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

Green manure plants enhance atrazine degradation in agriculture soil through modulating rhizosphere microbial communities

The widespread use of atrazine in agriculture threatens soil health and the safety of agricultural products. In this study, the removal and mechanism of green manure plants (GMPs) hairy vetch (Vicia villosa Roth, VV) and ryegrass (Lolium perenne L., LP) to atrazine were investigated. The results showed that VV and LP show a certain tolerance to 5-25 mg/kg atrazine contamination compared to VV and LP without atrazine (VV0 and LP0), with LP exhibiting higher tolerance. Moreover, compared to CK, VV and LP significantly promoted the removal of atrazine by 13.49%∼26.41% and 13.98%∼23.42%, respectively. VV was more effective at lower concentrations (5-10 mg/kg), while LP showed better results at 25 mg/kg. Soil enzyme activities (catalase and urease), as well as bacterial abundance and diversity, were significantly increased by VV and LP treatments. LP had a stronger effect. The function analysis revealed that VV enhances the Cell growth and death pathway in the rhizosphere soil, while LP primarily boosts the Replication and repair pathway to cope with atrazine stress. This difference likely results from the distinct root structures of the two plants, which create varying rhizosphere environments. Additionally, VV and LP upregulate the Atrazine degradation pathway by enriching atrazine-degrading bacteria, thereby promoting atrazine removal. VV growth was affected under 25 mg/kg atrazine treatment, which may lead to lower Atrazine degradation pathway abundance in the rhizosphere compared to LP. This study provides a theoretical basis for selecting plant species for the remediation of atrazine-contaminated soils.

Saprotrophic Wood Decay Ability and Plant Cell Wall Degrading Enzyme System of the White Rot Fungus Crucibulum laeve: Secretome, Metabolome and Genome Investigations

The basidiomycete Crucibulum laeve strain LE-BIN1700 (Agaricales, Nidulariaceae) is able to grow on agar media supplemented with individual components of lignocellulose such as lignin, cellulose, xylan, xyloglucan, arabinoxylan, starch and pectin, and also to effectively destroy and digest birch, alder and pine sawdust. C. laeve produces a unique repertoire of proteins for the saccharification of the plant biomass, including predominantly oxidative enzymes such as laccases (family AA1_1 CAZymes), GMC oxidoreductases (family AA3_2 CAZymes), FAD-oligosaccharide oxidase (family AA7 CAZymes) and lytic polysaccharide monooxygenases (family LPMO X325), as well as accompanying acetyl esterases and loosenine-like expansins. Metabolomic analysis revealed that, specifically, monosaccharides and carboxylic acids were the key low molecular metabolites in the C. laeve culture liquids in the experimental conditions. The proportion of monosaccharides and polyols in the total pool of identified compounds increased on the sawdust-containing media. Multiple copies of the family AA1_1, AA3_2, AA7 and LPMOs CAZyme genes, as well as eight genes encoding proteins of the YvrE superfamily (COG3386), which includes sugar lactone lactonases, were predicted in the C. laeve genome. According to metabolic pathway analysis, the litter saprotroph C. laeve can catabolize D-gluconic and D-galacturonic acids, and possibly other aldonic acids, which seems to confer certain ecological advantages.

Current trends in bioremediation and bio-integrated treatment of petroleum hydrocarbons

Petroleum hydrocarbons and their derivatives constitute the leading group of environmental pollutants worldwide. In the present global scenario, petroleum and natural gas production, exploration, petroleum refining, and other anthropogenic activities produce huge amounts of hazardous petroleum wastes that accumulate in the terrestrial and marine environment. Due to their carcinogenic, neurotoxic, and mutagenic characteristics, petroleum pollutants pose severe risks to human health and exert ecotoxicological effects on the ecosystems. To mitigate petroleum hydrocarbons (PHs) contamination, implementing "green technologies" for effective cleanup and restoration of an affected environment is considered as a pragmatic approach. This review provides a comprehensive outline of newly emerging bioremediation technologies, for instance; nanobioremediation, electrokinetic bioremediation, vermiremediation, multifunctional and sustainably implemented on-site applied biotechnologies such as; natural attenuation, biostimulation, bioaugmentation, bioventing, phytoremediation and multi-process hybrid technologies. Additionally, the scope of the effectiveness and limitations of individual technologies in treating the petroleum hydrocarbon polluted sites are also evaluated.

Enhancing soil petrochemical contaminant remediation through nutrient addition and exogenous bacterial introduction

Biostimulation (providing favorable environmental conditions for microbial growth) and bioaugmentation (introducing exogenous microorganisms) are effective approaches in the bioremediation of petroleum-contaminated soil. However, uncertainty remains in the effectiveness of these two approaches in practical application. In this study, we constructed mesocosms using petroleum hydrocarbon-contaminated soil. We compared the effects of adding nutrients, introducing exogenous bacterial degraders, and their combination on remediating petroleum contamination in the soil. Adding nutrients more effectively accelerated total petroleum hydrocarbon (TPH) degradation than other treatments in the initial 60 days' incubation. Despite both approaches stimulating bacterial richness, the community turnover caused by nutrient addition was gentler than bacterial degrader introduction. As TPH concentrations decreased, we observed a succession in microbial communities characterized by a decline in copiotrophic, fast-growing bacterial r-strategists with high rRNA operon (rrn) copy numbers. Ecological network analysis indicated that both nutrient addition and bacterial degrader introduction enhanced the complexity and stability of bacterial networks. Compared to the other treatment, the bacterial network with nutrient addition had more keystone species and a higher proportion of negative associations, factors that may enhance microbial community stability. Our study demonstrated that nutrient addition effectively regulates community succession and ecological interaction to accelerate the soil TPH degradation.

Biological machinery for the production of biosurfactant and their potential applications

The growing biotechnology industry has focused a lot of attention on biosurfactants because of several advantages over synthetic surfactants. These benefits include worldwide public health, environmental sustainability, and the increasing demand from sectors for environmentally friendly products. Replacement with biosurfactants can reduce upto 8% lifetime CO2 emissions avoiding about 1.5 million tons of greenhouse gas released into the atmosphere. Therefore, the demand for biosurfactants has risen sharply occupying about 10% (∼10 million tons/year) of the world production of surfactants. Biosurfactants' distinct amphipathic structure, which is made up of both hydrophilic and hydrophobic components, enables these molecules to perform essential functions in emulsification, foam formation, detergency, and oil dispersion-all of which are highly valued characteristic in a variety of sectors. Today, a variety of biosurfactants are manufactured on a commercial scale for use in the food, petroleum, and agricultural industries, as well as the pharmaceutical and cosmetic industries. We provide a thorough analysis of the body of knowledge on microbial biosurfactants that has been gained over time in this research. We also discuss the benefits and obstacles that need to be overcome for the effective development and use of biosurfactants, as well as their present and future industrial uses.

Basidiomycetes to the rescue: Mycoremediation of metal-organics co-contaminated soils

The increasing need for metals leads to contaminated post-mining landscapes. At the same time, the contamination with organic, recalcitrant contamination increases. This poses a problem of reuse of large areas, often co-contaminated with both, metals, and organic pollutants. For the remediation of areas contaminated with multiple contaminants and combining many stress factors, technical solutions including groundwater treatment, where necessary, have been devised. However, this is applied to highly contaminated, small sites. The reuse of larger, co-contaminated landscapes remains a major challenge. Mycoremediation with fungi offers a good option for such areas. Fungi cope particularly well with heterogeneous conditions due to their adaptability and their large hyphal network. This chapter summarizes the advantages of basidiomycetes with a focus on wood rot fungi in terms of their ability to tolerate metals, radionuclides, and organic contaminants such as polycyclic aromatic hydrocarbons. It also shows how these fungi can reduce toxicity of contaminants to other organisms including plants to allow for restored land-use. The processes based on diverse molecular mechanisms are introduced and their use for mycoremediation is discussed.

The Combination of Buchloe dactyloides Engelm and Biochar Promotes the Remediation of Soil Contaminated with Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) cause serious stress to biological health and the soil environment as persistent pollutants. Despite the wide use of biochar in promoting soil improvement, the mechanism of biochar removing soil PAHs through rhizosphere effect in the process of phytoremediation remain uncertain. In this study, the regulation of soil niche and microbial degradation strategies under plants and biochar were explored by analyzing the effects of plants and biochar on microbial community composition, soil metabolism and enzyme activity in the process of PAH degradation. The combination of plants and biochar significantly increased the removal of phenanthrene (6.10%), pyrene (11.50%), benzo[a]pyrene (106.02%) and PAHs (27.10%) when compared with natural attenuation, and significantly increased the removal of benzo[a]pyrene (34.51%) and PAHs (5.96%) when compared with phytoremediation. Compared with phytoremediation, the combination of plants and biochar significantly increased soil nutrient availability, enhanced soil enzyme activity (urease and catalase), improved soil microbial carbon metabolism and amino acid metabolism, thereby benefiting microbial resistance to PAH stress. In addition, the activity of soil enzymes (dehydrogenase, polyphenol oxidase and laccase) and the expression of genes involved in the degradation and microorganisms (streptomyces, curvularia, mortierella and acremonium) were up-regulated through the combined action of plants and biochar. In view of the aforementioned results, the combined application of plants and biochar can enhance the degradation of PAHs and alleviate the stress of PAH on soil microorganisms.

Influences of extracellular polymeric substances (EPS) recovered from waste sludge on the ability of Jiaozhou Bay to self-remediate of diesel-polluted seawater

The introduction of EPS recovered from waste sludge may have an impact on the process of microbial remediation of oil-contaminated seawater. This study investigated the effect of EPS on the self-remediation capacity of diesel-polluted seawater in Jiaozhou Bay. Hydrocarbon attenuation and microbial activity were monitored in seawater collected from five islands after diesel and N, P addition, with and without EPS, incubated under aerobic conditions. Compared to seawater without EPS, degradation of TPH (total petroleum hydrocarbon) doubled and improved degradation of non-volatile (C16-C24) hydrocarbons to some extent in EPS-added seawater. The introduction of EPS led to changes in microbiota richness and diversity, significantly stimulating the growth of Proteobacteria and Firmicutes phyla or Bacillus and Pseudomonas genera. RT-qPCR analysis indicated EPS caused higher increases in cytochrome P450 gene copies than alkB. Prediction of alkane decay genes from 16S rRNA sequencing data revealed that EPS addition obviously promoted genes related to ethanol dehydrogenation function in the microbial community. Additionally, EPS enhanced the enzymatic activities of alkane hydroxylase, ethanol dehydrogenase, phosphatase and lipase, but increased protease and catalase inconspicuously. The above outlook that environmental sustainability of EPS from waste sludge for diesel-contaminated seawater remediation may provide new perspectives for oil spill bioremediation.

New insights into thermal desorption remediation of pyrene-contaminated soil based on an optimized numerical model

Thermal desorption (TD) is known as an effective technique to remediate PAHs-contaminated sites. However, effectively removing PAHs using TD while saving time, and energy, and minimizing soil damage remains a challenge. In this study, we examined the combined effects of various factors on the removal efficiency of pyrene (PYR) by TD and developed an optimal numerical model based on conducting a series of soil experiments. The results showed that temperature (T) and time (t) promoted the desorption of PYR, while water (Sw) and organic matter (fom) were just the opposite. Besides, water and organic matter had a synergistic effect proportionally. It was found that adjusting the soil-water ratio (which can be controlled by organic matter) maximized the desorption rate of PYR. An ideal Sw/fom 1.56 and a minimized recommended temperature (173 °C) were proposed based on the model. Finally, the efficacy of the optimized scheme was validated in real-world site soil. These findings not only mechanistically revealed the desorption behavior of PYR under the influence of various factors, but also provided an optimized scheme for efficiently removing PAHs using TD, thereby accelerating the remediation process and reducing energy consumption. The modeling ideas and conclusions obtained may be applicable to other PAHs, guiding the effective remediation of PAHs-polluted sites.

The effect of exogenous plant growth regulators on elevated Cd phytoremediation by Solanum nigrum L. in contaminated soil

Maximizing amendment potential is an emphasis in the HM-contaminated field of phytoremediation by hyperaccumulators due to the low bioavailability of HMs in soils and small biomass yields of plants. This study investigated the influence of different types and concentrations of plant growth regulators on Cd phytoremediation by Solanum nigrum in contaminated soil. Our conclusions showed that the shoot Cd extractions (μg plant-1) and the root and shoot biomasses at all the treatments remarkedly increased compared with that of the CK (p < 0.05), while the Cd concentrations at root and aboveground parts by S. nigrum, the extractable Cd concentrations, and pH value of soils did not change significantly compared with the CK (p < 0.05). Furthermore, correlation analysis showed that the shoot Cd phytoaccumulation and the root and aboveground biomasses of S. nigrum were particularly dependent upon the application of CTK and GA3 concentration gradient (p < 0.05). Moreover, some related physicochemical indexes were determined for supervising the growth conditions of plants, and these results pointed out that after exogenous PGRs treatments, the chlorophyll content and antioxidative enzymes POD and SOD activities in vivo of plants clearly advanced, while the H2O2 and MDA contents and CAT apparently declined. These consequence demonstrated that the exogenous PGR addition prominently reinforced the Cd phytoextraction capacity of S. nigrum in contaminated soil by stimulating plant growth and increasing shoot yields.

Effect of electric fields strength on soil factors and microorganisms during electro-bioremediation of benzo[a]pyrene-contaminated soil

Electro-bioremediation is a promising technology for remediating soils contaminated with polycyclic aromatic hydrocarbons (PAHs). However, the resulting electrokinetic effects and electrochemical reactions may inevitably cause changes in soil factors and microorganism, thereby reducing the remediation efficiency. To avoid negative effect of electric field on soil and microbes and maximize microbial degradability, it is necessary to select a suitable electric field. In this study, artificial benzo [a]pyrene (BaP)-contaminated soil was selected as the object of remediation. Changes in soil factors and microorganisms were investigated under the voltage of 1.0, 2.0, and 2.5 V cm-1 using chemical analysis, real-time PCR, and high-throughput sequencing. The results revealed noticeable changes in soil factors (pH, moisture, electrical conductivity [EC], and BaP concentration) and microbes (PAHs ring-hydroxylating dioxygenase [PAHs-RHDα] gene and bacterial community) after the application of electric field. The degree of change was related to the electric field strength, with a suitable strength being more conducive to BaP removal. At 70 d, the highest mean extent of BaP removal and PAHs-RHDα gene copies were observed in EK2.0 + BIO, reaching 3.37 and 109.62 times those in BIO, respectively, indicating that the voltage of 2.0 V cm-1 was the most suitable for soil microbial growth and metabolism. Changes in soil factors caused by electric fields can affect microbial activity and community composition. Redundancy analysis revealed that soil pH and moisture had the most significant effects on microbial community composition (P < 0.05). The purpose of this study was to determine the appropriate electric field that could be used for electro-bioremediation of PAH-contaminated soil by evaluating the effects of electric fields on soil factors and microbial communities. This study also provides a reference for efficiency enhancement and successful application of electro-bioremediation of soil contaminated with PAHs.

Understanding the role of graphene oxide in affecting PAHs biodegradation by microorganisms: An integrated analysis using 16SrRNA, metatranscriptomic, and metabolomic approaches

Graphene oxide (GO)-promoted microbial degradation technology is considered an important strategy to eliminate polycyclic aromatic hydrocarbons (PAHs) in the environment; however, the mechanism by which GO affects microbial degradation of PAHs has not been fully studied. Thus, this study aimed to analyze the effect of GO-microbial interaction on PAHs degradation at the microbial community structure, community gene expression, and metabolic levels using multi-omics combined technology. We treated PAHs-contaminated soil samples with different concentrations of GO and analyzed the soil samples for microbial diversity after 14 and 28 days. After a short exposure, GO reduced the diversity of soil microbial community but increased potential degrading microbial abundance, promoting PAHs biodegradation. This promotion effect was further influenced by the GO concentration. In a short period of time, GO upregulated the expression of genes involved in microbial movement (flagellar assembly), bacterial chemotaxis, two-component system, and phosphotransferase system in the soil microbial community and increased the probability of microbial contact with PAHs. Biosynthesis of amino acids and carbon metabolism of microorganisms were accelerated, thereby increasing the degradation of PAHs. With the extension of time, the degradation of PAHs stagnated, which may be due to the weakened stimulation of GO on microorganisms. The results showed that screening specific degrading microorganisms, increasing the contact area between microorganisms and PAHs, and prolonging the stimulation of GO on microorganisms were important means to improve the biodegradation efficiency of PAHs in soil. This study elucidates how GO affects microbial PAHs degradation and provides important insights for the application of GO-assisted microbial degradation technology.

Field measures of strengthen plant-microbial remediation of PAHs-FQs compound pollution

In this study, five PAHs (benzo [b] fluoranthene (BbF), phenanthrene (Phe), fluoranthene (Flu), fluorene (Fl), benzo [A] pyrene (Bap)), and five FQs (ofloxacin (OFL), enrofloxacin (ENR), ciprofloxacin (CIP), norfloxacin (NOR), lomefloxacin (LOM)) were selected as ligands; peroxidase (1NML) was selected as receptor degrading protein. In the plant-microbial degradation, the factors with significant inhibitory effects are NOR, Bap, CIP, ENR, OFL, Flu, LOM, Phe, Fl, and BbF by the fractional factorial design experiment and molecular docking-assisted molecular dynamics methods. Using Taguchi experiment and molecular dynamics simulation methods, the main external field measures were designed and screened to effectively promote the degradation of PAHs-FQs under the combined pollution scenarios of Bap-CIP and BbF-NOR, respectively. The peroxidase mutation design plans with enhanced substrate affinity were then designed and screened using the DS software by predicting the virtual key amino acid of peroxidase. The novel biodegradable enzymes 2YCD-1, 2YCD-4, 2YCD-5, 2YCD-7, and 2YCD-9 had better structures and showed excellent degradability for PAHs and FQs. This study explored the degradation rules of the composite pollutants in the coexistence systems of multiple PAHs and FQs, providing the best external field measures for the control and treatment of the combined pollution effects of different PAHs and FQs. Overall, the current study has important practical significance for promoting the plant-microbial joint remediation of PAHs-FQs pollution and for reducing the combined pollution of PAHs and FQs in farmland systems.

Integrative effects of microbial inoculation and amendments on improved crop safety in industrial soils co-contaminated with organic and inorganic pollutants

Soils co-contaminated by organic and inorganic pollutants usually pose major ecological risks to soil ecosystems including plants. Thus, effective strategies are needed to alleviate the phytotoxicity caused by such co-contamination. In this study, microbial agents (a mixture of Bacillus subtilis, Sphingobacterium multivorum, and a commercial microbial product named OBT) and soil amendments (β-cyclodextrin, rice husk, biochar, calcium magnesium phosphate fertilizer, and organic fertilizer) were evaluated to determine their applicability in alleviating toxicity to crops (maize and soybean) posed by polycyclic aromatic hydrocarbon (PAHs) and potentially toxic metals co-contaminated soils. The results showed that peroxidase, catalase, and superoxide dismutase activity levels in maize or soybean grown in severely or mildly contaminated soils were significantly enhanced by the integrative effects of amendments and microbial agents, compared with those in single plant treatments. The removal rates of Zn, Pb, and Cd in severely contaminated soils were 49 %, 47 %, and 51 % and 46 %, 45 %, and 48 %, for soybean and maize, respectively. The total contents of Cd, Pb, Zn, and PAHs in soil decreased by day 90. Soil organic matter content, levels of nutrient elements, and enzyme activity (catalase, urease, and dehydrogenase) increased after the amendments and application of microbial agents. Moreover, the amendments and microbial agents also increased the diversity and distribution of bacterial species in the soil. These results suggest that the amendments and microbial agents were beneficial for pollutant purification, improving the soil environment and enhancing both plant resistance to pollutants and immune systems of plants.

Fungal bioproducts for petroleum hydrocarbons and toxic metals remediation: recent advances and emerging technologies

Petroleum hydrocarbons and toxic metals are sources of environmental contamination and are harmful to all ecosystems. Fungi have metabolic and morphological plasticity that turn them into potential prototypes for technological development in biological remediation of these contaminants due to their ability to interact with a specific contaminant and/or produced metabolites. Although fungal bioinoculants producing enzymes, biosurfactants, polymers, pigments and organic acids have potential to be protagonists in mycoremediation of hydrocarbons and toxic metals, they can still be only adjuvants together with bacteria, microalgae, plants or animals in such processes. However, the sudden accelerated development of emerging technologies related to the use of potential fungal bioproducts such as bioinoculants, enzymes and biosurfactants in the remediation of these contaminants, has boosted fungal bioprocesses to achieve higher performance and possible real application. In this review, we explore scientific and technological advances in bioprocesses related to the production and/or application of these potential fungal bioproducts when used in remediation of hydrocarbons and toxic metals from an integral perspective of biotechnological process development. In turn, it sheds light to overcome existing technological limitations or enable new experimental designs in the remediation of these and other emerging contaminants.

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.

Response of microbial community to the remediation of neonicotinoid insecticide imidacloprid contaminated wetland soil by Phanerochaete chrysosporium

Imidacloprid (IMI), a typic neonicotinoid insecticide, is widely used and persist in soils with long half-time causing serious threat to ecosystem and human health. It is urgent to develop suitable and effective methods to accelerate it degradation and alleviate its negative impacts in soil. In this study, the introduction of functional microbe white-rot fungus Phanerochaete chrysosporium to remediate IMI contaminated wetland soil was carried out. The remediation performance and the response of the soil microbial community were examined. The results showed that P. chrysosporium could improve the degradation of IMI in soil no matter the soil was sterilized or not. The bioaugmentation was especially observed in non-sterilized soil under the inoculation patterns of FE and SP with the maximum IMI degradation rate of 91% and 93% in 7 days, respectively. The invertase activity in soil was also enhanced with P. chrysosporium inoculation. Microbial community analysis revealed that P. chrysosporium inoculation could increase the diversity and richness of bacterial community, and stimulate some IMI degraders genera including Ochrobactrum, Leifsonia, Achromobacter, and Bacillus. Moreover, the xenobiotic degradation and metabolism pathway was generally enhanced with P. chrysosporium inoculation based on PICRUSt analysis. These obtained results demonstrated that the introduction of white-rot fungus is of great potentially enabling the remediation of neonicotinoids contaminated soil.

Comparison of the efficiency and microbial mechanisms of chemical- and bio-surfactants in remediation of petroleum hydrocarbon

Surfactant-enhanced remediation (SER) is one of the most effective methods for petroleum hydrocarbon-contaminated sites compared to single physical and chemical methods. However, biosurfactants are not as commonly used as chemical surfactants, and the actual remediation effects and related mechanisms remain undefined. Therefore, to comprehensively compare the remediation effects and biological mechanisms of biosurfactants and chemical surfactants, soil column leaching experiments including two biosurfactants (rhamnolipids and lipopeptide) and three commercially used chemical surfactants (Tween 80, Triton X-100, and Berol 226SA) were conducted. After seven days of leaching, rhamnolipids exhibited the highest petroleum hydrocarbon removal rate of 61.01%, which was superior to that of chemical surfactants (11.73-18.75%) in n-alkanes C10-C30. Meanwhile, rhamnolipids exhibited a great degradation advantage of n-alkanes C13-C28, which was 1.22-30.55 times that of chemical surfactants. Compared to chemical surfactants, biosurfactants significantly upregulated the soil's biological functions, including soil conductivity (80.90-155.56%), and soil enzyme activities of lipase (90.31-497.10%), dehydrogenase (325.00-655.56%), core enzyme activities of petroleum hydrocarbon degradation, and quorum sensing between species. Biosurfactants significantly changed the composition of Pseudomonas, Citrobacter, Acidobacteriota, and Enterobacter at the genus level. Meanwhile, chemical surfactants had less influence on the bacterial community and interactions between species. Moreover, the biosurfactants enhanced the microbial interactions and centrality of petroleum hydrocarbon degraders in the community based on the network. Overall, this work provides a systematic comparison and understanding of the chemical- and bio-surfactants used in bioremediation. In the future, we intend to apply biosurfactants to practical petroleum hydrocarbon-contaminated fields to observe realistic remediation effects and compare their functional mechanisms.

Occurrence of polycyclic aromatic compounds and potentially toxic elements contamination and corresponding interdomain microbial community assembly in soil of an abandoned gas station

Bacteria, archaea and fungi usually coexist in various soil habitats and play important roles in biogeochemical cycle and remediation of contamination. Despite their significance, their combined bioassembly pattern, ecological interactions and driving factors in contaminated soils still remain obscure. To fill the gap, a systemic investigation on the characteristics of microbial community including bacteria, archaea and fungi, assembly patterns and environmental driving factors was conducted in an abandoned gas station soils which were contaminated by polycyclic aromatic compounds and potentially toxic elements for decades. The results showed that the soils were contaminated excessively by benzo[a]pyrene (0.46-2.00 mg/kg) and Dibenz[a,h]anthracene (0.37-1.30 mg/kg). Multitudinous contaminant-degrading/resistant microorganisms and unigenes were detected, indicating potential of the soils to mitigate the pollution. Compared with fungi and archaea, the bacteria had higher community diversity and were more responsive to seasonal shifts. Functional genes (nidB, nahAb, nahAa, adhP, adh, adhC, etc.) involved in biodegradation were highly enriched in summer (1.96% vs 1.80%). The co-occurrence network analysis showed summer communities exhibit a more robust network structure and positive interactions than winter communities. The fungi Neocucurbitaria, Penicillium, Fusarium, Chrysosporium, Knufia, Filobasidium, Wallemia and Rhodotorula were identified as the keystone taxa, indicating that fungi also had important positions in the interdomain molecular ecological networks of both seasons. The network topological properties and |βNTI| (66.7%-93.3% greater than 2) results indicated the deterministic assembly processes of the microbial communities in the contaminated soil. Acenaphthylene, benzo[b]fluoranthene, indeno[1,2,3-cd]perylene, benzo[g,h,i]pyrene and 9-fluorenone were the key environmental factors driving the deterministic assembly processes of the interdomain microbial community in the contaminated soil. These findings extended our knowledge of interdomain microbial community assembly mechanisms and ecological patterns in natural attenuation and provide valuable guidance in associated bioremediation strategies.

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.

Nitrogen addition facilitates phytoremediation of PAH-Cd cocontaminated dumpsite soil by altering alfalfa growth and rhizosphere communities

Thousands of unlined landfills and open dumpsites seriously threatened the safety of soil and groundwater due to leachate leakage with a mass of pollutants, particularly heavy metals, organic contaminants and ammonia. Phytoremediation is widely used in the treatment of cocontaminated soils because it is cost-effective and environmentally friendly. However, the extent to which phytoremediation efficiency and plant physiological responses are affected by the high nitrogen (N) content in such cocontaminated soil is still uncertain. Here, pot experiments were conducted to investigate the effects of N addition on the applicability of legume alfalfa remediation for polycyclic aromatic hydrocarbon‑cadmium (PAHCd) co-/contaminated soil and the corresponding microbial regulation mechanism. The results showed that the PAH dissipation rates and Cd removal rates in the high-contamination groups increased with the external N supply, among which the pyrene dissipation rates in the cocontaminated soil was elevated most significantly, from 78.10% to 87.25%. However, the phytoremediation efficiency weakened in low cocontaminated soil, possibly because the excessive N content had inhibitory effects on the rhizobium Ensifer and restrained alfalfa growth. Furthermore, the relative abundance of PAH-degrading bacteria in the rhizosphere dominated PAH dissipation. As reflected by principal coordinate analysis (PCoA) analysis and hierarchical dendrograms, the microbial community composition changed with N addition, and a more pronounced shift was found in the rhizosphere relative to the endosphere or shoots of alfalfa. This study will provide a theoretical basis for legume plant remediation of dumpsites as well as soil contaminated with multiple pollutants.

Biological machinery for polycyclic aromatic hydrocarbons degradation: A review

Polycyclic aromatic hydrocarbons (PAHs) are hazardous environmental pollutants with widespread and well-recognized health concerns. Amidst more than a hundred known PAHs, 16 are categorized as priority pollutants. Use of widely diverse biological machinery comprising bacteria, fungi, and algae harnessed from contaminated sites has emerged as an ecologically safe and sustainable approach for PAH degradation. The potential of these biological systems has been thoroughly examined to maximize the degradation of specific PAHs by understanding their detailed biochemical pathways, enzymatic system, and gene organization. Recent advancements in microbial genetic engineering and metabolomics using modern analytical tools have facilitated the bioremediation of such xenobiotics. This review explores the role of microbes, their biochemical pathways, genetic regulation of metabolic pathways, and the effect of biosurfactants against the backdrop of PAH substrate structures.

Bibliometric analysis of global research on white rot fungi biotechnology for environmental application

In recent years, white rot fungi (WRFs) have received tremendous attention as a biotechnological tool for environmental pollution control. In order to systematically and comprehensively describe the progress, trends, and hotspots of WRF biotechnology in the field of environmental pollution control, the 3967 related publications from 2003 to 2020 were collected from Web of Science Core Collection database, and the bibliometric characteristics including publication output, country, institution, journal, author, citation frequency, h-index, and research focus were evaluated by using Excel 2007, CiteSpace V, and VOSviewer. The results indicated that the number of research publications increased rapidly before 2009, but after that, the number of publications fluctuated in a certain range. China and USA were the most productive countries and the most active country in international cooperation. In this field, most authors tend to cooperate within a small group. The journal and subject category with the largest number of publications are "International Biodeterioration & Biodegradation" and "Biotechnology Applied Microbiology", respectively. The analysis of high-frequency keywords revealed that "laccase", "biodegradation", "decolorization", and "Phanerochaete chrysosporium" were the most cited terms among all publications. The pretreatment of biomass waste, decolorization of dye wastewater, and bioremediation of polluted environment are the key research directions of WRF biotechnology. Finally, the frontier topics and active authors in this research field were identified using burst detection. We believe that this bibliometric study provides a comprehensive and systematic overview and promoted the future cooperative research and knowledge exchange in this field of WRF biotechnology for environmental applications.

Plant-microbial remediation of chlorpyrifos contaminated soil

With the development of modern agriculture, the pollution caused by the use of chemical fertilizers and pesticides has become a serious problem, posing a threat to human health and the living environment. The remediation of plant microorganisms has been seen as an economical, effective, and eco-friendly method of cleaning up soils contaminated with organophosphorus pesticides. In this study, white-rot fungi were immobilized by adsorption method, a plant-microbial remediation met was established. The data results show that after 30 days, the combined remediation system for corn microbes increased the rate of chlorpyrifos degradation by 18% compared to the single remediation of the plant, and the rate of combined remediation of ryegrass microbes increased by 23%. The effect of CPF content in soil on the combined remediation is mainly reflected in the significant difference in the number of microorganisms (P < 0.05). In this article, plant-microbial remediation were applied to soil contaminated by CPF, which provides a new idea for the remediation of pesticide-contaminated soil. Combined bioremediation may be a better alternative to mitigate the impact of high pollution on microorganisms at different pollutant concentrations compared to single microbial remediation or phytoremediation.

Insights into the vertical distribution of the microbiota in steel plant soils with potentially toxic elements and PAHs contamination after 60 years operation: Abundance, structure, co-occurrence network and functionality

Both potentially toxic elements (PTEs) and polycyclic aromatic hydrocarbons (PAHs) are widely present in soil contaminated by steel industries. This study assessed the vertical variation (at 20 cm, 40 cm, 60 cm, 80 cm, 120 cm, and 150 cm depth) of bacterial abundance, community structure, functional genes related to PAHs degradation, and community co-occurrence patterns in an old steel plant soils which contaminated by PTEs and PAHs for 60 years. The excessive PAHs and PTEs in steel plant soils were benzo (a) pyrene, benzo (b) fluoranthene, dibenzo (a, h) anthracene, indeno (1,2,3-c, d) pyrene, and lead (Pb). The abundance and composition of bacterial community considerably changed with soil depth in two study areas with different pollution degrees. The results of co-occurrence network analysis indicated that the top genera in blast furnace zone identified as the potential keystone taxa were Haliangium, Blastococcus, Nitrospira, and Sulfurifustis. And in coking zone, the top genera were Gaiella. The predictions of bacterial metabolism function using PICRUSt showed that the PAHs-PTEs contaminated soil still had the potential for PAHs degradation, but most PTEs negatively correlated with PAHs degradation genes. The total sulfur (TS), acenaphthene (ANA), and Zinc (Zn) were the key factors to drive development of bacterial communities in the steel plant soils. As far as we know, this is the first investigation of vertical distribution and interaction of the bacterial microbiota in the aging soils of steel plant contaminated with PTEs and PAHs.

A compartmentalized microsystem helps understanding the uptake of benzo[a]pyrene by fungi during soil bioremediation processes

Hydrophobic organic soil contaminants such as polycyclic aromatic hydrocarbons (PAH) are poorly mobile in the aqueous phase and tend to sorb to the soil matrix, resulting in low bioavailability. Some filamentous fungi are efficient in degrading this kind of pollutants. However, the mechanism of mobilization of hydrophobic compounds by non-motile microorganisms such as filamentous fungi needs investigations to improve pollutant bioavailability and bioremediation efficiency. Usual homogeneous media for microbial growth in the lab are poorly suited to model the soil, which is a compartmentalized and heterogeneous habitat. A microfluidic device was designed to implement a compartmentalization of the fungal inoculum and the source of the pollutant benzo[a]pyrene (BaP) as a deposit of solid crystals in order to gain a further insight into the mechanisms involved in the access to the contaminant and its uptake in soils. Thus in this device, two chambers are connected by an array of parallel microchannels that are wide enough to allow individual hyphae to grow through them. Macro-cultures of Talaromyces helicus in direct contact with BaP have shown its uptake and intracellular storage in lipid bodies despite the low propensity of BaP to cross aqueous phases as shown by simulation. Observations of T. helicus in the microfluidic device through laser scanning confocal microscopy indicate preferential uptake of BaP at a close range and through contact with the cell wall. However faint staining of some hyphae before contact with the deposit also suggests an extracellular transport phenomenon. Macro-culture filtrates analyses have shown that T. helicus releases extracellular non-lipidic surface-active compounds able to lower the surface tension of culture filtrates to 49.4 mN/m. Thus, these results highlight the significance of active mechanisms to reach hydrophobic contaminants before their uptake by filamentous fungi in compartmentalized micro-environments and the potential to improve them through biostimulation approaches for soil mycoremediation.

Indigenous bacterial community and function in phenanthrene-polluted coastal wetlands: Potential for phenanthrene degradation and relation with soil properties

The Yellow River Delta, adjacent to Shengli Oilfield, has a potential risk of petroleum pollution. In this study, soil samples were collected from phenanthrene (PHE)-polluted (adjacent to abandoned oil well, Zone D) and non-polluted (far away from abandoned oil well, Zone E) coastal wetlands. The influence of PHE pollution on indigenous bacterial community and function, and their relationship with soil characteristics were investigated. The levels of PHE, salinity and NH₄⁺-N were higher in Zone D than in Zone E. PHE-degrading bacteria Achromobacter and Acinetobacter were mainly distributed in Zone E, whereas Halomonas, Marinobacter, and Roseovarius were highly abundant in Zone D. Halomonas and Marinobacter had the potential for denitrification and could achieve PHE degradation through mutual cooperation. PHE pollution could increase the abundance of functional bacteria but reduce the diversity of microbial community. PHE and salinity played key roles in shaping microbial community structure and function. High PHE level inhibited microbial metabolism but stimulated self-protection potential. PHE aerobic degradation associated with the catechol and phthalic acid pathways was found in Zone D, whereas the catechol pathway dominated in Zone E. Interestingly, PHE anaerobic degradation with nitrate reduction also dominated in Zone D, whereas the process coupled with multiple electron acceptors co-existed in Zone E, which was associated with tidal seawater carrying nutrients. This study illustrated the importance of comprehensive consideration of microbial community structure and function under PHE pollution, suggesting indigenous microorganisms as potential microbial consortium for bioremediation in coastal wetlands.