Cometabolism mechanisms of organic pollutants in environmental microbes have not been fully understood. In this study, a global analysis of Mycobacterium sp. strain A1-PYR transcriptomes on different PAH substrates (single or binary of pyrene (PYR) and phenanthrene (PHE)) was conducted. Comparative results demonstrated that expression levels of 23 PAH degradation enzymes were significantly higher in the binary substrate than in the PYR-only one. These enzymes constituted an integrated enzymatic system to actualize all transformation steps of PYR, and most of their encoded genes formed a novel gene cascade in the genome of strain A1-PYR. The roles of different genotypes of enzymes in PYR cometabolism were also discriminated even though all of their gene sequences were presented in the genome of this strain. NidAB and PdoA2B2 instead of NidA3B3 served the initial oxidization of PAHs, and PcaL replaced PcaCD to catalyze the formation of 3-oxoadipate. Novel genes associated with PYR cometabolism was also predicted by the relationships between their transcription profiles and PYR removal. The results showed that ABC-type transporters probably played important roles in the transport of PAHs and their metabolites through cell membrane, and [4Fe-4S] ferredoxin might be essential for dioxygenases (NidAB and PdoA2B2) to achieve oxidative activities. This study provided molecular insight in that microbial degrader subtly cometabolized recalcitrant PAHs with relatively more degradable ones.

Nitrogen runoff from fertiliser intensive land uses has become an issue worldwide, contributing to algal blooms, hypoxic waters and aquatic biodiversity losses. This study assessed potential nutrient pollution from blueberry farms in subtropical Australia and examines whether nutrient loads were driven by groundwater discharge and/or surface water runoff. Streams downstream of eight blueberry farms were compared to eight nearby control sites without any blueberry activity. In the 90 day sample period, there were three rain events >90 mm day⁻¹ that produced runoff sufficient to create flooding. Overall, the results revealed a clear link between blueberry farming and nitrogen runoff in headwater streams. While NOX (nitrate + nitrite) was the dominant nitrogen species downstream of blueberry farms, dissolved organic nitrogen (DON) was the dominant species in control sites. The concentrations and loads of NOₓ were one order of magnitude lower in the eight non-blueberry (6.3 ± 2.0 μmol L⁻¹; 1.6 ± 1.2 kg N-NOX ha⁻¹ yr⁻¹) than the eight blueberry (56.9 ± 14.2 μmol L⁻¹; 21.8 ± 8.0 kg N-NOX ha⁻¹ yr⁻¹) sites. NOX concentrations and loads were highest following rain events. Radon (²²²Rn, a natural groundwater tracer) observations and low nitrogen concentration in groundwater samples further suggest that surface runoff dominates the delivery of nitrogen to the creeks investigated. NOX concentrations and loads in creeks correlated with blueberry farm density. At >15% of blueberry land use in a catchment, there was a detectable influence in NOX concentrations and loads in the headwater streams. Assuming that our load estimates can be up-scaled to annual nitrogen creek exports, and that local farmers use the recommended amount of fertiliser (121 kg N ha⁻¹ yr⁻¹), between 18 and 25% of the used fertiliser was lost to the creeks. This implies that there are opportunities for decreasing the use of fertilisers in this catchment and managing any nitrogen that escapes to the creeks.

Carbamazepine (CBZ) is an antiepileptic drug that is frequently detected in wastewater treatment plants, soil and plants after irrigation with treated wastewater or application of biosolids. However, little information is available on the fate and uptake of CBZ in edible vegetables. In this study, radioautographic visualization of the ¹⁴C distribution revealed that ¹⁴C-CBZ can be taken up by all three ready-to-eat vegetables. Furthermore, a mass-balance study was conducted to evaluate the dynamic processes of the uptake and translocation of CBZ by ¹⁴C labeling. ¹⁴C-CBZ was gradually taken up with the growth of vegetables, with maximum uptake ratios of 2.19 ± 0.15, 2.86 ± 0.24 and 0.25 ± 0.05% of applied ¹⁴C in celery, carrot and pak choi, respectively. The bioconcentration factors (BCFs) based on ¹⁴C measurements ranged from 7.6 to 26.1 for celery, 3.6–12.9 for carrot, and 4.4–44 for pak choi. ¹⁴C-CBZ was easily translocated from the roots to the leaves and/or stems. The amendment of biosolids had a significant inhibitory effect on the uptake and translocation of ¹⁴C-CBZ from soil.

Although the hepatotoxicity of thifluzamide in zebrafish has been characterized, its toxic mechanisms have not been fully explored. The present study demonstrated that thifluzamide damaged the zebrafish liver and endoplasmic reticulum (ER). In addition, thifluzamide significantly changed the expression of genes encoding antioxidant proteins and increased the malondialdehyde (MDA) content, leading to oxidative damage in zebrafish liver. Additionally, the autophagic ultrastructure was observed by transmission electron microscopy (TEM), and LC3-I/LC3-II conversion was obviously upregulated under western blotting (WB) measurements, verifying that autophagy was induced by thifluzamide. Moreover, the activities of Caspase-3 and Caspase-9 were obviously decreased, indicating that apoptosis was inhibited in adult zebrafish exposed to a higher concentration of thifluzamide. In summary, oxidative damage and autophagy but not apoptosis under ER injury might lead to the hepatotoxicity of thifluzamide in zebrafish. Our findings provide a new mechanistic insight into the toxicity of thifluzamide in zebrafish.

In corneal epithelium, tight junctions play a vital role in its barrier function. Human cornea is highly susceptible to damage by dust. Continued daily exposure to dust has been associated with increased risks of corneal injury. Studies demonstrated that water extract of dust induced cytotoxicity in human corneal epithelial cells (HCECs); however, its effects on corneal epithelial barrier function are unknown. In this study, we determined the concentrations of heavy metals in water extracts of dust, with office dust having higher concentrations of heavy metals than housedust, and Cu and Zn being highest among metals for both dust. Changes in barrier function and its associated mechanism after exposing HCECs to water extracts of dust at 48 μg/100 μ L for 7 d were evaluated. Water extracts of both dust caused decrease of TEER value (39–73%), down-regulation of gene expression related to tight junction and mucin (0.2–0.8 fold), and loss of ZO-1 immunoreactivity from cellular borders, with office dust having greater potential than housedust to disrupt corneal epithelial barrier function. Our data implied the importance to reduce heavy metals in dust to reduce their adverse impacts on human eyes.

Efficiency and the preservation of soil functions are key requirements for sustainable remediation of contaminated soil. Microbial decomposition and conversion of substrates is a fundamental soil function. Pilot-scale EDTA-based soil washing recycled chelant generated no wastewater and removed 78% of Pb from acidic farmland soil with 860 mg kg⁻¹ Pb and 60% of Pb from calcareous garden soil with 1030 mg kg⁻¹ Pb. Remediation had an insignificant effect on microbial respiration in acidic soil induced by sequential additions of glucose, micro-cellulose, starch and alfa-alfa sprout powder (mimicking litter components, C-cycle). In contrast, remediation of calcareous soil reduced cumulative CO₂ production after glucose (simple) and alfalfa (complex substrate) addition, by up to 40%. Remediation reduced the nitrification rate (denoting the N-cycle) in acidic soil by 30% and halved nitrification in calcareous soil. Remediation in both soils slightly or positively affected dehydrogenase and β-glucosidase activity (associated with C-cycle), and decreased urease activity (N-cycle). Generally, EDTA remediation modestly interfered with substrate utilisation in acidic soil. A more prominent effect of remediation on the functioning of calcareous soil could largely be attributed to the use of a higher EDTA dose (30 vs. 100 mmol kg⁻¹, respectively).

Oil spills offshore can cause long-term ecological effects on coastal marine ecosystems. Despite their important ecological roles in the cycling of energy and nutrients in food webs, effects on bacteria, protists or arthropods are often neglected. Environmental DNA (eDNA) metabarcoding was applied to characterize changes in the structure of micro- and macro-biota communities of surface sediments over a 7-year period since the occurrence of Hebei Spirit oil spill on December 7, 2007. Alterations in diversities and structures of micro- and macro-biota were observed in the contaminated area where concentrations of polycyclic aromatic hydrocarbons were greater. Successions of bacterial, protists and metazoan communities revealed long-term ecological effects of residual oil. Residual oil dominated the largest cluster of the community-environment association network. Presence of bacterial families (Aerococcaceae and Carnobacteriaceae) and the protozoan family (Platyophryidae) might have conferred sensitivity of communities to oil pollution. Hydrocarbon-degrading bacterial families (Anaerolinaceae, Desulfobacteraceae, Helicobacteraceae and Piscirickettsiaceae) and algal family (Araphid pennate) were resistant to adverse effects of spilt oil. The protistan family (Subulatomonas) and arthropod families (Folsomia, Sarcophagidae Opomyzoidea, and Anomura) appeared to be positively associated with residual oil pollution. eDNA metabarcoding can provide a powerful tool for assessing effects of anthropogenic pollution, such as oil spills on sediment communities and its long-term trends in coastal marine environments.

Agriculture-based climate change mitigation may occur through enhancing the carbon sink or through reducing greenhouse gases (GHGs) emissions from agricultural residue treatment, as open burning of agricultural residues produces millions of tons of GHGs and air pollutants annually worldwide. Charring slashed biomass, termed as slash-and-char, has been considered as a promising alternative to open burning in dealing with agricultural residues such as rice straw. Previous studies, however, focused on relatively sophisticated slash-and-char systems, which could not be practiced easily by smallholder farmers in developing countries. Here we introduce a simple slash-and-char system to mitigate the environmental problems associated with open burning of rice straw. This system could convert 30.7% of the initial carbon in rice straw into biochar, much higher than that retained in the ash generated by open burning (3.95%). It could also cut GHGs, particulate matters and polycyclic aromatic hydrocarbons (PAHs) emissions by 26.9%, 99.0% and 99.4%, respectively. If open burning of rice straw was replaced by the slash-and-char, the annual emissions of GHGs, particulate matters and PAHs in China would decrease by at least 15.4 Tg, 1.51 Tg and 1.27 Gg, correspondingly. This decrease is nearly twice the size of China's estimated forest C sink (8.81 Tg).

In this study, the formation of nitrate aerosol from 16 to 24 December 2015 in the Guanzhong basin, China is simulated using the WRF-Chem model. The predicted near-surface O₃, NO₂, and fine particulate matters (PM₂.₅) in the basin and inorganic aerosols and nitrous acid (HONO) in Xi'an are generally in good agreement with the observations. Sensitivity studies show that the heterogeneous HONO sources play an appreciable role in the nitrate formation in the basin, contributing 9.2% of nitrate mass concentrations during heavy haze days. Nitrate formation is also affected by sulfate due to their competition for ammonia, particularly in urban areas. A 50% decrease in SO₂ emissions enhances the nitrate concentration by 6.2% during heavy haze days on average in the basin, and a 50% increase in SO₂ emission reduces the nitrate concentration by 9.7%. The roles of HONO and sulfate competition in nitrate formation are strongly modulated by ammonia. Agricultural emissions predominate the nitrate level in the basin (93.5%), but the non-agricultural sources cannot substantially influence nitrate formation (3.7%–14.6%). Reducing agricultural emission is an effective control strategy to mitigate nitrate pollution in the basin.

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.