Effect of copper and zinc as sulfate or nitrate salts on soil microbiome dynamics and blaVIM-positive Pseudomonas aeruginosa survival

Insight into farming native microbiome by bioinoculant in soil-plant system

Applying beneficial microorganisms (BM) as bioinoculants presents a promising soil-amendment strategy while impacting the native microbiome, which jointly alters soil-plant performance. Leveraging the untapped potential of native microbiomes alongside bioinoculants may enable farmers to sustainably regulate soil-plant systems via natural bioresources. This review synthesizes literature on native microbiome responses to BMs and their interactive effects on soil and plant performance. We highlight that native microbiomes harbor both microbial "helpers" that can improve soil fertility and plant productivity, as well as "inhibitors" that hinder these benefits. To harness the full potential of resident microbiome, it is crucial to elucidate their intricate synergistic and antagonistic interplays with introduced BMs and clarify the conditions that facilitate durable BM-microbiome synergies. Hence, we indicate current challenges in predicting these complex microbial interactions and propose corresponding strategies for microbiome breeding via BM bioinoculant. Overall, fully realizing the potential of BMs requires clarifying their interactions with native soil microbiomes and judiciously engineering microbiome to harness helpful microbes already present within agroecosystems.

Tackling Carbapenem Resistance and the Imperative for One Health Strategies-Insights from the Portuguese Perspective

Carbapenemases, a class of enzymes specialized in the hydrolysis of carbapenems, represent a significant threat to global public health. These enzymes are classified into different Ambler's classes based on their active sites, categorized into classes A, D, and B. Among the most prevalent types are IMI/NMC-A, KPC, VIM, IMP, and OXA-48, commonly associated with pathogenic species such as Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The emergence and dissemination of carbapenemase-producing bacteria have raised substantial concerns due to their ability to infect humans and animals (both companion and food-producing) and their presence in environmental reservoirs. Adopting a holistic One Health approach, concerted efforts have been directed toward devising comprehensive strategies to mitigate the impact of antimicrobial resistance dissemination. This entails collaborative interventions, highlighting proactive measures by global organizations like the World Health Organization, the Center for Disease Control and Prevention, and the Food and Agriculture Organization. By synthesizing the evolving landscape of carbapenemase epidemiology in Portugal and tracing the trajectory from initial isolated cases to contemporary reports, this review highlights key factors driving antibiotic resistance, such as antimicrobial use and healthcare practices, and underscores the imperative for sustained vigilance, interdisciplinary collaboration, and innovative interventions to curb the escalating threat posed by antibiotic-resistant pathogens. Finally, it discusses potential alternatives and innovations aimed at tackling carbapenemase-mediated antibiotic resistance, including new therapies, enhanced surveillance, and public awareness campaigns.

Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs is the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

Potential risks of organic contaminated soil after persulfate remediation: Harmful gaseous sulfur release

Persulfate is considered a convenient and efficient remediation agent for organic contaminated soil. However, the potential risk of sulfur into the soil remediation by persulfate remains ignored. In this study, glass bottles with different persulfate dosages and groundwater tables were set up to simulate persulfate remediation of organic pollutants (aniline). The results found sulfate to be the main end-product (83.0%‒99.5%) of persulfate remediation after 10 days. Moreover, H2S accounted for 93.4%‒99.4% of sulfur reduction end-products, suggesting that H2S was the final fate of sulfur. H2S was released rapidly after one to three days at a maximum concentration of 33.0 ppm, which is sufficient to make a person uncomfortable. According to the fitted curve results, H2S concentration decreased to a safe concentration (0.15 ppm) after 20‒85 days. Meanwhile, the maximum concentration of methanethiol reached 0.6 ppm. These results indicated that secondary pollution from persulfate remediation could release harmful gases over a long time. Therefore, persulfate should be used more carefully as a remediation agent for soil contamination.

Characteristics of groundwater microbial communities' structure under the impact of elevated nitrate concentrations in north China plain

In groundwater environments, the interaction between microbial communities and the hydrogeochemical parameters have been investigated extensively in the past years. However, little is known whether the maximum contamination level (MCL) is a threshold value that dictates the microbial composition. In this study, we analyzed 10 groundwater samples for their nitrate, nitrite, COD and sulfate concentrations, and characterized their microbial compositions using 16 S rRNA based high-throughput sequencing methods. All the 10 samples had oxygen demands higher than the corresponding MCL of China (10 mg L^-1); moreover, 4 out of 10 samples also had nitrate concentrations higher than the corresponding MCL, which indicated that the groundwater quality was negatively impacted by anthropogenic activities. Comparing the microbial composition of groundwater that had higher-than-MCL nitrate concentrations to those that had lower-than-MCL nitrate concentrations, no significant differences were detected in communities' richness and diversity. However, the non-metric multi-dimensional analysis suggested that the 4 groundwater samples whose nitrate concentration exceed MCL are distinctly different from those of the rest 6 samples, indicating that MCL does have a significant impact on microbial structures. Pearson's correlation analysis suggested that none of the four analyzed hydrochemical parameters had significant impact on microbial communities' richness and diversity; however, at the genus level, the correlation results suggested that JG30-KM-CM45, Sphingomonas and Rhodococcus are closely correlated with nitrate concentration. The findings of this study deepened our understanding with respect to the relationships between the environmental quality indices and the microbial compositions of groundwater.

Damage and elimination of soil and water antibiotic and heavy metal pollution caused by livestock husbandry

The combination of antibiotics and heavy metals (HMs) increases the toxicity range of influence and requires additional research attention. This article analyzed the toxicity mechanisms and damage of combined pollution. Cross-resistance, co-resistance, and co-regulation are the primary toxicity mechanisms. Combined pollution increases antibiotic resistance genes (ARGs), increases bacterial resistance, and promotes the horizontal transfer of ARGs, affecting the types and distribution of microorganisms. The hazard of combined pollution varies with concentration and composition. The physicochemical and biological technologies for eliminating combined pollution are primarily elaborated. Adsorption, photocatalytic degradation, and microbial treatment show high removal rates and good recyclability, indicating good application potential. This review provides a basis and reference for the further study the elimination of combined antibiotic and HM pollution.

Pseudomonas aeruginosa Detection Using Conventional PCR and Quantitative Real-Time PCR Based on Species-Specific Novel Gene Targets Identified by Pangenome Analysis

Mining novel specific molecular targets and establishing efficient identification methods are significant for detecting Pseudomonas aeruginosa, which can enable P. aeruginosa tracing in food and water. Pangenome analysis was used to analyze the whole genomic sequences of 2017 strains (including 1,000 P. aeruginosa strains and 1,017 other common foodborne pathogen strains) downloaded from gene databases to obtain novel species-specific genes, yielding a total of 11 such genes. Four novel target genes, UCBPP-PA14_00095, UCBPP-PA14_03237, UCBPP-PA14_04976, and UCBPP-PA14_03627, were selected for use, which had 100% coverage in the target strain and were not present in nontarget bacteria. PCR primers (PA1, PA2, PA3, and PA4) and qPCR primers (PA12, PA13, PA14, and PA15) were designed based on these target genes to establish detection methods. For the PCR primer set, the minimum detection limit for DNA was 65.4 fg/μl, which was observed for primer set PA2 of the UCBPP-PA14_03237 gene. The detection limit in pure culture without pre-enrichment was 10⁵ colony-forming units (CFU)/ml for primer set PA1, 10³ CFU/ml for primer set PA2, and 10⁴ CFU/ml for primer set PA3 and primer set PA4. Then, qPCR standard curves were established based on the novel species-specific targets. The standard curves showed perfect linear correlations, with R² values of 0.9901 for primer set PA12, 0.9915 for primer set PA13, 0.9924 for primer set PA14, and 0.9935 for primer set PA15. The minimum detection limit of the real-time PCR (qPCR) assay was 10² CFU/ml for pure cultures of P. aeruginosa. Compared with the endpoint PCR and traditional culture methods, the qPCR assay was more sensitive by one or two orders of magnitude. The feasibility of these methods was satisfactory in terms of sensitivity, specificity, and efficiency after evaluating 29 ready-to-eat vegetable samples and was almost consistent with that of the national standard detection method. The developed assays can be applied for rapid screening and detection of pathogenic P. aeruginosa, providing accurate results to inform effective monitoring measures in order to improve microbiological safety.