Occurrence of antibiotic resistome in farmland soils near phosphorus chemical industrial area

Assessment of antibiotic resistance genes in soils polluted by chemical and technogenic ways with poly-aromatic hydrocarbons and heavy metals

Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.

Inactivation of antibiotic-resistant bacteria in hospital wastewater by ozone-based advanced water treatment processes

The emergence and spread of antimicrobial resistance (AMR) continue on a global scale. The impacts of wastewater on the environment and human health have been identified, and understanding the environmental impacts of hospital wastewater and exploring appropriate forms of treatment are major societal challenges. In the present research, we evaluated the efficacy of ozone (O3)-based advanced wastewater treatment systems (O3, O3/H2O2, O3/UV, and O3/UV/H2O2) for the treatment of antimicrobials, antimicrobial-resistant bacteria (AMRB), and antimicrobial resistance genes (AMRGs) in wastewater from medical facilities. Our results indicated that the O3-based advanced wastewater treatment inactivated multiple antimicrobials (>99.9%) and AMRB after 10-30 min of treatment. Additionally, AMRGs were effectively removed (1.4-6.6 log10) during hospital wastewater treatment. The inactivation and/or removal performances of these pollutants through the O3/UV and O3/UV/H2O2 treatments were significantly (P < 0.05) better than those in the O3 and O3/H2O2 treatments. Altered taxonomic diversity of microorganisms based on 16S rRNA gene sequencing following the O3-based treatment showed that advanced wastewater treatments not only removed viable bacteria but also removed genes constituting microorganisms in the wastewater. Consequently, the objective of this study was to apply advanced wastewater treatments to treat wastewater, mitigate environmental pollution, and alleviate potential threats to environmental and human health associated with AMR. Our findings will contribute to enhancing the effectiveness of advanced wastewater treatment systems through on-site application, not only in wastewater treatment plants (WWTPs) but also in medical facilities. Moreover, our results will help reduce the discharge of AMRB and AMRGs into rivers and maintain the safety of aquatic environments.

The role of pores in micro-zone distribution of Cd in a tropical paddy soil: Results from X-ray computed tomography combined energy dispersive spectroscopy analysis

Accurate description of Cd micro-zone distribution and accumulation is the prerequisite for revealing Cd transfer and transformation processes. However, to date, the role of soil pores in the Cd micro-zone distribution characteristics in undisturbed soil is still unclear. In this study, the obvious heterogeneous distribution of Cd in and around the soil pores at the cross-sectional surface of the tropical undisturbed topsoil was visualized by the combination of X-ray micro-computed tomography and scanning electron microscope-energy dispersive spectroscopy. For both the air space and water-holding pores, the micro-zone distribution characteristics of Cd around the pores were dominated by pore sizes. For macropores and mesopores, Cd preferred to distribute in the micro-zone within 167.5-335 µm from pores. But for micropores, the highest content percentage of Cd was exhibited in the micro-zone within 67-167.5 µm from pores. The random forest model revealed that the occurrence of Fe (13.83%) and P (13.59%) contributed most to Cd micro-zone distribution around air space pores. While for water-holding pores, Fe occurrence (18.30%) contributed more significantly than P (11.92%) to Cd micro-zone distribution. Our study provided new insights into Cd retention mechanism, which is help for accessing Cd migration and transformation.

Surveillance and mitigation of soil pollution through metagenomic approaches

Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.

Organic Carbon Controls Mercury Distribution and Storage in the Surface Soils of the Water-Level-Fluctuation Zone in the Three Gorges Reservoir Region, China

The particular condition of the water-level-fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR), the largest hydroelectric reservoir in China, raises great concerns about mercury (Hg) contamination and ecological risk. In addition, previous research found that soil organic carbon (SOC) plays an essential role in controlling Hg distribution and speciation. However, there is minimal information on the Hg storage distribution and their relationships with SOC in the WLFZ in TGR. This study investigated Hg distribution, storage, and their relationships with SOC in the surface soils in WLFZ. The results showed that the total Hg (THg) content in the surface soils ranged from 18.40 to 218.50 ng g-1, with an average value of 78.17 ± 41.92 ng g-1. About 89% of samples had THg content above the background value in Chongqing, showing specific enrichment of Hg in WLFZ due to contamination in the TGR. The surface soils have low SOC, with an average value of 8.10 ± 3.90 g kg-1. Moreover, THg content showed consistent distribution with the SOC in WLFZ, with a significantly positive correlation (R = 0.52, p < 0.01, n = 242). THg storage (201.82 ± 103.46 g ha-1) in the surface soils was also significantly positively correlated with the SOC storage (R = 0.47, p < 0.01, n = 242). The reduced SOC sequestration, due to the periodical alternative "flooding-draining" and frequent reclamation and utilization of WLFZ, decreased the Hg adsorption in soil. Those might result in the re-release of Hg into waters when WLFZ is flooded. Therefore, more attention should be directed towards Hg cycling and the consequent environmental risks in the TGR region.

Phosphorus fractions and iron oxides responsible for the variations in the Cd retention capacity in tropical soil aggregates under different cropping patterns

The environmental behavior of Cd in soil has been widely studied because of its close relationship with food security and soil environmental pollution. In this study, the roles of P fractions and Fe oxides in the retention of Cd in typical tropical soil from five cropping patterns were investigated. Although there was no evident relationship between the Cd adsorption capacity and soil aggregate particle sizes, strong spatial associations of P, Fe, and Cd at the soil aggregates were observed via energy dispersive spectroscopy analysis. Among five cropping patterns, citrus plantations exhibited highest ratios (calculated by pixel area) of P overlapped with Cd (8.61%) and Fe overlapped with Cd (9.53%) in the microaggregates. Furthermore, the random forest model revealed that humic P and labile organic P greatly contributed to the sorptivity of Cd²⁺ by < 0.053 mm (13.3%) and 0.25-0.053 mm (13.4%) soil aggregates, respectively. Compared with the P fractions in different-sized soil aggregates, the contribution of Fe oxides to the sorption of Cd²⁺ by soil aggregates was more significant. Amorphous ferric oxide had the most significant contribution to the sorptivity of Cd²⁺ by < 0.053 mm (26.0%), 0.25-0.053 mm (23.0%), 2.0-0.25 mm (25.1%), and > 2.0 mm (33.9%) soil aggregates.

Spatial distribution and risk assessment of certain antibiotics in 51 urban wastewater treatment plants in the transition zone between North and South China

The release of antibiotics from WWTPs into the environment has raised increasing concern worldwide. The monitoring of antibiotics in WWTPs throughout a region is crucial for emerging pollutant management. A large-scale survey of the occurrence, distribution, and ecological risk of seven antibiotics in 51 WWTPs was conducted in Shaanxi Province, China. Norfloxacin and ofloxacin had the highest detection concentrations of 474.2 and 656.18 ng L^-1, respectively. Antibiotic residues in effluents were decreased by 5.88-94.16 % after different treatment processes. In particular, A²O or mixed processes performed well in removing target antibiotic compounds simultaneously. The ecological risk posed by antibiotic compounds detected in effluents was calculated using the risk quotient (RQ). Norfloxacin, ofloxacin, tetracycline, and roxithromycin posed different levels of potential ecotoxicological risk (RQ = 0.02-7.59). Based on the sum of the RQ values of individual antibiotic compounds, each investigated WWTP showed potential ecological risk. WWTPs with high risk levels were mainly found in the central region, while those in the southern region exhibited low risk levels, and those in the northern region showed risk levels between medium and high. This comprehensive investigation provides promising results to support the safe use and control of antibiotics in the study area.

Distinct aggregate stratification of antibiotic resistome in farmland soil with long-term manure application

Agricultural soils, which are closely linked to human health via food supply, have been recognized as an important reservoir for antibiotic resistance genes (ARGs). However, there is still a lack of knowledge regarding the role of soil aggregates in shaping ARG profile. In this study, we collected soils from long-term experimental farmland plots receiving inorganic and/or organic fertilizers and examined the patterns of antibiotic resistome distribution among differently sized soil aggregates using high-throughput quantitative polymerase chain reaction (HT-qPCR). Our results showed that the distribution of soil ARGs could be affected by manure application and aggregate size individually but not interactively. More diverse and abundant ARGs were found in the manured soils, compared to the non-manured soils. The aggregate size fraction of <53 μm exhibited the highest diversity and abundance of ARGs. Variation partitioning analysis revealed that soil traits, mobile genetic elements, and bacterial community collectively contributed to the variation of soil antibiotic resistance. The knowledge about aggregation stratification of soil ARGs obtained in this study is fundamental and essential to understanding the fate of soil ARGs at the microscale.

The performance and mechanism of simultaneous removal of calcium and heavy metals by Ochrobactrum sp. GMC12 with the chia seed (Salvia hispanica) gum as a synergist

A bacterium Ochrobactrum sp. GMC12, capable of biomineralization and denitrification, was employed to investigate the performance and mechanism of heavy metals removal. A chia seeds (Salvia hispanica) gum was proposed as a synergist for the first time. The results showed that strain GMC12 reduced Ca²⁺, Cd²⁺, Zn²⁺, and nitrate by 83.38, 98.89, 98.95, and 100% (2.09, 0.29, 0.55, and 0.79 mg L^-1 h^-1), respectively, over 96 h continuous determination experiments. The concentration gradient test revealed that strain GMC12 would effectively remove Cd²⁺ and Zn²⁺ by 99.80 and 99.91% (0.67 and 1.35 mg L^-1 h^-1), respectively, under the synergistic effect of gum (1.0%, w/v). The SEM-EDS and XRD manifested that Ca²⁺, HMs ions, and anionic groups coated on the bacteria surface to form CaCO₃, Ca₅(PO₄)₃OH, CdCO₃, Cd₅(PO₄)₃OH, ZnCO₃, and Zn₂(PO₄)OH. The fluorescence spectrometry and fourier transform infrared (FTIR) spectra illustrated that extracellular polymeric substance (EPS) was the key product for the nucleation site of bacteria, and the gum promoted the accumulation of bio-precipitates and accelerated the removal of HMs. In this research, Ochrobactrum sp. GMC12 exhibited great potential in wastewater treatment and chia seeds gum would go deep into material preparation and wastewater treatment due to its non-toxic nature, high viscosity, and advantageous morphology.

Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils

The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 - 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of bla_ampC showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p＞0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., bla_ampC, bla_TEM-1) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.