New Delhi Metallo-β-lactamase-1(NDM-1) is an enzyme that hydrolyzes a wide range of β-lactams antibiotics, including carbapenems. The presence of the NDM-1 inhibits the potential of β–lactam antibiotics in treating infections caused by bacterial strains carrying such resistances, thus leaving minimal treatment options available. Due to this, the rapid distribution of NDM-1 harboring bacteria accounts for a significant public health menace worldwide. These bacteria have been detected in clinical specimens and environmental compartments where bacterial infections are ubiquitous. In this study, identification and absolute quantification of NDM-1 in sixteen lake sediment samples collected in and around Hyderabad, India, was carried out using a real-time quantitative polymerase chain reaction (qPCR), and the results were expressed in gene copy number/ng (nanogram) of template DNA. Thirteen samples (out of sixteen) displayed a positive signal for NDM-1 during the qPCR analysis with the highest gene copy number/ng of template DNA (71.8) being observed in the Amberpet STP. Three samples, samples from Durgamcheru lake, Kandi lake, and Singur dam, were negative for the NDM-1 during the qPCR analysis. Hierarchical clustering analysis was performed to categorize the sampling location into different clusters based on pollution sources and the observed results were expressed in the form of a dendrogram.

In recent years, Feammox has made it possible to remove NH₄⁺-N under anaerobic conditions; however, its application in practical wastewater treatment processes has not been extensively reported. In this study, an up-flow anaerobic biological filter based on limonite (Lim-UAF) was developed to facilitate long-term and stable treatment of domestic sewage. Lim-UAF achieved the highest removal efficiency of chemical oxygen demand (COD) and NH₄⁺-N at a hydraulic retention time (HRT) of 24 h (Stage II). Specifically, the COD and NH₄⁺-N content decreased from 240.8 and 30.0 mg/L to about 7.5 and 0.35 mg/L, respectively. To analyze the potential nitrogen removal mechanism, the Lim-UAF was divided into three layers according to the height of the reactor. The results showed that COD and NH₄⁺-N removal had remarkable characteristics in Lim-UAF. More than 55.0% of influent COD was removed in the lower layer (0–30 cm) of Lim-UAF, while 60.2% of NH₄⁺-N was removed in the middle layer (30–60 cm). Microbial community analysis showed that the community structure in the middle and upper layers (60–90 cm) was relatively similar, but quite different from that of the lower layer. Heterotrophic bacteria were dominant in the lower layer, whereas iron-reducing and iron-oxidizing bacteria were enriched in the upper and middle layers. The formation of secondary minerals (siderite and Fe(OH)₃) indicated that the Fe(III)/Fe(II) redox cycle occurred in Lim-UAF, which was triggered by the Feammox and NDFO processes. In summary, limonite was used to develop a single-stage wastewater treatment process for simultaneously removing organic matter and NH₄⁺-N, which has excellent application prospects in domestic sewage treatment.

Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of AMR, and human activities can strongly influence their resistome.The main goal of this work was to study the resistome of wild boar faecal microbiome, one of the most important game species in Europe using metagenomic and culturing approaches. The most abundant genes identified by the high-throughput qPCR array encode mobile genetic elements, including integrons, which can promote the dissemination of AMR determinants. A diverse set of genes (n = 62) conferring resistance to several classes of antibiotics (ARGs), some of them included in the WHO list of critically important antimicrobials were also detected. The most abundant ARGs confer resistance to tetracyclines and aminoglycosides. The phenotypic resistance of E. coli and Enterococcus spp. were also investigated, and together supported the metagenomic results.As the wild boar is an omnivorous animal, it can be a disseminator of AMR bacteria and ARGs to livestock, humans, and the environment. This study supports that wild boar can be a key sentinel species in ecosystems surveillance and should be included in National Action Plans to fight AMR, adopting a One Health approach.

Bio-stimulation of the indigenous microbial community is considered as an effective strategy for the bioremediation of polluted environments. This examination explored the near effects of various bio-stimulants on pyrene degradation, prokaryotic community compositions, and functions using 16S rRNA amplicon sequencing and qPCR. At first, the results displayed significant differences (p < 0.05) between the prokaryotic community structures of the control group, PYR (contains pyrene only), and bio-stimulants amended groups. Among the bio-stimulants, biochar, oxalic acid, salicylate, NPK, and ammonium sulfate augmented the pyrene degradation potential of microbial communities. Moreover, the higher abundance of genera, such as Flavobacterium, Hydrogenophaga, Mycobacterium, Rhodococcus, Flavihumibacter, Pseudomonas, Novosphingobium, etc., across the treatments indicated that these genera play a vital role in pyrene metabolism. Based on the higher abundance of GP-RHD and nidA genes, we speculated that Gram-positive prokaryotic communities are more competent in pyrene dissipation than Gram-negative. Furthermore, the marked abundance of nifH, and pqqC genes in the NPK and SA treatments, respectively, suggested that different bio-stimulants might enrich certain bacterial assemblages. Besides, the significant distinctions (p < 0.05) between the bacterial consortia of HA (humic acid) and SA (sodium acetate) groups from NPK, OX (oxalic acid), UR (urea), NH4, and SC (salicylate) groups also suggested that different bio-stimulants might induce distinct ecological impacts influencing the succession of prokaryotic communities in distinct directions. This work provides new insight into the bacterial degradation of pyrene using the bio-stimulation technique. It suggests that it is equally important to investigate the community structure and functions along with studying their impacts on degradation when devising a bio-stimulation technology.

Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12–24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.

An increase in polycyclic aromatic hydrocarbon (PAH) pollution poses significant challenges to human and ecosystem health in the Three Gorges Reservoir (TGR) of the Yangtze River. Based on the combination of PAH analysis with qPCR and high-throughput sequencing of bacteria, 32 topsoil samples collected from 16 sites along the TGR were used to investigate the distribution and biodegradation pathways of PAHs in the water-level-fluctuation zone (WLFZ). The results indicated that the concentrations of PAHs were 43.8–228.2 and 30.8–206.3 ng/g soil (dry weight) under the high- and low-water-level (HWL and LWL) conditions, respectively. The PAH concentration in urban areas was higher than that in rural areas. Under both the HWL and LWL conditions, the abundance of the bamA gene, a biomarker of anaerobic PAH biodegradation, was significantly higher than that of the ring-hydroxylating-dioxygenase (RHD) gene, a biomarker of aerobic PAH biodegradation. The abundance of the bamA gene was significantly positively correlated with PAHs (R² = 0.8), and the biodegradation percentage of PAHs incubated anaerobically was greater than that in the aerobically incubated microcosm experiments. These data implicated a key role of the anaerobic pathway in PAH biodegradation. Co-occurrence network analysis suggested that anaerobic Anaerolineaceae, Dechloromonas, Bacteroidetes_vadin HA17 and Geobacter were key participants in the biodegradation of PAHs. The diversity analysis of functional bacteria based on the bamA gene and microcosm experiments further demonstrated that nitrate was the primary electron acceptor for PAH biodegradation. These findings provide a new perspective on the mechanism of PAH biodegradation in the TGR and knowledge that can be used to develop strategies for environmental management.

Antimicrobial resistance genes (ARGs) are considered emerging environmental pollutants, posing potential risks for human and animal health: the misuse of antimicrobials in food-producing animals could favour the maintenance and spread of resistances (RMS) in bacteria. The occurrence of ARGs in Italian swine farming – which has specific characteristics – was investigated in order to explore RMS dynamics. Two farrow-to-finish pig farms were longitudinally monitored: faecal samples from animals and environmental samples were collected. DNA was extracted and tetA, ermB, qnrS and mcr1 ARGs were analysed by qPCR for their ability to confer resistance to highly or critically important antimicrobials (CIAs). Moreover, 16SrDNA gene was analysed to assess bacterial abundance. ermB and tetA genes were found in animal samples and manure samples. On the contrary, mcr1 was exclusively found in weaners, while qnrS occurred in all animal categories but sows and finishers. Among the analysed genes, ermB and tetA showed the highest absolute and relative abundances. Our results indicate that ermB and tetA ARGs are widely disseminated in the explored farms, suggesting efficient maintenance among bacteria and persistence in the environment. Interestingly, the presence of qnrS and mcr1, limited to just a few animal categories, highlights inefficient dissemination of these genes in the farm environment, in particular for mcr1, a stable plasmid gene conferring resistance to the last-resort antimicrobial, colistin. Paying close attention only to the finishing phase would have hampered the discovery of resistances to CIAs at farm level, which we instead identified thanks to an intensive longitudinal monitoring programme.

Marine mammals in the Barents Sea region have among the highest levels of contaminants recorded in the Arctic and the Atlantic walrus (Odobenus rosmarus rosmarus) is one of the most contaminated species within this region. We therefore investigated the relationships bewteen blubber concentrations of lipophilic persistent organic pollutants (POPs) and plasma concentrations of perfluoroalkyl substances (PFASs) and markers of endocrine and immune functions in adult male Atlantic walruses (n = 38) from Svalbard, Norway. To do so, we assessed plasma concentrations of five forms of thyroid hormones and transcript levels of genes related to the endocrine and immune systems as endpoints; transcript levels of seven genes in blubber and 23 genes in blood cells were studied. Results indicated that plasma total thyroxine (TT4) concentrations and ratio of TT4 and reverse triiodothyronine decreased with increasing blubber concentrations of lipophilic POPs. Blood cell transcript levels of genes involved in the function of T and B cells (FC like receptors 2 and 5, cytotoxic T-lymphocyte associated protein 4 and protein tyrosine phosphatase non-receptor type 22) were increased with plasma PFAS concentrations. These results suggest that changes in thyroid and immune systems in adult male walruses are linked to current levels of contaminant exposure.

The control of agricultural pests is key to maintain economically viable crops. Increasing environmental awareness, however, is leading to more restrictive European policies regulating the use of certain pesticides due to their impact on human health and the soil system. Given this context, we evaluated the efficacy of three alternatives to the soil fumigant 1,3-dichloropropene (1,3-D), which is currently banned in Europe: two non-fumigant nematicides [oxamyl (OX) and fenamiphos (FEN)] and the soil fumigant dimethyl disulfide (DMDS). We analysed the efficiency of these pesticides against root-knot nematodes and soil fungal pathogens (determined by qPCR) as well as the soil biological quality after treatments application (estimated by enzyme activities). Among treatments, 1,3-D and DMDS significantly reduced nematode populations. FEN was more effective in sandy soil, while OX had no effect in any soil. OX and FEN had no effect on fungal pathogens, whereas DMDS reduced the abundance of Rhizoctonia solani and Fusarium solani at the root level in clay-loam soil. Soil quality decreased after treatment application but then recovered throughout the experiment, indicating the possible dissipation of the pesticides. Our findings support DMDS as a potential sustainable alternative for controlling root-knot nematodes and fungal pathogens due to its effectiveness in both studied soils, although its negative impact on soil biological quality in sandier soils must be taken into account.Main finding of the work. DMDS is a reliable alternative to 1,3-D for controlling agricultural pest but its inhibitory effect on soil enzyme activities varied according to the soil characteristics.

Aquatic ecosystems and drinking water supply systems worldwide are increasingly affected by taste and odor episodes. In this study, molecular approaches including next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) were used to study the diversity and dynamics of cyanobacteria and 2-methylisoborneol (2-MIB)-producing cyanobacteria in Yuqiao Reservoir, a eutrophicated drinking water reservoir in Tianjin city, northern China. NGS revealed that the entire cyanobacterial community consisted of 16 genera, with Planktothrix (28.8%), Pseudanabaena (18.4%), Cylindrospermosis (7.8%), and Microcystis (7.6%) being the dominant genera, while microscopic examination identified only eight cyanobacterial genera. NGS of the 2-MIB synthesis gene revealed that Pseudanabaena and Planktothricoides were the main 2-MIB producers, with Pseudanabaena being dominant. This finding demonstrated that NGS can identify 2-MIB producers quickly and accurately and it can thus play an important role in the practical monitoring of aquatic ecology. The qPCR test showed 2-MIB synthesis gene with 4.27 × 10⁶ copies/L to 2.24 × 10⁹copies/L occurring at the three sampling sites. The mic gene copy number increased before the 2-MIB concentration increased, indicating that forecasting role in dealing with the 2-MIB concentration by gene copy number. Predicting 2-MIB by qPCR in the field must be verified with additional studies. The combination of NGS and qPCR can be an even more comprehensive method to provide early warning information to managers of reservoirs and water utilities facing taste and odor incidents. This is the first amplicon NGS dataset based on 2-MIB gene to study the diversity and dynamics of 2-MIB-producing cyanobacteria.