Metabolic and Microbial Profiling of Soil Microbial Community under Per- and Polyfluoroalkyl Substance (PFAS) Stress

Nanoplastic and phthalate induced stress responses in rhizosphere soil: Microbial communities and metabolic networks

The widespread use of plastic products in agriculture has introduced micro-nano plastics (MNPs) and dibutyl phthalate (DBP) into soil ecosystems, disrupting microbial communities and altering metabolite profiles. However, their effects on the rhizosphere soil characteristics of medicinal plants like dandelion remain understudied. This study systematically examined the impact of PS NPs and DBP on rhizosphere microbial communities and metabolites by integrating high-throughput sequencing with liquid chromatography-mass spectrometry. Results demonstrated that individual and combined exposures to PS NPs and DBP decreased soil pH, organic matter content, and enzyme activities while reshaping the diversity, structure, and composition of rhizosphere bacteria and fungi. Notably, bacterial network stability and complexity increased under combined exposure, while fungal networks became more simplified, with a 33.72 % decrease in positive correlations. We identified potential PS NPs and DBP-degrading bacteria and biomarkers, including Nocardioides, Pseudarthrobacter, and Arenimonas. We revealed that co-exposure elevated differential soil metabolites associated with tyrosine metabolism and steroid biosynthesis. The significant positive associations between rhizosphere microorganisms and metabolites highlighted that metabolite accumulation was a key microbial response mechanism to stress. However, within the complex soil environment, the compensatory actions of microorganisms and metabolites were insufficient to mitigate the detrimental effects of PS NPs and DBP, resulting in continued inhibition of dandelion growth by 38.66 %. Consequently, these findings highlight that soil fungi and metabolism play key roles in responding to stress and influencing crop growth, providing novel insights into the impact of nanoparticle and plasticizer exposure on medicinal plant cultivation.

Metagenomics deciphers the function of biochar in alleviating zinc ion stress during sulfur autotrophic denitrification process

Sulfur autotrophic denitrification (SAD) process has significant potential in treating low carbon/nitrogen ratio wastewater. However, the presence of zinc ions (Zn2+) adversely affects the denitrification performance. This study investigated the effect of biochar prepared at 300 °C (BC300) and 600 °C (BC600), as well as dosing strategy, on denitrification performance in the SAD process under Zn2+ inhibition. Firstly, BC600 had a higher maximum adsorption capacity for Zn2+ than BC300 in nitrogen-containing wastewater. Surface complexation was mainly adsorption mechanism. BC300 exhibited a greater ability in enhancing denitrification ability than BC600. The strategy of synchronous addition is more effective than pre-adsorption. Firstly, BC300 enhancing humic-like component secretion. BC300 enriched higher abundance of sulfur-oxidizing bacteria. More importantly, BC300 counteracted the negative effect of Zn2+ by enhancing glycan biosynthesis and metabolism, enriching functional genes, and increased the level of quorum sensing. The study presents a sustainable approach for maintaining denitrification performance under environmental stress.

Fatty Acid Metabolic Impairment in Soil Microbes Induced by PFAS: Dependence on the Fluorocarbon Chain Length, Headgroups, and Ether Attached

Per- and polyfluoroalkyl substances (PFASs) with varying chain lengths, headgroups, and alternative structures are widespread and persistent in soil, yet knowledge of their biological effects and toxic mechanisms on soil microorganisms is limited. This study identified the structure-dependent impacts of PFAS on microbial fatty acid (FA) profiles by integrated field-laboratory investigations. The field investigation uncovered distinct PFAS-FA interaction patterns, varying by PFAS fluorocarbon (FC) chain length and functional group, and FA hydrocarbon (HC) chain length and unsaturation degree. Specifically, long-chain perfluoroalkyl carboxylic acids (PFCAs, FC7-17) increased medium/long-chain FAs (HC ≤ 17) and monounsaturated FAs (MUFAs), while long-chain perfluoroalkyl sulfonic acids (PFSAs, FC6-8) enhanced longer-chain FAs (HC > 17) and MUFAs. Additionally, perfluoroether carboxylic acids (PFECAs) as well as short-chain PFCAs (FC < 7) and PFSAs (FC < 6), which commonly used as alternatives to long-chain PFCAs/PFSAs, were associated with polyunsaturated FAs (PUFAs). The laboratory investigation with Pseudomonas aeruginosa PAO1 validated these FA metabolic disruptions and revealed broader perturbations in phospholipids, acetyl-CoA, and secondary metabolite metabolisms, providing insights into dysregulated membrane synthesis, C/N metabolisms, and bacteria quorum sensing (QS) processes. These findings reveal novel structure-dependent effects of PFASs on microorganisms, highlighting microbial FA profiles as potential metabolic biomarkers for assessing PFAS toxicity and soil health.

Co-occurrence of PFASs, TPHs, and BTEX in subsurface soils: Impacts on native microbial communities and implications for bioremediation

This study investigates the co-occurrence of per- and polyfluoroalkyl substances (PFASs), petroleum hydrocarbons (TPHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) and their effects on the indigenous microbial communities in soils at a contaminated site with a history of petroleum refinery operations. PFASs concentrations were in the range of 5.65-6.73 ng/g, and fluorooctane sulfonate (PFOS) and perfluorobutane sulfonic acid (PFBS) were the dominating compounds. No significant difference was observed in the PFASs concentration profiles between the site and background locations, indicating that PFASs detected in the soil samples were mainly contributed from non-point sources, due to the long-distance transport of PFASs in the region. The concentrations of TPHs and BTEX ranged from 227 to 72,360 mg/kg and 0.06-2109.77 mg/kg, respectively, mainly contributed by the historical refinery activities. The presence of PFASs, TPHs, and BTEX significantly impacted soil microbial community diversity and abundance, altering microbial compositions and enriching bacteria with higher resistance or metabolic capabilities against contamination. Strong correlations were observed between TPHs and its degraders such as Pseudomonas, Azoarcus, and Polaromonas. Significant positive relationship between PFASs and Trichlorobacter implied the potential defluorination capabilities of Trichlorobacter, warranting further investigation. Moreover, the higher energy metabolism including carbon, nitrogen and sulfur metabolisms and higher abundance of metabolic enzymes for alkane, cyclohexane and toluene in the refinery site revealed the potential occurrence of natural biodegradation of contaminants with indigenous microbial community. These findings highlight the complexity of sites contaminated with a mixture of traditional and emerging contaminants, providing valuable insights into the potential for biodegradation of mixed contaminants and underscoring the need for integrated approaches in environmental remediation strategies. This study contributes to understanding the ecological impacts of co-occurring contaminants and emphasizes the importance of considering multiple contaminant types in environmental risk assessments and remediation efforts.

Metabolomic interpretation of bacterial and fungal contribution to per- and polyfluoroalkyl substances interface migration in waterlogged paddy fields

Per- and polyfluoroalkyl substances (PFAS) are widely distributed in paddy soils, and their multi-phase partitioning in soil fractions was proved to be strongly interact with soil microbial community composition and functions. Despite this, soil bacterial and fungal metabolic molecular effects on PFAS water-soil interface migration in waterlogged paddy fields still remain unclear. This study integrated soil untargeted metabolomics with microbial amplicon sequencing to elucidate soil metabolic modulations of 15 PFAS interface release. Inhibition of bacterial and fungal metabolic activity both significantly altered PFAS cross-media translocation (p < 0.05). Gemmatimonadota, Desulfobacterota, Acidobacteriota, Actinobacteriota, and Bacteroidota were vital bacterial taxa affecting PFAS transport, while Basidiobolomycota and Chytridiomycota were vital fungal taxa. Fungi regulated PFAS migration more (R2 = 0.379-0.526) than bacteria (R2 = 0.021-0.030) due to the higher metabolic stability of stochastic-dominated fungi than deterministic-dominated bacteria. At the water-soil interface, the amino acid-like dissolved organic matter (Tyrosine and Tryptophan) contributed most (48.5-58.6 %) to the PFAS multiphase distribution. Untargeted metabolomics further clarified that fungal amino acid-like metabolites, including Phosphoenolpyruvate and Methionine, were key triggers stimulating Tyrosine and Tryptophan biosynthesis (p < 0.001), which were vital in modulating PFAS interface translocation (p < 0.001). These results provide novel insights into soil microbial metabolites' participation in PFAS water-soil interface migration, benefiting PFAS pollution control and agricultural security risk assessment in waterlogged paddy ecosystems.

Cadmium immobilization by mercapto-palygorskite in alkaline soil: Impacts on soil microbial communities and wheat rhizosphere metabolism

Weakly alkaline cadmium (Cd) contaminated soil in China has aroused great concern regarding its impact on food security and human health. Mercapto-modified palygorskite (MP) has exhibited good potential to minimize Cd accumulation in wheat, it is imperative to understand the underlying mechanisms within the soil-wheat-microbial system for sustainable development of agrochemicals. This study evaluated the effects of various MP dosages on soil Cd bioavailability, rhizosphere metabolomics, microbial community structure and wheat growth. The results indicated that MP (0.05-0.2 %) application significantly reduced Cd accumulation in wheat grains by 59.0-83.2 % (p < 0.05) and inhibited Cd translocation from root to grain. MP also promoted Mn oxide formation and redistributed the exchangeable Cd to Fe-Mn oxide-bound forms (44.2-109.6 %), thus lowering soil Cd bioavailability by 17.9-32.5 %. Additionally, MP reduced wheat rhizosphere organic acid levels, altered rhizosphere carbon and nitrogen pools, and stimulated the growth of Cd-tolerant Alternaria and Cladosporium, while inhibiting the growth of Fusarium. These findings highlight the potential of MP to modulate soil rhizosphere metabolism and microbial communities, offering a novel perspective on its environmental implications and supporting agrochemical sustainability.

Occurrence, risk assessment and source apportionment of perfluoroalkyl acids in the river of a hill-plain intersection region: The impacts of land use and river network structure

Studying the impacts of land use and river network structure on perfluoroalkyl acids (PFAAs) footprint in rivers is crucial for predicting the fate of PFAAs in aquatic environments. This study investigated the distribution, ecological risks, sources and influence factors of 17 PFAAs in water and sediments of rivers from hills to plain areas. The results showed that the detection frequencies were higher for short-chain PFAAs than long-chain PFAAs in water, whereas an opposite pattern was found in sediments. The concentration of ∑PFAAs ranged from 59.2 to 414 ng/L in water and from 1.4 to 60.1 ng/g in sediments. Perfluorohexanoic acid and perfluorooctanoic acid were identified as the main pollutants in the river. The average concentrations of PFAAs were higher in the aquaculture areas (water: 309.8 ng/L; sediments: 43.27 ng/g) than in residential areas (water: 206.03 ng/L; sediments: 11.7 ng/g) and farmland areas (water: 123.12 ng/L; sediments: 9.4 ng/g). Environmental risk assessment showed that PFAAs were mainly low risk or no risk in water, but were moderate risk and even high risk in sediments, especially for perfluorooctane sulfonate. Source apportionment found that PFAA sources were mostly from industry, wastewater discharge, and surface runoff. Dissolved oxygen, chemical oxygen demand, water system circularity, network connectivity and organic matter were significantly correlated to PFAA concentration, indicating that the physicochemical properties and river network might directly influence the environmental behavior of PFAAs. The built-up area was positively correlated with PFAAs. These findings indicated that a comprehensive understanding of the influences of land use and river network structure on PFAAs in rivers is essential for managers to formulate effective PFAA control strategies.

Soil amendments reduce PFAS bioaccumulation in Eisenia fetida following exposure to AFFF-impacted soil

The efficacy of RemBind® 300 to immobilize per- and polyfluoroalkyl substances (PFAS) in aqueous film forming foam (AFFF)-impacted soil (∑28 PFAS 1280-8130 ng g-1; n = 8) was assessed using leachability (ASLP) and bioaccumulation (Eisenia fetida) endpoints as the measure of efficacy. In unamended soil, ∑28 PFAS leachability ranged from 26.0 to 235 μg l-1, however, following the addition of 5% w/w RemBind® 300, ∑28 PFAS leachability was reduced by > 99%. Following exposure of E. fetida to unamended soil, ∑28 PFAS bioaccumulation ranged from 18,660-241,910 ng g-1 DW with PFOS accumulating to the greatest extent (15,150-212,120 ng g-1 DW). Biota soil accumulation factors (BSAF) were significantly (p < 0.05) higher for perfluoroalkyl sulfonic acids (PFSA; 13.2-50.9) compared to perfluoroalkyl carboxylic acids (PFCA; 1.2-12.7) while for individual PFSA, mean BSAF increased for C4 to C6 compounds (PFBS: 42.6; PFPeS: 52.7; PFHxS: 62.4). In contrast, when E. fetida were exposed to soil amended with 5% w/w RemBind® 300, significantly lower PFAS bioaccumulation occurred (∑28 PFAS: 339-3397 ng g-1 DW) with PFOS accumulation 23-246 fold lower compared to unamended soil. These results highlight the potential of soil amendments for reducing PFAS mobility and bioavailability, offering an immobilization-based risk management approach for AFFF-impacted soil.

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.

Discrepant soil microbial community and C cycling function responses to conventional and biodegradable microplastics

Biodegradable microplastics (MPs) are promising alternatives to conventional MPs and are of high global concern. However, their discrepant effects on soil microorganisms and functions are poorly understood. In this study, polyethylene (PE) and polylactic acid (PLA) MPs were selected to investigate the different effects on soil microbiome and C-cycling genes using high-throughput sequencing and real-time quantitative PCR, as well as the morphology and functional group changes of MPs, using scanning electron microscopy and Fourier transform infrared spectroscopy, and the driving factors were identified. The results showed that distinct taxa with potential for MP degradation and nitrogen cycling were enriched in soils with PLA and PE, respectively. PLA, smaller size (150-180 µm), and 5% (w/w) of MPs enhanced the network complexity compared with PE, larger size (250-300 µm), and 1% (w/w) of MPs, respectively. PLA increased β-glucosidase by up to 2.53 times, while PE (150-180 µm) reduced by 38.26-44.01% and PE (250-300 µm) increased by 19.00-22.51% at 30 days. Amylase was increased by up to 5.83 times by PLA (150-180 µm) but reduced by 40.26-62.96% by PLA (250-300 µm) and 16.11-43.92% by PE. The genes cbbL, cbhI, abfA, and Lac were enhanced by 37.16%- 1.99 times, 46.35%- 26.46 times, 8.41%- 69.04%, and 90.81%- 5.85 times by PLA except for PLA1B/5B at 30 days. These effects were associated with soil pH, NO3--N, and MP biodegradability. These findings systematically provide an understanding of the impact of biodegradable MPs on the potential for global climate change.