Microbiology combined with metabonomics revealing the response of soil microorganisms and their metabolic functions exposed to phthalic acid esters

Improving key gene expression and di-n-butyl phthalate (DBP) degrading ability in a novel Pseudochrobactrum sp. XF203 by ribosome engineering

Di-n-butyl phthalate (DBP) is one of the important phthalates detected commonly in soils and crops, posing serious threat to human health. Pseudochrobactrum sp. XF203 (XF203), a new strain related with DBP biodegradation, was first identified from a natural habitat lacking human disturbance. Genomic analysis coupled with gene expression comparison assay revealed this strain harbors the key aromatic ring-cleaving gene catE203 (encoding catechol 2,3-dioxygenase/C23O) involved DBP biodegradation. Following intermediates identification and enzymatic analysis also indicated a C23O dependent DBP lysis pathway in XF203. The gene directed ribosome engineering was operated and to generate a desirable mutant strain XF203R with highest catE203 gene expression level and strong DBP degrading ability. The X203R removed DBP in soil jointly by reassembling bacterial community. These results demonstrate a great value of XF203R for the practical DBP bioremediation application, highlighting the important role of the key gene-directed ribosome engineering in mining multi-pollutants degrading bacteria from natural habitats where various functional genes are well conserved.

Microplastics in heavy metal-contaminated soil drives bacterial community and metabolic changes

Microplastic (MP) and heavy metal pollution in soil are global issues. When MPs invade the soil, they combine with heavy metals and adversely affect soil organisms. Six common MPs-polyethylene, polypropylene, polystyrene, polyvinyl chloride, polyethylene terephthalate, and polytetrafluoroethylene-were selected for this study to examine the effects of various concentrations and MP types on the physicochemical properties, bacterial community, and soil metabolism of heavy metal-contaminated soil. MP enhanced predation and competition among heavy metal-contaminated soil bacteria. Heavy metal-MPs alter metabolites in lipid metabolism, other pathways, and the bacterial community. MP treatment promotes energy production and oxidative stress of soil bacteria to resist the toxicity of heavy metals and degrade MP pollution. In conclusion, MP treatment changed the metabolism of the microbiome in heavy metal-contaminated soil and increased the abundance of Proteobacteria that responded to MPs and heavy metal pollution by 11.54 % on average. This study explored bacteria for the ecological regeneration and provided ideas for MPs and heavy metal-contaminated soil remediation.

Effects of biodegradable (PBAT/PLA) and conventional (LDPE) mulch film residues on bacterial communities and metabolic functions in different agricultural soils

Soil health is a crucial aspect of sustainable agriculture and food production, necessitating attention to the ecological risks associated with substantial amounts of mulch film residues. Biodegradable mulch films (BDMs) carry the same risk of mulch film residues formation as low-density polyethylene (LDPE) mulch films during actual use. More information is needed to elucidate the specific impacts of mulch film residues on the soil environment. Integrated 16S rRNA gene sequencing and non-targeted metabolomics, this study revealed the response patterns of bacterial communities, metabolites, and metabolic functions in the soil from three different agricultural regions to the presence of mulch film residues. LDPE mulch film residues negatively impacted the bacterial communities in the soils of Heilongjiang (HLJ) and Yunnan (YN) and had a lesser impact on the metabolic spectrum in the soils of HLJ, YN, and Xinjiang (XJ). BDM residues had a greater negative impact on all three soils in terms of both the bacterial communities and metabolites. The impact of BDM treatment on the soils of HLJ, YN, and XJ increased sequentially in that order. It is recommended that, when promoting the use of biodegradable mulch films, a fuller assessment should be made, accounting for local soil properties.

The concentrations and behavior of classic phthalates and emerging phthalate alternatives in different environmental matrices and their biological health risks

Because of their excellent plasticity, phthalates or phthalic acid esters (PAEs) are widely used in plastic products. However, due to the recognized toxicity of PAEs and legislative requirements, the production and use of emerging PAE alternatives have rapidly grown, such as di-isononyl cyclohexane-1,2-dicarboxylate (DINCH) and di(2-ethylhexyl) terephthalate (DEHTP) which are the primary replacements for classic PAEs. Nowadays, PAEs and emerging PAE alternatives are frequently found in a variety of environmental media, including the atmosphere, sludge, rivers, and seawater/sediment. PAEs and emerging PAE alternatives are involved in endocrine-disrupting effects, and they affect the reproductive physiology of different species of fish and mammals. Therefore, their presence in the environment is of considerable concern due to their potential effects on ecosystem function and public health. Nevertheless, current research on the prevalence, destiny, and conduct of PAEs in the environment has primarily focused on classic PAEs, with little attention given to emerging PAE alternatives. The present article furnishes a synopsis of the physicochemical characteristics, occurrence, transport, fate, and adverse effects of both classic PAEs and emerging PAE alternatives on organisms in the ecosystem. Our analysis reveals that both classic PAEs and emerging PAE alternatives are widely distributed in all environmental media, with emerging PAE alternatives increasingly replacing classic PAEs. Various pathways can transform and degrade both classic PAEs and emerging PAE alternatives, and their own and related metabolites can have toxic effects on organisms. This research offers a more extensive comprehension of the health hazards associated with classic PAEs and emerging PAE alternatives.

Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

Co-exposure effects of butyl benzyl phthalate and TiO2 nanomaterials (anatase) on Metaphire guillelmi gut health

Phthalic acid esters (PAEs) and TiO2 nanomaterials (nTiO2) are commonly used as plastic additives, nano-fertilizers or nano-pesticides. Their excessive co-applications led to the co-occurrence, which can induce damage to soil organisms such as Metaphire guillelmi (an earthworm widespread in farmland). However, the co-exposure effects of butyl benzyl phthalate (BBP, a typical PAEs) and nTiO2 on Metaphire guillelmi at environmental-relevant concentrations remain unclear. In this study, 1 mg kg-1 BBP and 1 mg kg-1 nTiO2 (anatase) were added into the soil to assess: (1) their effects on oxidative damage, digestive system, and neurotoxicity in Metaphire guillelmi gut on days 14 and 28; and (2) whether BBP and nTiO2 affected Metaphire guillelmi gut health by disrupting intestinal microorganisms. The results demonstrated that BBP and nTiO2 had the potential to inhibit the activity of superoxide dismutase, cellulase, protease, Na+K+-ATPase, and Ca2+-ATPase, as well as cause oxidative damage by altering intestinal bacteria such as Marmoricola and Microvirga at genus levels after 28 d-exposure. However, the exposure did not cause disorders of the intestinal bacteria. The present study provides more evidence for the sustainable application and scientific management of BBP and nTiO2, thus providing better guidance for PAEs and engineered nanomaterials regulations in agroecosystems.

Release of Additives from Agricultural Plastic Films in Water: Experiment and Modeling

Globally, more than 6 million metric tons of agricultural plastic films are used to increase crop yields and reduce the use of water and herbicides, resulting in the contamination of soil and water by plastic debris and additives. However, knowledge of the occurrence and release of additives from agricultural films is limited. In this study, suspect screening with high-resolution mass spectrometry, one-dimensional Fickian diffusion models, and linear free energy relationships (LFERs) were used to determine the occurrence and mass transfer of various additives from agricultural plastic films. A total of 89 additives were tentatively identified in 40 films, and 62 of them were further validated and quantified. The aqueous concentrations of 26 released additives reached mg L^-1 after a 28 day incubation at 25 °C. Diffusion models and LFERs demonstrated that the film-water partition coefficient and the diffusivity in the polymer, the two critical parameters controlling the mass transfer, could be predicted using Abraham descriptors. The findings of this study highlighted the need for future research on the environmental fate and risk assessment of previously neglected additives in agricultural plastic films and other similar products.

Effects of long-term microplastic pollution on soil heavy metals and metal resistance genes: Distribution patterns and synergistic effects

Heavy metals (HMs) and microplastics (MPs) are two emerging factors threatening global food security. Whether long-term MPs pollution will affect the distribution of HMs and their resistance genes (MRGs) in soil is unknown. Here, metagenomic approach was used to decipher the fate of MRGs in cropland soils with long-term film MPs residues. Similar distribution pattern of MRGs was formed in long-term film MPs contaminated soil. A total of 202 MRG subtypes were detected, with resistance genes for Multimetal, Cu, and As being the most prevalent type of MRGs. MRGs formed a modular distribution of five clusters centered on MRGs including ruvB in long-term film MPs contaminated soil. MRGs also formed tight co-occurrence networks with mobile genetic elements (MGEs: integrons, insertions and plasmids). Redundancy analysis showed that HMs together with microbial communities and MGEs affected the distribution of MRGs in soil. Thirteen genera including Pseudomonas were identified as potential hosts for MRGs and MGEs. The research provides preliminary progress on the synergistic effect of HMs and MPs in affecting soil ecological security. The synergistic effect of MPs and HMs needs to be considered in the remediation of contaminated soils.

Characteristics of organic pollutants and their effects on the microbial composition and activity in the industrial soils of Pearl River Delta, China

To investigate the interaction between organic pollutants and soil microorganisms, industrial soils were collected from Pearl River Delta region of China for determining semi-volatile organic pollutants, the community structure and activity of microorganisms. The results showed that polycyclic aromatic hydrocarbons (PAHs) (63.3-4956 μg kg^-1) and phthalate esters (PAEs) (272-65,837 μg kg^-1) were main organic pollutants in the research area soils. Chemical manufacturing industry and plastics manufacturing industry contributed greatly to PAH pollution and PAE pollution, respectively. Organic pollutants changed the biomass of microorganisms. In most industrial soils, the biomass of actinomycetes was the highest in the industrial soils, followed by G^- bacteria, G⁺ bacteria and fungi. The exception was that the biomass of fungi in the soil near chemical manufacturing industry was greater than that of G⁺ bacteria. The soil microbial biomass (including soil microbial biomass carbon, soil microbial biomass nitrogen, the biomass of actinomycetes, bacteria, and fungi) and soil enzyme activities (sucrase and urease) positively correlated with the organic pollutant residues, and the microbial species diversity and microbial species abundance decreased with organic pollutant residues increasing. Based on the correlation analysis, the urease activity, actinomycetes biomass, and fungi biomass were appropriate biological indicators for evaluating the stress of organic pollutants. Our research provides a new perspective for understanding the soil biological response in industrial soils.

Daphnia magna sub-lethal exposure to phthalate pollutants elicits disruptions in amino acid and energy metabolism

Phthalic acid esters (PAEs) are a class of chemicals that are usually incorporated as additives in the manufacturing of plastics. PAEs are not covalently bound to the material matrix and can, consequently, be leached into the environment. PAEs have been reported to act as endocrine disruptors, neurotoxins, metabolic stressors, and immunotoxins to aquatic organisms but there is a lack of information regarding the impact of sub-lethal concentrations to target organisms. The freshwater crustacean Daphnia magna, a commonly used model organism in aquatic toxicity, was exposed to four phthalate pollutants: dimethyl phthalate (DMP), diethyl phthalate (DEP), monomethyl phthalate (MMP), and monoethyl phthalate (MEP). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed in a targeted metabolomic approach to quantify polar metabolites extracted from a single Daphnia body. Individual metabolite percent changes and hierarchical clustering heatmap analysis showed unique metabolic profiles for each phthalate pollutant. Metabolite percent changes were mostly downregulated or presented opposing responses for the low and high concentrations tested. Meanwhile, pathway analyses suggest the disruption of related and unique pathways, mostly connected with amino acid and energy metabolism. The pathways aminoacyl-tRNA biosynthesis, arginine biosynthesis, and glutathione metabolism were disrupted by most selected PAEs. Overall, this study indicates that although phthalate pollutants can elicit distinct metabolic perturbations to each PAE, they still impacted related biochemical pathways. These chemical-class based responses could be associated with a common toxic mechanism of action. The reported findings show how targeted metabolomic approaches can lead to a better understanding of sub-lethal exposure to pollutants, revealing metabolomic endpoints do not hold a close relationship with traditional acute toxicity endpoints.

Fluorescent labeling and tracing of immobilized efficient degrading bacterium DNB-S1 and its remediation efficiency of DBP contaminated soil

Dibutyl phthalate (DBP) is an organic pollutant frequently detected in soil, and is a reproductive poison that harms animals both before and after birth and has mutagenic, teratogenic, and carcinogenic effects. DBP removal from farmland has been the subject of extensive research in recent years. Efficient DBP degrading bacterial strains were screened in the laboratory. GFP (Green fluorescent protein) labeled degradation strain GFP-DNB-S1 was analyzed for its activity and dynamics. Using sodium alginate (SA) and nano-hydroxyapatite (n-HAP) as carrier materials and CaCl₂ as a cross-linking agent, the immobilized microbial agent n-HAP/SA + DNB-S1 was prepared by embedding cross-linking immobilization technology to study the remediation effect of DBP contaminated soil. The best formation effect of immobilized materials (n-HAP/SA) was found when the SA to n-HAP ratio was 3:2. When compared to single SA immobilized bacteria, n-HAP/SA immobilized bacteria improved the surface roughness and porosity of the microspheres. After 70 days, LED light revealed that the immobilized bacteria's GFP green fluorescent protein expression was stable. At 70 days, the initial DBP concentration of 500 mg ∙ L^-1 degraded at a rate of 69.9%. The degrading bacteria had no effect on DBP degradation before and after being labeled with GFP. The n-HAP/SA immobilized bacteria offered a better living environment for microorganisms due to their rougher surface and a greater number of pores. This protected the microorganisms and increased the efficiency of DBP degradation. When the concentration of DBP in contaminated soil was set to 20 mg ∙ kg^-1 and the n-HAP/SA + DNB-S1 immobilized bacterial agent was applied to the soil, the rate of DBP degradation was determined to be 93.34%. The degradation process followed First-order degradation kinetics, which improved the physical and chemical properties of the soil as well as its fertility.

Alterations of gut and oral microbiota in the individuals consuming take-away food in disposable plastic containers

Microplastics (MP) and nanoplastics (NP) exist in the disposable plastic take-away containers. This study aims to determine the gut and oral microbiota alterations in the individuals frequently and occasionally consuming take-away food in disposable plastic containers (TFDPC), and explore the effect of micro/nanoplastics (MNP) reduction on gut microbiota in mice. TFDPC consumption are associated with greater presences of gastrointestinal dysfunction and cough. Both occasional and frequent consumers have altered gut and oral microbiota, and their gut diversity and evenness are greater than those of non-TFDPC consuming cohort. Multiple gut and oral bacteria are associated with TFDPC consumers, among which intestinal Collinsella and oral Thiobacillus are most associated with the frequent consumers, while intestinal Faecalibacterium is most associated with the occasional consumers. Although some gut bacteria associated with the mice treated with 500 µg NP and 500 µg MP are decreased in the mice treated with 200 µg NP, the gut microbiota of the three MNP groups are all different from the control group. This study demonstrates that TFDPC induces gut and oral microbiota alterations in the consumers, and partial reduction of the size and amount of MNP cannot rectify the MNP-induced gut microbial dysbiosis.

Tracking antibiotic resistance genes in microplastic-contaminated soil

Agricultural soils and microplastics (MPs) are hotspots for antibiotic resistance genes (ARGs). Plastic mulch is the most important source of MPs in agricultural soil. ARGs, mobile genetic elements (MGEs), and their host profiles in long-term mulch MP-exposed soils remain unclear. In the present study, metagenomics was used to investigate the distribution patterns of ARGs and MGEs in eight Chinese provinces with a long history of plastic mulch use. A total of 204 subtypes of ARGs and thousands of MGEs (14 integrons, 28 insertions, and 2993 plasmids) were identified. A similar diversity of ARGs was found among MPs film-contaminated sites. The types of ARGs with a high abundance were more concentrated, and multidrug resistance genes were the dominant ARGs. Soils from regions with a longer history of plastic film use (such as Xinjiang province) had a higher abundance of ARGs and MGEs. The distribution of ARGs and MGEs exhibited a modular network distribution pattern. A total of 27 ARG subtypes and 29 MGEs showed co-occurrence network relationships. More than 10 common hosts of ARGs and MGEs, such as Pseudomonas, were found, and their abundances were highest in three provinces, including Xinjiang. This study may help elucidate the impact mechanism of long-term MP residues on the occurrence and spread of ARGs in soil.

Deciphering the diversity, composition, function, and network complexity of the soil microbial community after repeated exposure to a fungicide boscalid

Boscalid is a novel, highly effective carboximide fungicide that has been substantially and irrationally applied in greenhouses. However, little is known about the residual characteristics of boscalid and its ecological effects in long-term polluted greenhouse soils. Therefore, actual boscalid pollution status in greenhouse soils was simulated by repeatedly introducing boscalid into the soil under laboratory conditions. The degradation characteristics of boscalid, and its effects on the diversity, composition, function, and co-occurrence patterns of the soil microbial community were systematically investigated. Boscalid degraded slowly, with its degradation half-lives ranging from 31.5 days to 180.1 days in the soil. Boscalid degradation was further delayed by repeated treatment and increasing its initial concentration. Boscalid significantly decreased soil microbial diversity, particularly at the recommended dosage. Amplicon sequencing analysis showed that boscalid altered the soil microbial community and further stimulated the phylum Proteobacteria and four potential boscalid-degrading bacterial genera, Sphingomonas, Starkeya, Citrobacter, and Castellaniella. Although the network analysis revealed that boscalid significantly reduced the microbial network complexity, it enhanced the vital roles of Proteobacteria by increasing its proportion and strengthening the relationships among the internal bacteria in the network. The soil microbial function in the boscalid treatment were simulated at the recommended dosage and two-fold recommended dosage but showed an inhibition-recovery-stimulation trend at the five-fold recommended dosage with an increase in treatment frequency. Moreover, the expression of nitrogen cycling functional genes, nifH, AOA amoA, AOB amoA, nirK, and nirS in all boscalid treatments displayed an inhibition-recovery-stimulation trend during the entire experimental period, and the effects were more pronounced at the five-fold recommended dosage. In conclusion, repeated boscalid treatments delayed degradation, reduced soil microbial diversity and network complexity, disturbed soil microbial community, and interfered with soil microbial function.

Effects of phthalate esters on soil microbial community under different planting patterns in Northern China: Case study of Hebei Province

Soil microorganisms are biological factors involved in the farmland environment. The factors that shape soil microbial communities and how these are influenced by geographic location, planting pattern (open-field or greenhouse), and soil organic pollutants (phthalate esters, PAEs) remain poorly understood at large scales. Using 16 S rRNA gene and ITS sequencing, we characterized the soil microbiota in open-field and greenhouse soils in Hebei Province, China, and correlated their structure and composition to geographic location, planting pattern and PAEs. Compared with geographic location, planting pattern is more decisive for shaping soil microbes and has more significant effects on bacteria, and the effects are shaped by the number and types of core OTUs. PAEs participated in the shaping of soil microbial communities by altering the relative abundances of dominant microorganisms in the two planting patterns, and the effects of PAEs with high K_ow were more significant. PAEs have a greater impact on bacteria than fungi in both planting patterns. Bacteria in the greenhouse soil were sensitive to the 9 kinds of PAEs detected, however in the open-field samples, mainly responded to PAEs with high K_ow and rarely respond to PAEs with low K_ow. DEHP and DBP, as two monomers with the highest concentration, have significant effects on dominant genera of microorganisms under both planting patterns, with inhibiting effect on bacteria and significantly promotion on fungi. Our study clarified the factors that have a substantial impact on soil microorganisms at the provincial scale and the mechanisms involved in shaping soil microbial community structure, as well as the significant impact of PAEs on soil microbial dominant microorganisms.