytoremediation of petroleum contaminated soil by a newly designed rhizobox system

To understand the plant (Vigna unguiculata) and plant-growth promoting bacteria (PGPB) (Microcococcus luteus WN01) interactions in crude oil contaminated soil, experiments were conducted based on the newly designed rhizobox system. The rhizobox was divided into three main compartments namely the rhizosphere zone, the mid-zone, and the bulk soil zone, in accordance with the distance from the plant. Plants were grown in these three-chambered pots for 30 days under natural conditions. The plant root exudates were determined by analyzing for carbohydrates, amino acids, and phenolic compounds. The degradation of alkane, polycyclic aromatic hydrocarbons (PAHs), and total petroleum hydrocarbons (TPHs) were quantified by GC-FID. Soil catalase, dehydrogenase, and invertase activities were determined. The microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE). Results showed that the inoculation of M. luteus WN01 significantly enhanced cowpea root biomass and exudates, especially the phenolic compounds. Bioaugmented phytoremediation by cowpea and M. luteus promoted rhizodegradation of TPH. Cowpea stimulated microbial growth, soil dehydrogenase, and invertase activities and enhanced bacterial community diversity in oil contaminated soil. The rhizosphere zone of cowpea inoculated with M. luteus showed the highest removal efficiency, microbial activities, microbial population, and bacterial community diversity indicating the strong synergic interactions between M. luteus and cowpea.

Toward understanding submersed macrophyte Vallisneria natans-microbe partnerships to improve remediation potential for PAH-contaminated sediment

Rhizodegradation using submersed macrophytes Vallisneria natans (V. natans) is a promising biotechnology with the potential to restore polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. However, how different sediment types influence the rhizoremediation outcome and the characterization of microbial community along the sediment-V. natans continuum is poorly understood. Here, we collect V. natans, sediments and overlying water from two types of vegetation zones with different levels of PAHs pollutions and set up sediment microcosms for phytoremediation tests. V. natans presence was particularly useful for PAHs remediation in the highly contaminated sites and had a significant effect on PAHs rhizodegradation and microbial communities, especially rhizosphere sediments. The structural composition of microbial communities along the sediment-plant continuum was shaped predominantly by compartment niche of V. natans. Moreover, selective enrichment of specific microbial taxa like Herbaspirillum (relative abundance = 94.80%) in endosphere of V. natans was observed. Herbaspirillum could use PAH as carbon source and promote the growth of plants. In the highly contaminated sediment, V. natans could recruit these bacteria for toxicant degradation into the root interior. Thus, understanding the complex V. natans-microbe interactions could help set up novel decontamination strategies based on the rhizosphere and root interior interactions between plants and their microbial associates.

Mechanism of salicylic acid in promoting the rhizosphere benzo[a]pyrene biodegradation as revealed by DNA-stable isotope probing

Benzo[a]pyrene (BaP) is a typical high-molecular-weight PAH with carcinogenicity. Rhizoremediation is commonly applied to remove soil BaP, but its mechanism remains unclear. The role of inducers in root exudates in BaP rhizoremediation is rarely studied. Here, to address this problem, we firstly investigated the effect of the inducer salicylic acid on BaP rhizoremediation, rhizosphere BaP degraders, and PAH degradation-related genes by combining DNA-stable-isotope-probing, high-throughput sequencing, and gene function prediction. BaP removal in the rhizosphere was significantly increased by stimulation with salicylic acid, and the rhizosphere BaP-degrading microbial community structure was significantly changed. Fourteen microbes were responsible for the BaP metabolism, and most degraders, e.g. Aeromicrobium and Myceligenerans, were firstly linked with BaP biodegradation. The enrichment of the PAH-ring hydroxylating dioxygenase (PAH-RHD) gene in the heavy fractions of all ¹³C-treatments further indicated their involvement in the BaP biodegradation, which was also confirmed by the enrichment of dominant PAH degradation-related genes (e.g. PAH dioxygenase and protocatechuate 3,4-dioxygenase genes) based on gene function prediction. Overall, our study demonstrates that salicylic acid can enhance the rhizosphere BaP biodegradation by altering the community structure of rhizosphere BaP-degrading bacteria and the abundance of PAH degradation-related genes, which provides new insights into BaP rhizoremediation mechanisms in petroleum-contaminated sites.

Influence of destructive bacteria and red clover (trifolium pratense L.) on the pesticides degradation in the soil

Lindane and DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) are pesticides from the group of persistent organic pollutants. These compounds, due to lipophilic properties, accumulate in tissues of organisms, are transmitted through the food chain and ultimately threaten human health. The long-term use of pesticides led to soil and water pollution. Microbial degradation of organochlorine compounds is the most eco-friendly method of polluted soil recultivation. Effective degradation of lindane and DDT soil pollution under the influence of introduced destructive bacteria was shown in the laboratory conditions. The concentration of lindane in the soil decreased by 75% and of DDT-by 56% in 30 days. The red clover seedlings increased pesticides degradation in the soil by 20%. The destruction of pesticides in soil was more intense than in the mineral medium. The DGGE analysis of microorganism associations introduced in contaminated soil was possible to follow the survival of the introduced associations. The use of microorganisms-destructors of organochlorine compounds, and plants as well as the biodegradation potential of the soil is a promising direction in the recultivation of polluted soils.

Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation

Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics-contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.

Interactions between pyrene and heavy metals and their fates in a soil-maize (Zea mays L.) system: Perspectives from the root physiological functions and rhizosphere microbial community

The co-occurrence of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in agricultural soils has become a worldwide food crop security concern. Pot experiments, rhizosphere microbial metagenomic sequencing, and root metatranscriptomic sequencing were performed to investigate the interactions among pyrene, Cu, and Cd in a soil-maize (Zea mays L.) system. This study provided direct evidence that the co-presence of PAHs and heavy metals changed the root physiological functions and the rhizosphere microbial community, which subsequently influenced the fate of the contaminants. Co-contamination at low levels tended to enhance the uptake potential and biodegradation performance of the plant, whereas increased contaminant concentrations produced opposite effects. The co-presence of 1000 mg/kg Cu decreased the abundance of Mycobacterium in the rhizosphere and reduced pyrene degradation by 12%-16%. The presence of 400-750 mg/kg pyrene altered the metabolic processes, molecular binding functions, and catalytic activity of enzymes in the maize roots, thus impeding the phytoextraction of Cu and Cd. Competitive absorption between Cu and Cd was observed for the 800-1000 mg/kg Cu and 50-100 mg/kg Cd co-treatment, in which Cu showed a competitive advantage, enhancing its root-to-shoot translocation. These findings provide important information for the production of safe crops and for the development of phytoremediation technologies.

Organic amendment improves rhizosphere environment and shapes soil bacterial community in black and red soil under lead stress

Heavy metal pollution is a worldwide problem affecting the quality of agricultural production and human health. In this study, spent mushroom substrate (SMS) and its compost (CSMS) were used to remedy black soil and red soil with simulated Pb contamination, aiming to discover their role in the improving rhizosphere environment and structuring rhizosphere bacterial community under lead stress. We designed an ultra-small-scale plot experiment to separate the rhizosphere from non-rhizosphere soil when planting water spinach (Ipomoea aquatica Forsk). The results showed that under 600 mg/kg of lead pollution, CSMS and SMS had no significant effect on the rhizosphere bacterial diversity in the black soil, but CSMS significantly increased the rhizosphere bacterial diversity in the red soil. The amendments significantly increased the percentage of Proteobacteria and Bacteroidetes in rhizosphere soil, and the relative abundance of some beneficial genera, such as Pseudoxanthomonas, Rhizomicrobium, Lysobacter etc., which subsequently restructured the bacterial community. The compositions of bacterial community of the red soil remediated by both amendments evolved to those of the black soil.

Responses of oil degrader enzyme activities, metabolism and degradation kinetics to bean root exudates during rhizoremediation of crude oil contaminated soil

During rhizoremediation process, plant roots secrete the specific exudates which enhance or stimulate growth and activity of microbial community in the rhizosphere resulting in effective degradation of pollutants. The present study characterized cowpea (CP) and mung bean (MB) root exudates and examined their influences on the degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) by the two oil degraders Micrococcus luteus WN01 and Bacillus cereus W2301. The effects of root exudates on soil microbial population dynamic and their enzymes dehydrogenase (DHA), and catechol 2,3 dioxygenase (C23O) activities were assessed. Both root exudates enhanced the degradation by both oil degraders. Cowpea root exudates maximized the removal of TPHs and PAHs by M. luteus WN01. Both bacterial population and DHA increased significantly in the presence of both root exudates. However, the C23O activities were significantly higher in WN01 treated. No significant influence of root exudates was observed on the C23O activities of W2301 treated. By using gas chromatography -mass spectroscopy, the dominant compounds found in cowpea and mung bean root exudates were 4-methoxy-cinnamic acid and terephthalic acid. Found in lower amount were propionic, malonic acid, and citric acid which were associated with enhanced PAHs desorption from soil and subsequent degradation. Novelty statement This is the first study to characterize the low molecular weight organic acids from root exudates of cowpea and mung bean and their influences on hydrocarbon desorption and hence enhancing the biodegradation process. The findings of the present study will greatly contribute to a better understanding of plant-microbe interaction in total petroleum hydrocarbons contaminated soil.

Effects of Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) and Mycobacterium sp. on the degradation of PAHs and bacterial community in soil

Phytomicrobial remediation technology of PAH-contaminated soils has drawn great attention due to its low-cost, eco-friendly, and effective characteristics, but the mechanism underlying the removal of PAHs by rhizosphere in wastewater-irrigated soil is so far not clear. To evaluate the dissipation of PAHs and the shifts of bacterial community structure under plant-microorganism symbiotic system in an agricultural soil, a rhizo-box experiment with Fire Phoenix (a genotype mixture of Fesctuca arundinecea L.) or/and inoculated Mycobacterium sp. was conducted for 60 days. The changes of bacterial community structure and the contents of PAHs were analyzed by denaturing gradient gel electrophoresis (DGGE) and high-performance liquid chromatography (HPLC), respectively. The results showed that the removal rate of PAHs in phytomicrobial combined treatment was 53.7% after 60 days. The PAH-degraders were dominated by Microbacterium sp., Sphingomonas sp., Mycobacterium sp., and Flavobacterium sp. The plant of Fire Phoenix induced the appearance of Pseudomonas sp. and TM7 phylum sp. oral clone. The highest of bacterial diversity index was observed in unrhizosphere soils (MR-), rather than that in rhizosphere soils (MR+). In combination, phytomicrobial combined treatment of Fire Phoenix and Mycobacterium strain enhanced the removal rate of PAHs and changed the structure of bacterial community and bacterial diversity. Bacterial community has great effect on PAH degradation in PAH-contaminated soil from the wastewater-irrigated site. Our study can provide support information for PAH degradation enhancement by the synergetic effect of Fire Phoenix and Mycobacterium sp.

Long-Term Field Study on Fate, Transformation, and Vertical Transport of Tetrabromobisphenol A in Soil-Plant Systems

Soil contamination with tetrabromobisphenol A (TBBPA) has been an environmental concern for many years, but in situ studies of the fate and potential risk of TBBPA are lacking. In this study, we investigated the dissipation, metabolism, strong alkali-hydrolytic (SAH-TBBPA), and vertical movement of TBBPA in the field with and without rice-wheat rotation and reed growth for 1225 days. After 342 days of incubation, 21.3% of the TBBPA remained in the surface soil accompanied by obvious leaching to deeper soil layers in the first 92 days. By day 1225, TBBPA was nearly absent from the surface soil layer. A very low amount of SAH-TBBPA (2.31-3.43 mg/kg) was detected during the first 342 days of incubation. In the surface soil, five metabolites were identified that represented four interconnected pathways: oxidative skeletal cleavage, O-methylation, type II ipso-substitution, and reductive debromination. Both rice-wheat rotation and monocultural reed growth accelerated TBBPA removal in the field by stimulating the anaerobic debromination and aerobic O-methylation, especially the oxidative skeletal cleavage of TBBPA in the rhizosphere soil. Though far from comprehensive, our study investigated the natural attenuation and metabolism of TBBPA in situ and the influence by crops to estimate the environmental risk of TBBPA in a field scale.

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.

Phenanthrene contamination and ploidy level affect the rhizosphere bacterial communities of Spartina spp

Spartina spp. are widely distributed salt marsh plants that have a recent history of hybridization and polyploidization. These events have resulted in a heightened tolerance to hydrocarbon contaminants, but the effects of this phenomenon on the rhizosphere microbial communities are unknown. Here, we grew two parental Spartina species, their hybrid and the resulting allopolyploid in salt marsh sediments that were contaminated or not with phenanthrene. The DNA from the rhizosphere soil was extracted and the bacterial 16S rRNA gene was amplified and sequenced, whereas the abundances of the genes encoding for the PAH (polycyclic aromatic hydrocarbon) ring-hydroxylating dioxygenase (RHD) of Gram-negative and Gram-positive bacteria were quantified by real-time PCR. Both the contamination and the plant genotype significantly affected the bacterial communities. In particular, the allopolyploid S. anglica harbored a more diverse bacterial community in its rhizosphere. The interspecific hybrid and the allopolyploid also harbored significantly more copies of the PAH-RHD gene of Gram-negative bacteria in their rhizosphere than the parental species, irrespective of the contamination treatments. Overall, our results are showing that the recent polyploidization events in the Spartina affected its rhizosphere bacterial communities, both under normal and contaminated conditions, possibly increasing its phytoremediation potential.

DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil

DNA-stable isotope probing (SIP) with ¹³C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.

Rhizodegradation of Pyrene by a Non-pathogenic Klebsiella pneumoniae Isolate Applied With Tagetes erecta L. and Changes in the Rhizobacterial Community

The non-clinical Klebsiella pneumoniae variants, isolated from different environments, are now well acknowledged for their role in plant-growth promotion and biodegradation of pollutants. In the present study, a non-clinical environmental isolate K. pneumoniae AWD5 is being described for rhizoremediation of pyrene, applied through the rhizosphere of an ornamental plant, Tagetes erecta L (marigold). The non-pathogenic nature of AWD5 was established using an in vivo mouse model experiment, where AWD5 was unable to cause lung infection in tested mice. Degradation of pyrene, in the presence of succinate as co-substrate, was observed to be 87.5% by AWD5, after 21 days of incubation in minimal (Bushnell–Hass) medium in vitro conditions. Consequently, the bacterial inoculation through the rhizosphere of T. erecta L. plants resulted in 68.61% degradation of pyrene, which was significantly higher than control soil. Inoculation of AWD5 also improved plant growth and exhibited an increase in root length (14.64%), dry root weight (80.56%), shoot length (3.26%), and dry shoot weight (45.35%) after 60 days of incubation. T. erecta L., an ornamental plant, was also found to be suitable for bioremediation of pyrene. The effect of AWD5 application, and rhizoremediation process, on rhizosphere bacterial diversity and community structure has been studied using the metagenomic analysis of the 16S (V3–V4) region of rRNA. 37 bacterial phyla constituted the core microbiome, which was dominated by Proteobacteria followed by Actinobacteria, Actinobacteria, and Planctomycetes for all the treatments. AWD5 inoculation enhanced the relative abundance of Firmicutes and Acidobacteria as compared with other treatments. Genus Kaistobacter and Verrucomicrobia were found to be an abundant indigenous population in pyrene-spiked soils. Bacterial richness and diversity were analyzed using the Shannon–Wiener (H) index. A lower diversity index was observed in pyrene-spiked soils. Canonical correspondence analysis (CCA) showed a possible linkage with plant growth attributes and available nitrogen content that influences diversity and abundance of the bacterial community.

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.

Assessment of PAH degradation potential of native species from a coking plant through identifying of the beneficial bacterial community within the rhizosphere soil

Understanding the mechanisms underlying plant-rhizobacteria interactions in field-contaminated soils is crucial for designing effective rhizoremediation strategies. This study aimed to test the ability of four native herb species to remove polycyclic aromatic hydrocarbons (PAHs) and to analyze their associated bacterial community structures and functional genes within the rhizosphere from the abandoned site of a former Shenyang coking plant in China; the bulk soil was collected as control. All four species removed PAHs, of which the rhizosphere of Kochia scoparia had the highest PAH removal rate (almost 30.2%). Although the composition of the bacterial community within the rhizosphere varied among plant species, all plant species could promote the growth of Sphingomonas, Pedomicrobium, Rhodoplanes, Blastoccus, Mycobacterium, Devosia, and Pseudomonas, and their relative abundance positively correlated with the removal rates of PAHs, soil moisture, and total carbon/total nitrogen in the rhizosphere. Moreover, the activities of 1-aminocyclopropane-1 -carboxylic deaminase gene and Gram-negative ring-hydroxylating dioxygenase gene significantly (P < 0.05) increased compared with those in the control, and these activities had a strong positive correlation with the removal rates of PAHs [r = 0.759 (P < 0.01) and 0.87 (P < 0.01), respectively]. The findings of this study indicated that PAHs were the main factor driving the composition of beneficial bacteria in PAH rhizodegradation, and the PAH rhizoremediation of native plants grown in coking plant can be controlled though altering soil properties.

Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere

Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The K_a/K_s values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most K_a/K_s values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The K_a/K_s values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered K_a/K_s values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.

Soil microbial community succession and interactions during combined plant/white-rot fungus remediation of polycyclic aromatic hydrocarbons

Despite combined plant/white-rot fungus remediation being effective for remediating polycyclic aromatic hydrocarbon (PAH)-contaminated soil, the complex organismal interactions and their effects on soil PAH degradation remain unclear. Here, we used quantitative PCR, analysis of soil enzyme activities, and sequencing of representative genes to characterize the ecological dynamics of natural attenuation, mycoremediation (MR, using Crucibulum laeve), phytoremediation (PR, using Salix viminalis), and plant-microbial remediation (PMR, using both species) for PAHs in soil for 60 days. On day 60, PMR achieved the highest removal efficiency of all three representative PAHs (65.5%, 47.5%, and 62.4% for phenanthrene, pyrene, and benzo(a)pyrene, respectively) when compared with the other treatments. MR significantly increased the relative abundance of Rhizobium and Bacillus but antagonized the other putative indigenous PAH-degrading bacteria, which were enriched by PR. PR significantly reduced soil nutrients, such as NO₃^- and NH₄⁺, and available potassium (AK), thereby changing the microbial community composition as reflected by redundancy analysis, significantly reducing the soil bacterial biomass relative to that in other treatments. These disadvantages hampered phenanthrene and pyrene removal. MR provided additional nutrients, which counteracted the nutrient consumption associated with PR, thereby maintaining the microbial community diversity and bacterial biomass of PMR at a level achieved in the NA treatment. Combination remediation therefore overcame the disadvantages of using PR alone. These results indicated that inoculation with the combination of S. viminalis and C. laeve synergistically stimulated the growth of indigenous PAH-degrading microorganisms and maintained bacterial biomass, thus accelerating the dissipation of soil PAHs.

Soil Characteristics Constrain the Response of Microbial Communities and Associated Hydrocarbon Degradation Genes during Phytoremediation

Rhizodegradation is a promising cleanup technology where microorganisms degrade soil contaminants in the rhizosphere. A symbiotic relationship is expected to occur between plant roots and soil microorganisms in contaminated soils that enhances natural microbial degradation. However, little is known about how different initial microbiotas influence the rhizodegradation outcome. Recent studies have hinted that soil initial diversity has a determining effect on the outcome of contaminant degradation. To test this, we either planted (P) or not (NP) balsam poplars (Populus balsamifera) in two soils of contrasting diversity (agricultural and forest) that were contaminated or not with 50 mg kg^-1 of phenanthrene (PHE). The DNA from the rhizosphere of the P and the bulk soil of the NP pots was extracted and the bacterial genes encoding the 16S rRNA, the PAH ring-hydroxylating dioxygenase alpha subunits (PAH-RHDα) of Gram-positive and Gram-negative bacteria, and the fungal ITS region were sequenced to characterize the microbial communities. The abundances of the PAH-RHDα genes were quantified by real-time quantitative PCR. Plant presence had a significant effect on PHE degradation only in the forest soil, whereas both NP and P agricultural soils degraded the same amount of PHE. Fungal communities were mainly affected by plant presence, whereas bacterial communities were principally affected by the soil type, and upon contamination the dominant PAH-degrading community was similarly constrained by soil type. Our results highlight the crucial importance of soil microbial and physicochemical characteristics in the outcome of rhizoremediation.IMPORTANCE Polycyclic aromatic hydrocarbons (PAH) are a group of organic contaminants that pose a risk to ecosystems' health. Phytoremediation is a promising biotechnology with the potential to restore PAH-contaminated soils. However, some limitations prevent it from becoming the remediation technology of reference, despite being environmentally friendlier than mainstream physicochemical alternatives. Recent reports suggest that the original soil microbial diversity is the key to harnessing the potential of phytoremediation. Therefore, this study focused on determining the effect of two different soil types in the fate of phenanthrene (a polycyclic aromatic hydrocarbon) under balsam poplar remediation. Poplar increased the degradation of phenanthrene in forest, but not in agricultural soil. The fungi were affected by poplars, whereas total bacteria and specific PAH-degrading bacteria were constrained by soil type, leading to different degradation patterns between soils. These results highlight the importance of performing preliminary microbiological studies of contaminated soils to determine whether plant presence could improve remediation rates or not.

Both artificial root exudates and natural Koelreuteria paniculata exudates modify bacterial community structure and enhance phenanthrene biodegradation in contaminated soils

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants that represent a serious threat to the health of humans and ecosystems. The effects of plant root and artificial root exudates (ARE) on the biodegradation of phenanthrene (PHE) and their impact on soil bacterial community structure was the focus of this work using four treatments for 180 days. Treatments included; control treatment (CK), low concentration of ARE (AREL), high concentration of ARE (AREH), and planting Koelreuteria paniculata saplings (KOE). The diversity and composition of soil bacterial community were analyzed using high-throughput sequencing. The results showed that KOE treatments had the most significant effect on the biodegradation of PHE compared to controls. ARE treatments had the similar effects on the biodegradation of PHE in soil with high efficiency in AREH than AREL. Both KOE and ARE treatments reduced diversity of bacterial community but increased the abundance of PAHs degrading bacterial populations within representative phyla, including Proteobacteria and Firmicutes. During the study, the total bacterial OTUs showed the number of unique genus types initially increased, then lowered in the later stages of the incubation process. Specific bacterial populations enriched by the treatments and supported by the exudates seemed to determine the biodegradation of PHE and not the overall bacterial diversity.

Response of soil bacterial communities to polycyclic aromatic hydrocarbons during the phyto-microbial remediation of a contaminated soil

Rhizo-box experiments were conducted to analyze the phyto-microbial remediation potential of a grass (Lolium multiflorum L.) and a crop (Glycine max L.) combined with exogenous strain (Pseudomonas sp.) for polycyclic aromatic hydrocarbons (PAHs) contaminated soils. The dynamics of bacterial community composition, abundances of 16 S rDNA and ring hydroxylating dioxygenases (RHDα) genes, and removal of PAHs were evaluated and compared on four culture stages (days 0, 10, 20, and 30). The results showed that 8.65%-47.42% of Σ12 PAHs were removed after 30 days of cultivation. Quantitative polymerase chain reaction (qPCR) analysis indicated that treatments with soybean and ryegrass rhizosphere markedly increased the abundances of total bacteria and PAH-degraders, especially facilitated the growth of gram-negative degrading bacteria. Flavobacterium sp. and Pseudomonas sp. were the main and active strains in the control soil. However, the presence of plants and/or exogenous Pseudomonas sp. changed the soil bacterial community structure and modified the bacterial diversity of PAH-degraders. On the whole, this study showed that the high molecular weight PAHs removal efficiency of phyto-microbial remediation with ryegrass was better than those of remediation with soybean. Furthermore, the removals of PAHs strongly coincided with the abundance of PAH-degraders and bacterial community structure.

Transportation and degradation of decabrominated diphenyl ether in sequential anoxic and oxic crop rotation

This work evaluated the debromination and uptake of ¹⁴C-labeled BDE-209 in rice cultivars grown in anoxic soil for 120 days (d) followed by cultivation of vegetables (peanut, eggplant and pepper) in oxic soil (120 d). Degradation of BDE-209 to lower polybrominated diphenyl ethers (PBDEs) occurred in cultivated soils, and more metabolites were released in oxic soil than in anoxic soil. The crop rotation from anoxic to oxic greatly enhanced the dissipation of BDE-209 in the soil (P < 0.05), in which the dissipation in anoxic soil planted with Huanghuazhan (HHZ, indica) and Yudao 1 (YD1, indica) were 6.8% and 2.4%, respectively, while in oxic soil with peanut and pepper were increased to 25.8% and 21.7%, respectively. The crop rotation also enhanced the degradation of BDE-209 in the soil, the recovered BDE-209 in soil after 120 d anoxic incubation with YD1 was 81.1%, but it decreased to 47.8% and 45.8% after another 120 d oxic incubation. Bioconcentration factors were between 0.23 and 0.36 for rice, eggplant and pepper but reached to 0.5 in peanut, which contains more lipids in the edible portion than the other test crops. The estimated daily intake for vegetables was 0.01-0.07 μg BDE-209-equivalent kg^-1 bw day^-1, which is at least two orders of magnitude below the maximum acceptable oral dose (7 μg kg^-1 bw day^-1). Our work confirms that crop rotation from rice to vegetable enhanced the dissipation and debromination of BDE-209 in the soil, and indicate that sequential anoxic-oxic rotation practice is considered to be effective in remediation of environmental pollutants.

Advanced treatment of coal chemical reverse osmosis concentrate with three-stage MABR

The issue of reverse osmosis concentrate (ROC) has attracted significant attention due to its complex and toxic constituents under high salinity conditions. In this work, a three-stage membrane-aerated biofilm reactor (MABR) system was constructed to treat such wastewater without an external carbon source. The effects of operating conditions including aeration pressure, reflux ratio, temperature and hydraulic retention time on the removal performance of the integrated system were evaluated and optimized. Under the optimal operating parameters, the removal efficiencies of COD, NH4 +-N, NO3 --N, and TN reached 69.36%, 80.95%, 54.55%, and 54.36%, respectively. Three-dimensional fluorescence analysis indicated that humic acid was mostly removed from raw water. Moreover, microbial diversity analysis indicated that the microbial community structure of each reactor could be individually modulated to exert different functions and enhance the system performance. The integrated MABR system exhibits great feasibility and potential for the advanced treatment of coal chemical ROC.

The Degradation of Phenanthrene, Pyrene, and Fluoranthene and Its Conversion into Medium-Chain-Length Polyhydroxyalkanoate by Novel Polycyclic Aromatic Hydrocarbon-Degrading Bacteria

Screening of high-efficient polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is important due to environmental contamination by PAHs. In this study, sediment contaminated with phenanthrene (Phe), pyrene (Pyr), and fluoranthene (Fluo) was used as a source of bacteria. The ability of these isolated bacteria to convert PAHs into valuable products was determined. Based on a primary screening, 20 bacterial isolates were obtained; however, only three strains showed a good PAH-degrading ability, and were identified as Pseudomonas aeruginosa, Pseudomonas sp., and Ralstonia sp. PAH-degrading genes were detected in all isolates. Notably, all selected strains could degrade PAHs using the ortho or meta cleavage pathways due to the presence of catechol dioxygenase genes. The ability of isolated strains to convert PAHs into polyhydroxyalkanoate (PHA) was also evaluated in both single and mixed cultures. Single cultures of P. aeruginosa PAH-P02 showed 100% degradation of PAHs, with the highest biomass (1.27 ± 0.02 g l^-1) and PHA content (38.20 ± 1.92% dry cell weight). However, degradative ability and PHA production were decreased when mixtures of PAHs were used. This study showed that P. aeruginosa, Pseudomonas sp., and Ralstonia sp. were able to degrade PAHs and convert them into medium-chain-length (mcl)-PHA. A high content of 3-hydroxydecanoate (3HD, C10) was observed in this study. The formation of mcl-PHA with high 3HD content from Pyr and Fluo, and the assessment of mixed cultures converting PAHs to mcl-PHA, were novel contributions.

Characterization and genomic function analysis of phenanthrene-degrading bacterium Pseudomonas sp. Lphe-2

A stain of Pseudomonas sp. Lphe-2, which could degrade phenanthrene as the main carbon and energy source, was isolated from the aerobic sludge of a coking plant. Then its biodegradation characteristics, whole genome sequence and biodegradation pathway were examined. The Lphe-2 strain exhibited broad-spectrum degradation activities for various polycyclic aromatic hydrocarbons (PAHs), including naphthalene (NAP), phenanthrene (PHE), and pyrene (PYR). Under the optimal conditions, the degradation efficiency of phenanthrene (100 mg/L) is 92.76% on the 7th day, and 2-carboxybenzaldehyde and 1-hydroxy-2-naphthoic acid are the major metabolites found in phenanthrene metabolism. Genomic analysis of Pseudomonas sp. Lphe-2 showed that a total of 3879 genes from the Lphe-2 strain were annotated based on the COG classification, and the genomic information was annotated to 185 metabolic pathways. Based on the intermediate metabolites detected by Gas Chromatography-Mass Spectrometer (GC-MS) and all potential phenanthrene-degrading genes identified by BLAST search, a phenanthrene biodegradation pathway of Lphe-2 strain was proposed. These results suggested that Lphe-2 strain has a good prospect in the bioremediation of PAHs pollution.

Can biochar and oxalic acid alleviate the toxicity stress caused by polycyclic aromatic hydrocarbons in soil microbial communities?

It remains unclear whether biochar amendment can mediate changes in soil microbial communities caused by organic contaminants in the rhizosphere. In this study, phenanthrene-contaminated soil was amended with biochar and oxalic acid (OA) alone or in combination and incubated for 21 days. Phospholipid fatty acids (PLFAs) and high-throughput sequencing were used to evaluate shifts in bacterial and fungal community structure. Phenanthrene stress led to significant shifts in both soil bacterial and fungal community structure, in particularly, 82% of microbial phyla decreased in abundance. Biochar and/or OA improved the phenanthrene-polluted soil by positively mediating shifts in soil microbial communities stressed by phenanthrene. Specifically, biochar and/or OA led to the survival of certain microbial taxa that were inhibited by phenanthrene stress. In addition, many functional microbial individuals and genes participating in polycyclic aromatic hydrocarbon (PAH) degradation were positively stimulated by high phenanthrene stress and further stimulated by the simultaneous application of biochar and OA. Based on these findings, tandem biochar and rhizoremediation may be a feasible strategy for relieving PAH toxicity to soil microbial communities.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

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.

Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.

Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community

Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.

Distribution of bacterial polycyclic aromatic hydrocarbon (PAH) ring-hydroxylating dioxygenases genes in oilfield soils and mangrove sediments explored by gene-targeted metagenomics

PAH ring-hydroxylating dioxygenases (PAH-RHDα) gene, a useful biomarker for PAH-degrading bacteria, has been widely used to examine PAH-degrading bacterial community in different contaminated sites. However, the distribution of PAH-RHDα genes in oilfield soils and mangrove sediments and their relationship with environmental factors still remain largely unclear. In this study, gene-targeted metagenomics was first used to investigate the diversity of PAH-degrading bacterial communities in oilfield soils and mangrove sediments. The results showed that higher diversity of PAH-degrading bacteria in the studied samples was revealed by gene-targeted metagenomics than traditional clone library analysis. Pseudomonas, Burkholderia, Ralstonia, Polymorphum gilvum, Mycobacterium, Sciscionella marina, Rhodococcus, and potential new degraders were prevailed in the oilfield area. For mangrove sediments, novel PAH degraders and Mycobacterium were predominated. The spatial distribution of PAH-RHDα gene was dependent on geographical location and regulated by local environmental variables. PAH content played a key role in shaping PAH-degrading bacterial communities in the studied samples, which would enrich PAH-degrading bacterial population and decrease PAH-degrading bacterial diversity. This work brings a more comprehensive and some new insights into the distribution and biodegradation potential of PAH-degrading bacteria in soil and sediments ecosystems.

Enhanced polycyclic aromatic hydrocarbons degradation in rhizosphere soil planted with tall fescue: Bacterial community and functional gene expression mechanisms

To investigate the bacterial mechanisms of polycyclic aromatic hydrocarbons (PAHs) degradation in an aged-contaminated agricultural soil planted with tall fescue (Festuca arundinacea), a rhizo-box experiment was carried out for 60 d. Shifts in bacterial community structure in the soils during the experiment were performed using denaturing gradient gel electrophoresis. The abundance and activity of total bacteria and PAH-degraders were measured by quantification of 16S rDNA, PAH-ring hydroxylating dioxygenase (PAH-RHDα) genes and their transcripts, respectively. The residual PAH concentrations were monitored using high-performance liquid chromatography analysis. Results showed that the removal percentage of total PAHs in rhizosphere soil was 11% higher than that in unplanted soil. Soil bacteria were dominated by Alphaproteobacteria (48.4%) and Gammaproteobacteria (25.8%). Tall fescue positively affected the abundance and activity of total bacteria in the soil, and stimulated RHDα gram-negative (GN) gene expression while inhibiting RHDα gram-positive gene expression. PAH dissipation in rhizosphere soil could be ascribed to modifications in the bacterial community structure, increase in the abundance of PAH-degraders, and enhancement of the RHDα GN gene expression during the incubation.

Vanillic acid changed cucumber (Cucumis sativus L.) seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities

Soil microorganisms are key drivers of plant productivity in terrestrial ecosystems, yet controls on their diversities and abundances are not fully elucidated. Phenolic acids, released through plant root exudation and residues decomposition, are usually referred as autotoxins of several crops, including cucumber. In this study, effects of vanillic acid (VA) on cucumber rhizosphere microbial communities were investigated by treating cucumber seedlings with VA every two days for five times. Amplicon sequencing, PCR-denaturing gradient gel electrophoresis and quantitative PCR were used to analyzed the 16S rRNA genes of total bacterial, Pseudomonas and Bacillus spp. communities. Results showed that VA at 0.05 μmol g⁻¹ soil changed total bacterial community diversity and composition. In particular, VA inhibited the relative abundances of genera with plant-beneficial potentials, such as Bacillus and Lysobacter spp. Moreover, VA changed Pseudomonas and Bacillus spp. community compositions by altering the number and/or relative abundances of their OTUs; and decreased Bacillus spp. community abundance at 0.02 to 0.2 μmol g⁻¹ soil and Pseudomonas spp. community abundance at 0.2 μmol g⁻¹ soil. Overall, VA changed cucumber seedling rhizosphere total bacterial, Pseudomonas and Bacillus spp. communities, which maybe be associated with the adverse effects of VA on cucumber growth under soil conditions.

Autochthonous Bioaugmentation-Modified Bacterial Diversity of Phenanthrene Degraders in PAH-Contaminated Wastewater as Revealed by DNA-Stable Isotope Probing

To reveal the mechanisms of autochthonous bioaugmentation (ABA) in wastewater contaminated with polycyclic aromatic hydrocarbons (PAHs), DNA-stable-isotope-probing (SIP) was used in the present study with the addition of an autochthonous microorganism Acinetobacter tandoii LJ-5. We found LJ-5 inoculum produced a significant increase in phenanthrene (PHE) mineralization, but LJ-5 surprisingly did not participate in indigenous PHE degradation from the SIP results. The improvement of PHE biodegradation was not explained by the engagement of LJ-5 but attributed to the remarkably altered diversity of PHE degraders. Of the major PHE degraders present in ambient wastewater ( Rhodoplanes sp., Mycobacterium sp., Xanthomonadaceae sp. and Enterobacteriaceae sp.), only Mycobacterium sp. and Enterobacteriaceae sp. remained functional in the presence of strain LJ-5, but five new taxa Bacillus, Paenibacillus, Ammoniphilus, Sporosarcina, and Hyphomicrobium were favored. Rhodoplanes, Ammoniphilus, Sporosarcina, and Hyphomicrobium were directly linked to, for the first time, indigenous PHE biodegradation. Sequences of functional PAH-RHD_α genes from heavy fractions further proved the change in PHE degraders by identifying distinct PAH-ring hydroxylating dioxygenases between ambient degradation and ABA. Our findings indicate a new mechanism of ABA, provide new insights into the diversity of PHE-degrading communities, and suggest ABA as a promising in situ bioremediation strategy for PAH-contaminated wastewater.

Investigations of microbial degradation of polycyclic aromatic hydrocarbons based on 13C-labeled phenanthrene in a soil co-contaminated with trace elements using a plant assisted approach

Co-contaminations of soils with organic and inorganic pollutants are a frequent environmental problem. Due to their toxicity and recalcitrance, the heterogeneous pollutants may persist in soil. The hypothesis of this study was that degradation of polycyclic aromatic hydrocarbons (PAHs) is enhanced if heavy metals in soil are immobilized and their bioavailability reduced. For metal immobilization and enhanced biodegradation, distinct mineral and organic soil amendments (iron oxides, gravel sludge, biochar) were deployed in an incubation batch experiment. The second part of the experiment consisted of a greenhouse pot experiment applying fast-growing and pollution-tolerant woody plants (willow and black locust). Soil amendments initially immobilized NH₄NO₃-extractable zinc, cadmium, and lead; after 100 days of incubation, soil amendments showed reductions only for cadmium and a tendency to enhance arsenic mobility. In order to monitor the remediation success, a ¹³C-phenanthrene (PHE) label was applied. ¹³C-phospholipid fatty acid analysis (¹³C-PLFA) further enabled the identification of PHE-degrading soil microorganisms. Both experiments exhibited a similar PLFA profile. Gram-negative bacteria (esp. cy17:0, 16:1ω7 + 6, 18:1ω7c) were the most significant microbial group taking up ¹³C-PHE. Plants effectively increased the label uptake by gram-positive bacteria and increased the biomass of the fungal biomarker, although their contribution to the degradation process was minor. Plants tended to prolong PAH dissipation in soil; at the end of the experiment, however, all treatments showed equally low total PAH concentrations in soil. While black locust plants tended not to take up potentially toxic trace elements, willows accumulated them in their leaves. The results of this study show that the chosen treatments did not enhance the remediation of the experimental soil.

Biochar reduces the bioaccumulation of PAHs from soil to carrot (Daucus carota L.) in the rhizosphere: A mechanism study

The aim of this study was to reveal the mechanisms on how biochar reduces bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) in tuberous vegetables. Corn straw-derived biochar pyrolyzed at 300°C (CB300) or bamboo-derived biochar pyrolyzed at 700°C (BB700) was amended into PAH-contaminated soil planted with carrot (Daucus carota L.). After 150days, 2% CB300 or 2% BB700 amendments significantly reduced the bioaccumulation of PAHs in carrot root (p<0.05), especially for high-molecular-weight PAHs. In the non-rhizosphere, either CB300 or BB700 suppressed PAH dissipation and decreased the bioavailability via adsorption processes. Compared to the control, the total concentration of PAHs in the rhizosphere was higher in the 2% BB700 treatment but the bioavailable concentration was lower. This indicates that BB700 decreased the bioavailability of PAHs primarily via immobilization (adsorption processes). By contrast, the total and bioavailable PAH concentrations were both lower in the 2% CB300 treatment than those in the control. The abundance of bacteria such as Arthrobacter and Flavobacterium and the total number of genes playing important roles in microbial PAH degradation processes increased significantly (p<0.05), which were likely responsible for the rapid dissipation of PAHs in the 2% CB300 treatment in the rhizosphere. These results indicate that CB300 decreased the PAH bioavailability primarily via increasing degradation of PAHs by indigenous microorganisms. The two biochars both showed better effectiveness at reducing the bioavailability of high-molecular-weight PAHs than the low-molecular-weight PAHs in the rhizosphere. Therefore, the mechanisms on how biochar reduces the PAH uptake into carrot are dependent on the type of biochar (e.g., pyrolysis temperature and feedstock) and root presence.