Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau

Applications of different forms of nitrogen fertilizers affect soil bacterial community but not core ARGs profile

The objective of this study was to investigate the impact of various chemical nitrogen fertilizers on the profile of antibiotic resistance genes (ARGs) in soil. A microcosm experiment was conducted with four treatments, including CK (control with no nitrogen), AN (ammonium nitrogen), NN (nitrate nitrogen), and ON (urea nitrogen), and the abundance of ARGs was assessed over a 30-day period using a metagenomic sequencing approach. The levels of core ARGs varied between 0.16 and 0.22 copies per cell across different treatments over time. The abundance of core ARGs in the ON treatment closely resembled that of the CK treatment, suggesting that environmentally friendly nitrogen fertilizers, particularly those in controlled release formulations, may be preferable. The core ARG abundance in the AN and NN treatments exhibited noticeable fluctuations over time. Overall, chemical nitrogen fertilizers had minimal effects on the core ARG profile as determined by principal component analysis and clustering analyses. Conversely, distinct and significant changes in bacterial communities were observed with the use of different nitrogen fertilizers. However, the influence of nitrogen fertilizers on the core ARGs is limited due to the unaffected potential bacterial hosts. Nitrogen-cycling-related genes (NCRGs), such as those involved in nitrogen-fixing (nifK, nifD, nifH) and denitrification (narG, napA, nirK, norB, nosZ) processes, exhibit a positive correlation with ARGs (rosA, mexF, bacA, vanS), indicating a potential risk of ARG proliferation during intense denitrification activities. This study indicates that the application of chemical nitrogen has a minimal effect on the abundance of ARGs in soil, thereby alleviating concerns regarding the potential accumulation of ARGs due to the use of chemical nitrogen fertilizers.

Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake

Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.

High-generation tetracyclines shifted microbial community composition and induced the emergence of antibiotic resistant bacteria in soil

Tetracyclines (TCs) have been widely detected in agricultural soil due to their widespread use in animal husbandry. The impact of low-generation TCs, i.e., the first- and second- generations, on soil ecosystem has attracted widespread attention. However, the dynamic response of soil microbial community to high-generation TCs, i.e., the third- and fourth- generations, remains largely unknown. Herein, we characterized the variations in the composition, diversity and succession of microbial community and the proliferation of antibiotic resistance genes (ARGs) under the stress of four generations of TCs in brown soil and red soil. The results demonstrated that the exposure of low- and high- generation TCs consistently decreased the alpha diversity and stimulated the succession rate of microbial community in soil. High-generation TCs strongly shifted microbial community composition by reducing community resilience. The complexity of microbial networks and cross-module associations were strengthened to cope with the stress of high-generation TCs in soil. The abundance of ARGs was exacerbated by 1.75 times in response to the fourth-generation TCs compared to control in brown soil. The potential bacterial hosts of ARGs were more diverse in brown soil exposed to high-generation TCs, but the dominant hosts were not changed. These results highlight the potential ecological risk of the newly developed antibiotics, which is helpful for a comprehensive risk assessment of emerging contaminants.

Antimicrobial resistance and its risks evaluation in wetlands on the Qinghai-Tibetan Plateau

Amidst the global antimicrobial resistance (AMR) crisis, antibiotic resistance has permeated even the most remote environments. To understand the dissemination and evolution of AMR in minimally impacted ecosystems, the resistome and mobilome of wetlands across the Qinghai-Tibetan Plateau and its marginal regions were scrutinized using metagenomic sequencing techniques. The composition of wetland microbiomes exhibits significant variability, with dominant phyla including Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Notably, a substantial abundance of Antibiotic Resistance Genes (ARGs) and Mobile Genetic Elements (MGEs) was detected, encompassing 17 ARG types, 132 ARG subtypes, and 5 types of MGEs (Insertion Sequences, Insertions Sequences, Genomic Islands, Transposons, and Integrative Conjugative Elements). No significant variance was observed in the prevalence of resistome and mobilome across different wetland types (i.e., the Yellow River, other rivers, lakes, and marshes) (R=-0.5882, P=0.607). The co-occurrence of 74 ARG subtypes and 22 MGEs was identified, underscoring the pivotal role of MGEs in shaping ARG pools within the Qinghai-Tibetan Plateau wetlands. Metagenomic binning and analysis of assembled genomes (MAGs) revealed that 93 out of 206 MAGs harbored ARGs (45.15 %). Predominantly, Burkholderiales, Pseudomonadales, and Enterobacterales were identified as the primary hosts of these ARGs, many of which represent novel species. Notably, a substantial proportion of ARG-carrying MAGs also contained MGEs, reaffirming the significance of MGEs in AMR dissemination. Furthermore, utilizing the arg_ranker framework for risk assessment unveiled severe contamination of high-risk ARGs across most plateau wetlands. Moreover, some prevalent human pathogens were identified as potential hosts for these high-risk ARGs, posing substantial transmission risks. This study aims to investigate the prevalence of resistome and mobilome in wetlands, along with evaluating the risk posed by high-risk ARGs. Such insights are crucial for informing environmental protection strategies and facilitating the management of water resources on the Qinghai-Tibetan Plateau.

NO3- as an electron acceptor elevates antibiotic resistance gene and human bacterial pathogen risks in managed aquifer recharge (MAR): A comparison with O2

Managed aquifer recharge (MAR) stands out as a promising strategy for ensuring water resource sustainability. This study delves into the comparative impact of nitrate (NO3-) and oxygen (O2) as electron acceptors in MAR on water quality and safety. Notably, NO3-, acting as an electron acceptor, has the potential to enrich denitrifying bacteria, serving as hosts for antibiotic resistance genes (ARGs) and enriching human bacterial pathogens (HBPs) compared to O2. However, a direct comparison between NO3- and O2 remains unexplored. This study assessed risks in MAR effluent induced by NO3- and O2, alongside the presence of the typical refractory antibiotic sulfamethoxazole. Key findings reveal that NO3- as an electron acceptor resulted in a 2 times reduction in dissolved organic carbon content compared to O2, primarily due to a decrease in soluble microbial product production. Furthermore, NO3- significantly enriched denitrifying bacteria, the primary hosts of major ARGs, by 747%, resulting in a 66% increase in the overall abundance of ARGs in the effluent of NO3- MAR compared to O2. This escalation was predominantly attributed to horizontal gene transfer mechanisms, as evidenced by a notable 78% increase in the relative abundance of mobile ARGs, alongside a minor 27% rise in chromosomal ARGs. Additionally, the numerous denitrifying bacteria enriched under NO3- influence also belong to the HBP category, resulting in a significant 114% increase in the abundance of all HBPs. The co-occurrence of ARGs and HBPs was also observed to intensify under NO3- influence. Thus, NO3- as an electron acceptor in MAR elevates ARG and HBP risks compared to O2, potentially compromising groundwater quality and safety.

Effects of Microtopography on Soil Microbial Community Structure and Abundance in Permafrost Peatlands

Soil microorganisms play crucial roles in the stability of the global carbon pool, particularly in permafrost peatlands that are highly sensitive to climate change. Microtopography is a unique characteristic of peatland ecosystems, but how microtopography affects the microbial community structures and their functions in the soil is only partially known. We characterized the bacterial and fungal community compositions by amplicon sequencing and their abundances via quantitative PCR at different soil depths in three microtopographical positions (hummocks, flats, and hollows) in permafrost peatland of the Greater Xing'an Mountains in China. The results showed that the soil of hummocks displayed a higher microbial diversity compared to hollows. Microtopography exerted a strong influence on bacterial community structure, while both microtopography and soil depth greatly impacted the fungal community structure with variable effects on fungal functional guilds. Soil water content, dissolved organic carbon, total phosphorus, and total nitrogen levels of the soil mostly affected the bacterial and fungal communities. Microtopography generated variations in the soil water content, which was the main driver of the spatial distribution of microbial abundances. This information stressed that the hummock-flat-hollow microtopography of permafrost peatlands creates heterogeneity in soil physicochemical properties and hydrological conditions, thereby influencing soil microbial communities at a microhabitat scale. Our results imply that changes to the water table induced by climate warming inducing permafrost degradation will impact the composition of soil microbes in peatlands and their related biogeochemical functions, eventually providing feedback loops into the global climate system.

Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network

The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.

Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem

Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.

A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau

The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.

The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers

Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4+ and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4+ with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.

Coupling of submerged macrophytes and epiphytic biofilms reduced methane emissions from wetlands: Evidenced by an antibiotic inhibition experiment

Wetlands are the largest natural methane source, but how submerged macrophytes affect methane emission remains controversial. In this study, the impacts of submerged macrophytes on methane fluxes, water purification, and epiphytic microbial community dynamics were investigated in simulated wetlands (with and without Hydrilla verticillata) treated with norfloxacin (NOR) for 24 days. Mean methane fluxes were significantly lower in treatments with Hydrilla verticillata (56.84-90.94 mg/m2/h) than bulks (65.96-113.21 mg/m2/h) (p < 0.05) during the experiment regardless of NOR. The relative conductivity (REC) values, H2O2, and malondialdehyde (MDA) contents increased in plant leaves, while water nutrients removal rates decreased with increasing NOR concentration at the same sampling time. The partial least squares path model analysis revealed that plant physiological indices and water nutrients positively affected methane fluxes (0.72 and 0.49, p < 0.001). According to illumina sequencing results of 16S rRNA and pmoA genes, α-proteobacteria (type II) and γ-proteobacteria (type I) were the dominant methanotroph classes in all epiphytic biofilms. The ratio of type I/type II methanotrophs and pmoA gene abundance in epiphytic biofilm was considerably lower in treatment with 16 mg/L NOR than without it (p < 0.05). pmoA gene abundance was negatively correlated with methane fluxes (p < 0.05). Additionally, the assembly of epiphytic bacterial community was mainly governed by deterministic processes, while stochastic dispersal limitation was the primary assembly process in the epiphytic methanotrophic community under NOR stress. The deterministic process gained more importance with time both in bacterial and methanotrophic community assembly. Network analysis revealed that relationships among bacteria in epiphytic biofilms weakened with time but associations among methanotrophic members were enhanced under NOR stress over time. It could be concluded that submerged macrophytes-epiphytic biofilms symbiotic system exhibited potential prospects to reduce methane emissions from wetlands under reasonable management.

Maize straw application reduced cadmium and increased arsenic uptake in wheat and enhanced the rhizospheric bacterial communities in alkaline-contaminated soil

Many fields where wheat is grown in northern China are co-polluted by arsenic (As) and cadmium (Cd). Thus, remediation of As and Cd-contaminated alkaline soils is crucial for safe wheat production. In this study, a pot experiment was carried out to investigate the impact of 1% and 2% maize straw (MS) incorporation on As and Cd bioavailability, binding forms, uptake by winter wheat (Triticum aestivum L.), and bacterial communities in smelter (SS) and irrigation (IS) alkaline contaminated soils. The results indicated that 2% MS incorporation significantly (p < 0.05) increased bioavailable-As by 37% (SS) and 39% (IS) with no significant change in the bioavailable-Cd in SS2% (31.95%) from 31.95% (SSCK) and IS2% (33.33%) from 32.82% (ISCK). Incorporation of 2% MS increased the grain As concentration from 0.22 mg kg-1 (SSCK) to 0.51 mg kg-1 (SS2%) and from 0.59 mg kg-1 (ISCK) to 0.84 mg kg-1 (IS2%) which is above the acceptable standard of 0.5 mg kg-1 (GB2726-2017). In contrast, the Cd content in grains was maintained at 0.09 (SS1%), 0.04 (SS2%) and 0.03 (IS1%), 0.02 (IS2%) below the acceptable standard of 0.10 mg kg-1 (GB2762-2017). The amendment through dissolved organic carbon mediated As desorption enhanced As transfer to wheat grain, decreasing DTPA-Cd in the soils and its consequent translocation to wheat leaves and grain. The 2% MS incorporation increased the active As fractions, reduced mobile Cd into immobile fractions, and promoted the abundance of Actinobacteria, Bacteroidetes, and Firmicutes in the two soils. These attributes of MS in decreasing the accumulation of Cd in wheat leaves and grains signified its potential as a suitable ingredient for Cd sequestration and food safety in Cd-contaminated soils.

Distribution and relationship of antibiotics, heavy metals and resistance genes in the upstream of Hanjiang River Basin in Shiyan, China

The upstream basin of Hanjiang River is an important water source for the middle route of China's South-to-North Water Diversion Project. The quality of water and soil in the Hanjiang River have enormous biological and environmental impacts, and resistant genetic contamination has emerged, but only few studies are concerned the correlation between heavy metals and metal resistance genes (MRGs). In this study, 8 antibiotics and 19 heavy metals were analyzed, the results showed that the highest antibiotic content was tetracycline, with mean concentrations of 43.201 µg/kg and 0.022 µg/L. Mn was the highest heavy metal in soil with a content of 1408.284 µg/kg, and in water was Zn with a content of 10.611 µg/L. We found that the most abundant antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in the study area were bacA and arsT genes, coding for resistance mechanisms to bacitracin and arsenic, respectively. The data showed that heavy metals had a greater impact on antibiotic resistance genes than antibiotics, and the correlation between resistance genes was significantly positive. This work expands our understanding of the correlations of antibiotics, heavy metals, and resistance genes in the Hanjiang River, indicating that more attention should be paid to the effects of resistance genes and the quality of water.

Regional distribution and migration potential of antibiotic resistance genes in croplands of Qinghai Tibet Plateau

Agricultural activities have recently disturbed the ecosystem of the Qinghai-Tibet Plateau and the shift of antibiotic resistance genes (ARGs) in the different types of farmlands is not well understood, so more comprehensive ecological barrier management measures cannot be provided for the region. This research was performed to exploring ARG pollution in cropland soil on the Qinghai-Tibet Plateau to obtain information on the geographical and climatic factors shaping the ARG distribution. Based on high-throughput quantitative PCR (HT-qPCR) analysis, the ARG abundance in farmland ranged from 5.66 × 105 to 6.22 × 107 copies per gram of soil higher than previous research at soil and wetland in Qinghai-Tibet plateau, and it was higher in wheat and barley soils than in corn soil. The distribution of ARGs exhibited regional features as ARG abundance was adversely affected by mean annual precipitation and temperature with lower temperature and less rainfall at high altitude. According to network analysis and structural equation modeling (SEM), mobile genetic elements (MGEs) and heavy metals are the key drivers of ARG dissemination on the Qinghai-Tibet Plateau as they show negative relationship with ARGs, and selection copressure from heavy metals in cropland soil increases the horizontal gene transfer (HGT) potential of ARGs through synergistic selection effects, each contribution to the ARGs was 19% and 29% respectively. This research suggests the need to focus on controlling heavy metals and MGEs to constrain the dissemination of ARGs, as arable soil is already slightly contaminated by heavy metals.

Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau

As hotspots for the dissemination of antibiotic resistance genes (ARGs), wastewater treatment plants (WWTPs) have attracted global attention. However, there lacks a sufficient metagenomic surveillance of antibiotic resistome in the WWTPs located on the Qinghai-Tibet Plateau. Here, metagenomic approaches were used to comprehensively investigate the occurrence, mobility potential, and bacterial hosts of ARGs in influent and effluent of 18 WWTPs located on the Qinghai-Tibet Plateau. The total ARG relative abundances and diversity were significantly decreased from influent to effluent across the WWTPs. Multidrug, bacitracin, sulfonamide, aminoglycoside, and beta-lactam ARGs generally consisted of the main ARG types in effluent samples, which were distinct from influent samples. A group of 72 core ARGs accounting for 61.8-95.8 % of the total ARG abundances were shared by all samples. Clinically relevant ARGs mainly conferring resistance to beta-lactams were detected in influent (277 ARGs) and effluent (178 ARGs). Metagenomic assembly revealed that the genetic location of an ARG on a plasmid or a chromosome was related to its corresponding ARG type, demonstrating the distinction in the mobility potential of different ARG types. The abundance of plasmid-mediated ARGs accounted for a much higher proportion than that of chromosome-mediated ARGs in both influent and effluent. Moreover, the ARGs co-occurring with diverse mobile genetic elements in the effluent exhibited a comparable mobility potential with the influent. Furthermore, 137 metagenome-assembled genomes (MAGs) assigned to 13 bacterial phyla were identified as the ARG hosts, which could be effectively treated in most WWTPs. Notably, 46 MAGs were found to carry multiple ARG types and the potential pathogens frequently exhibited multi-antibiotic resistance. Some ARG types tended to be carried by certain bacteria, showing a specific host-resistance association pattern. This study highlights the necessity for metagenomic surveillance and will facilitate risk assessment and control of antibiotic resistome in WWTPs located on the vulnerable area.