Animals living in urban river systems play critical roles in the dissemination of microbiome and antibiotic resistance that poses a strong threat to public health. This study provides a comprehensive profile of microbiota and antibiotic resistance genes (ARGs) of sharpbelly (Hemiculter leucisculus) and the surrounding water from five sites along the Ba River. Results showed Proteobacteria, Firmicutes and Fusobacteria were the dominant bacteria in gut of H. leucisculus. With the aggravation of water pollution, bacterial biomass of fish gut significantly decreased and the proportion of Proteobacteria increased to become the most dominant phylum eventually. To quantify the contributions of influential factors on patterns of gut microbiome with structural equation model (SEM), water bacteria were confirmed to be the most stressors to perturb fish gut microbiome. SourceTracker model indicated that deteriorating living surroundings facilitated the invasion of water pathogens to fish gut eco-environments. Additionally, H. leucisculus gut is an important reservoir of ARGs in Ba River with relative abundance up to 9.86 × 10⁻¹/copies. Among the ARGs, tetracycline and quinolone resistance genes were detected in dominant abundance. Deterioration of external environments elicited the accumulation of ARGs in fish gut. Intestinal class I integron, environmental heavy metal residues and gut bacteria were identified as key drivers of intestinal ARGs profiles in H. leucisculus. Analysis of SEM and co-occurrence patterns between ARGs and bacterial hosts indicated that class I integron and bacterial community played vital roles in ARGs transmission through water-fish pathway. In general, this study highlighted hazards of water contamination to microbiome and ARGs in aquatic animals and provided a new perspective to better understand the bacteria and ARGs dissemination in urban river ecosystems.

The atmosphere as a temporary habitat for airborne microbial communities is a valuable topic to explore, and it is through aerobiological studies that the diversity of biological particles and their release, emission, transport, deposition, and impact are assessed. Specific microorganisms are involved in meteorological processes, and phytosanitary and public health concerns. Airborne microbial composition is related to factors such as geographic region and weather conditions.In this study a metagenomic approach was used to determine the composition of bacterial and fungal communities in the air of two different land-use areas (urban area and semi-rural area), during dry and rainy seasons in Mexico City. Air sampling was carried out with a Hirst-type spore trap, collecting the samples simultaneously in both study areas. Forty-two bioaerosol samples were collected, and the DNA obtained was sequenced using Next-Generation Sequencing. The results indicated that the bacterial communities were represented mainly by the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria, and the fungal communities by the phyla Ascomycota followed by Basidiomycota. The evident changes in microbial composition were related more to seasonality than to locality, since both UA and SRA showed a high degree of urbanization, despite some differences in land use. Continuous monitoring of atmospheric bioaerosols is essential to determine the influence of meteorological factors on the composition of the aerial microbiota.

Thermal desorption is widely adopted for the remediation of organic compounds, yet is generally considered a non-green-sustainable manner owing to its energy-intensive nature and potential to deteriorate soil reuse. Here, lube oil-contaminated soils were remediated at 200–500 °C in nitrogen atmosphere, upon which removal behaviors of lube oil and physicochemical properties of soils were explored. Illumina 16S ribosomal RNA (rRNA) and 18S rRNA amplicon sequencing were employed to determine the relative abundances and diversities of bacteria and fungi in soils, respectively. The results indicated that, after heating at 350 °C for 60 min, 93% of the lube oil was reduced, with the residual lube oil concentration lower than the Chinese risk intervention values (GB 36600–2018). The weakly-alkaline, multi-phosphorus and char-rich soils after indirect thermal desorption could provide a nutrient source and favorable habitat space for living organisms, and the decomposition of minerals in soils is more conducive to the survival of organisms. Microbial species in soils after heating at 350 °C became extinct, however, microbial species after 3 days of recolonization were enough to carry out DNA extraction when these soils were exposed to natural grass land. Though the microbial richness and diversity in heated soils after 3 days of recolonization were still little lower than those in contaminated soils, Firmicutes (29.41%) and Basidiomycota (9.33%) became dominant at phyla level, while Planomicrobium (16.37%), Massilia (10.09%), Jeotgalibaca (7.91%) and Psychrobacter (6.84%) were dominant at general level, whose ecological function was more conducive to nutrient cycling and ecological resiliency. Overall, this innovative research provides a new perspective: low temperature indirect thermal desorption may also achieve a sustainable remediation, due to its energy-saving (low temperature), favorable physicochemical properties and the rapid recolonization capacity of microbial communities in heated soils.

Combining hydrothermal treatment and composting is an effective method to dispose of penicillin fermentation residue (PFR), but the safety and related mechanism are still unclear. In this study, penicillin solution was hydrothermally treated to decipher its degradation mechanism, and then hydrothermally treated PFR (HT-PFR) was mixed with bulking agents at ratios of 2:0 (CK), 2:1.5 (T1), and 2:5 (T2) to determine the absolute abundance of antibiotic resistance genes (ARGs) and the succession of bacterial community. Results showed that penicillin was degraded to several new compounds without the initial lactam structure after hydrothermal treatment. During composting, temperature and pH of the composts increased with the raising of HT-PFR proportion, except the pH at days 2. After 52 days of composting, the absolute copies of ARGs (blaTEM, blaCMY2, and blaSFO) and the relative abundance of bacteria related to pathogens were reduced significantly (P < 0.05). Especially, the total amount of ARGs in the samples of CK and T1 were decreased to equal level (around 5 log₁₀ copies/g), which indicated that more ARGs were degraded in the latter by the composting process. In the CK samples, Bacteroidetes and Proteobacteria accounted for ~69.8% of the total bacteria, but they were gradually replaced by Firmicutes with increasing proportions of HT-PFR, which can be caused by the high protein content in PFR. Consisting with bacterial community, more gram-positive bacteria were observed in T1 and T2, and most of them are related to manganese oxidation and chitinolysis. As composting proceeded, bacteria having symbiotic or pathogenic relationships with animals and plants were reduced, but those related to ureolysis and cellulolysis were enriched. Above all, hydrothermal treatment is effective in destroying the lactam structure of penicillin, which makes that most ARGs and pathogenic bacteria are eliminated in the subsequent composting.

The water and sediments of urban rivers are spatially heterogeneous because of the influence of environmental and anthropogenic factors. However, the spatial and functional diversity of bacterial communities in urban river sediments are unclear. We investigated the spatial distribution of microbial compositions in sediments in Qingdao section of the Dagu River, and the effects of sediment physiochemical properties on the variation were explored. Among the seven heavy metals analyzed, only the average concentration of Cd significantly exceeded the safety limit for sediments. The detailed composition and spatial distribution of bacterial communities fluctuated substantially between sites along the river. Bacterial datasets were separated into three clusters according to the environmental characteristics of sampling areas (the urbanized, scenic, and intertidal zones). For the urbanized zone, Acidobacteria, Firmicutes, Gemmatimonadetes, Bacteroidetes, and Gammaproteobacteria were significantly enriched, implying the effects of human activity. In the intertidal zone, Alphaproteobacteria and Deltaproteobacteria were significantly enriched, which are associated with S redox processes, as in the marine environment. Variation partitioning analysis showed that the amount of variation independently explained by variables of Na, Al, total S and Zn was largest, followed by sediment nutrients, while heavy metals and pH explained independently 13% and 9% of the variance, respectively. Overall, microbial structures in the Dagu River exhibited spatial variation and functional diversity as a result of natural and anthropogenic factors. The results will enable the prediction of the changes in urban river ecosystems that maintain their ecological balance and health.

Various microplastics (MPs) are found in the environment and organisms. MP residues in organisms can affect health; however, their impacts on metabolism in aquatic organisms remain unclear. In this study, zebrafish embryos were exposed to polyethylene MPs with sizes ranging from 1 to 4 μm at concentrations of 0, 10, 100, and 1000 μg/L for 7 days. Through qPCR technology, the results indicated that zebrafish exposed to polyethylene MPs exhibited significant change in microbes of the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Verrucomicrobia, etc. Moreover, 16S RNA gene sequencing revealed that there was a significant difference in alpha diversity between the control and 1000 μg/L MP-treated groups. At the genus level, the abundance of Aeromonas, Shewanella, Microbacterium, Nevskia and Methyloversatilis have increased remarkably. Conversely, the abundance of Pseudomonas, Ralstonia and Stenotrophomonas were significant reduction after MPs exposure. In addition, the levels of TG (triglyceride), TCHO (total cholesterol), NEFA (nonesterified fatty acid), TBA (total bile acid), GLU (glucose) and pyruvic acid significantly changed in MP-treated larval zebrafish, indicating that their metabolism was disturbed by MPs. Transcriptional levels of glucose and lipid metabolism-related genes showed a decreasing trend. Furthermore, LC/MS-based nontargeted metabolomics analysis demonstrated that a total of 59 phospholipid-related substances exhibited significant changes in larval fish treated with 1000 μg/L MPs. The mRNA levels of phospholipid metabolism-related genes were also obviously changed. Pearson correlation analysis indicated that the abundance of Aeromonas, Shewanella and Chitinibacter bacteria showed a negative correlation with most phospholipids, while Nevskia, Parvibacter and Lysobacter showed a positive correlation with most phospholipids. Based on these results, it is suggested that 1–4 μm PE-MPs could impact the microbiome and metabolism of larval zebrafish. All of these results indicated that the health risk of MPs cannot be ignored.

Phenanthrene (Phe), among the most ubiquitous polycyclic aromatic hydrocarbons (PAHs) existing in nature and foodstuffs, has severe effects on hepatic lipids metabolism. However, the detailed mechanism involved is still unknown. For environmental chemicals can disturb intestinal microbiota, which plays a vital role in lipids metabolism, we hypothesized that oral exposure to Phe may disrupt the intestinal microbiota, leading to the induction of an abnormal inflammatory response and lipid metabolism dysfunction. Herein, male mice were orally exposed to Phe (0.05, 0.5 and 5 mg/kg/2d) for ten weeks and the results showed that long term exposure to Phe induced significant alteration in relative Bacteroidetes, Firmicutes and Proteobacteria abundance in male mice. Histopathological anomalies, and significantly increased hepatic levels of free fatty acid, cholesterol and triglyceride were observed as well. The expression of hepatic proteins linked to lipid metabolism including peroxisome proliferator-activated receptors (PPARs), liver X receptor β (LXRβ) and retinoid X receptors (RXRs) were upregulated. The importance of the gut microbiota in Phe-altered lipid metabolism disorder was further confirmed by fecal microbiota transplantation (FMT). FMT intervention boosted microbial diversity and attenuated Phe-induced elevation in liver somatic index and hepatic total lipids levels. These results demonstrated that environmental-level Phe altered the composition of gastrointestinal bacteria and subsequently induced hepatic lipid metabolism disorder. These results would be helpful for understanding the health risk posed by Phe.

Manure pH may vary depending on its inherent composition or additive contents. However, the effect of pH on the fate of antibiotics and antibiotic resistance determinants in manure remains unclear. This work demonstrated that pH adjustment promoted the removal of different sulfonamide antibiotics (SAs) within swine manure under incubation conditions, which increased from 26–60.8% to 75.0–86.0% by adjusting the initial pH from neutral (7.4) to acidic (5.4–4.8). Acidification was also demonstrated to inhibit the accumulation of antibiotic resistance genes in manure during incubation. Acidified manure contained both lower absolute and relative abundances of sul1 and sul2 than those at a neutral pH like 7.4. Further investigation indicated that acidification promoted the reduction of sul genes in manure by restricting sulfonamide-resistant bacteria (SRB) proliferation and inhibiting IntI1 accumulation. Furthermore, pH adjustment significantly influenced the composition of the manure bacterial community after incubation, which increased Firmicutes and decreased Proteobacteria. Close relationships were observed between pH-induced enrichment of the Firmicutes bacterial phylum, enhanced SAs degradation, and the fates of antibiotic resistance determinants. Overall, lowering the pH of manure promotes the degradation of SAs, decreases sul genes and SRB, and inhibits horizontal sul gene transfer, which could be a simple yet highly-effective manure management option to reduce antibiotic resistance.

Tributyltin (TBT), an organotin compound once widely used in agriculture and industry, has been reported to induce obesity and endocrine disruption. Gut microbiota has a strong connection with the host’s physiology. Nevertheless, the influences of TBT exposure on gut microbiota and whether TBT-influenced gut microbiota is related to TBT-induced toxicity remain unclear. To fill these gaps, ICR (CD-1) mice were respectively exposed to TBT at NOEL (L-TBT) and tenfold NOEL (H-TBT) daily by gavage for 8 weeks in the current study. The results showed that TBT exposure significantly increased body weight as well as epididymal fat, and led to adipocyte hypertrophy, dyslipidemia and impaired glucose and insulin homeostasis in mice. Additionally, TBT exposure significantly decreased the levels of T4, T3 and testosterone in serum. Also of note, TBT exposure changed gut microbiota composition mainly by decreasing Bacteroidetes and increasing Firmicutes proportions. To confirm the role of gut microbiota in TBT-induced overweight and hormonal disorders, fecal microbiota transplantation was performed and the mice receiving gut microbiota from H-TBT mice had similar phenotypes with their donor mice including significant body weight and epididymal fat gain, glucose and insulin dysbiosis and hormonal disorders. These results suggested that gut microbiome altered by TBT exposure was involved in the TBT-induced increased body weight, impaired glucose and insulin homeostasis and endocrine disruption in mice, providing significant evidence and a novel perspective for better understanding the mechanism by which TBT induces toxicity.

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.