Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils

Unlocking the potential of soil microbial communities for bioremediation of emerging organic contaminants: omics-based approaches

The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions.

Bioremediation of environmental organic pollutants by Pseudomonas aeruginosa: Mechanisms, methods and challenges

The development of the chemical industry has led to a boom in daily consumption and convenience, but has also led to the release of large amounts of organic pollutants, such as petroleum hydrocarbons, plastics, pesticides, and dyes. These pollutants are often recalcitrant to degradation in the environment, whereby the most problematic compounds may even lead to carcinogenesis, teratogenesis and mutagenesis in animals and humans after accumulation in the food chain. Microbial degradation of organic pollutants is efficient and environmentally friendly, which is why it is considered an ideal method. Numerous studies have shown that Pseudomonas aeruginosa is a powerful platform for the remediation of environmental pollution with organic chemicals due to its diverse metabolic networks and its ability to secrete biosurfactants to make hydrophobic substrates more bioavailable, thereby facilitating degradation. In this paper, the mechanisms and methods of the bioremediation of environmental organic pollutants (EOPs) by P. aeruginosa are reviewed. The challenges of current studies are highlighted, and new strategies for future research are prospected. Metabolic pathways and critical enzymes must be further deciphered, which is significant for the construction of a bioremediation platform based on this powerful organism.

Biodegradation of soil agrochemical contamination mitigates the direct horizontal transfer risk of antibiotic resistance genes to crops

Microorganisms can drive a substrate-specific biodegradation process to mitigate soil contamination resulting from extensive agrochemical usage. However, microorganisms with high metabolic efficiency are capable of adapting to the co-occurrence of non-substrate contaminants in the soil (particularly antibiotics). Therefore, the utilization of active microorganisms for biodegradation raises concerns regarding the potential risk of antibiotic resistance development. Here, the horizontal transfer risk of antibiotic-resistance genes (ARGs) in the soil-plant biota was assessed during biodegradation by the newly isolated Proteus terrae ZQ02 (which shortened the half-life of fungicide chlorothalonil from 9.24 d to 2.35 d when exposed to tetracycline). Based on metagenomic analyses, the distribution of ARGs and mobile genetic elements (MGEs) was profiled. The ARGs shared with ∼118 core genes and mostly accumulated in the rhizosphere and maize roots. After ZQ02 was inoculated, the core genes of ARGs reduced significantly in roots. In addition, the Pseudomonas and Proteus genera were identified as the dominant microbial hosts of ARGs and MGEs after ZQ02 adoption. The richness of major ARG hosts increased in soil but barely changed in the roots, which contributed to the mitigation of hosts-mediated ARGs transfer from soil to maize. Finally, the risk of ARGs has been assessed. Compared with the regular planting system, the number of risky ARGs declined from 220 (occupied 4.77 % of the total ARGs) to 143 (occupied 2.67 %) after biodegradation. Among these, 23 out of 25 high-risk genes were aggregated in the soil whereas only 2 genes were identified in roots, which further verified the low antibiotic resistance risk for crop after biodegradation. In a nutshell, this work highlights the critical advantage of ZQ02-based biodegradation that alleviating the ARGs transfer risks from soil to crop, which offers deeper insights into the versatility and feasibility of bioremediation techniques in sustainable agriculture.

Biochar as functional amendment for antibiotic resistant microbial community survival during hen manure composting

The study aim was to reveal the mechanism of impact of two type biochar on composting of hen manure (HM) and wheat straw (WS). Biochar derived from coconut shell and bamboo used as additives to reduce antibiotic resistant bacteria (ARB) in HM compost. The results manifested that effect of biochar amendment was significant to reduce ARB in HM composting. Compared with control, the microbial activity and abundance were increased in both biochar applied treatment, and bacterial community was changed. Additionally, network analysis revealed that biochar amendment increased the quantity of microorganisms related to organic matter degrading. Among them, coconut shell biochar (CSB) played a pioneering role to mitigate ARB to better exert its effects. Structural correlation analysis showed that CSB reduce ARB mobility and promote organic matter degradation via improving beneficial bacterial community structure. Overall, composting with participation of biochar amendment stimulated antibiotic resistance bacterial dynamics. These results evidence practical value for scientific research and lay the foundation for agricultural promotion of composting.

Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance

As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.

Biochar can mitigate co-selection and control antibiotic resistant genes (ARGs) in compost and soil

Heavy metals (HMs) contamination raises the expression of antibiotic resistance (AR) in bacteria through co-selection. Biochar application in composting improves the effectiveness of composting and the quality of compost. This improvement includes the elimination and reduction of antibiotic resistant genes (ARGs). The use of biochar in contaminated soils reduces the bioaccessibility and bioavailability of the contaminants hence reducing the biological and environmental toxicity. This decrease in contaminant bioavailability reduces contaminants induced co-selection pressure. Conditions which favour reduction in HMs bioavailable fraction (BF) appear to favour reduction in ARGs in compost and soil. Biochar can prevent horizontal gene transfer (HGT) and can eliminate ARGs carried by mobile genetic elements (MGEs). This effect reduces maintenance and propagation of ARGs. Firmicutes, Proteobacteria, and Actinobacteria are the major bacteria phyla identified to be responsible for dissipation, maintenance, and propagation of ARGs. Biochar application rate at 2-10% is the best for the elimination of ARGs. This review provides insight into the usefulness of biochar in the prevention of co-selection and reduction of AR, including challenges of biochar application and future research prospects.

Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species

The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.

An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR’s negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

Cost reduction strategies in the remediation of petroleum hydrocarbon contaminated soil

Petroleum hydrocarbon spill on land pollutes soil and reduces its ecosystem. Hydrocarbon transport in the soil is aided by several biological, physical, and chemical processes. However, pore characteristics play a major role in the distribution within the soil matrix. Restoring land use after spills necessitates remediation using cost-effective technologies. Several remediation technologies have been demonstrated at different scales, and research is ongoing to improve their performances towards the reduction of treatment costs. The process of removing the contaminants in the soil is through one or a combination of containment, separation, and degradation methods under the influence of biological, physical, chemical, and electrically-dominated processes. Generally, performance improvement is achieved through the introduction of products/materials and/or energy. Nevertheless, the technologies can be categorized based on effectiveness period as short, medium, and long term. The treatment cost of short, medium, and long-term technologies are usually in the range of $39 - 331/t (/tonne), $22 - 131/t, and $8 - 131/t, respectively. However, the total cost depends on other factors such as site location, capital cost, and permitting. This review compiles cost-saving strategies reported for different techniques used in remediating petroleum hydrocarbon polluted soil. We discuss the principles of contaminant removal, performance enhancing methods, and the cost-effectiveness analysis of selected technologies.

Removal of antibiotic thiamphenicol by bacterium Aeromonas hydrophila HS01

Thiamphenicol (TAP) is an amphenicol antibiotic, which has a broad-spectrum inhibitory effect on both gram-positive and gram-negative bacteria. Since it is widely used in animals and aquaculture, its residues in environment may bring potential risk for human health and ecosystems. While TAP can be removed through conventional physical or chemical methods, its bioremediation using microorganisms is less studied. Here, we report the removal of TAP by a bacterial strain, Aeromonas hydrophila HS01, which can remove more than 90.0% of TAP in a living cell-dependent manner. Our results indicated that its removal efficiency can be greatly affected by the growth condition. Proteomics studies revealed a number of differentially expressed proteins of HS01 in the presence of TAP, which may play critical roles in the transportation and degradation of TAP. All these results indicate bacterial strain A. hydrophila HS01 is a new microbial resource for efficiently removing TAP, and may shed new insights in developing bioremediation approaches for TAP pollution.

Bio-Based Waste’ Substrates for Degraded Soil Improvement—Advantages and Challenges in European Context

The area of degraded sites in the world is constantly expanding and has been a serious environmental problem for years. Such terrains are not only polluted, but also due to erosion, devoid of plant cover and organic matter. The degradation trends can be reversed by supporting remediation/reclamation processes. One of the possibilities is the introduction of biodegradable waste/biowaste substrates into the soil. The additives can be the waste itself or preformed substrates, such composts, mineral-organic fertilizers or biochar. In EU countries average value of compost used for land restoration and landfill cover was equal 4.9%. The transformation of waste in valuable products require the fulfillment of a number of conditions (waste quality, process conditions, law, local circumstances). Application on degraded land surface bio-based waste substrates has several advantages: increase soil organic matter (SOM) and nutrient content, biodiversity and activity of microbial soil communities and change of several others physical and chemical factors including degradation/immobilization of contaminants. The additives improve the water ratio and availability to plants and restore aboveground ecosystem. Due to organic additives degraded terrains are able to sequestrate carbon and climate mitigate. However, we identified some challenges. The application of waste to soil must comply with the legal requirements and meet the end of use criteria. Moreover, shorter or long-term use of bio-waste based substrate lead to even greater soil chemical or microbial contamination. Among pollutants, “emerging contaminants” appear more frequently, such microplastics, nanoparticles or active compounds of pharmaceuticals. That is why a holistic approach is necessary for use the bio-waste based substrate for rehabilitation of soil degraded ecosystems.

Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH₄⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH₄⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

Plasmid profiling of multiple antibiotic-resistant Pseudomonas aeruginosa isolated from soil of the industrial area in Chittagong, Bangladesh

Background

Multiple antibiotic-resistant (MAR) Pseudomonas aeruginosa (P. aeruginosa) plays a significant role in triggering nosocomial infection in clinical settings. While P. aeruginosa isolated from the environment is often regarded as non-pathogenic, the progressive development of antibiotic resistance necessitates exploring the MAR patterns and transposable genetic elements like plasmid in the isolates.

Results

Using ecfX gene-based PCR, 32 P. aeruginosa isolates among 48 soil samples collected from the industrial region have been confirmed. The antibiotic susceptibility pattern of those isolates revealed that 5 (15.63%) of them were resistant to a range of antibiotics, and they were categorized as MAR isolates. Nevertheless, all MAR isolates were found resistant to piperacillin and gentamicin, but none of them to ceftazidime, aztreonam, and ciprofloxacin. Moreover, the isolates were also showed resistance to amikacin (60%), tobramycin (80%), netilmicin (80%), imipenem (60%), doripenem (40%), meropenem (60%), and cefixime (40%). Furthermore, 60% of MAR isolates possessed double plasmids of 1000–2000 bp sizes which indicates the distribution of antibiotic resistance genes in MAR P. aeruginosa might be correlated with the presence of those plasmids. The MAR index’s high threshold values (> 0.20) implied that the isolates were from high-risk environmental sites where the presence of numerous antibiotic residues happened.

Conclusions

These findings highlighted the presence of multiple antibiotic resistance in P. aeruginosa of the industrial soil and a considerable prospect of transferring antibiotic resistance genes in the microbial community by plasmids. We recommend taking immediate stringent measures to prohibit the unnecessary and overuse of antibiotics in agricultural, industrial, or other purposes.

Impact of spent engine oil contamination on the antibiotic resistome of a tropical agricultural soil

Profiling of hydrocarbon-contaminated soils for antibiotic resistance genes (ARGs) is becoming increasingly important due to emerging realities of their preponderance in hydrocarbon-inundated matrices. In this study, the antibiotic resistome of an agricultural soil (1S) and agricultural soil contaminated with spent engine oil (AB1) were evaluated via functional annotation of the open reading frames (ORFs) of their metagenomes using the comprehensive antibiotic database (CARD) and KEGG KofamKOALA. CARD analysis of AB1 metagenome revealed the detection of 24 AMR (antimicrobial resistance) gene families, 66 ARGs, and the preponderance (69.7%) of ARGs responsible for antibiotic efflux in AB1 metagenome. CARD analysis of 1S metagenome revealed four AMR gene families and five ARGs. Functional annotation of the two metagenomes using KofamKOALA showed 171 ARGs in AB1 and 29 ARGs in 1S, respectively. Majority of the detected ARGs in AB1 (121; 70.8%) and 1S (16; 55.2%) using KofamKOALA are responsible for antibiotic efflux while ARGs for other resistance mechanisms were also detected. All the five major antibiotic efflux pump systems were detected in AB1 metagenome, though majority of the ARGs for antibiotic efflux belong to the RND (resistance-nodulation-cell division) and MFS (major facilitator superfamily) efflux systems. Significant differences observed in the ARGs recovered from 1S and AB1 metagenomes were statistically validated (P < 0.05). SEO contamination is believed to be responsible for ARGs increase in AB1 metagenome via mechanisms of cross-resistance especially with efflux pumps. The detection of these ARGs is of great public health concern in this era of multidrug resistant isolates resurgence.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Paradigm shift in antibiotic-resistome of petroleum hydrocarbon contaminated soil

The increasing prevalence of antibiotic-resistant microorganisms in both clinical and environmental samples is of great concern for public health. In the present study, environmental samples from seven different sites, heavily contaminated with petroleum hydrocarbons has been examined for the antimicrobial resistome through metagenomic approach. The soil samples were found to be contaminated with high concentration of total petroleum hydrocarbons (average 45 g/kg), polyaromatic hydrocarbons (average ∑16PAH = 280 mg/kg), and heavy metals, which shapes the microbial community and their function. Proteobacteria was found to be predominant phylum in the contaminated habitat with the highest diversity (55.91%) followed by Actinobacteria (9.86%). Although the taxonomical abundance of the non-contaminated sample was not significantly different from contaminated samples, the functional abundance of genes related to antibiotic resistance was found to be higher up to 2 fold in contaminated samples. The comparative metagenomic analysis revealed a higher abundance of different antibiotic resistance genes, especially genes for fluoroquinolones was found to be higher up to 10 fold in contaminated samples. Moreover, the study has shown a significant difference in total functional diversity and abundance, mainly genes for aromatic compound metabolism and genes for phages, mobile genetic elements. These higher abundances of well recognized antibiotic resistance genes, multidrug efflux pumps, and integrons, suggest that the petroleum hydrocarbon contaminated sites can act as reservoirs for development of antibiotic resistance genes (ARGs). From this study, a significant link between the presence of petroleum hydrocarbon and the development of antibiotic resistance in the microbiome of contaminated habitat has been established.