Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances

Three-year field study on the temporal response of soil microbial communities and functions to PFOA exposure

Contamination of per- and polyfluoroalkyl substances (PFAS) poses a significant threat to soil ecosystem health, yet there remains a lack of understanding regarding the responses of soil microbial communities to prolonged PFAS exposure in field conditions. This study involved a three-year field investigation to track changes in microbial communities and functions in soil subjected to the contamination of a primary PFAS, perfluorooctanoic acid (PFOA). Results showed that PFOA exposure altered soil bacterial and fungal communities in terms of diversity, composition, and structure. Notably, certain bacterial communities with a delayed reaction to PFOA contamination showed the most significant response after one year of exposure. Fungal communities were sensitive to PFOA in soil, exhibiting significant responses within just four months of exposure. After two years, the impact of PFOA on both bacterial and fungal communities was lessened, likely due to the long-term adaptation of microbial communities to PFOA. Moreover, PFOA exposure notably inhibited alkaline phosphatase activity and reduced certain phosphorus cycling-related functional genes after three years of exposure, suggesting potential disruptions in soil fertility. These new insights advance our understanding of the long-term effects of PFOA on soil microbial communities and functions at a field scale.

The potential of ferrihydrite-synthetic humic-like acid composite as a soil amendment for metal-contaminated agricultural soil: Immobilization mechanisms by combining abiotic and biotic perspectives

In-situ passivation technique has attracted increasing attention for metal-contaminated agricultural soil remediation. However, metal immobilization mechanisms are mostly illustrated based on metal speciation changes and alterations in soil physicochemical properties from a macroscopic and abiotic perspective. In this study, a ferrihydrite-synthetic humic-like acid composite (FH-SHLA) was fabricated and applied as a passivator for a 90-day soil incubation. The heavy metals immobilization mechanisms of FH-SHLA were investigated by combining both abiotic and biotic perspectives. Effects of FH-SHLA application on soil micro-ecology were also evaluated. The results showed that the 5%FH-SHLA treatment significantly decreased the DTPA-extractable Pb, Cd and Zn by 80.75%, 46.82% and 63.63% after 90 days of incubation (P < 0.05), respectively. Besides, 5% FH-SHLA addition significantly increased soil pH, soil organic matter content and cation exchange capacity (P < 0.05). The SEM, FTIR, and XPS characterizations revealed that the abiotic metal immobilization mechanisms by FH-SHLA included surface complexation, precipitation, electrostatic attraction, and cation-π interactions. For biotic perspective, in-situ microorganisms synergistically participated in the immobilization process via sulfide precipitation and Fe mineral production. FH-SHLA significantly altered the diversity and composition of the soil microbial community, and enhanced the intensity and complexity of the microbial co-occurrence network. Both metal bioavailability and soil physiochemical parameters played a vital role in shaping microbial communities, while the former contributed more. Overall, this study provides new insight into the heavy metal passivation mechanism and demonstrates that FH-SHLA is a promising and environmentally friendly amendment for metal-contaminated soil remediation.

Life in the PFAS lane: The impact of perfluoroalkyl substances on photosynthesis, cellular exudates, nutrient cycling, and composition of a marine microbial community

Perfluoroalkyl substances (PFAS) are of great ecological concern, however, exploration of their impact on bacteria-phytoplankton consortia is limited. This study employed a bioassay approach to investigate the effect of unary exposures of increasing concentrations of PFAS (perfluorooctane sulfonate (PFOS) and 6:2 fluorotelomer sulfonate (6:2 FTS)) on microbial communities from the northwestern Gulf of Mexico. Each community was examined for changes in growth and photophysiology, exudate production and shifts in community structure (16S and 18S rRNA genes). 6:2 FTS did not alter the growth or health of phytoplankton communities, as there were no changes relative to the controls (no PFOS added). On the other hand, PFOS elicited significant phototoxicity (p < 0.05), altering PSII antennae size, lowering PSII connectivity, and decreasing photosynthetic efficiency over the incubation (four days). PFOS induced a cellular protective response, indicated by significant increases (p < 0.001) in the release of transparent exopolymer particles (TEP) compared to the control. Eukaryotic communities (18S rRNA gene) changed substantially (p < 0.05) and to a greater extent than prokaryotic communities (16S rRNA gene) in PFOS treatments. Community shifts were concentration-dependent for eukaryotes, with the low treatment (5 mg/L PFOS) dominated by Coscinodiscophyceae (40 %), and the high treatment (30 mg/L PFOS) marked by a Trebouxiophyceae (50 %) dominance. Prokaryotic community shifts were not concentration dependent, as both treatment levels became depleted in Cyanobacteriia and were dominated by members of the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. Further, PFOS significantly decreased (p < 0.05) the Shannon diversity and Pielou's evenness across treatments for eukaryotes, and in the low treatment (5 mg/L PFOS) for prokaryotes. These findings show that photophysiology was not impacted by 6:2 FTS but PFOS elicited toxicity that impacted photosynthesis, exudate release, and community composition. This research is crucial in understanding how PFOS impacts microbial communities.

High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas

Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.

Characterization of the composition, structure, and functional potential of bamboo rhizosphere archaeal communities along a chromium gradient

Introduction

Bamboo can be used in the phytoremediation of heavy metal pollution. However, the characteristics of the bamboo rhizosphere archaeal community in Cr-contaminated soil under field conditions remain unclear.

Methods

In this study, high-throughput sequencing was used to examine the rhizosphere soil archaeal communities of Lei bamboo (Phyllostachys precox) plantations along a Cr pollution gradient.

Results

The results revealed U-shaped relationships between Cr [total Cr (TCr) or HCl-extractable Cr (ACr)] and two alpha indices (Chao1 and Shannon) of archaea. We also established that high Cr concentrations were associated with a significant increase in the abundance of Thaumarchaeota and significant reductions in the abundances of Crenarchaeota and Euryarchaeota. The archaeal co-occurrence networks reduced in complexity with Cr pollution, decreasing the community's resistance to environmental disturbance. Candidatus nitrosotalea and Nitrososphaeraceae_unclassified (two genera of Thaumarchaeota) were identified as keystone taxa. The community structure of soil archaeal communities was also found to be affected by TCr, ACr, pH, total organic C, and available nutrient (N, P, and K) concentrations, with pH being identified as the most reliable predictor of the archaeal community in assessed soils.

Discussion

These findings enhance our understanding of microbial responses to Cr pollution and provide a basis for developing more refined approaches for the use of bamboo in the remediation of Cr-contaminated soils.

Comparison of microbial communities in unleached and leached ionic rare earth mines

The leaching of ionic rare earth elements has caused serious environmental pollution and ecological damage. Microorganisms play a crucial role in soil ecosystems and are one of the most important components of these systems. However, there are fewer studies related to the changes that occur in microbial community structure and diversity before and after leaching in ionic rare earth mines. In this study, Illumina high-throughput sequencing was used to examine the diversity and composition of soil microorganisms on the summit, hillside, and foot valley surfaces of unleached and leached mines after in situ leaching. The results showed that microbial diversity and abundance in the surface soil of the unleached mine were higher than those in the leached mine, and leaching had a significant impact on the microbial community of mining soil. pH was the main factor affecting the microbial community. Proteobacteria, Actinobacteriota, and Chloroflexi were phyla that showed high abundance in the soil. Network analysis showed that microbial interactions can improve microbial adaptation and stability in harsh environments. PICRUSt2 predictions indicate functional changes and linkages in soil microbial communities.

Aerobic biotransformation of 6:2 fluorotelomer sulfonate in soils from two aqueous film-forming foam (AFFF)-impacted sites

Although 6:2 fluorotelomer sulfonate (6:2 FTS) is a common ingredient in aqueous film-forming foam (AFFF) formulations, its environmental fate at AFFF-impacted sites remains poorly understood. This study investigated the biotransformation of 6:2 FTS in microcosms prepared with soils collected from two AFFF-impacted sites; the former Loring Air Force Base (AFB) and Robins AFB. The half-life of 6:2 FTS in Loring soil was 43.3 days; while >60 mol% of initially spiked 6:2 FTS remained in Robins soil microcosms after a 224-day incubation. Differences in initial sulfate concentrations and the depletion of sulfate over the incubation likely contributed to the different 6:2 FTS biotransformation rates between the two soils. At day 224, stable transformation products, i.e., C4C7 perfluoroalkyl carboxylates, were formed with combined molar yields of 13.8 mol% and 1.2 mol% in Loring and Robins soils, respectively. Based on all detected transformation products, the biotransformation pathways of 6:2 FTS in the two soils were proposed. Microbial community analysis suggests that Desulfobacterota microorganisms may promote 6:2 FTS biotransformation via more efficient desulfonation. In addition, species from the genus Sphingomonas, which exhibited higher tolerance to elevated concentrations of 6:2 FTS and its biotransformation products, are likely to have contributed to 6:2 FTS biotransformation. This study demonstrates the potential role of biotransformation processes on the fate of 6:2 FTS at AFFF-impacted sites and highlights the need to characterize site biogeochemical properties for improved assessment of 6:2 FTS biotransformation behavior.

Performance and mechanism of chromium reduction in denitrification biofilm system with different carbon sources

In the process of biological reduction of Cr(VI), the type of carbon sources affects the rate and effect of Cr(VI) reduction, but its specific performance and influencing mechanism have not yet been explored. In this study, four denitrification biofilm reactors were operated under four common carbon sources (C6H12O6, CH3COONa, CH3OH, CH3COONa:C6H12O6 1:1) to reveal the impact of carbon sources on Cr(VI) reduction. Through preliminary experimental concentration research, 75 mg/L Cr(VI) was selected as the dosing concentration. In long-term operation, the composite carbon sources of CH3COONa and C6H12O6 demonstrated excellent stability and achieved an impressive Cr(VI) removal efficiency of 99.5 %. The following sequence was C6H12O6, CH3COONa, and CH3OH. Among them, CH3OH was less competitive and the system was severely unbalanced with lowest Cr(VI) reduction efficiency. The toxicity reactions, changes in EPS and its functional groups, and electron transfer revealed the reduction and fixation mechanism of chromium on denitrification biofilm. The changes in microbial communities indicated that microbial communities in composite carbon sources can quickly adapt to the high toxic environment. The proportion of Trichococcus reached 43.6 %, which played an important role in denitrification and Cr(VI) reduction. Meanwhile, the prediction of microbial COG function reflected its excellent metabolic ability and defense mechanism.

Effect of heavy metal co-contaminants on the sorption of thirteen anionic per- and poly-fluoroalkyl substances (PFAS) in soils

Understanding the sorption behavior of per- and poly-fluoroalkyl substances (PFAS) in soils are essential for assessing their mobility and risk in the environment. Heavy metals often coexist with PFAS depending on the source and history of contamination. In this study, we investigated the effect of heavy metal co-contaminants (Pb2+, Cu2+ and Zn2+) on the sorption of 13 anionic PFAS with different perfluorocarbon chain length (C3-C9) in two soils with different properties. Results revealed that Pb2+, Cu2+ and Zn2+ had little effect on the sorption of most short-chain compounds, while the presence of these heavy metals enhanced the sorption of long-chain PFAS in two soils. The distribution coefficients (Kd) of several long-chain PFAS linearly increased with increasing concentrations of heavy metal, especially in the presence of Pb2+ (ΔKd/Δ [Pb2+] > 3 for PFOS and PFNA vs <1 for PFPeS and PFHxS). While several mechanisms may have contributed to the enhancement of sorption of PFAS, the heavy metals most likely contributed through enhanced hydrophobic interactions of PFAS by neutralizing the negative charge of adsorption surfaces in soils and thus making it more favorable for their partitioning onto the solid phase. Moreover, the increase in the concentrations of heavy metals led to a decrease in the pH of the system and promoted sorption of long-chain compounds, especially in soil with lower organic carbon content. Overall, this study provides evidence that the presence of co-existing heavy metal cations in soils can significantly enhance the sorption of long-chain PFAS onto soil, thereby potentially limiting their mobility in the environment.

Are PFBS, PFHxS, and 6:2FTSA more friendly to the soil environment compared to PFOS? A new insight based on ecotoxicity study in soil invertebrates (Eisenia fetida)

As alternatives to perfluorooctane sulfonate (PFOS) with shorter carbon chains or lower proportion of fluorine atoms, perfluorobutane sulfonate (PFBS), perfluorohexane sulfonate (PFHxS), and 6:2 fluorotelomer sulfonic acid (6:2FTSA) have been detected in various environmental media. However, it is unclear whether the toxicity of these alternatives is lower than that of PFOS. Therefore, this study investigated the toxicity and differences in PFBS, PFHxS, 6:2FTSA, and PFOS (0.2 mg/kg) after 56 d of exposure using the common invertebrate Eisenia fetida in soil as the test organism. The results showed that although PFOS, PFBS, PFHxS, and 6:2FTSA induced oxidative stress and apoptosis in earthworms and led to developmental and reproductive toxicity in terms of comprehensive toxicity, PFHxS > PFOS > PFBS >6:2FTSA. To reveal the mechanisms underlying the differences in toxicity between the alternatives and PFOS, we conducted molecular docking and transcriptomic analyses. The results indicated that, unlike PFOS, PFBS, and PFHxS, 6:2FTSA did not cause significant changes in antioxidant enzyme activity at the molecular level. Furthermore, PFOS exposure caused disorder in the nervous and metabolic systems of earthworms, and PFHxS disrupted energy balance and triggered inflammatory responses, which may be important reasons for the higher toxicity of these compounds. In contrast, exposure to 6:2FTSA did not result in adverse transcriptomic effects, suggesting that 6:2FTSA exerted the least molecular-scale toxicity in earthworms. The results of this study provide new insights into the environmental safety of using PFBS, PFHxS, and 6:2FTSA as alternatives to PFOS.

The effects of per- and polyfluoroalkyl substances on environmental and human microorganisms and their potential for bioremediation

Utilised in a variety of consumer products, per- and polyfluoroalkyl substances (PFAS) are major environmental contaminants that accumulate in living organisms due to their highly hydrophobic, lipophobic, heat-resistant, and non-biodegradable properties. This review summarizes their effects on microbial populations in soils, aquatic and biogeochemical systems, and the human microbiome. Specific microbes are insensitive to and even thrive with PFAS contamination, such as Escherichia coli and the Proteobacteria in soil and aquatic environments, while some bacterial species, such as Actinobacteria and Chloroflexi, are sensitive and drop in population. Some bacterial species, in turn, have shown success in PFAS bioremediation, such as Acidimicrobium sp. and Pseudomonas parafulva.

Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties

Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.

Impact of biological activated carbon filtration and backwashing on the behaviour of PFASs in drinking water treatment plants

PFASs are present in surface water, tap water and even commercial drinking water and pose a risk to human health. In this study, the treatment efficiency of 14 PFASs was studied in a large drinking water treatment plant (DWTP) using Taihu Lake as the source, and it was found that the ozone/biological activated carbon (O₃-BAC) process was the most effective process for the removal of PFASs in DWTPs. For the O₃-BAC process, there were differences in the removal of PFASs by BACs (1,4,7,13 years) of different ages. The sterilization experiments revealed that for GAC, its physical adsorption capacity reached saturation after one year, while for BAC with mature biofilms, biosorption was the main mechanism for the removal of PFASs. The abundance of Alphaproteobacteria and Gammaproteobacteria in biofilms was positively correlated with the age of the BAC. The microbial community with higher abundance is beneficial to the biodegradation of organic matter and thus provides more active sites for the adsorption of PFASs. PFASs can leak in the early stage of filtration after backwashing, so it is necessary to pay close attention to the influent and effluent concentrations of PFASs during biofilm maturation after backwashing.

Assessing aerobic biotransformation of 8:2 fluorotelomer alcohol in aqueous film-forming foam (AFFF)-impacted soils: Pathways and microbial community dynamics

Production of 8:2 fluorotelomer alcohol (8:2 FTOH) for industrial and consumer products, including aqueous film-forming foams (AFFFs) used for firefighting, has resulted in its widespread occurrence in the environment. However, the fate of 8:2 FTOH at AFFF-impacted sites remains largely unknown. Using AFFF-impacted soils from two United States Air Force Bases, microcosm experiments evaluated the aerobic biotransformation of 8:2 FTOH (extent and byproduct formation) and the dose-response on microbial communities due to 8:2 FTOH exposure. Despite different microbial communities, rapid transformation of 8:2 FTOH was observed during a 90-day incubation in the two soils, and 7:2 secondary fluorotelomer alcohol (7:2 sFTOH) and perfluorooctanoic acid (PFOA) were detected as major transformation products. Novel transformation products, including perfluoroalkane-like compounds (1H-perfluoroheptane, 1H-perfluorohexane, and perfluoroheptanal) were identified by liquid chromatography-high resolution mass spectrometry (LC-HRMS) and used to develop aerobic 8:2 FTOH biotransformation pathways. Microbial community analysis suggests that species from genus Sphingomonas are potential 8:2 FTOH degraders based on increased abundance in both soils after exposure, and the genus Afipia may be more tolerant to and/or involved in the transformation of 8:2 FTOH at elevated concentrations. These findings demonstrate the potential role of biological processes on PFAS fate at AFFF-impacted sites through fluorotelomer biotransformation.

Negatively charged nano-hydroxyapatite can be used as a phosphorus fertilizer to increase the efficacy of wollastonite for soil cadmium immobilization

Improper application of phosphorus (P) fertilizer during soil cadmium (Cd) immobilization reduces the efficiency of fertilizer and Cd remediation. In this study, we synthesized three types of nano-hydroxyapatite (NHAP) with different surface charges as slow-release P fertilizers during Cd immobilization. We also evaluated the effects of wollastonite application with or without NHAP addition, in comparison with triple superphosphate (TSP) or bulk hydroxyapatite, on Cd accumulation in Amaranthus tricolor L. The results showed that adding wollastonite significantly reduced P availability (23.5%) in the soil, but it did not inhibit plant P uptake. In wollastonite-amended soil, the application of negatively/positively charged NHAP significantly increased plant biomass by 643-865% and decreased Cd uptake by 74.8-75.1% compared to the unamended soil as well as showed greater efficiency than those with TSP. This was ascribed to the increased soil pH (from 3.94 to 6.52-6.63) and increased abundance of organic acids (including citric acid, malic acid, lactic acid, and acetic acid) secreted by plants. In addition, the P-preferring bacterial class Bacteroidia was specific to soils amended with both wollastonite and NHAP-. These results suggest that NHAP- may be an appropriate P fertilizer for soil Cd immobilization using wollastonite.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Critical review on phytoremediation of polyfluoroalkyl substances from environmental matrices: Need for global concern

Poly- and perfluoroalkyl substances (PFAS) are a class of emerging organic contaminants that are impervious to standard physicochemical treatments. The widespread use of PFAS poses serious environmental issues. PFAS pollution of soils and water has become a significant issue due to the harmful effects of these chemicals both on the environment and public health. Owing to their complex chemical structures and interaction with soil and water, PFAS are difficult to remove from the environment. Traditional soil remediation procedures have not been successful in reducing or removing them from the environment. Therefore, this review focuses on new phytoremediation techniques for PFAS contamination of soils and water. The bioaccumulation and dispersion of PFAS inside plant compartments has shown great potential for phytoremediation, which is a promising and unique technology that is realistic, cost-effective, and may be employed as a wide scale in situ remediation strategy.

Ecological risk assessment for perfluorohexanesulfonic acid (PFHxS) in soil using species sensitivity distribution (SSD) approach

Perfluorohexanesulfonic acid (PFHxS) is one of the persistent organic pollutants that has been recommended to be listed in Annex A of the Stockholm Convention. It has gained increasing attention in recent years due to its toxic effects. The guideline values of PFHxS are commonly associated with PFOS in various countries and regulatory agencies. In this study, multispecies bioassays were conducted to determine the ecological toxic effects of PFHxS, including plants, soil invertebrates, and soil microorganisms, which indicated the EC10/NOEC values ranged from 2.9 to 250 mg/kg. Where possible, logistic models were used to calculate the EC30 values for various endpoints. The species sensitivity distributions were employed to estimate the ecological investigation levels for PFHxS contamination in soils using toxicity results from literature and this study. The calculation using EC10/NOEC values from both literature and this study indicated a most conservative HC5 as 1.0 mg/kg (hazardous concentration for 5 % of the species being impacted). However, utilisation of EC30 values derived from this study resulted in a much higher HC5 for PFHxS in contaminated soils (13.0 mg/kg) which is at the higher end of the existing guideline values for PFOS for protecting ecological systems. The results obtained in this study can be useful in risk assessment processes to minimize any uncertainty using combined values with PFOS.

Biotransformation of 8:2 Fluorotelomer Alcohol in Soil from Aqueous Film-Forming Foams (AFFFs)-Impacted Sites under Nitrate-, Sulfate-, and Iron-Reducing Conditions

The environmental fate of per- and polyfluoroalkyl substances (PFAS) in aqueous film-forming foams (AFFFs) remains largely unknown, especially under the conditions representative of natural subsurface systems. In this study, the biotransformation of 8:2 fluorotelomer alcohol (8:2 FTOH), a component of new-generation AFFF formulations and a byproduct in fluorotelomer-based AFFFs, was investigated under nitrate-, iron-, and sulfate-reducing conditions in microcosms prepared with AFFF-impacted soils. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (HRMS) were employed to identify biotransformation products. The biotransformation was much slower under sulfate- and iron-reducing conditions with >60 mol % of initial 8:2 FTOH remaining after ∼400 days compared to a half-life ranging from 12.5 to 36.5 days under nitrate-reducing conditions. Transformation products 8:2 fluorotelomer saturated and unsaturated carboxylic acids (8:2 FTCA and 8:2 FTUA) were detected under all redox conditions, while 7:2 secondary fluorotelomer alcohol (7:2 sFTOH) and perfluorooctanoic acid (PFOA) were only observed as transformation products under nitrate-reducing conditions. In addition, 1H-perfluoroheptane (F(CF₂)₆CF₂H) and 3-F-7:3 acid (F(CF₂)₇CFHCH₂COOH) were identified for the first time during 8:2 FTOH biotransformation. Comprehensive biotransformation pathways for 8:2 FTOH are presented, which highlight the importance of accounting for redox condition and the related microbial community in the assessment of PFAS transformations in natural environments.

Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community

Archaea are important participants in biogeochemical cycles of metal(loid)-polluted ecosystems, whereas archaeal structure and function in response to metal(loid) contamination remain poorly understood. Here, the effects of multiple metal(loid) pollution on the structure and function of archaeal communities were investigated in three zones within an abandoned sewage reservoir. We found that the high-contamination zone (Zone I) had higher archaeal diversity but a lower habitat niche breadth, relative to the mid-contamination zone (Zone II) and low-contamination zone (Zone III). Particularly, metal-resistant species represented by potential methanogens were markedly enriched in Zone I (cumulative relative abundance: 32.24%) compared to Zone II (1.93%) and Zone III (0.10%), and closer inter-taxon connections and higher network complexity (based on node number, edge number, and degree) were also observed compared to other zones. Meanwhile, the higher abundances of potential metal-resistant and methanogenic functions in Zone I (0.24% and 9.24%, respectively) than in Zone II (0.08% and 7.52%) and Zone III (0.01% and 1.03%) suggested archaeal functional adaptation to complex metal(loid) contamination. More importantly, six bioavailable metal(loid)s (titanium, tin, nickel, chromium, cobalt, and zinc) were the main contributors to archaeal community variations, and metal(loid) pollution reinforced the role of deterministic processes, particularly homogeneous selection, in the archaeal community assembly. Overall, this study provides the first integrated insight into the survival strategies of archaeal communities under multiple metal(loid) contamination, which will be of significant guidance for future bioremediation and environmental governance of metal(loid)-contaminated environments.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Insight into functional microorganisms in wet–dry conversion to alleviate the toxicity of chromium fractions in red soil

Soil contamination with potentially toxic element such as chromium (Cr) poses a threat to the environment and human health. The environmental toxicity of Cr is related not only to the total Cr content but also to the distribution of Cr fractions. In this study, laboratory simulation experiments were conducted to explore the characteristics of Cr fractions and responses of the functional microbial community during dynamic leaching and static drying processes. The results showed that acid-soluble Cr and reducible Cr transformed into other relatively stable fractions under dry conditions, and ammonium nitrogen promoted the transformation. Nitrate-nitrogen was significantly positively correlated with Cr fractions in the wet stage (p < 0.05), while ammonium nitrogen showed the same relation in the dry process. Analysis of the microbial community showed that the bacterial and fungal genera Flavihumibacter, Altererythrobacter, Methylobacillus, Flavisolibacter, Lysobacter, and Cladosporium were related to the Cr fractions (acid-soluble Cr, reducible Cr, and oxidizable Cr) under wet conditions, while the microbial genera Ellin6067, MND1, and Ramlibacter were related to Cr fractions under dry conditions. Moreover, the proliferation of the functional microbial genera Methylobacillus, Ellin6067, and MND1 related to Cr fractions in the wet–dry conversion process alleviated the environmental toxicity of Cr. These findings provide useful information for the remediation of Cr-contaminated soils by monitoring the distribution fractions of Cr and the functional microbial community under wet–dry conditions.

Effects of co-occurrence of PFASs and chlorinated aliphatic hydrocarbons on microbial communities in groundwater: A field study

The effects of per- and polyfluoroalkyl substances (PFASs) and chlorinated aliphatic hydrocarbons (CAHs) co-contamination on the microbial community in the field have not been studied. In this study, we evaluated the presence of PFASs and CAHs in groundwater collected from a fluorochemical plant (FCP), and carried out Illumina MiSeq sequencing to understand the impact of mixed PFASs and CAHs on the indigenous microbial community. The sum concentrations of 20 PFASs in FCP groundwater ranged from 2.05 to 317.40 μg/L, and the highest PFOA concentration was observed in the deep aquifer (60 m below ground surface), co-contaminated by dense non-aqueous-phase liquid (DNAPL). The existence of PFASs and CAHs co-contamination in groundwater resulted in a considerable decrease in the diversity of microbial communities, while the abundance of metabolisms associated with contaminants biodegradation has increased significantly compared to the background wells. Furthermore, Acinetobacter, Pseudomonas and Arthrobacter were the dominant genera in PFASs and CAHs co-contaminated groundwater. The presence of high concentrations of PFASs and CAHs has been positively associated with the genus of Citreitalea. Finally, geochemical parameters, such as ORP, sulfate and nitrate were the key factors to shape up the structure of the microbial community and sources to rich the abundance of the potential functional bacteria.

Bio-capture of Cr(VI) in a denitrification system: Electron competition, long-term performance, and microbial community evolution

Chromium is widely applied in industries as an important metal resource, but the discharge of Cr(VI) containing wastewater leads to the loss of chromium resources. This study proposed a bio-capture process of chromium in a denitrification system. The bio-capture potentiality was explored by investigating the electron competition between Cr(VI) and nitrogen compounds reduction, the long-term bio-capture performance, and the microbial community evolution. In the competition utilization of electron donors, both NO₃^--N and NO₂^--N took precedence over Cr(VI), and NO₂^--N reduction was proved to be the rate-limiting step. Under the optimum conditions of 20 mg/L NO₃^--N and 6 h HRT, 99.95% of 30 mg/L Cr(VI) could be reduced, and 220980 μg Cr/g MLSS was captured by the biofilm, which was fixed in intercellular as Cr(III). Microbiological analysis confirmed that the bio-reduction of Cr(VI) and NO₃^--N was mediated by synergistic interactions of a series of dominant bacteria, including genera Acidovorax, Thermomonas, and Microbacterium, which contained both the denitrification genes (narG, narZ, nxrA, and nirK) and chromate reduction genes (chrA and chrR). This study proved the feasibility of chromium bio-capture in denitrification systems and provided a new perspective for the Cr(VI) pollution treatment.

Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community

The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.

In-situ active Bisphenol A-degrading microorganisms in mangrove sediments

Bisphenol A (BPA), as both an endocrine disrupting compound and an important industrial material, is broadly distributed in coastal regions and may cause adverse effects on mangrove ecosystems. Although many BPA degraders have been isolated from various environments, the in-situ active BPA-degrading microorganisms in mangrove ecosystem are still unknown. In this study, DNA-based stable isotope probing in combination with high-throughput sequencing was adopted to pinpoint the microbes actually involved in BPA metabolism in mangrove sediments. Five bacterial genera were speculated to be associated with BPA degradation based on linear discriminant analysis (LDA) effect size (LEfSe) analysis, including Truepera, Methylobacterium, Novosphingobium, Rhodococcus and Rhodobacter. The in-situ BPA degraders were different between mudflat and forest sediments. The Shannon index of microbes in heavy fractions was significantly lower than that in light fractions. Besides, phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) demonstrated that the functional genes relevant to cytochrome P450, benzoate degradation, bisphenol degradation and citrate cycle were up-regulated significantly in in-situ BPA-degrading microbes. These findings greatly expanded the knowledge of indigenous BPA metabolic microorganisms in mangrove ecosystems.

Occurrence of PFASs and its effect on soil bacteria at a fire-training area using PFOS-restricted aqueous film-forming foams

Fire-training areas (FTAs) are an important source of perfluoroalkyl and polyfluoroalkyl substances (PFASs) pollution. However, the effect of PFASs on soil bacterial communities remains limited. Here, we detected the PFASs in soils ranging from 3.4 to 531.7 μg kg⁻¹ dry weight in seven plots at an FTA where PFOS-restricted aqueous film-forming foams (AFFFs) have been used for 6 years. PFOS was still the dominant homologue despite the restriction by Stockholm Convention, but it was almost three orders of magnitude lower than that in previous studies. PFASs played an important role in shaping the bacterial community, and high levels of PFASs (>100 μg kg⁻¹ dw) reduced the biodiversity and connectivity of soil bacteria. The extreme condition-tolerant bacteria were identified as biomarkers at the FTA. Our study provides valuable insights into the effect of PFOS-restricted AFFFs on soil bacterial communities at the FTA.

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PFOS was still the dominant PFAS despite the restriction by Stockholm Convention

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PFASs played an important role in shaping bacterial community

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High level of PFASs reduced the biodiversity and connectivity of soil bacteria

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The extreme condition-tolerant bacteria were identified as biomarkers at the FTA

Anaerobic degradation of perfluorooctanoic acid (PFOA) in biosolids by Acidimicrobium sp. strain A6

Anaerobic incubations were performed with biosolids obtained from an industrial wastewater treatment plant (WWTP) that contained perfluorooctanoic acid (PFOA), and with per- and polyfluoroalkyl substances- (PFAS) free, laboratory-generated, biosolids that were spiked with PFOA. Biosolid slurries were incubated for 150 days as is, after augmenting with either Acidimicrobium sp. Strain A6 or ferrihydrite, or with both, Acidimicrobium sp. Strain A6 and ferrihydrite. Autoclaved controls were run in parallel. Only the biosolids augmented with both, Acidimicrobium sp. Strain A6 and ferrihydrite showed a decrease in the PFOA concentration, in excess of 50% (total, dissolved, and solid associated). Higher concentrations of PFOA in the biosolids spiked with PFOA and no previous PFAS exposure allowed to track the production of fluoride to verify PFOA defluorination. The buildup of fluoride over the incubation time was observed in these biosolid incubations spiked with PFOA. A significant increase in the concentration of perfluoroheptanoic acid (PFHpA) over the incubations of the filter cake samples from the industrial WWTP was observed, indicating the presence of a non-identified precursor in these biosolids. Results show that anaerobic incubation of PFAS contaminated biosolids, after augmentation with Fe(III) and Acidimicrobium sp. Strain A6 can result in PFAS defluorination.

Comparative characterization of microbial communities that inhabit PFAS-rich contaminated sites: A case-control study

The historic usage and discharge of per- and polyfluoroalkyl substances (PFAS) containing chemicals have produced many contaminated sites and PFAS contamination has become a global concern due to their persistence, widespread distribution, and potential adverse impacts for human and environmental health. However, there have been limited investigations on the specific behavior of bacterial communities in PFAS contaminated soils. In this study, a quantitative PCR assay and Illumina MiSeq sequencing were used to investigate the variations of bacterial communities in a regional Australian airport contaminated with PFAS. The dominate PFAS detected in soil samples was Perfluorooctanesulfonic acid (PFOS), which accounted for 82% of total PFAS and the maximum PFOS level was noted (20,947±1824 ng.PFOS/mg.Soil) at the top soil. Irrespective of the degree of PFAS contamination at different depths, the comparable percentile contribution of each PFAS was observed in soil samples. Significantly higher bacteria amplicon sequence variant (ASV) and diversity were noted in uncontaminated soil than PFAS contaminated soil. Bacterial genera Rhodanobacter and Chujaibacter were dominant in the PFAS contaminated soil. Three different bacterial genera of Alphaproteobacteria, Ambiguous taxa of Acidobacteriia, and genus Chujaibacter of Gammaproteobacteria showed a significant positive correlation and RB41, Gaiella showed a significant negative correlation with 11 different PFAS concentrations. Overall, the results presented in this study suggest that the counts and species diversity of soil microorganisms are adversely influenced by PFAS contamination.

The Co-Transport of PFAS and Cr(VI) in porous media

PFAS and Cr are present at some sites as co-contaminants. The objective of this research was to investigate the co-transport behavior of per- and polyfluoroalkyl substances (PFAS) and hexavalent chromium (Cr(VI)) in porous media. Miscible-displacement experiments were conducted using two soils and an aquifer sediment with different geochemical properties. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were employed as model PFAS. The retardation of PFOS was decreased in the presence of Cr(VI). Conversely, the transport and retardation of PFOA was not affected by the presence of Cr(VI). The reduction of PFOS retardation caused by Cr(VI) is likely due to sorption competition for both organic-carbon and inorganic (metal-oxides and clay minerals) domains. The relative contributions of the three soil constituents to PFOS sorption and the potential for competition between PFOS and Cr(VI) is a function of the geochemical composition of the porous media (i.e., organic carbon, metal-oxides and clay minerals). The PFAS had minimal impact on the retention and transport of Cr(VI). To our knowledge, the results presented herein represent the first reported data for PFOS and Cr(VI) co-transport in porous media. The results of this study indicate that the presence of Cr(VI) has the potential to increase the migration potential of PFOS in soil and groundwater, which should be considered when characterizing electroplating facilities, leather tanning facilities, and other co-contaminated sites.

Bioconversion of organic wastes into value-added products: A review

Rapid urbanization has increased the demand for food, feed, and chemicals that have in turn augmented the use of fossil-based resources and generation of organic waste. Owning to the characteristics like high abundance, renewability, and ease of accessibility, valorization of organic wastes serves as a potential solution for waste management issues. Several industrial wastes, due to their organic and nutrient-rich composition, have been utilized as a resource for the production of value-added products such as biofuels, biopesticides, biohydrogen, enzymes, and bioplastics via microbial fermentation processes. The process consists of pre-treatment of the waste biomass, production of value-added product in reactors and downstream processing for product's recovery. The integration of new comprehensive technologies for organic waste utilization will also stimulate the transition towards a circular economy. Therefore, the feasibility and sustainability of the production of various value-added products from biowastes and byproduct streams will be discussed in the present review.

Controlling pathogenic risks of water treatment biotechnologies at the source by genetic editing means

Antimicrobial-resistant pathogens in the environment and wastewater treatment systems, many of which are also important pollutant degraders and are difficult to control by traditional disinfection approaches, have become an unprecedented treat to ecological security and human health. Here, we propose the adoption of genetic editing techniques as a highly targeted, efficient and simple tool to control the risks of environmental pathogens at the source. An 'all-in-one' plasmid system was constructed in Aeromonas hydrophila to accurately identify and selectively inactivate multiple key virulence factor genes and antibiotic resistance genes via base editing, enabling significantly suppressed bacterial virulence and resistance without impairing their normal phenotype and pollutant-degradation functions. Its safe application for bioaugmented treatment of synthetic textile wastewater was also demonstrated. This genetic-editing technique may offer a promising solution to control the health risks of environmental microorganisms via targeted gene inactivation, thereby facilitating safer application of water treatment biotechnologies.

A review of responses of terrestrial organisms to perfluorinated compounds

Perfluorinated compounds (PFCs) are a class of persistent organic pollutants with widespread distribution in the environment. Since the soil environment has become a significant sink for PFCs, the toxicological assessment about their potential effects on terrestrial organisms is necessary. This review compiles the toxicity researches of regular and emerging PFCs on classical terrestrial biota i.e. microorganisms, earthworms, and plants. In the soil environment, the bioavailability of PFCs much depends on their adsorption in soil, which is affected by soil properties and PFCs structure. By the exploration of bacterial community richness and structure, the gene expression, the influences of PFCs on soil microorganisms were revealed; while the plants and earthworms manifested the PFCs disruption not only through macroscopic indicators, but also from molecular and metabolite responses. Basically, the addition of PFCs would accelerate the production of reactive oxygen species (ROS) in terrestrial organisms, while the excessive ROS could not be eliminated by the defense system causing oxidative damage. Nowadays, the PFCs toxic mechanisms discussed are limited to a single strain, Escherichia coli; thus, the complexity of the soil environment demands further in-depth researches. This review warrants studies focus on more potential quantitative toxicity indicators, more explicit elaboration on toxicity influencing factors, and environmentally relevant concentrations to obtain a more integrated picture of PFCs toxicity on terrestrial biota.

Metagenomic analysis of microbial communities continuously exposed to Bisphenol A in mangrove rhizosphere and non-rhizosphere soils

Bisphenol A (BPA) is widely distributed in littoral zones and may cause adverse impacts on mangrove ecosystem. Biodegradation and phytoremediation are two primary processes for BPA dissipation in mangrove soils. However, the rhizosphere effects of different mangrove species on BPA elimination are still unresolved. In this study, three typical mangrove seedlings, namely Avicennia marina, Bruguiera gymnorrhiza (L.) and Aegiceras corniculatum, were cultivated in soil microcosms for four months and then subjected to 28-day continuous BPA amendment. Un-planted soil microcosms (as control) were also set up. The BPA residual rates and root exudates were monitored, and the metabolic pathways as well as functional microbial communities were also investigated to decipher the rhizosphere effects based on metagenomic analysis. The BPA residual rates in all planted soils were significantly lower than that in un-planted soil on day 7. Both plantation and BPA dosage had significant effects on bacterial abundance. A distinct separation of microbial structure was found between planted and un-planted soil microcosms. Genera Pseudomonas and Lutibacter got enriched with BPA addition and may play important roles in BPA biodegradation. The shifts in bacterial community structure upon BPA addition were different among the microcosms with different mangrove species. Genus Novosphingobium increased in Avicennia marina and Bruguiera gymnorrhiza (L.) rhizosphere soils but decreased in Aegiceras corniculatum rhizosphere soil. Based on KEGG annotation and binning analysis, the proposal of BPA degradation pathways and the quantification of relevant functional genes were achieved. The roles of Pseudomonas and Novosphingobium may differ in lower BPA degradation pathways. The quantity variation patterns of functional genes during the 28-day BPA amendment were different among soil microcosms and bacterial genera.

Understanding variations in soil properties and microbial communities in bamboo plantation soils along a chromium pollution gradient

With high biomass productivity and resistance to heavy metals (HM) stress, bamboo has strong potential for HM phytoremediation. However, few studies have been conducted under field conditions to explore changes in soil physicochemical and microbial properties of bamboo forests with HM-contaminated soils. This study established bamboo (Phyllostachys praecox) plantations in five Cr-contaminated sites with different pollution levels (low, L; low-moderate, LM; moderate, M; moderate-high, MH; and high, H). We determined soil chemical properties, total and available Cr content, as well as bacterial and fungal community structures from 0 to 20 cm depth along the pollution gradient, and evaluated their interactions. The results revealed a corresponding decrease in soil pH, alkali-hydrolysable N (AN), along with urease and sucrase activities, as Cr pollution increased. In contrast, total organic carbon (TOC) increased with increasing Cr pollution. Soil available P (AP) and acid phosphatase activity did not differ significantly. Different pollution level resulted in distinct bacterial and fungal communities, with Proteobacteria, Acidobacteria, Actinobacteria, Ascomycota, and Basidiomycota being the dominant phyla across the five bamboo soils. Both total Cr (TCr) and HCl-extractable Cr (ACr) negatively correlated with alpha indices (Chao1 and Shannon) for bacteria but not for fungi, indicating that the latter is more resistant to Cr pollution. Decrease in soil pH and increase in TCr and ACr from L to H were closely related to the shift of bacterial and fungal communities. These changes reduced soil N and C cycles. Our findings suggest that improving soil acidic conditions and N availability enhances carbon and nitrogen cycles via altering soil microbial structure and activities. This, in turn, can increase phytoremediation efficiency in the bamboo ecosystem.

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.

High-throughput sequencing clarifies the spatial structures of microbial communities in cadmium-polluted rice soils

Soil microbial communities are affected by environmental factors. Contamination with heavy metals such as cadmium (Cd) can decrease soil microbial species richness and substantially alter soil microbial species composition. Investigations of the microbial communities in Cd-contaminated soils are necessary to obtain data for soil bioremediation efforts. However, depth-associated variations in microbial community composition and structure in Cd-contaminated paddy soils are not well understood. Here, the effects of various degrees of long-term Cd pollution on soil microorganisms were investigated at different soil depths within the plough layer using 16S rRNA gene amplicon sequencing. We found that, in Cd-polluted soils, microbial communities were more similar between the surface soil and the underlying soil. In addition, microbial community richness and/or diversity were significantly reduced in the Cd-polluted underlying soil as compared with the non-polluted underlying soil. However, species richness in the surface layer was significantly greater in the mildly and severely Cd-polluted soils. The soil microbial communities in the same soil layer differed significantly between the non-polluted and polluted soils. Furthermore, Cd contamination affected the microbial communities of different soil layers differently. Soil pH had a synergistic effect on microbial community abundance and composition. The potential functions of the soil microbiota were mainly related to environmental processing, genetic processing, and metabolic pathways. Notably, our identification of the phyla that were differently abundant among sites with different levels of Cd pollution will provide experimental guidance for further explorations of the effects of Cd on soil microbes in natural environments. Our results not only demonstrate that long-term Cd pollution leads to a marked reduction in microbial richness and diversity in the underlying soil layer, but they also help to clarify how long-term heavy metal contamination affects the soil bacterial community.

Improved immobilization of soil cadmium by regulating soil characteristics and microbial community through reductive soil disinfestation

Cadmium (Cd) contamination arising from industrialization has attracted increasing attention in recent years. Reductive soil disinfestation (RSD) as an effective agricultural practice has been widely applied for soil sterilization. However, there is little research regarding RSD affecting Cd immobilization. Here, five treatments, namely untreated soil (CK), flooding-treated soil (FL), RSD with 2% ethyl alcohol (EA), 2% sugarcane bagasse (SB), and 2% bean dregs (BD) were designed to detect their performance for Cd immobilization in contaminated soils, and the change of soil properties and microbial communities were monitored. The results revealed that pH significantly increased in FL and RSD-treated soils, but was negatively correlated with the exchangeable fraction of Cd (EX-Cd), while Oxidation-Reduction Potential (Eh) significantly decreased in FL and RSD-treated soils, and was positively correlated with EX-Cd. BD treatment might contribute to the increase of CaCO₃ as shown by X-Ray Diffractomer analysis and strongly decreased the EX-Cd in the soil, but increased the relative abundances of Firmicutes, Planctomycetes, Acidobacteria, and Gemmatimonadetes, which may promote Fe (III) reduction or induce resistance to Cd. Bacterial communities at the phylum and genus levels were closely related to Cd fraction. The FL and RSD treatments moderately altered bacterial specific functions, including iron respiration, which may contribute to remediation of Cd-polluted soil by Fe (III) reduction. Field experiments were conducted to confirm that BD treatment resulted in a significant increase in pH whereas the content of total available Cd was reduced in soils. Compared to the control, concentration of total available Cd of red amaranth, sweet potato, towel gourd, and cowpeas were reduced by approximately 46%, 74%, 72%, and 76% in a BD-treated field, respectively. Our study highlights the potential of RSD as an effective method for Cd immobilization in contaminated soils by improving soil characteristics and altering the composition of the microbial community.

Bisphenol A biodegradation differs between mudflat and mangrove forest sediments

Bisphenol A (BPA) is one of the widely detected endocrine disrupting chemicals in coastal sediment. Biodegradation is a vital pathway of BPA elimination in sediment. However, the impact of vegetation on BPA degradation in coastal sediment is still unclear. In this study, the differences of BPA biodegradation and the functional microbial community and metabolic pathway were explored between mangrove forest and mudflat sediments. A nearly complete BPA attenuation was detected in 4 days in mudflat sediment but 8 days in forest sediment. Bacterial abundance varied greatly in different sediment types. Bacterial community structure changed with BPA biodegradation, dependent on sediment type. During the degradation, the proportions of Alphaproteobacteria and Gammaproteobacteria were higher in BPA amended microcosms than in un-amended microcosms. With BPA biodegradation, a substantial increase in Novosphingobium and Croceicoccus occurred in forest sediment and mudflat sediment, respectively. Additionally, two divergent BPA biodegradation pathways were proposed based on functional annotation and KEGG pathway database. The abundance of functional genes also varied with BPA biodegradation, dependent on sediment type. Gene pcaGH decreased, while genes ligK and pcaD increased in both sediment types. Gene pcaB showed a remarkable increase in forest sediment but a decrease in mudflat sediment. Therefore, BPA degradation and the associated microbial community and metabolic pathway differed between mudflat and mangrove forest sediments.

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

An Overview of Per- and Polyfluoroalkyl Substances (PFAS) in the Environment: Source, Fate, Risk and Regulations

The current article reviews the state of art of the perfluoroalkyl and polyfluoroalkyl substances (PFASs) compounds and provides an overview of PFASs occurrence in the environment, wildlife, and humans. This study reviews the issues concerning PFASs exposure and potential risks generated with a focus on PFAS occurrence and transformation in various media, discusses their physicochemical characterization and treatment technologies, before discussing the potential human exposure routes. The various toxicological impacts to human health are also discussed. The article pays particular attention to the complexity and challenging issue of regulating PFAS compounds due to the arising uncertainty and lack of epidemiological evidence encountered. The variation in PFAS regulatory values across the globe can be easily addressed due to the influence of multiple scientific, technical, and social factors. The varied toxicology and the insufficient definition of PFAS exposure rate are among the main factors contributing to this discrepancy. The lack of proven standard approaches for examining PFAS in surface water, groundwater, wastewater, or solids adds more technical complexity. Although it is agreed that PFASs pose potential health risks in various media, the link between the extent of PFAS exposure and the significance of PFAS risk remain among the evolving research areas. There is a growing need to address the correlation between the frequency and the likelihood of human exposure to PFAS and the possible health risks encountered. Although USEPA (United States Environmental Protection Agency) recommends the 70 ng/L lifetime health advisory in drinking water for both perfluorooctane sulfonate (PFO) perfluorooctanoic acid (PFOA), which is similar to the Australian regulations, the German Ministry of Health proposed a health-based guidance of maximum of 300 ng/L for the combination of PFOA and PFOS. Moreover, there are significant discrepancies among the US states where the water guideline levels for the different states ranged from 13 to 1000 ng L−1 for PFOA and/or PFOS. The current review highlighted the significance of the future research required to fill in the knowledge gap in PFAS toxicology and to better understand this through real field data and long-term monitoring programs.

A comprehensive survey on the horizontal and vertical distribution of heavy metals and microorganisms in soils of a Pb/Zn smelter

Smelter emissions have brought serious heavy metal contamination. Comprehensive surveys of spatial heavy metal and microorganism distribution in soils of smelters aera are still limited. In this study, the horizontal and vertical profiles of heavy metals as well as microorganisms of 80 samples from 5 soil layers of 16 sites in a Pb/Zn smelter were studied. Pollution index indicated the pollution level as Cd > Zn > Pb > As > Cu > Mn > Co > Cr > V, and the severe pollutants were Cd, Zn, Pb, As and Cu. The hazard quotient and hazard index indicated that the topsoil might pose high chronic risk to children mainly due to high content of Pb, As and Cd. The whole smelter was heavily polluted even to the depth of 100 cm as revealed by Nemerow pollution indices. Depth-related microbiota analysis indicated high richness of indigenous microorganisms and significant differences in vertical microbial structure. Proteobacteria was the dominant phylum in all depth layers, followed by Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria as major phyla. pH and heavy metals Zn, Cu, As, Mn and Cd significantly influenced the microbiota composition. Metagenomic functional prediction suggested antioxidant response, metal exportation and biotransformation play roles in bio-resistance to and bioremoval of heavy metals.

Effect of perfluorooctanesulfonate (PFOS) on the rhizosphere soil nitrogen cycling of two riparian plants

Here, we examined the effects of low and high concentrations of perfluorooctanesulfonate (PFOS) on rhizosphere soil N cycling processes in the presence of Lythrum salicaria and Phragmites communis over 4 months. Compared with the control group, the nitrate nitrogen (NO₃^--N) content of the bulk soil in the low PFOS (0.1 mg kg^-1) treatment significantly decreased (27.7%), the ammonium nitrogen (NH₄⁺-N) content significantly increased (8.7%), and the pH value and total organic carbon (TOC) content slightly increased (0.3% and 1.1%, respectively). Compared with the low PFOS treatment, the content of NO₃^-N, NH₄⁺-N and pH value in the bulk soil of the high PFOS treatment (50 mg kg^-1) significantly increased (1.0%, 53.8% and 61.8%, respectively), and the TOC content significantly decreased (8.2%). Soil protease levels were high in the low PFOS treatment, but low in the high PFOS treatment. PFOS produced inverted U-shaped responses in the potential nitrification (1.5, 3.0, and 1.1 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), denitrification (0.19, 0.30, and 0.22 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively), and N₂O emission rates (0.01, 0.03, and 0.02 mg N d^-1 kg^-1 in no, low, and high PFOS, respectively) of bulk soil. The abundance of the archaea amoA gene decreased with increasing PFOS concentration, whereas that of bacterial amoA increased; inverted U-shaped responses were observed for narG, nirK, nirS, and nosZ. In the PFOS-contaminated rhizosphere soil, the observed changes differed from those in the bulk soil and differed between treatments. P. communis tended to upregulate each step of the nitrogen cycle under low PFOS conditions, whereas L. salicaria tended to inhibit them. Under high PFOS conditions, both test plants tended to act as inhibitors of the soil N-cycle; thus, the effects of PFOS on soil N transformation were plant-specific.

Influences of hexafluoropropylene oxide (HFPO) homologues on soil microbial communities

Hexafluoropropylene oxide (HFPO) homologues, as emerging perfluoroalkyl substances (PFASs) to replace legacy PFASs, have wide applications in the organofluorine industry and have been detected in the global environment. However, it is still unclear what effect HFPO homologues will exert on microbial abundance, community structure and function. The objective of this study was to assess potential impacts of HFPO homologue acids on archaea, bacteria, and ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the soil environment. Grassland soil microcosms were supplemented with low (0.1 mg/kg) or high (10 mg/kg) dosages of dimer, trimer and tetramer acids of HFPO (HFPO-DA, HFPO-TA, and HFPO-TeA), respectively. The amendment of HFPO homologues acids initially decreased the abundance of archaea and bacteria but increased them in the later period. The addition of HFPO homologues acids raised AOA abundance but restrained AOB growth during the whole incubation. AOA and AOB community structures showed considerable variations. Potential nitrifying rate (PNR) showed an increase in the initial period followed by a decline in the later period. HFPO-DA had a lasting and suppressive effect on AOB and PNR even at a nearly environmental level. Overall, HFPO homologues with different carbon chain lengths had different impacts on soil microbial community and ammonia oxidation.

Effects of co-contamination of heavy metals and total petroleum hydrocarbons on soil bacterial community and function network reconstitution

Due to the accumulation of heavy metals in soil ecosystems, the response of soil microorganisms to the disturbance of heavy metals were widely studied. However, little was known about the interactions among microorganisms in heavy metals and total petroleum hydrocarbons (TPH) co-contaminated soils. In the present study, the microbiota shifts of 2 different contamination types of heavy metal-TPH polluted soils were investigated. NGS sequencing approach was adopted to illustrate the microbial community structure and to predict community function. Networks were established to reveal the interactions between microbes and environmental pollutants. Results showed that the alpha diversity and OTUs number of soil microbiota were reduced under heavy metals and TPH pollutants. TPH was the major pollutant in HT1 group, in which Proteobacteria phylum increased significantly, including Arenimonas genus, Sphingomonadaceae family and Burkholderiaceae family. Moreover, the function structures based on the KEGG database of HT1 group was enriched in the benzene matter metabolism and bacterial motoricity in microbiota. In contrast, severe Cr-Pb-TPH co-pollutants in HT2 increased the abundance of Firmicutes. In details, the relative abundance of Streptococcus genus and Bacilli class raised sharply. The DNA replication functions in microbiota were enriched under severely contaminated soil as a result of high concentrations of heavy metals and TPH pollutants' damage to bacteria. Furthermore, according to the correlation analysis between microbes and the pollutants, Streptococcus, Neisseria, Aeromonas, Porphyromonas and Acinetobacter were suggested as the bioremediation bacteria for Cr and Pb polluted soils, while Syntrophaceae spp. and Immundisolibacter were suggested as the bioremediation bacteria for TPH polluted soil. The study took a survey on the microbiota shifts of the heavy metals and TPH polluted soils, and the microbe's biomarkers provided new insights for the candidate strains of biodegradation, while further researches are required to verify the biodegradation mechanism of these biomarkers.

Metagenomic analysis of soil microbial community under PFOA and PFOS stress

Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.

Enhanced reductive defluorination and inhibited infiltration of fluoroglucocorticoids in a river receiving reclaimed water amended by nano zero-valent iron-modified biochar: Performance and mechanisms

The main aim of this study was to investigate the effect of a nano zero-valent iron-modified biochar-amended composite riverbed (nZVI@BC-R) on inhibited infiltration and enhanced biodegradation of fluoroglucocorticoids (FGCs) in a river receiving reclaimed water. The results demonstrated that the removal efficiency of triamcinolone acetonide (TA), a representative FGC, increased from 38.40% and 77.91% to 91.60% in the nZVI@BC-R compared with that of a natural soil riverbed (S-R) and biochar-amended soil riverbed (BC-R). The main removal mechanismwas attributedto adsorption and biodegradation, of which the contribution rates were 32.2% and 59.4% in nZVI@BC-R, 18.9% and 19.5% in S-R, and 24.4% and 53.5% in BC-R, respectively. The removal process could be described by a two-compartment, first-order dynamic model with decay rate constants for adsorption and biodegradation of 4.02700, 22.44400, and 29.07300 d-1 and 0.00286, 0.01562, and 0.03484 d-1 in the S-R, BC-R and nZVI@BC-R, respectively. The mechanism of defluorination accounted for 42.2% of biodegradation in the nZVI@BC-R, which was accompanied by side-chain rupture, oxidation, and ringopening. Functional microbes with iron oxidizing ability and reductive dehalogenating genera, namely Pseudoxanthomonas, Pedobacter, and Bosea, contributed to the high removal rate of TA, particularly in the nZVI@BC-R. Overall, the nZVI@BC-R provided an effective method to inhibit glucocorticoids infiltration into groundwater.

Response of sediment bacterial communities to the drainage of wastewater from aquaculture ponds in different seasons

Bacterial communities play an important role in diffuse sediment pollution in aquaculture farms. Previous studies have revealed the short-term influence of wastewater drainage on the bacterial communities but the seasonal response of the sediment bacterial communities to wastewater drainage from aquaculture farms remains unclear. This study used the 16S rRNA approach to explore the profiles of bacterial communities over four seasons in a typical crab aquaculture farm that included a pond and an outlet ditch. Nineteen sediment samples and an equal number of water samples were collected and analysed during spring, summer, autumn, and winter during 2018-19. Our results showed that Proteobacteria, Chloroflexi, and Bacteroides were the predominant phyla in aquaculture pond sediment with the relative abundance of 28.95%, 17.32%, and 15.31%, respectively. The relative abundance of Proteobacteria and Bacteroides was higher in autumn and winter, and the relative abundance of Chloroflexi was highest in spring. The Shannon diversity index value ranged from 6.17 to 9.30 and showed significant positive correlation (P < 0.01) with the concentrations of TN, NH₄⁺-N, and TP in the water. The variation in the bacterial community and relative abundance in outlet ditch sediment were consistent with those in the pond sediment. Our results show that determinisation of the bacterial community composition in the outlet ditch sediment provides a novel tool to monitor watersheds sensitive to the influence of aquacultures.

Assessing Chromium Contamination in Red Soil: Monitoring the Migration of Fractions and the Change of Related Microorganisms

The improper stacking of chromium (Cr) slag poses a great threat to the environment and human health. The toxicity of Cr in soil is not only related to its total amount, but also to its fractions. A simulated experiment was conducted in laboratory to assess the environmental risk of Cr fractions migration and distribution in red soil. The results showed the content of acid-soluble and reducible Cr significantly decreased (P < 0.05) in top layer but increased in middle and substratum layers over time. This indicated that acid-soluble and reducible Cr migrated downward with time and the relative mobility of acid-soluble Cr (0.038 mg/kg·d·m) was higher than that of reducible Cr (0.028 mg/kg·d·m). Furthermore, correlation analysis between microbial community and chromium fraction showed the relative abundance of Lysobacter, Flavihumibacter, Flavisolbacter, and Altererythrobacter was significantly (P < 0.05) correlated with acid-soluble and reducible fractions. Thus, these microorganisms might be evaluators to assess the migration of acid-soluble and reducible fractions in red soil. In summary, this study provided a new comprehension on remediation of Cr-contaminated soil by monitoring the migration of acid-soluble and reducible fractions and the changes of related microbial groups.

Developing a roadmap to determine per- and polyfluoroalkyl substances-microbial population interactions

We collected over 40 groundwater samples from a per- and polyfluoroalkyl substances (PFAS) impacted legacy fire fighting training area in Canada to develop an in-depth assessment of the relationship between PFAS and in situ microbial communities. Results suggest differential transport of PFAS of differing chain-length and head group. There is also evidence of PFAS degradation, in particular 6:2 FTS degradation. Although PFAS constituents were not major drivers of microbial community structure, the relative abundance of over one hundred individual genera were significantly associated with PFAS chemistry. For example, lineages within the Oxalobacteraceae family had strong negative correlations with PFAS, whilst the Desulfococcus genus has strong positive correlations. Results also suggest a range of genera may have been stimulated at low to mid-range concentrations (e.g., Gordonia and Acidimicrobium), with some genera potentially inhibited at high PFAS concentrations. Any correlations identified need to be further investigated to determine the underlying reasons for observed associations as this is an open field site with the potential for many confounding factors. Positive correlations may ultimately provide important insights related to development of biodegradation technologies for PFAS impacted sites, while negative correlations further improve our understanding of the potential negative effects of PFAS on ecosystem health.