International audience | Radioactive contamination of the natural areas is one of the most long-lasting anthropogenic impacts on the environment. Scots pine (Pinus sylvestris L.) is a promising organism for radiation-related research because of its high radiosensitivity, but the genome size of Pinacea species has imposed obstacles for high-throughput studies so far. In this work, we conducted the analysis of the de novo assembled transcriptome of Scots pine populations growing in the Chernobyl-affected zone, which is still today contaminated with radionuclides because of the accident at the nuclear power plant in 1986. The transcriptome profiles indicate a clear pattern of adaptive stress response, which seems to be dose-dependent. The transcriptional response indicates a continuous modulation of the cellular redox system, enhanced expression of chaperones and histones, along with the control of ions balance. Interestingly, the activity of transposable element families is inversely correlated to the exposure levels to radiation. These adaptive responses, which are triggered by radiation doses 30 times lower than the one accepted as a safe for biota species by international regulations, suggest that the environmental management in radiation protection should be reviewed.

The presence of large amounts of antibiotic resistance genes (ARGs) in livestock manures poses an impending, tough safety risk to ecosystems. To investigate more comprehensively the mechanisms of ARGs removal from industrial-scale composting of livestock manure based on biochar addition, we tracked the dynamics of bacterial community and ARGs at various stages of aerobic composting of livestock manures with 10% biochar. There were no significant effects of biochar on the bacterial community and the profiles of ARGs. During aerobic composting, the relative abundance of ARGs and mobile genetic elements (MGEs) showed overall trends of decreasing and then increasing. The key factor driving the dynamics of ARGs was bacterial community composition, and the potential hosts of ARGs were Caldicoprobacter, Tepidimicrobium, Ignatzschineria, Pseudogracilibacillus, Actinomadura, Flavobacterium and Planifilum. The retention of the thermophilic bacteria and the repopulation of the initial bacteria were the dominant reasons for the increase in ARGs at maturation stage. Additionally, among the MGEs, the relative abundance of transposon gene was substantially removed, while the integron genes remained at high relative abundance. Our results highlighted that the suitability of biochar addition to industrial-scale aerobic composting needs to be further explored and that effective measures are needed to prevent the increase of ARGs content on maturation stage.

The development of antibiotic resistance and dissemination of its determinants is an emerging public health problem as it compromises treatment options of infections that were, until recently, treatable. Investigation of outbreaks of vancomycin resistant enterococci (VRE) suggests that the environment serves as a significant reservoir for antibiotic resistance genes (ARGs). However, there is a paucity of data regarding the presence of ARGs in the water sources in South Africa. In this study, water samples collected from wastewater treatment plants (WWTPs), surface water and hospital sewage were screened for enterococci harbouring genes conferring resistance to four classes of antibiotics. Enterococci isolates harbouring ARGs were detected in raw influent and treated wastewater discharge from WWTPs and hospital sewage water. Plasmid and transposon encoded ermB (macrolide), tetM and tetL (tetracycline) as well as aph(3’)-IIIa (aminoglycosides) genes were frequently detected among the isolates, especially in E. faecalis. The presence of enterococci harbouring ARGs in the treated wastewater suggest that ARGs are discharged into the environment where their proliferation could be perpetuated. Among the enterococci clonal complexes (CCs) recovered from wastewater were E. faecium CC17 (ST18), which is frequently associated with hospital outbreaks and a novel E. faecalis sequence type (ST), ST780.

Radioactive contamination of the natural areas is one of the most long-lasting anthropogenic impacts on the environment. Scots pine (Pinus sylvestris L.) is a promising organism for radiation-related research because of its high radiosensitivity, but the genome size of Pinacea species has imposed obstacles for high-throughput studies so far. In this work, we conducted the analysis of the de novo assembled transcriptome of Scots pine populations growing in the Chernobyl-affected zone, which is still today contaminated with radionuclides because of the accident at the nuclear power plant in 1986. The transcriptome profiles indicate a clear pattern of adaptive stress response, which seems to be dose-dependent. The transcriptional response indicates a continuous modulation of the cellular redox system, enhanced expression of chaperones and histones, along with the control of ions balance. Interestingly, the activity of transposable element families is inversely correlated to the exposure levels to radiation. These adaptive responses, which are triggered by radiation doses 30 times lower than the one accepted as a safe for biota species by international regulations, suggest that the environmental management in radiation protection should be reviewed.

Heavy metal contamination of source water frequently occurred in developing countries as a result of accidents. To address the problems, most of the previous studies have focused on engineering countermeasures. In this study, we investigated the effects of heavy metals, particularly copper, on the development of antibiotic resistance by establishing a copper shock loading test. Results revealed that co-selection occurred rapidly within 6 h. Copper, at the levels of 10 and 100 mg/L, significantly increased bacterial resistance to the antibiotics tested, including rifampin, erythromycin, kanamycin, and a few others. A total of 117 antimicrobial-resistance genes were detected from 12 types of genes, and the relative abundance of most genes (particularly mobile genetic elements intⅠand transposons) was markedly enriched by at least one fold. Furthermore, the copper shock loading altered the bacterial community. Numerous heavy metal and antibiotic resistant strains were screened out and enriched. These strains are expected to enhance the overall level of resistance. More noticeably, the majority of the co-selected antibiotic resistance could sustain for at least 20 h in the absence of copper and antimicrobial drugs. Resistance to vancomycin, erythromycin and lincomycin even could remain for 7 days. The prominent selection pressure by the copper shock loading implies that a real accident most likely poses similar impacts on the water environment. An accidental release of heavy metals would not only cause harm to the ecological environment, but also contribute to the development of bacterial antibiotic resistance. Broader concerns should be raised about the biological risks caused by sudden releases of pollutants by accidents.

Triclosan (TCS) is a broad-spectrum antimicrobial used in a variety of consumer products. While it was recently banned from hand soaps in the US, it is still a key ingredient in a top-selling toothpaste. TCS is a hydrophobic micropollutant that is recalcitrant under anaerobic digestion thereby resulting in high TCS concentrations in biosolids. The objective of this study was to determine the impact of TCS on the antibiotic resistome and potential cross-protection in lab-scale anaerobic digesters using shotgun metagenomics. It was hypothesized that metagenomics would reveal selection for antibiotic resistance genes (ARGs) not previously found in pure culture studies or mixed-culture studies using targeted qPCR. In this study, four different levels of TCS were continuously fed to triplicate lab-scale anaerobic digesters to assess the effect of TCS levels on the antibiotic resistance gene profiles (resistome). Blasting metagenomic reads against antibiotic/metal resistance gene database (BacMet) revealed that ARG diversity and abundance changed along the TCS concentration gradient. While loss of bacterial diversity and digester function were observed in the digester treated with the highest TCS concentration, FabV, which is a known TCS resistance gene, increased in this extremely high TCS environment. The abundance of several other known ARG or metal resistance genes (MRGs), including corA and arsB, also increased as the concentrations of TCS increased. Analysis of other functional genes using SEED database revealed the increase of potentially key genes for resistance including different types of transporters and transposons. These results indicate that antimicrobials can alter the abundance of multiple resistance genes in anaerobic digesters even when function (i.e. methane production) is maintained. This study also suggests that enriched ARGs could be released into environments with biosolids land application.

With the induction of various emerging environmental contaminants such as antibiotic resistance genes (ARGs), environment is considered as a key indicator for the spread of antimicrobial resistance (AMR). As such, the ARGs mediated environmental pollution raises a significant public health concern worldwide. Among various genetic mechanisms that are involved in the dissemination of ARGs, integrons play a vital role in the dissemination of ARGs. Integrons are mobile genetic elements that can capture and spread ARGs among environmental settings via transmissible plasmids and transposons. Most of the ARGs are found in Gram-negative bacteria and are primarily studied for their potential role in antibiotic resistance in clinical settings. As one of the most common microorganisms, Escherichia coli (E. coli) is widely studied as an indicator carrying drug-resistant genes, so this article aims to provide an in-depth study on the spread of ARGs via integrons associated with E. coli outside clinical settings and highlight their potential role as environmental contaminants. It also focuses on multiple but related aspects that do facilitate environmental pollution, i.e. ARGs from animal sources, water treatment plants situated at or near animal farms, agriculture fields, wild birds and animals. We believe that this updated study with summarized text, will facilitate the readers to understand the primary mechanisms as well as a variety of factors involved in the transmission and spread of ARGs among animals, humans, and the environment.

In recent years, concerns about using Bisphenol A (BPA) in daily consume products and its effects in many chronic human diseases have prompted the removal of BPA. However, the widely used BPA alternatives, including Bisphenol S (BPS), have a high structural similarity with BPA, suggesting that they may have similar biological effects towards human beings. Indeed, BPS was also found to have endocrine-disrupting effects. Epigenetic mechanism was reported to be involved in BPA-induced biological effects in both in vitro and in vivo models. However, there is no assessment on whether BPS could cause epigenetic changes. In this work, we investigated the possible epigenetic effects of BPS that might induce in human breast cancer cell line MCF-7. We found that BPS could change DNA methylation level of transposons. Besides, methylation status in promoter of breast cancer related genes CDH1, SFN, TNFRSF10C were also changed, which implied that BPS might play a role in the development of breast cancer. Gene expression profiling showed that some genes related to breast cancer progression were upregulated, including THBS4, PPARGC1A, CREB5, COL5A3. Gene ontology (GO) analysis of the differentially expressed genes revealed the significantly changes in PI3K-Akt signaling pathway and extracellular matrix, which were related to the proliferation, migration and invasion of breast cancer cells. These results illustrated that BPS exposure might play roles in the progression of breast cancer.

We evaluated the chronic impact of oxytetracycline (OTC) on performance and antibiotic resistance development during the mesophilic anaerobic digestion (AD) of antibiotic-containing biomass. Mesophilic AD was conducted in a completely stirred tank reactor by constantly feeding municipal excess sludge spiked with increasing concentrations of OTC (0–1000 mg L−1) under a solid retention time of 20 days over a period of 265 days. Results showed that methane generation of mesophilic AD was inhibited when the OTC concentration in digested sludge was increased to around 18,000 mg kg−1 (OTC dose, 1000 mg L−1), due to the inhibition of fermenting and acidogenic bacteria. Metagenomic sequencing and high-throughput quantitative PCR analysis demonstrated that tetracycline resistance genes were the most dominant type (38.47–43.76%) in the resistome, with tetG, tetX, tetM, tetR, tetQ, tetO, and tetL as the dominant resistant subtypes throughout the whole experimental period. The relative abundance of these tet genes increased from 2.10 × 10−1 before spiking OTC (OTC concentration in digested sludge, 8.97 mg kg−1) to 2.83 × 10−1 (p < 0.05) after spiking OTC at a dose of 40 mg L−1 (OTC concentration in digested sludge, 528.52 mg kg−1). Furthermore, mobile genetic elements, including integrons, transposons, and plasmids, were also enriched with the increase in OTC dose. Based on partial canonical correspondence analysis, the contributions of horizontal (mobile element alteration) and vertical (bacterial community shift) gene transfer to antibiotic resistome variation were 29.35% and 21.51%, respectively. Thus, considering the inhibition of hydrolytic acidification and enrichment of antibiotic resistome, mesophilic AD is not suggested to directly treat the biomass containing OTC concentration higher than 200 mg L−1.

Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.