High throughput sequencing analysis of the joint effects of BDE209-Pb on soil bacterial community structure

Polyethylene and sulfa antibiotic remediation in soil using a multifunctional degrading bacterium

To obtain a multifunctional bacterium that can effectively degrade polyethylene (PE) and sulfonamide antibiotics (SAs), PE and SAs were selected as the primary research objects. Multifunctional degrading bacteria were isolated and screened from an environment in which plastics and antibiotics have existed for a long time. An efficient degrading strain, Raoultella sp., was screened by measuring the degradation performance of PE and SAs. We analyzed the changes in the microbial community of indigenous bacteria using 16S rRNA. After 60 d of degradation at 28 °C, the Raoultella strain to PE degradation rate was 4.20 %. The SA degradation rates were 96 % (sulfonathiazole, (ST)), 86 % (sulfamerazine, (SM)), 72 % (sulfamethazine, (SM2)) and 64 % (sulfamethoxazole, (SMX)), respectively. This bacterium increases the surface roughness of PE plastic films and produces numerous gullies, pits, and folds. In addition, after 60 d, the contact angle of the plastic film decreased from 92.965° to 70.205°, indicating a decrease in hydrophobicity. High-throughput sequencing analysis of the degrading bacteria revealed that the Raoultella strain encodes enzymes involved in PE and SA degradation. The results of this study not only provide a theoretical basis for further study of the degradation mechanism of multifunctional and efficient degrading bacteria but also provide potential strain resources for the biodegradation of waste plastics and antibiotics in the environment.

Hydroquinone Ecotoxicity: Unveiling Risks in Soil and River Ecosystems with Insights into Microbial Resilience

Despite widespread industrial use, the environmental safety of hydroquinone (HQ), a benzene compound from plants used in processes like cosmetics, remains uncertain. This study evaluated the ecotoxicological impact of HQ on soil and river environments, utilizing non-target indicator organisms from diverse trophic levels: Daphnia magna, Aliivibrio fischeri, Allium cepa, and Eisenia fetida. For a more environmentally realistic assessment, microbial communities from a river and untreated soil underwent 16S rRNA gene sequencing, with growth and changes in community-level physiological profiling assessed using Biolog EcoPlate™ assays. The water indicator D. magna exhibited the highest sensitivity to HQ (EC50 = 0.142 µg/mL), followed by A. fischeri (EC50 = 1.446 µg/mL), and A. cepa (LC50 = 7.631 µg/mL), while E. fetida showed the highest resistance (EC50 = 234 mg/Kg). Remarkably, microbial communities mitigated HQ impact in both aquatic and terrestrial environments. River microorganisms displayed minimal inhibition, except for a significant reduction in polymer metabolism at the highest concentration (100 µg/mL). Soil communities demonstrated resilience up to 100 µg/mL, beyond which there was a significant decrease in population growth and the capacity to metabolize carbohydrates and polymers. Despite microbial mitigation, HQ remains highly toxic to various trophic levels, emphasizing the necessity for environmental regulations.

Effects of hexabromocyclododecane and polyethylene microplastics on soil bacterial communities

Hexabromocyclododecane (HBCD) and polyethylene (PE) microplastic are ubiquitous pollutants, and knowledge about the effects of HBCD and PE pollution on soil bacterial communities remains obscure. In this study, the effects of different HBCD and PE concentrations and combined HBCD and PE exposure on the diversity, composition, and function of agricultural soil bacterial communities over 4 months were systematically examined for the first time. Generally, soil bacterial communities were influenced in both the 1-month and 4-month scenarios through HBCD and PE separately as well as combined exposure. After 4 months of exposure, PE and combined exposure significantly affected soil bacterial alpha diversity, however, low concentration of HBCD showed no apparent influence. 1-month and 4-month HBCD, PE, and combined exposure significantly influenced bacterial beta diversity. Compared with 1 month of exposure, HBCD, PE, and combined exposure demonstrated remarkable influences on soil bacteria after 4 months of exposure, especially on Nitrospirae, Elusimicrobia, Rokubacteria at the phylum level, and on MND1, Ruminiclostridium, Lysobacter, Anaeromyxobacter, Alistipes, WCHB1 at the genus level. The bacterial function analysis indicated that amino acid metabolism, carbohydrate metabolism, and membrane transport were the three predominant enriched bacterial functions after 1-month and 4-month HBCD and PE exposure. This research provides a comprehensive grasp of the effects of HBCD and PE pollution on soil microbial communities, which could have a beneficial impact on future soil pollution control.

Insight into the spatiotemporal distribution of antibiotic resistance genes in estuarine sediments during long-term ecological restoration

In this study, we aimed to investigate the long-term spatiotemporal changes in hydrodynamics, antibiotics, nine typical subtypes of antibiotic resistance genes (ARGs), class 1 integron gene (intI1), and microbial communities in the sediments of a semi-enclosed estuary during ecological restoration with four treatment stages (influent (#1), effluent of the biological treatment area (#2), oxic area (#3), and plant treatment area (#4)). Ecological restoration of the estuary reduced common pollutants (nitrogen and phosphorus) in the water, whereas variations in ARGs showed noticeable seasonal and spatial features. The absolute abundance of ARGs at sampling site #2 considerably increased in autumn and winter, while it significantly increased at sampling site #3 in spring and summer. The strong intervention of biological treatment (from #1 to #2) and aerators (from #2 to #3) in the estuary substantially affected the distribution of ARGs and dominant antibiotic-resistant bacteria (ARB). The dominant ARB (Thiobacillus) in estuarine sediments may have low abundance but important dissemination roles. Meanwhile, redundancy and network analysis revealed that the microbial communities and intl1 were key factors related to ARG dissemination, which was affected by spatial and seasonal ecological restoration. A positive correlation between low flow velocity and certain ARGs (tetM, tetW, tetA, sul2, and ermC) was observed, implying that flow optimization should also be considered in future ecological restoration to remediate ARGs. Furthermore, the absolute abundance of ARGs can be utilized as an index to evaluate the removal capacity of ARGs by estuarine restoration.

Impact of microplastics on lead-contaminated riverine sediments: Based on the enzyme activities, DOM fractions, and bacterial community structure

Microplastics (MPs) are able to interact with diverse contaminants in sediments. However, the impacts of MPs on sediment properties and bacterial community structure in heavy metal-contaminated sediments remain unclear. In this study, we investigated the adsorption of Pb(II) by sediment-MPs mixtures and the effects of different concentration MPs on sediment enzyme activities, DOM fractions, and Pb bioavailability in riverine sediments, and further explored the response of sediment microbial community to Pb in the presence of MPs. The results indicated that the addition of MPs significantly decreased the adsorption amount of Pb(II) by sediments, especially decreased by 12.6% at 10% MPs treatment. Besides, the changes in enzyme activities, DOM fractions exhibited dose-dependent effects of MPs. The higher level of MPs (5% and 10%) tends to transform Pb into more bioavailable fractions in sediments. Also, MPs amendment was observed to alter sediment bacterial community structures, and community differences were evident in the uncontaminated and lead-contaminated sediments. Therein, significant increase of Bacteroidota, Proteobacteria and decrease of Firmicutes abundance in Pb-contaminated sediment at the phylum level were observed. These findings are expected to provide comprehensive information for assessing the combined ecological risks of heavy metals and MPs in riverine sediments.

Characterization of the responses of soil micro-organisms to azoxystrobin and the residue dynamics of azoxystrobin in wheat-corn rotation fields over two years

Azoxystrobin, a high-efficiency and broad-spectrum strobilurin fungicide, has been widely used in global agricultural production. However, the effects of azoxystrobin on soil micro-organisms have scarcely been studied, and relevant experiments are usually conducted under laboratory conditions using active ingredient. Therefore, the effects of azoxystrobin on soil micro-organisms when applied to actual farmland are unknown. We sought to address this knowledge gap in this study, where we studied the effects of azoxystrobin on soil micro-organisms in a wheat-corn rotation field over two years. The results indicate that after two years of azoxystrobin application the activities of soil enzymes were inhibited, and the abundance of functional genes related to the nitrogen and carbon cycle were inhibited, which change the abundance of soil microbial bacteria of genera. As a consequence, the soil nitrogen and carbon cycles were disturbed. In addition, azoxystrobin inhibited the abundance of functional bacteria related to organic pollutant degradation and soil metabolism, where the rate of azoxystrobin degradation diminished over time. Moreover, azoxystrobin significantly inhibited the soil-culturable microbial population. The integrated biomarker response (IBR) indicated that the soil-culturable microbial population can be used as a sensitive indicator of the effect of azoxystrobin on soil micro-organisms. The final levels of azoxystrobin residues measured in grains were less than 0.004 mg/kg, lower than the maximum residue limits in European Union and China. The results of this study provide a basis for suggestions regarding the appropriate use of azoxystrobin in addition to support for elucidating the interaction between biological macromolecules and pollutants.

Non-targeted metabolomics and 16s rDNA reveal the impact of uranium stress on rhizosphere and non-rhizosphere soil of ryegrass

As a radioactive heavy metal element with a long half-life, uranium causes environmental pollution when it enters the surrounding soil. This study analyzed the changes about soil enzyme activity, non-targeted metabolomics, microbial community structure and function microbial community structure and function to assess the differences in the effects of uranium stress on rhizosphere and non-rhizosphere soil. Results showed that uranium stress significantly inhibited the activities of urease and sucrase in rhizosphere and non-rhizosphere, which had less effect on rhizosphere. Compare to the non-rhizosphere soil, the uranium stress induced the production of gibberellin A1, to promoted several metabolic pathways, such as nitrogen and PTS (Phosphotransferase system) metabolic in rhizosphere soil. The species and abundance of Aspergillus, Acidobacter, and Synechococcus in both rhizosphere and non-rhizosphere soil were decreased by uranium stress. However, the microorganisms in rhizosphere soil were less inhibited according to the soil metabolism and microbial network map analysis. Furthermore, the Chujaibacter in rhizosphere soil under uranium stress was found significantly positively correlated with lipid and organic oxygen compounds. Overall, the results indicated that ryegrass roots significantly alleviated the effects of uranium stress on soil microbial activity and population abundances, thus playing a protective role. The study also provided a theoretical basis for in-depth understanding of the biological effects, prevention and control mechanisms of uranium-contaminated soil.

The thermal degradation and soil recovery of thermal treatment of field-weathered decabrominated diphenyl ether-contaminated soil

A farm at Taoyuan in Taiwan was highly contaminated with decabrominated diphenyl ether (BDE-209), a widely used commercial brominated flame retardant and persistent in the environment, more than 10 years. Since crops are able to absorb and accumulate BDE-209 from soils in our previous research, posing a hazardous risk for humans, it is essential to develop a practical method of soil treatment. Thermal treatment was studied among different approaches. In our previous study (Ko et al., 2022), we found that heating to 450 °C for 30 min achieved a complete removal of BDE-209 in soil. However, the high temperature significantly decreased the original soil organic matter (SOM) from 2.47% to 0.27%, altering the soil texture, damaging microbial biomass, and thus affecting the revegetation after the thermal treatment. Sugarcane bagasse, a common agricultural residue, served as an amendment to restore soil fertility. Current results indicate that 2.5% bagasse can improve the SOM in soil by up to 2.73% and restore its bacterial composition, making the plant growth conditions similar to those of the untreated contaminated soil. In light of the high removal efficiency provided by the 450°C-thermal treatment and the high recovery efficiency of sugarcane bagasse, the strategy presented in this study serves to be a promising method for sustainable remediation.

Occurrence, spatial distribution, and risk assessment of brominated flame retardants in farmland soils of typical provinces in China

In the present study, we investigated the occurrence, distribution, and potential risks of 4 brominated flame retardants in farmland soils across 18 provinces of China. The total mean concentrations of the BFRs were in order as DBDPE > BDE209 > HBB > TBB. DBDPE concentration was highest at 177.208 ng/kg, revealing its long-term use and persistence across the study areas. In parts of China, DBDPE was highest in the south (Sichuan, Shaanxi and Guangdong provinces), BDE209 was highest in the south (Sichuan province) and north (Jilin province), while HBB was highest in the south (Sichuan province) and east (Anhui and Zhejiang provinces) of China. Comparisons of the results in this study to other reported studies in different regions indicated that the studied BFRs concentrations were higher in the studied provinces of China. Pearson correlation between BFRs revealed both positive and negative associations within the BFRs groups and between BFRs and soil properties (SOM, CEC, pH, EC and PS%). The mean hazard quotients (HQ) of ecological risks ranged from 8.76 × 10^-6 to 1.16 × 10^-2 (HQ < 1) while non-carcinogenic human health risk evaluation for adults ranged from 7.05 × 10^-7 - 7.48 × 10^-4 (HQ < 1) and for children 2.99 × 10^-4 - 4.30 × 10^-2 (HQ < 1). Although the risk evaluations of BFRs from farmland soils in this study were low, the results serve as useful indicators of potential cumulative and long-term threats of BFR to rural areas where there is a high conversion of agricultural lands to non-agricultural use.

Effects of combined pollution of organic pollutants and heavy metals on biodiversity and soil multifunctionality in e-waste contaminated soil

Electronic waste (e-waste) is increasing globally, but the impact of this source of combined pollution on soil biodiversity and multiple soil functions (i.e., ecosystem multifunctionality) remains unclear. Here, we evaluated the effects of combined pollution on the biodiversity and soil multifunctionality using samples collected from upland and paddy soils chronically contaminated with e-waste. Overall biodiversity, as well as the relative abundance and biodiversity of key ecological clusters, as combined pollution concentrations increased in upland soil, while the opposite was true in paddy soil. Soil multifunctionality followed the same trend. Organic pollutants had significant negative effects on soil multifunctionality and were the main influencing factors in upland soil. Heavy metals had significant positive effects on soil multifunctionality in paddy soil. Moreover, driving soil multifunctionality was overall biodiversity in upland soil but key biodiversity in paddy soil. Importantly, a strong positive association between key organism biodiversity and soil multifunctionality was found in soil with low contamination. However, the relationship between key organism biodiversity and soil multifunctionality weakened or disappeared in highly contaminated soil, whereas overall biodiversity was significantly and positively correlated with multifunctionality. Our results emphasized that severe e-waste contamination would reduce soil biodiversity and soil multifunctionality and warrants high attention.

Airlift two-phase partitioning bioreactor for dichloromethane removal: Silicone rubber stimulated biodegradation and its auto-circulation

Solid non-aqueous phases (NAPs), such as silicone rubber, have been used extensively to improve the removal of volatile organic compounds (VOCs). However, the removal of VOCs is difficult to be further improved because the poor understanding of the mass transfer and reaction processes. Further, the conventional reactors were either complicated or uneconomical. In view of this, herein, an airlift bioreactor with silicone rubber was designed and investigated for dichloromethane (DCM) treatment. The removal efficiency of Reactor 1 (with silicone rubber) was significantly higher than that of Reactor 2 (without silicone rubber), with corresponding higher chloride ion and CO₂ production. It was found that Reactor 1 achieved a much better DCM shock tolerance capability and biomass stability than Reactor 2. Silicone rubber not only enhanced the mass transfer in terms of both gas/liquid and gas/microbial phases, but also decreased the toxicity of DCM to microorganisms. Noteworthily, despite the identical inoculum used, the relative abundance of potential DCM-degrading bacteria in Reactor 1 (91.2%) was much higher than that in Reactor 2 (24.3%) at 216 h. Additionally, the silicone rubber could be automatically circulated in the airlift bioreactor due to the driven effect of the airflow, resulting in a significant reduction of energy consumption.

Responses of microbial communities and metabolic profiles to the rhizosphere of Tamarix ramosissima in soils contaminated by multiple heavy metals

Heavy metals (HMs) contamination around smelters poses serious stress to soil microbiome. However, the co-effect of multiple HMs and native vegetation rhizosphere on the soil ecosystem remains unclear. Herein, effects of high HMs level and the rhizosphere (Tamarix ramosissima) on soil bacterial community structure and metabolic profiles in sierozem were analyzed by coupling high-throughput sequencing and soil metabolomics. Plant roots alleviated the threat of HMs by absorbing and stabilizing them in soil. High HMs level decreased the richness and diversity of soil bacterial community and increased numbers of special bacteria. Plant roots changed the contribution of HMs species shaping the bacterial community. Cd and Zn were the main contributors to bacterial distribution in non-rhizosphere soil, however, Pb and Cu became the most important HMs in rhizosphere soil. HMs induced more dominant metal-tolerant bacteria in non-rhizosphere than rhizosphere soil. Meanwhile, critical metabolites varied by rhizosphere in co-occurrence networks. Moreover, the same HMs-tolerant bacteria were regulated by different metabolites, e.g. unclassified family AKYG1722 was promoted by Dodecanoic acid in non-rhizosphere soil, while promoted by Octadecane, 2-methyl- in rhizosphere soil. The study illustrated that high HMs level and rhizosphere affected soil properties and metabolites, by which soil microbial community structure was reshaped.

How heavy metal stress promotes dissemination of antibiotic resistance genes in the activated sludge process

Heavy metals have been recently revealed as promoters to antibiotic resistance gene (ARG) dissemination in water environment, but their influence on ARG transfer in the activated sludge process has not been clear. In this study, a set of sequencing batch reactors (SBRs) and micro-scale microfluidic chips were established to quantify the impacts of heavy metals (0.5 mM of Pb, 0.1 mM of As, and 0.005 mM of Hg) on the ARG spreading in the activated sludge consortium. Under heavy metal stress, transfer frequencies were 1.7-3.6 folds increase compared to the control. Gram-negative bacteria increased significantly after heavy metal added, which were more prone to receiving resistant plasmid from donors. Meanwhile, the relative expression of genes related to conjugation changed in activated sludge, especially the expression of outer membrane protein and oxidative stress regulatory genes increased by 2.9-7.4 folds and 7.8-13.1 folds, respectively. Furthermore, using microfluidic chips, the dynamics of ARG transfer was observed at single cell level under heavy metal pressure. Heavy metals firstly promoted conjugation and then vertical gene transfer played an important part for ARG spreading. The results provided in-depth understanding of the influence of heavy metals on ARG behavior in the environment.

Isolation and Genome Sequence of a Novel Phosphate-Solubilizing Rhizobacterium Bacillus altitudinis GQYP101 and Its Effects on Rhizosphere Microbial Community Structure and Functional Traits of Corn Seedling

Bacillus altitudinis is a widely distributed soil bacterium that has various functional activities, including remediation of contaminated soil, degradation of herbicides, and enhancement of plant growth. B. altitudinis GQYP101 was isolated from the rhizosphere soil of Lycium barbarum L. and demonstrated potential as a plant growth-promoting bacterium. In this work, strain GQYP101 could solubilize phosphorus, and increased the stem diameter, maximum leaf area, and fresh weight of corn in a pot experiment. Nitrogen and phosphorus contents of corn seedlings (aerial part) increased by 100% and 47.9%, respectively, after application of strain GQYP101. Concurrently, nitrogen and phosphorus contents of corn root also increased, by 55.40% and 20.3%, respectively. Furthermore, rhizosphere soil nutrients were altered and the content of available phosphorus increased by 73.2% after application of strain GQYP101. The mechanism by which strain GQYP101 improved plant growth was further investigated by whole genome sequence analysis. Strain GQYP101 comprises a circular chromosome and a linear plasmid. Some key genes of strain GQYP101 were identified that were related to phosphate solubilization, alkaline phosphatase, chemotaxis, and motility. The findings of this study may provide a theoretical basis for strain GQYP101 to enhance crop yield as microbial fertilizer.

How microorganisms tell the truth of potentially toxic elements pollution in environment

Potentially toxic elements (PTEs) posed a major hazard to microbial community in river sediments, but the way how different kinds of microorganisms responses to elements pollution has not been clearly understood. The target of this research was to discriminate the apposite indicators for diagnosing elements pollution based on the sensitivity of microbial abundance, biodiversity, predicted metabolic functions to PTEs (Cu, Cd, Cr, Ni, Pb, Zn, As and Hg). Considering Huaihe River Basin as the main subject, sediment samples were gathered from 135 sites. Ni, Zn and Cd significantly influenced the microbial communities and predicted functions. In general, the microbial sensitivity to PTEs was bacteria > archaea. Geo-accumulation index and potential ecological risk (PER) index suggested Hg and Cd were the significant contaminates and posed the most serious ecological risk in sediments. Structural Equation Model identified the bioindicators 1/nitrate reduction and rara taxa (Azoarcus) as reflect and speculate Hg and Cd pollution, respectively. PER was predicted by 1/nitrate reduction and rare taxa (Phaeodactylibacter and Illumatobacter). Results elucidated the rather role of rare taxa in indicating PTEs pollution. The findings contributed to provide useful reference for bioremediation of contaminated sediments under PTEs stress.

Remediation of soils co-contaminated with cadmium and dichlorodiphenyltrichloroethanes by king grass associated with Piriformospora indica: Insights into the regulation of root excretion and reshaping of rhizosphere microbial community structure

Cadmium (Cd) and dichlorodiphenyltrichloroethane (DDT) are frequently detected in agricultural soils, which poses a threat to public health. This study investigated the effects of inoculation of king grass with Piriformospora indica on the remediation of soils co-contaminated with Cd and DDTs. After treatment for 90 days, the dry shoot and root biomass of king grass inoculated with P. indica markedly increased by 13.0-15.8% and 24.1-46.4%, respectively, compared with those of uninoculated plants. Inoculation with P. indica also increased the uptake of Cd and DDTs by shoots and roots of king grass. The removal efficiency of Cd and DDTs from soils reached 4.88-17.4% and 48.4-51.0%, respectively, in the presence of king grass inoculated with P. indica. Under three Cd-DDTs contamination conditions, root secretion of organic acids, alcohol, and polyamines was distinctively stimulated by P. indica inoculation of king grass compared with planting king grass alone. After phytoremediation, changes in soil bacterial and fungal community composition occurred at different contamination levels. Overall, the results showed that king grass associated with P. indica can be adopted for phytoextraction of Cd and DDTs from moderately contaminated soils by regulating root excretion and reshaping rhizosphere microbial community structure.

Response of microorganisms to phosphate nanoparticles in Pb polluted sediment: Implications of Pb bioavailability, enzyme activities and bacterial community

In recent years, various phosphate nanoparticles (PNPs) have been synthesized and applied for in situ Pb remediation in laboratory investigations. Here, three kinds of PNPs, CMC-nClAP (carboxymethyl cellulose stabilized nano-chlorapatite), SDS-nClAP (sodium dodecyl sulfate stabilized nano-chlorapatite) and Rha-nClAP (rhamnolipid stabilized nano-chlorapatite) were used to investigate the influence of PNPs on Pb bioavailability, enzyme activities and bacterial community in Pb polluted sediment. Pb bioavailability can be reduced by the application of CMC-nClAP, SDS-nClAP and Rha-nClAP with the maximum increases of residual fraction to 57.2 %, 58.3 % and 61.4 %, respectively. Alternatively, catalase activity, urease activity and protease activity also changed with the remediation of PNPs. Microbes responded quickly to PNPs in different ways: bacterial richness was all increased while bacterial diversity was only increased with the application of SDS-nClAP. Three dominant species, Proteobacteria, Firmicutes and Bacteroidetes were redistributed differentially during the treatment of PNPs. Interestingly, PNPs didn't significantly change the bacterial community structure in treated samples and CMC-nClAP induced fewer changes in microbial activity and community as compared with SDS-nClAP and Rha-nClAP. Overall, our findings suggested that long-term exposure to PNPs would decrease Pb bioavailability, regulate enzyme activities and affect bacterial community in sediments. The Pb bioavailability, physical-chemical properties of PNPs and properties of chemical/bio-surfactant may determine the response of microorganisms to PNPs in Pb polluted sediment.

Tuber flours improve intestinal health and modulate gut microbiota composition

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Tuber flours decreased the body weight gain in rats compared with starches.

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Gut integrity and digestive/absorptive function were improved by whole flour diets.

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Gut microbiota in cecum and colon were reshaped by different diets.

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Butyric acid content in ileum, cecum and colon were increased by tuber flours.

The different health effects between starch and whole flour from tubers are rarely studied. Here, we investigated the effects of cassava flour (CF), cassava starch (CS), potato flour (PF), and potato starch (PS) on gut health and gut microbiota of normal rats. Feed analysis showed that CF and PF diet provided significantly more slowly digestible and resistant starch, less rapidly digestible starch. Compared with rats fed with PS and CS diets, rats fed with PF and CF diets gained less body weight and have tighter intestinal barrier. Butyric acid contents were increased by tuber flours. CF and PF selectively promoted the relative abundance of Akkermansia and Eubacterium ruminantium in cecal and colonic content. In conclusion, tuber flour has intestinal protection, body weight control, and gut microbiota improving ability compared with starch. The different composition of starch might be the basis for these effects.

Bacterial communities and their bioremediation capabilities in oil-contaminated agricultural soils

Rapid industrialization and development in petrochemical industries have resulted in increased hydrocarbon pollution causing substantial damage to the natural ecosystems including agricultural soils. In the recent, past efforts have been made to treat the contaminated soils using microorganisms by natural processes. Soil bacteria, known for their potential to degrade the soil contaminants, play a vital role in maintaining soil health. In the current study, we observed the influence of hydrocarbon contamination on the physicochemical characteristics and enzymatic activities of the soil. Proteobacteria (30.48%), Actinobacteria (13.91%), and Acidobacteria (12.57%) flourished in the non-contaminated soil whereas contaminated sites were dominated by Proteobacteria (44.02 ± 15.65%). In contrast, the sites experiencing the different degrees of exposure to the hydrocarbon pollution allowed specific augmentation of bacterial taxa (in decreasing order of exposure time), viz. Proteobacteria (60.47%), Firmicutes (32.48%), and Bacteroidetes(13.59%), based on culture-independent approach that suggested their potential role in hydrocarbon degradation as compared to the non-contaminated site. The imputation of metabolic function also supported the positive correlation to the exposure to hydrocarbon pollution, with site 2 being highly abundant for gene families involved in xenobiotics biodegradation. The study provides insights into bacterial community structure with special emphasis on their efficiency to degrade hydrocarbons. The results from the study can help in designing appropriate biodegradation strategies to mitigate the serious problems of oil contamination in agricultural soil.

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

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

Effects of antimony (III/V) on microbial activities and bacterial community structure in soil

Antimony (Sb) primarily exists in trivalent (III) and pentavalent (V) speciation in the soil environment and poses a potential threat to ecological soil function as a toxic metalloid element. To evaluate the ecological effect of Sb in soil, the effects of different concentrations of Sb(III) and Sb(V) on microbial biomass carbon (MBC), soil basal respiration (SBR), potential nitrification rate (PNR), five enzyme activities and bacterial community structure were investigated using biochemical methods and high-throughput sequencing technology during the 1st and 8th weeks of exposure. The results of these experiments indicated that MBC and SBR were influenced, and PNR, FDA hydrolysis activity and urease activity were significantly inhibited by Sb(III) and Sb(V), while the activities of dehydrogenase, acid phosphatase and β-glucosidase had no clear effects on the amounts of Sb(III) or Sb(V). Meanwhile, there are some discrepancies regarding the effects of Sb(III) and Sb(V) on the same microbial indicators, and incubation time is not a neglected factor. Sequencing analysis revealed that Sb(III) decreased the bacterial diversity indexes and abundances of specific bacteria at the phylum level, whereas Sb(V) had little effect on them. The bacterial community structure at the genus level was altered by Sb(III) and Sb(V), in which the abundances of some functional microbes were increased, while the abundances of some functional microbes were reduced under Sb pollution. In general, PNR, FDA hydrolysis activity, urease activity and the abundances of specific functional microbes (i.e., Nitrospira) could be considered as sensitive indicators of Sb contamination. This study highlights the ecological effect of Sb(III) and Sb(V) on agricultural soil and will provides references for environmental monitoring and assessment.

Bacterial community structure of aged oil sludge contaminated soil revealed by illumina high-throughput sequencing in East China

Screening of the dominant or core oil resistant bacteria in Aged Oil Sludge (AOS) contaminated soil in Daqing and Shengli oilfields (DQ and SL) in China was investigated through High-Throughput Sequencing method. Enhanced total organic carbon (TOC, 12.53 to 28.35 g/kg in DQ and 3.07 to 4.97 g/kg in SL) and total petroleum hydrocarbons (TPHs, 21 to 2837 mg/mg in DQ and 13 to 1558 mg/kg in SL) were observed. The internal transcribed spacer (ITS) sequencing by Illumine Miseq platform at each taxonomic level revealed the notable toxicological effect of AOS on the diversity and community structure of bacteria. In this study, sequence analyses showed 77-89% and 92-98% reduction of Firmicutes at phylum level in DQ and SL respectively after treated with AOS. Enhanced universal gene location was observed in Proteobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes in DQ and SL. The universal dominant family in the two oilfields was anaerolineaceae. At the genus level, Algiphilus in DQ and Pseudomonas in SL were the majority respectively. In total, 3 negligible genera (Perlucidibaca, Alcanivorax and Algiphilus) in DQ and 13 negligible genera (Salinisphaera, Microbulbifer and Idiomarina, et al.,) in SL were significantly enriched after oil treatment indicating their possible role in the attenuation of petroleum hydrocarbons.

Effects of cloransulam-methyl and diclosulam on soil nitrogen and carbon cycle-related microorganisms

Cloransulam-methyl and diclosulam are applied to soybean fields to control broad-leaved weeds. These herbicides have become a focus of attention because of their low application dose and high-efficiency advantages. However, the effects of these two herbicides on soil microorganisms are unknown. The present study investigated the effects of 0.05, 0.5, and 2.5 mg kg^-1 of cloransulam-methyl or diclosulam on soil microbes after 7, 14, 28, 42, and 56 days of exposure. The results showed that the two herbicides increased the abundances of functional bacteria related to pesticide degradation. Based on the genetic expression results, we speculated that 0.05 mg kg^-1 of these two herbicides inhibited the nitrification reaction but promoted the denitrification reaction. Diclosulam at a concentration of 0.5 mg kg^-1 may enhance the ability of microbes to fix carbon. β-glucosidase activity was activated by the two herbicides at a concentration of 2.5 mg kg^-1. Diclosulam had a positive effect on urease, but cloransulam-methyl activated urease activity only at concentrations of 0.05 and 0.5 mg kg^-1. The results of the integrated biomarker response showed that the toxicity of diclosulam was greater than that of cloransulam-methyl. Our research provides data for evaluating the environmental risks of cloransulam-methyl and diclosulam.

Effects of heavy metals on microbial communities in sediments and establishment of bioindicators based on microbial taxa and function for environmental monitoring and management

Heavy metals have always been a research hotspot due to their persistence, hazard and bioaccumulation. Microorganisms are highly sensitive to heavy metal pollution and play an important role in the material cycling and energy flow of the ecosystem. In order to further explore the influence of heavy metals on the diversity, composition, and function of microbial communities in the wetland sediment ecosystem, and to find suitable indicators to reflect heavy metal pollution status, we collected sediments from Huangjinxia nature reserve and determined the physicochemical properties, heavy metal (Cu, Cr, Ni, Pb, Zn, and Mn) concentrations, and microbial information. We found that: the contamination status of the study area stood at a moderate level evaluated by the pollution load index (PLI); heavy metals explained more of microbial community variation than the sediment physicochemical properties; in particular, Cr and Mn negatively affected microbial α-diversity; heavy metals significantly affected the structure of microbial communities, elements Cr, Pb, and Zn showed uniformly negative associations with the relative abundance of bacteria Nitrospirae (including class Nitrospira and order Nitrospirales), Bacteroidetes (including class Bacteroidia), and Verrucomicrobia; moreover, heavy metals affected predicted functions of microbial communities, including metabolic functions, genetic information processes, and functions related to the carbon cycle and the nitrogen cycle. Based on the relative abundance of sensitive microbial taxa and predicted functions, bioindicators [Bacteroidia], 1/[Nitrospira], 1/[Nitrification], and 1/[Aerobic nitrite oxidation] were established to reflect and predict the contamination status of heavy metals in sediments. Our in-depth research on the effects of heavy metals on microorganisms and the establishment of bioindicators provide references and new perspectives for environmental monitoring and management.

Global occurrence, chemical properties, and ecological impacts of e-wastes (IUPAC Technical Report)

The waste stream of obsolete electronic equipment grows exponentially, creating a worldwide pollution and resource problem. Electrical and electronic waste (e-waste) comprises a heterogeneous mix of glass, plastics (including flame retardants and other additives), metals (including rare Earth elements), and metalloids. The e-waste issue is complex and multi-faceted. In examining the different aspects of e-waste, informal recycling in developing countries has been identified as a primary concern, due to widespread illegal shipments; weak environmental, as well as health and safety, regulations; lack of technology; and inadequate waste treatment structure. For example, Nigeria, Ghana, India, Pakistan, and China have all been identified as hotspots for the disposal of e-waste. This article presents a critical examination on the chemical nature of e-waste and the resulting environmental impacts on, for example, microbial biodiversity, flora, and fauna in e-waste recycling sites around the world. It highlights the different types of risk assessment approaches required when evaluating the ecological impact of e-waste. Additionally, it presents examples of chemistry playing a role in potential solutions. The information presented here will be informative to relevant stakeholders seeking to devise integrated management strategies to tackle this global environmental concern.

River bacterial community structure and co-occurrence patterns under the influence of different domestic sewage types

Bacterial communities play a critical role in food webs and the biogeochemical cycles of fundamental elements. However, there remains a substantial gap in our knowledge of the anthropogenic impacts on bacterial co-occurrence patterns and ecosystem functions. In this study, we used Illumina high-throughput sequencing to characterize and compare the diversity, composition, co-occurrence patterns, and functional changes in bacterial communities in the Qingliu River under the influence of different types of domestic sewage. Twelve samples had similar dominant phyla, mainly Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, differing only in the proportions of the microorganisms. However, there was a large difference at the genus level, for example, the relative abundance of the genus Dechloromonas in the school sewage water samples (XXW) was much higher than that in the other samples, the genus Chryseobacterium was the dominant bacteria in the residential sewage water samples (JMW), and there were significant differences between the different samples (P < 0.01). This may indicate that external pollution and environmental induction deeply affect the bacterial community assembly in rivers. Network analysis showed that the river bacterial co-occurrence network has a modular structure (divided into 6 modules), and that the microbial taxonomic units from the same module were involved in the carbon and nitrogen cycle (e.g., the CL500-29 marine group and the genus Pseudomonas) and degradation of organic pollutants and toxic compounds (e.g., the genera Massilia and Exiguobacterium). Functional predictions indicate that the function of ABC transporter was highest in the hospital sewage water samples (YYW), while two-component system was more abundant in the XXW samples. In summary, our research provides a new perspective of community assembly in rivers under the influence of human activity.

Activation of integrated stress response and disordered iron homeostasis upon combined exposure to cadmium and PCB77

Both cadmium and polychlorinated biphenyls (PCBs) can induce diverse detrimental effects on human health. Though these compounds co-exist in various environmental contexts and in the human body, studies on their joint toxicities are limited. Activation of the integrated stress response (ISR) and iron homeostasis are crucial for erythropoiesis. The impact of cadmium and PCBs on the ISR activation and iron homeostasis of erythroid progenitors is unknown. We investigated the adverse effects and mechanisms of CdCl₂ and PCB77 on HEL cells, a human cell model of erythroid progenitors. We found that at high concentrations of CdCl₂ and PCB77, cytotoxicity and apoptosis of HEL cells were mainly induced by CdCl₂. At low concentrations of CdCl₂ and PCB77, iron homeostasis inside HEL cells was disturbed by both of these two compounds. Both CdCl₂ and PCB77 activated ISR to combat stress, which at high concentration was mainly induced by ROS, leading to apoptosis, and at low concentration was partly induced by disordered iron homeostasis. The patterns of ISR activation and iron homeostasis disorder were different between CdCl₂ and PCB77. Their combined exposure exhibited synergetic effect on activating ISR but antagonistic effect on disturbing iron homeostasis. Our study demonstrates some previously unrecognized harmful characteristics and mechanisms of cadmium and PCB77.

Effects of Bacillus velezensis FKM10 for Promoting the Growth of Malus hupehensis Rehd. and Inhibiting Fusarium verticillioides

Bacillus velezensis is a novel species of Bacillus that has been widely investigated and used because of its direct or indirect growth improvement effect for many plants. B. velezensis FKM10 was previously isolated from rhizosphere soil of apple trees and shows potential as a plant growth-promoting and biocontrol bacterium. In this study, strain FKM10 was verified to inhibit some fungal pathogens of soil-borne plant diseases, produce siderophores to absorb ferric iron for plants, and degrade proteins. Pot experiments showed that the application of strain FKM10 could directly promote the growth of Malus hupehensis Rehd. by increasing biomass, promoting the absorption of nutrients, improving soil fertility, changing the soil microbial community structure, and reducing fungal diversity. The results of this study provided a basis for using strain FKM10 to improve crop yield and overcome diseases of plants. The mechanism of strain FKM10 to control the phytopathogenic fungus Fusarium verticillioides was studied by interoperation with RNA sequencing. Strain FKM10 can destroy the cell wall and cell membrane of F. verticillioides. The secretion of glucosidases, such as β-glucanase, might be one of the causes of the destruction of the fungal cell wall. The regulation of amino acid metabolism might also play an important role in the antibacterial process of strain FKM10. During the antibacterial process, strain FKM10 attacks F. verticillioides and strain FKM10 itself is also affected: the expression of spores is increased, the number of viable cells is decreased, and the ribonucleoprotein complex and flagellar assembly-related genes are downregulated. The results of this study indicate that both strain FKM10 and F. verticillioides have mutually inhibitory activities in a liquid environment. Comparative genome analysis of B. velezensis FKM10 reveals that the general features of their genomes are similar overall and contain the core genome for this species. The results of this study further reveal that B. velezensis can also serve as a basis for developing new biocontrol agents or microbial fertilizers.

The effects of ectomycorrhizal fungi on heavy metals' transport in Pinus massoniana and bacteria community in rhizosphere soil in mine tailing area

Pinus massoniana is one of the potential tree species of afforestation in barren mine tailing area, and ectomycorrhizal fungi contributes remarkably to its survival. However, how ectomycorrhizal fungi interacts with Pinus massoniana under heavy metals' stress is unknown. Two systems (Pinus massoniana inoculated with and without ectomycorrhizal fungi) were designed, and each system contained rhizosphere and non-rhizosphere, while bulk soil was sampled as control. The results showed that treatment of ectomycorrhizal fungi inoculation could obviously improved the absorption of soil moisture, total carbon/total nitrogen and nutrients, while reduced the bulk density and heavy metals of soil when compared with control (p＜0.05). The heavy metals accumulating in plants' roots with ectomycorrhizal fungi were greater than that without ectomycorrhizal fungi. Conversely, they were lower in shoots with ectomycorrhizal fungi. The bacterial community were affiliated with 23 bacterial phyla, 70 classes, 115 orders, 201 families, and 363 genera. Constrained Principal Coordinate Analysis and redundancy analysis demonstrated that bacterial communities structure in the soil inoculated with or without ectomycorrhizal fungi and bulk soil were distinguishable, but no difference between rhizosphere and non-rhizosphere. The LEfSe analysis showed Acidobacteria, Actinobacteria, and Proteobacteria were the dominant phyla that contributed to the difference among treatments.

Effects of decabromodiphenyl ether on activity, abundance, and community composition of phosphorus mineralizing bacteria in eutrophic lake sediments

Polybrominated diphenyl ethers (PBDEs) are typical persistent organic pollutants (POPs) in the environment. However, little is known about their effects on phosphorus mineralizing bacteria (PMB) in eutrophic lake sediments, despite the critical role of PMB in phosphorus (P) biogeochemical cycling. In this study, we carried out a 60-day microcosm experiment to understand the effects of 2 and 20 mg kg^-1 dry weight decabromodiphenyl ether (BDE-209) on the activity, abundance, diversity, and community composition of PMB in the sediment of Taihu Lake, a typical eutrophic lake in China. The results showed that BDE-209 contamination, regardless of the contamination levels, significantly increased the orthophosphate concentration in overlying water and available phosphorus concentration in sediments on day 60. Such increases may be explained by the stimulatory effects of BDE-209 on alkaline phosphatase (ALP) activity and PMB abundance. Moreover, based on Miseq sequencing of the phoD gene encoding ALP, Actinobacteria was the dominant PMB phylum in all treatments, and BDE-209 significantly increased the diversity of PMB and altered their community composition. In particular, the relative abundances of some PMB genera such as Bradyrhizobium were increased significantly after 60 days of the High treatment. A co-occurrence network analysis further revealed that the high level of BDE-209 contamination strengthened the connectivity and interspecific co-operative relationships in the PMB community. These results will help us to understand the effects of POPs on P biogeochemical cycling in eutrophic lakes and the associated microbial mechanisms.

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

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

The activation and extraction systems using organic acids and Lentinus edodes to remediate cadmium contaminated soil

To develop a high efficient and eco-friendly approach to remediate cadmium (Cd) contaminated soil, we designed the activation and extraction systems, on the basis of combined effects between the ability of organic acids to activate Cd and the ability of mushroom accumulator (Lentinus edodes) to extract Cd. The results showed that the proportion of acetic acid-extractable Cd significant increased with the application of exogenous organic acids. Additionally, soil microecology analysis indicated that exogenous organic acids evidently enhanced the numbers of microbial cells and the activities of soil enzymes. Besides, high throughput sequencing analysis revealed exogenous organic acids improved the diversity and structure of soil bacterial community after remediation. Particularly, the combination application of mushroom and exogenous citric acid had highest accumulation efficiency of Cd, and its efficiency was 59.19% higher than single mushroom treatment. Hence, exogenous organic acids could alleviate soil microecology and increase mycoextraction efficiency, which suggested it was a feasible route to remediate Cd contaminated soil by the activation and extraction systems.

Phytoremediation of cadmium-contaminated soil by Sorghum bicolor and the variation of microbial community

In this paper, the growth of S. bicolor in Cd-polluted sandy clay loam soil in north China, Cd accumulation in plant and the corresponding soil microbial community were characterized when the plant matured (140 d of growth). Cadmium promoted the growth of mature S. bicolor with higher height and heavier dry mass, especially at the spiked level of 1 mg kg^-1 soil (P < 0.05). The higher microbial diversity was found under Cd stress at the spiked level of 15 mg kg^-1, which basically corresponded with its influence on the plant growth. High-throughput sequencing data demonstrated that the predominant bacterial phyla include Proteobacteria (35.99% for Cd-polluted soil and 35.22% for the control soil), Chloroflexi (21.33% and 20.58%), Actinobacteria (12.00% and 12.89%), Acidobacteria (7.47% and 11.14%), Bacteroidetes (7.37% and 6.96%), Gemmatimonadetes (5.60% and 6.65%), Firmicutes (2.82% and 1.86%), Planctomycetes (2.47% and 0.95%), Saccharibacteria (1.26% and 1.11%). The predominant fungal phyla was Ascomycota, with the relative abundance of 89.96% for the control soil and 86.2% for the Cd-polluted soil. S. bicolor could grow well in sandy clay loam soil in northern China at low Cd lvel, but it could not accumulate cadmium at higher cadmium level. S. bicolor could be used for phytoextraction of cadmium from the lightly Cd-polluted soil.

Biodegradability and ecological impacts of polyethylene-based mulching film at agricultural environment

Discarded Polyethylene (PE) mulches have posed a persistent pollution in the agricultural field. Although PE degraded by microbes has been reported, the effect on in situ soil environment is not completely understood. To determine the biodegradability and ecological impacts of PE-based mulches, we tested the biodegradation related properties of screened strains and analyzed change in soil quality and microbial community after covering with different mulches. Strain Bacillus aryabhattai 5-3 showed 3.85 ± 0.50% gravimetric weight loss after a 30 days incubation with PE-based mulch as the sole carbon source; Considerable pits and vast cavities were found on the surface using AFM and SEM. The hydrophobicity of mulch sheet was decreased to 68.9 ± 0.8°, FTIR identified that new oxidized groups were formed on the surfaces of incubated mulch. Additionally, the fluctuations of microbial communities indicate that synthetic mulch could replace the current commercial product to minimise agricultural pollution.

Enhanced reductive dechlorination of 1,1,1-trichloroethane using zero-valent iron-biochar-carrageenan microspheres: preparation and microcosm study

In this study, a composite remediation material for the enhanced reductive dechlorination (ERD) of 1,1,1-trichloroethane (1,1,1-TCA) in aqueous solution was prepared. This material was comprised of biochar as the carrier and adsorbent, and carrageenan (CG) as the embedding medium to entrap the organic carbon sources and zero-valent iron (ZVI). We determined the suitable biochar dosage and organic carbon source in the composite alongside the optimal preparation conditions. Furthermore, using an anaerobic microcosm study, we discussed the performance and possible mechanisms of the composite on 1,1,1-TCA removal in aqueous solution. From this, we found that the suitable dosage of biochar in water during the preparation of composite microspheres was 0.2% (w/v). Under this condition, the biochar had a strong capacity to adsorb 1,1,1-TCA with a removal efficiency of 84.2%. Soluble starch was selected as the appropriate organic carbon source, because starch-microspheres show an excellent slow-release effect in water. The optimal preparation conditions of microspheres were identified as follows: 2% CG (w/v) colloidal solution, 6% CaCl₂ (w/v) solution, and a 12-h curing time. After 25-day incubation with the composite prepared under optimized conditions, the removal efficiency of 1,1,1-TCA was 95.68%, which was 24.69% higher than that observed in the microcosm with a commercial remediation material. The scanning electron microscopy (SEM) images show that the amounts of ZVI and soluble starch inside the microsphere decreased obviously, while the biochar amount remained about the same. This indicates that 1,1,1-TCA in aqueous solution was mainly removed via soluble starch-enhanced biotic reductive dechlorination and ZVI-enhanced abiotic reductive dechlorination. The changes in microbial community structure demonstrate that the composite stimulated the activities of functional anaerobic bacteria, in particular, regarding dechlorination and fermentation abilities in the microcosm, therefore enhancing the anaerobic biodegradation of 1,1,1-TCA. This study suggests that the composite, entrapping biochar, ZVI, and organic carbon source in CG microspheres can significantly enhance the reductive dechlorination of 1,1,1-TCA in aqueous solution. We anticipate this novel remediation material could be successfully applied to the in situ ERD remediation of natural groundwater mainly contaminated with 1,1,1-TCA.

Effects of soil properties, heavy metals, and PBDEs on microbial community of e-waste contaminated soil

Heavy metals and polybrominated diphenyl ethers (PBDEs) are ubiquitous pollutants at electronic waste (e-waste) contaminated sites, their individual impacts on soil microbial community has attracted wide attention, however, limited research is available on the combined effects of heavy metals and PBDEs on microbial community of e-waste contaminated. Therefore, combined effects of heavy metals and PBDEs on the microbial community in the e-waste contaminated soil were investigated in this study. Samples were collected from Ziya e-waste recycling area in Tianjin, northern China, and the soil microbial communities were then analyzed by the high-throughput MiSeq 16S rRNA sequencing to assess the effects of soil properties, heavy metals, and PBDEs on the soil microbial community. Candidatus Nitrososphaera, Steroidobacter and Kaistobacter were the dominant microbial species in the soils. Similar microbial metabolic functions, including amino acid metabolism, carbohydrate metabolism and membrane transport, were found in all soil samples. Redundancy analysis and variation partition analysis revealed that the microbial community was mainly influenced by PBDEs (including BDE 183, BDE 99, BDE 100 and BDE 154) in horizontal soil samples. However, TN, biomass, BDE 100, BDE 99 and BDE 66 were the major drivers shaping the microbial community in vertical soil samples.

Diagnosis of soil contamination using microbiological indices: A review on heavy metal pollution

Heavy metal contamination of soil has become a serious global issue because of their persistence in the environment and the non-biodegradable nature leading to their accumulation to toxic levels. In order to achieve early warning and prevent soil quality from deteriorating, it is necessary to select suitable indices to diagnose heavy metal pollution. Microbiological indices for monitoring soil pollution by heavy metals are gaining attention. However, the related researches are scattered, and critical review is imperative. This review is mainly to provide readers with an in-depth understanding of the merits and limitations of microbiological indices for heavy metals contaminated and remediated soils. Microbiological indicators include microbial abundance, community diversity and structure, functional activity. The changes of different microbiological indices and the mechanism of microbial response to heavy metal stress in soils are comprehensively summarized. Furthermore, research gaps and future directions of the microbial ecotoxicological diagnosis of soil contamination by heavy metals are also proposed and discussed.

Analyses of artificial morel soil bacterial community structure and mineral element contents in ascocarp and the cultivated soil

This study explored the differences among various artificial morel cultivations as well as the factors that influence these differences, including soil bacterial community structure, yield, and mineral element contents of ascocarp and the cultivated soil. High-throughput sequencing results revealed that the dominant bacterial phyla in all the samples, including Proteobacteria, Acidobacteria, Chloroflexi, Bacteroides, and Gemmatimonadetes, were found not only in morel soils (experimental group) but also in wheat soil (control group); the highest richness and diversity in the soil bacteria were observed during the primordial differentiation stage. The M6 group exhibited the highest yield (271.8 g/m²) and had an unexpectedly high proportion of Pseudomonas (25.30%) during the primordial differentiation stage, which was 1.77∼194.62 times more than the proportion of Pseudomonas in other samples. Pseudomonas may influence the growth of morel. The mineral element contents of the different soil groups and the ascocarp were determined by electrothermal digestion and inductively coupled plasma mass spectrometry. The results revealed that morel had high enrichment effects on phosphorus (P, bioconcentration factor = 16.83), potassium (K, 2.18), boron (B, 1.47), zinc (Zn, 1.36), copper (Cu, 1.15), and selenium (Se, 2.27). P levels were the highest followed by Se and K, and the mineral element contents in ascocarp were positively correlated with the soil element contents.

Assessment of bacterial communities in Cu-contaminated soil immobilized by a one-time application of micro-/nano-hydroxyapatite and phytoremediation for 3 years

Heavy metals contamination of soil has been considered as a global environmental problem, and consequently various soil amendments have been widely used in immobilization. Previous studies have reported that micro-/nano-hydroxyapatite (MHA/NHA) as a novel chemical material could alleviate soil acidity and reduce the bioavailability of heavy metals. However, the mechanism of soil microorganism responding to the application of MHA/NHA is little studied. Presently, an in-situ field experiment was conducted to determine the effects of MHA/NHA and the other three traditional amendments including alkali slag (AS), lime (L) and apatite (AP) on soil copper (Cu) bioavailability and dominate bacterial population. The results showed that the application of MHA/NHA effectively increased soil pH and decreased soil available Cu content, and showed the highest increasing effects on the activities of urease, catalase and acid phosphatase. Compared with the control, MHA/NHA significantly changed the soil bacterial community structure and increased the bacterial abundance and diversity. Besides, analysis of the dominate population showed that the application of MHA/NHA decreased the relative abundance of acidophiles and the indicator of soil degradation. Additionally, the relative abundance of potential plant growth promoting bacteria increased with the addition of MHA/NHA, which was confirmed by the characteristics (the ability of producing indole acetic acid and siderophore) of bacterial strains. These results suggested that these dominate bacterial populations with significant changes may be regarded as the biomarkers for the recovery of soil ecological environment, which provides a theoretical basis for the ecological evaluation of MHA/NHA.

Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems

Soil bacterial communities have complex regulatory networks, which are mainly associated with soil fertility and ecological functions, and are likely to be disturbed due to antibiotics applications. The impact of antibiotics, particularly in mixtures form, on bacterial communities in different paddy soils is poorly understood. Using pyrosequencing techniques of 16 S rRNA genes, this study investigated the synergistic effects of veterinary antibiotics (sulfadiazine, sulfamethoxazole, trimethoprim, florfenicol, and clarithromycin) on bacterial communities in a soil-bacteria-plant system. Rice was grown under controlled greenhouse conditions where unplanted and planted treatments were doped with 200 µg kg^-1 of combined antibiotics over a period of 3 months. Bacterial richness remained unaltered, while a significant decline was observed in bacterial diversity due to antibiotics in the four paddy soils. Bacteroidetes and Acidobacteria were increased, while Actinobacteria and Firmicutes decreased under antibiotics exposure. Despite antibiotics perturbation, compositional variations were mainly attributed to the different paddy soils which harbor distinct bacterial communities. Haliangium and Gaiella were among the sensitive genera that were negatively correlated to antibiotics perturbation. Additionally, electrical conductivity, total organic carbon, and total nitrogen of soil solution were the key physiochemical indices which significantly influenced the structure of bacterial communities in the paddy soils. These findings expanded our knowledge of effects from synergistic antibiotics application and variations in bacterial communities among different paddy soils.

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community

Heavy metal contamination is a serious problem worldwide threatening soil environment and human health. In the present study, concentrations of 6 heavy metals at an electronic waste (e-waste) site in Nigeria were correlated to their mobility, showing distinct distribution pattern between surface soils and subsoils. Proteobacteria, Firmicutes, Acidobacteria and Planctomycetes dominated the indigenous soil microbial communities, and there was significant discrimination of bacterial taxonomic composition between the heavy metal contaminated and uncontaminated areas. The abundance of most bacterial taxa changed with heavy metal contamination level to different extent. The multivariate regression tree (MRT) analyses illustrated that main environmental variables influencing bacterial taxonomic composition included soil texture (31%) and organic carbon (14%), whereas microbial diversity was affected by soil pH (32%) and soil texture (14%). Our results surprisingly indicated that soil properties were more influential in determining soil bacterial composition and diversity than heavy metals even at the e-waste site which was seriously contaminated by heavy metals. The present study contributes to a deeper insight into the key environmental variables shaping the diversity and composition of soil microbes at heavy metal contaminated e-waste sites.

The soil bacterial community in cropland is vulnerable to Cd contamination in winter rather than in summer

Potentially toxic metal contamination exerts a significant impact on soil microbes, thus deteriorating soil quality. The seasonality also has effects in shaping soil microbial community. The soil microbial community is a crucial factor representing soil health. However, whether the influence of potentially toxic metals on the microbial community differs in different seasons are still unknown. In this study, we established nine mesocosms of three cadmium treatments to investigate the impact of Cd amendments on the bacterial community of croplands in winter and summer. High bacterial diversity was revealed from the soil samples with 31 phyla. In winter, the abundance of dominant phylum Bacteroidetes, Gemmatimonadetes, and Verrucomicrobia increased, but Firmicutes decreased in Cd-contaminated soil in winter. Meanwhile, the abundance of Actinobacteria, Planctomycetes, and Chloroflexi showed Cd dose-dependent pattern in winter. In summer, the phylum Gemmatimonadetes and Verrucomicrobia decreased along with Cd dosing, while the dose-effect of Cd was found on the abundance of Actinobacteria and Chloroflexi. At the genus level, 55 genera of bacteria were significantly affected by Cd stress in winter, 24 genera decreased, 11 genera increased along with Cd gradients, and 20 genera changed depending on Cd dosage. In particular, genera Lactococcus, Psychrobacter, Brochothrix, Enhydrobacter, and Carnobacterium disappeared in Cd treatments, suggesting high sensitivity to Cd stress in winter. In summer, one genus decreased, seven genera increased with Cd dosing, and three genera were dose-dependent. The contrasting effects of Cd on soil bacterial community could be due to different edaphic factors in winter (moisture, available phosphorus, and total Cd) and summer (available Cd). Collectively, the winter-induced multiple stressors increase the impact of Cd on bacterial community in cropland. In further studies, the seasonal factor should be taken into consideration during the sampling stage.

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China

Sediment is the one of most important storage of heavy metal. Microbiotas in sediment can be used as the effective indicators of heavy metals. The goal of this study was to understand the bacterial communities responding to heavy metal enrichment in sediments and prioritize some factors that affected significantly to bacterial community. Sediments were sampled from five river-lake systems in the Poyang Lake in dry season, and the bacterial community was analyzed using Illumina high-throughput sequencing. Relationships between sediment environment and the diversity and structure of bacterial communities were determined by correlation analysis and redundancy analysis (RDA). The result indicated that Cd and Sb were identified as the heavy metals of the great risk in sediments. Sediments from five river-lake systems shared 31.83% core operational taxonomic units (OTUs) of bacterial communities. Proteobacteria (33.54% of total sequences) and Actinobacteria (15.04%) were the dominant phyla across all sites. High enrichment of heavy metals (MRI and mC_d) resulted in low diversity of bacterial communities (Simpson index). The RDA revealed pH, OC, mCd, and Efs of As, Pb, Cd were major factors related to bacterial community structure changes. The dominant phylum Actinobacteria was regarded as tolerant bacteria, while the dominant phylum Proteobacteria was named as resistant bacteria in sediment with high anthropogenic Cd enrichment.

Toxicity responses of bacterial community as a biological indicator after repeated exposure to lead (Pb) in the presence of decabromodiphenyl ether (BDE209)

Continuous exposure of chemicals could cause various environmental impacts. Decabromodiphenyl ether (BDE209) and lead (Pb) can co-exist and are discharged simultaneously at e-waste recycling sites (EWRSs). Extensive concerns have been attracted by their toxic effects on soil microorganisms. Thus, by using high-throughput sequencing, this study explored bacterial community responses in a soil system after repeated Pb exposure in the presence of BDE209 in the laboratory during 90-day indoor incubation period. Gene sequencing of 16S rDNA performed on an Illumina MiSeq platform proved that one-off Pb exposure caused higher microbial abundance and community diversity. Additionally, both repetitive Pb treatment and exogenous BDE209 input could change bacterial community composition. Twenty-three different bacterial phyla were detected in the soil samples, while more than 90% of the sequences in each treatment belonged to a narrow variety. The sequence analyses elucidated that Proteobacteria, Acidobacteria, and Bacteroidetes were the top three dominant phyla. Our observations could provide a few insights into the ecological risks of Pb and BDE209 co-existed contamination in soils at EWRSs.

Effects of Aged Oil Sludge on Soil Physicochemical Properties and Fungal Diversity Revealed by High-Throughput Sequencing Analysis

The oilfield soil was contaminated for years by large quantities of aged oil sludge generated in the petroleum industry. In this study, physicochemical properties, contents of main pollutants, and fungal diversity of the aged oil sludge-contaminated soil were analyzed. Results revealed that aged oil sludge significantly changed physical and chemical properties of the receiving soil and increased the contents of main pollutants (petroleum hydrocarbons and heavy metals) in soil. Meanwhile, the internal transcribed spacer (ITS) sequencing by Illumina Miseq platform at each taxonomic level demonstrated that the toxicological effect of oil pollutants obviously influenced the fungal diversity and community structure in soil. Moreover, it was found that the presence of three genera (Cephalotheca, Lecanicillium, and Septoriella) appeared in aged oil sludge-contaminated soil. And oil pollutants promoted the growth of certain genera in Ascomycota (70.83%) and Basidiomycota (10.78%), such as Venturia, Alternaria, and Piloderma. Nevertheless, the growth of Mortierella (9.16%), Emericella (6.02%), and Bjerkandera (0.00%) was intensively limited. This study would aid thorough understanding of microbial diversity in oil-contaminated soil and thus provide new point of view to soil bioremediation.

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi

Organic and inorganic xenobiotic compounds can affect the potential ecological function of the soil, altering its biodiversity. Therefore, the response of microbial communities to environmental pollution is a critical issue in soil ecology. Here, a high-throughput sequencing approach was used to investigate the indigenous bacterial and fungal community structure as well as the impact of pollutants on their diversity and richness in contaminated and noncontaminated soils of a National Interest Priority Site of Campania Region (Italy) called "Terra dei Fuochi". The microbial populations shifted in the polluted soils via their mechanism of adaptation to contamination, establishing a new balance among prokaryotic and eukaryotic populations. Statistical analyses showed that the indigenous microbial communities were most strongly affected by contamination rather than by site of origin. Overabundant taxa and Actinobacteria were identified as sensitive biomarkers for assessing soil pollution and could provide general information on the health of the environment. This study has important implications for microbial ecology in contaminated environments, increasing our knowledge of the capacity of natural ecosystems to develop microbiota adapted to polluted soil in sites with high agricultural potential and providing a possible approach for modeling pollution indicators for bioremediation purposes.

Soil Microbial Community Structure and Diversity around the Aging Oil Sludge in Yellow River Delta as Determined by High-Throughput Sequencing

Microorganisms are sensitive indicators of edaphic environmental variation. The Illumina MiSeq sequencing technology was used to analyze soil bacterial community diversity around an aging oil sludge in the Yellow River Delta. The alpha diversity index of soil bacterial community results (Ace, Chao, Shannon, and Simpson) determined that bacterial community diversity sampling within the scope of a 20 cm radius from the center of an aging oil sludge spot showed the most abundant diversity. The level of diversity distributed symmetrically with radial direction from the center of the aging oil sludge spot. Over the distance of 100 m from the center, bacterial community diversity tends to be monotonous, with small differences especially in the horizontal direction underground. The alpha-diversity indicators also showed that the bacterial diversity of samples were close under the aging oil sludge. In addition, the aging oil sludge inhibited the growth of bacteria compared with the referenced unpolluted soil sample and also increased the diversities of soil bacteria. At the phylum level, the Proteobacteria, Chloroflexi, and Actinobacteria existing in the aging oil sludge-contaminated wetland soil constituted a larger proportion of the community, while the proportion of Firmicute was relatively less. On the contrary, Firmicute showed the highest content of 63.8% in the referenced soil. Under the genus level and family level, the corresponding strains that resisted the aging oil sludge were selected. According to the bacterial diversity analysis, the basic structure of the bacterial community which could be used for remediation of aging oil sludge-contaminated soil was also developed.

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient

Screening for tolerant and high biomass producing plants is important for phytoextraction efforts in remediating agricultural soils contaminated by heavy metals. We carried out a greenhouse experiment involving a soil cadmium (Cd) concentration gradient (0.1, 0.5, 1, 2, 4, and 8 mg kg^-1) to assess growth and phytoextraction capacity of king grass (Pennisetum sinese Roxb.) in soils contaminated by Cd and to explore changes in diversity and structure of rhizosphere soil bacterial communities in response to long-term Cd pollution. A significant positive relationship was observed between Cd concentrations in P. sinese stems, leaves, and roots and soil Cd concentration. The highest Cd concentrations in shoots and roots were 28.87 and 34.01 mg kg^-1, respectively, at 8 mg kg^-1of soil Cd supply. Total extraction amounts of Cd in P. sinese were 0.22-1.86 mg plant^-1 corresponding to treatment with 0.5-8 mg kg^-1 Cd. Most of the Cd was stored in shoots, and the largest accumulation was 1.56 mg plant^-1 with 54.02 g dry shoot weight. After phytoextraction, changes in rhizobacterial community composition were found with different levels of Cd application, whereas there were no clear trends in diversity and richness. Results of this study show the feasibility of P. sinese in accumulating Cd and provide support for its application in remediation of soil moderately contaminated by Cd.