Change in microbial community in landfill refuse contaminated with antibiotics facilitates denitrification more than the increase in ARG over long-term

Impact of antibiotics, iron oxide, and sodium sulfate on microbial community composition in laboratory-built municipal solid waste microcosms

Municipal solid waste (MSW) landfills represent underexplored microbial ecosystems. Landfills contain variable amounts of antibiotic and construction and demolition (C&D) wastes, which have the potential to alter microbial metabolism due to biocidal or redox active components, and these effects are largely underexplored. To circumvent the challenge of MSW heterogeneity, we conducted a 65-day time series study on simulated MSW microcosms to assess microbiome changes using 16S rRNA sequencing in response to 1) Fe(OH)3 and 2) Na2SO4 to represent redox active components of C&D waste as well as 3) antibiotics. The addition of Fe(OH)3 altered the overall community composition and increased Shannon diversity and Chao1 richness. The addition of a mixture of seven antibiotics (1000 ng/L each) altered the community composition without affecting diversity metrics. Sulfate addition had little effect on microbial community composition or diversity. These results suggest that the microbial community composition in fresh MSW may be significantly impacted by influxes of iron waste and a single application of antibiotics.

Performances of a novel BAF with ferromanganese oxide modified biochar (FMBC) as the carriers for treating antibiotics, nitrogen and phosphorus in aquaculture wastewater

In this paper, a biological aerated filter (BAF) based on ferromanganese oxide-biochar (FMBC) was constructed to investigated the removal performance and mechanism for conventional pollutants and four kinds of antibiotic, in contrast of conventional zeolite loaded BAF (BAF-A) and bamboo biochar filled BAF (BAF-B). Results showed that the average removal efficiency of total nitrogen (TN), total phosphorus (TP) and antibiotics in a FMBC-BAF (named by BAF-C) were 52.97 ± 2.27%, 51.58 ± 1.92% and 70.36 ± 1.00% ~ 81.65 ± 0.99% respectively in running period (39-100 d), which were significantly higher than those of BAF-A and BAF-B. In the BAF-C, the expression of denitrification enzyme activities and the secretion of extracellular polymeric substance (EPS) especially polyprotein (PN) were effectively stimulated, as well as accelerated electron transfer activity (ETSA) and lower electrochemical impedance spectroscopy (EIS) were acquired. After 100 days of operation, the abundance of nitrogen, phosphorus and antibiotic removal functional bacteria like Sphingorhabdus (4.52%), Bradyrhizobium (1.98%), Hyphomicrobium (2.49%), Ferruginibacter (7.80%), unclassified_f_Blastoca tellaceae (1.84%), norank_f_JG30-KF-CM45 (6.82%), norank_f_norank_o_SBR1031 (2.43%), Nitrospira (2.58%) norank_f_Caldilineaceae (1.53%) and Micropruina (1.11%) were enriched. Mechanism hypothesis of enhanced performances of nutrients and antibiotics removal pointed that: The phosphorus was removed by adsorption and precipitation, antibiotics removal was mainly achieved through the combined action of adsorption and biodegradation, while nitrogen removal was realized by biologic nitrification and denitrification in a FMBC-BAF for aquaculture wastewater treatment.

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.

Effects of Florfenicol on nirS-Type Denitrification Community Structure of Sediments in an Aquatic Microcosm Model

Florfenicol is one of the most widely used antibiotics in aquaculture and veterinary clinics because of its low side effects and strong bactericidal effect. A total of 45~60% of florfenicol is not absorbed by the animal body and accumulates in the aquatic environment through a variety of pathways, which affects denitrification. Indoor aquatic microcosm models were constructed and sediment samples were collected at different florfenicol concentrations (0.1, 1, 10, and 100 mg/L) on days 0, 7, 30, and 60 to extract the microbial genome DNA and determine the water properties. qPCR and amplicon sequencing were used to study the dynamic changes in the nirS gene and nirS-type denitrification community structure, diversity, and abundance, respectively. The results showed that high florfenicol stress influenced the sediment's physicochemical properties, reducing conductivity, alkaline dissolved nitrogen, and organic matter content. In addition, the abundance of nirS, a functional denitrification gene, increased obviously with increased florfenicol concentrations but decreased the diversity of nirS-type denitrification microorganisms. Proteobacteria was the dominant denitrifying phylum in the sediment. Our study provides a scientific basis for the rational use of florfenicol in aquaculture to maintain a healthy and stable microecological environment and also provides a preliminary understanding of the response characteristics of water denitrifying microorganisms to florfenicol exposure.

Sediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystems

The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

Delineating the impact of COVID-19 on antimicrobial resistance: An Indian perspective

The COVID-19 pandemic has shattered millions of lives globally and continues to be a challenge to public health due to the emergence of variants of concern. Fear of secondary infections following COVID-19 has led to an escalation in antimicrobial use during the pandemic, while some antimicrobials have been repurposed as treatments for SARS-CoV-2, further driving antimicrobial resistance. India is one of the largest producers and consumers of antimicrobials globally, hence the task of curbing antimicrobial resistance is a huge challenge. Practices like empirical antimicrobial prescription and repurposing of drugs in clinical settings, self-medication and excessive use of antimicrobial hygiene products may have negatively impacted the prevalence of antimicrobial resistance in India. However, the expanded production of antimicrobials and disinfectants during the pandemic in response to increased demand may have had an even greater impact on the threat of antimicrobial resistance through major impacts on the environment. The review provides an outline of the impact COVID-19 can have on antimicrobial resistance in clinical settings and the possible outcomes on the environment. This review calls for the upgrading of existing antimicrobial policies and emphasizes the need for research studies to understand the impact of the pandemic on antimicrobial resistance in India.

Profiling of co-metabolic degradation of tetracycline by the bio-cathode in microbial fuel cells

In this paper, a system of tetracycline (TEC) degradation by the bio-cathode in a microbial fuel cell (MFC) was constructed. Overall, the co-metabolic degradation performance of TEC was studied through single factor experiments and the ecological risk was evaluated using the E. coli growth inhibition rate and resistance genes. High throughput sequencing (HTS) was utilized to profile the biofilm community structure of the bio-cathode. Results showed that the degradation rate of TEC reached greater than 90% under optimal conditions, which was 10 mg L⁻¹ initial TEC concentration, 0.2–0.7 g L⁻¹ sodium acetate concentration and 12–18 L h⁻¹ aeration. Furthermore, compared with the aerobic biodegradation of TEC, the degradation efficiency of the MFC bio-cathode for TEC was significantly increased by 50% and the eco-toxicity of TEC after 36 hour degradation was reduced by 60.9%, and TEC ARGs in effluent were cut down. HTS results showed that electrochemically active bacteria Acetobacter and TEC-resistant degradation bacteria Hyphomicrobium, Clostridium and Rhodopseudomonas were the main dominant bacteria in the cathode biofilm. Besides, based on 5 intermediates, degradation pathways involving deamidation, denitro dimethylation, dedimethylation and dehydroxylation of TEC were proposed. The degradation of TEC on the bio-cathode was mainly caused by microbial co-metabolism action. This study would enrich the study of MFC bio-cathodic degradation of antibiotics in water.

In this paper, a system of tetracycline (TEC) degradation by the bio-cathode in a microbial fuel cell (MFC) was constructed.

The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing

Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.

Impact of acyl-homoserine lactones on the response of nitrogen cycling in sediment to florfenicol stress

Antibiotic residuals disrupt environmental microbial metabolism and can alter the nitrogen cycle. Quorum sensing has both inter- and intra-species effects that are directly related to the population densities necessary for microbial nitrogen cycling. Here, we explored how acyl-homoserine lactones (AHLs) can change the response of nitrogen cycling to florfenicol in sediments. AHLs might promote microbial reproduction in sediment under florfenicol stress. The relative abundances of Proteobacteria and Euryarchaeota in the antibiotic and AHL treatment groups were higher than those in the control group. AHLs reduced the effects of antibiotics on the abundance of Nitrospira at sampling times of 3d, 10d, and 20d. In the annotation results, nitrate reductase showed the highest abundance, followed by nitrite reductase, nitrogenase, nitric oxide (NO) reductase, nitrous oxide reductase, and ammonia monooxygenase. The abundances of these genes have changed in response to pressure by florfenicol and the addition of AHLs. We also found significant associations between the nitrogen cycle-related functional genes and dominant genera. In particular, glutamate metabolic enzymes and nitrate/nitrite transporters were the primary participants in correlation. Florfenicol can rapidly alter microbial community structures in sediments, affect the functional diversity of microorganisms, and hinder the nitrogen cycle. The response of microorganisms to florfenicol was regulated by the addition of AHLs. This process might alter the use and production of nitrogenous substances in the environment by functional communities in sediments.

Bacterial community compositions and nitrogen metabolism function in a cattle farm wastewater treatment plant revealed by Illumina high-throughput sequencing

Bacteria play an important role in pollutant transformation in activated sludge-based wastewater treatment plants (WWTPs). Exploring the microbial community structure and diversity is essential to improving the performance of wastewater treatment processes. This study employed Illumina MiSeq high-throughput sequencing to investigate the microbial community composition and diversity in a cattle farm wastewater treatment plant (Cf-WWTP). The results showed that the dominant phyla in the whole process were Proteobacteria, Bacteroidetes, and Firmicutes. The principal coordinate analysis (PCoA) indicated that the different stages had a significant impact on the microbial community structure; Bacteroidetes was the dominant phylum in the anearobic stage and Proteobacteria was the dominant phylum in the anoxic-oxic stage. Redundancy analysis (RDA) revealed that total phosphorus (TP) was the most significant factor that regulated the microbial community composition, followed by chemical oxygen demand (COD), total nitrogen (TN), and pH. Proteobacteria, Patescibacteria, and Chloroflexi were simultaneously negatively correlated with TN, COD, and TP. Nitrogen metabolic pathway and transformation mechanism was elucidated by a complete denitrification function predicted with phylogenetic investigation of communities with reconstruction of unobserved states (PICRUSt), as well as detection of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). These results provide new insights into our understanding of microbial community and metabolic functions of Cf-WWTP.

Potential Environmental and Human Health Risks Caused by Antibiotic-Resistant Bacteria (ARB), Antibiotic Resistance Genes (ARGs) and Emerging Contaminants (ECs) from Municipal Solid Waste (MSW) Landfill

The disposal of municipal solid waste (MSW) directly at landfills or open dump areas, without segregation and treatment, is a significant concern due to its hazardous contents of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and metal resistance genes (MGEs). The released leachate from landfills greatly effects the soil physicochemical, biological, and groundwater properties associated with agricultural activity and human health. The abundance of ARB, ARGs, and MGEs have been reported worldwide, including MSW landfill sites, animal husbandry, wastewater, groundwater, soil, and aerosol. This review elucidates the occurrence and abundance of ARB, ARGs, and MRGs, which are regarded as emerging contaminants (ECs). Recently, ECs have received global attention because of their prevalence in leachate as a substantial threat to environmental and public health, including an economic burden for developing nations. The present review exclusively discusses the demands to develop a novel eco-friendly management strategy to combat these global issues. This review also gives an intrinsic discussion about the insights of different aspects of environmental and public health concerns caused due to massive leachate generation, the abundance of antibiotics resistance (AR), and the effects of released leachate on the various environmental reservoirs and human health. Furthermore, the current review throws light on the source and fate of different ECs of landfill leachate and their possible impact on the nearby environments (groundwater, surface water, and soil) affecting human health. The present review strongly suggests the demand for future research focuses on the advancement of the removal efficiency of contaminants with the improvement of relevant landfill management to reduce the potential effects of disposable waste. We propose the necessity of the identification and monitoring of potential environmental and human health risks associated with landfill leachate contaminants.

Antibiotic and metal resistance genes are closely linked with nitrogen-processing functions in municipal solid waste landfills

Landfilled antibiotics and metals were related to the occurrences of their resistance genes, whose decade-long development in leachates with the dynamic landfilling environmental conditions, especially with the varying nitrogen contents, has yet to be studied. Here, we sampled leachates from five representative municipal solid waste landfills in China. The total concentrations of antibiotics (5000 - 50000 ng/L) and metals (10 - 60 mg/L) in leachates were significantly different among different sites and they were only closely related to sulfonamide and tetracycline resistance genes (P < 0.05). Regarding the abundance of subtype resistance genes, sul1 and ermB were dominant antibiotic resistance genes (ARGs) and terc, arsc, and mer were dominant heavy metal resistance genes (HMRGs); and meanwhile the observed huge variations of these genes appeared to be related to environmental factors like nitrate and pH (P < 0.05). The GeoChip results further indicated that more than 85% of sequenced ARGs/HMRGs and nitrogen processing genes, particularly of the denitrification genes, were hosted by the same bacterial species, such as Pseudomonas sp. and Bacillus sp., which belonged to the predominant phylum in leachates. These results extended our knowledge about the linkages among ARGs, HMRGs and nitrogen-processing functions in leachates.

Dynamics of denitrification performance and denitrifying community under high-dose acute oxytetracycline exposure and various biorecovery strategies in polycaprolactone-supported solid-phase denitrification

Solid-phase denitrification (SPD) is a promising technology for nitrate-rich water purification. This study aimed to examine the variation in denitrification performance and denitrifying community under high-dose acute oxytetracycline (OTC) exposure and various biorecovery strategies. The denitrification performance was impaired significantly after one-day OTC shock at 50 mg L^-1 in a continuous-flow SPD system supported by a polycaprolactone (PCL) carrier but could rapidly recover without the addition of OTC. When 50 mg L^-1 OTC stress was applied for a longer time in the batch tests, a natural recovery period of more than 20 days was required to reach more than 95% nitrate reduction. Under the same conditions, the addition of both mature biofilm-attached PCL carrier and fresh biofilm-free PCL carrier significantly shortened the recovery time for efficient nitrate reduction, mainly due to the increase in organic availability from the PCL carriers. However, the composition of the microbial community notably changed due to the effects of OTC according to high-throughput sequencing and metagenomic analysis. Genes encoding NAR and NIR were much more sensitive than those encoding NOR and NOS to OTC shock. Tetracycline resistance gene (TRG) enrichment was 15.86% higher in the biofilm that experienced short-term OTC shock than in the control biofilm in the continuous-flow SPD system.

The formation mechanism of antibiotic-resistance genes associated with bacterial communities during biological decomposition of household garbage

Food wastes are significant reservoir of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) available for exchange with clinical pathogens. However, food wastes-related changes of antibiotic resistance in long-period decomposition have been overlooked. Here, we evaluated the comprehensive ARG profile and its association with microbial communities, explained how this might vary with household garbage decomposition. Average of 128, 150 and 91 ARGs were detected in meat, vegetable and fruit wastes, respectively, with multidrug and tetracycline as the predominant ARG types. ARG abundance significantly increased at initial stage of waste fermentation and then decreased. High abundance of Eubacterium-coprostanoligenes, Sporanaerobacter, Peptoniphilus, Peptostreptococcus might be explained for the high relative abundance of ARGs in meat, while high abundance of Advenella, Prevotella, Solobacterium was attributed to the high diversity of ARGs in vegetables. Significant correlations were observed among volatile organic compounds, mobile genetic elements and ARGs, implying that they might contribute to transfer and transport of ARGs. Network analysis revealed that aph(2')-Id-01, acrA-05, tetO-1 were potential ARG indicators, while Hathewaya, Paraclostridium and Prevotellaceae were possible hosts of ARGs. Our work might unveil underlining mechanism of the effects of food wastes decomposition on development and spread of ARGs in environment and also clues to ARG mitigation.

Comparative analysis of denitrification performance, denitrifying community and functional genes to oxytetracycline exposure between single and hybrid biodegradable polymers supported solid-phase denitrification systems

Biodegradable carrier are vital for the solid-phase denitrification (SPD) systems for treating nitrate-rich water. Two solid-phase denitrification reactors were developed with both 200 g L^-1 of single (polycaprolactone, PCL) (R1) and hybrid solid carbon sources (PCL/polylactic acid (PLA) /polyhydroxyalkanoates (PHA)) (R2) to examine the denitrification performance, denitrifying community and functional genes to various oxytetracycline (OTC) exposure in this study, respectively. Complete denitrification performance was achieved in the both SPD systems at low stress of OTC (1 mg L^-1), but then dramatically reduced to less than 20% of nitrate reduction efficiency after one-month high OTC stress (10 mg L^-1), and rapidly recovered to stable nitrate removal rates of 76.77 ± 5.48% (R1) and 40.68 ± 4.40% (R2) after the next day of no OTC stress. However, the reactor R1 with single PCL carriers acquired more efficient nitrate removal rate than that of reactor R2 at the high OTC stress and recovery phase with OTC stress, mainly due to the more organics availability from the single PCL carriers. The richness and diversity of nirK and nirS deintrifiers significantly declined at high OTC stress, and much more of those occurred in biofilm R1 with more organics availability. Besides, biofilm R1 achieved much more abundant periplasmic nitrate reductase, nitrite reductase genes and tetracycline resistance genes after high OTC stress, which explained the potential resistance to OTC and rapid recovery efficiency after no stress of OTC. Thus, the organics availability played an important role in assuring SPD system to be efficient under high OTC stress.

A Review of Landfill Microbiology and Ecology: A Call for Modernization With 'Next Generation' Technology

Engineered and monitored sanitary landfills have been widespread in the United States since the passage of the Clean Water Act (1972) with additional controls under RCRA Subtitle D (1991) and the Clean Air Act Amendments (1996). Concurrently, many common perceptions regarding landfill biogeochemical and microbiological processes and estimated rates of gas production also date from 2 to 4 decades ago. Herein, we summarize the recent application of modern microbiological tools as well as recent metadata analysis using California, USEPA and international data to outline an evolving view of landfill biogeochemical/microbiological processes and rates. We focus on United States landfills because these are uniformly subject to stringent national and state requirements for design, operations, monitoring, and reporting. From a microbiological perspective, because anoxic conditions and methanogenesis are rapidly established after daily burial of waste and application of cover soil, the >1000 United States landfills with thicknesses up to >100 m form a large ubiquitous group of dispersed 'dark' ecosystems dominated by anaerobic microbial decomposition pathways for food, garden waste, and paper substrates. We review past findings of landfill ecosystem processes, and reflect on the potential impact that application of modern sequencing technologies (e.g., high throughput platforms) could have on this area of research. Moreover, due to the ever evolving composition of landfilled waste reflecting transient societal practices, we also consider unusual microbial processes known or suspected to occur in landfill settings, and posit areas of research that will be needed in coming decades. With growing concerns about greenhouse gas emissions and controls, the increase of chemicals of emerging concern in the waste stream, and the potential resource that waste streams represent, application of modernized molecular and microbiological methods to landfill ecosystem research is of paramount importance.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Validated predictive modelling of sulfonamide and beta-lactam resistance genes in landfill leachates

The spread of antimicrobial resistance via landfill leachates jeopardizes millions of people's health, which can be exacerbated due to the unclear quantitative relationships between leachate characteristics and occurrences of antibiotic resistance genes (ARGs). Here, in parallel with sampling raw leachates from a real landfill, we constructed a lab-scale landfill and collected its leachates for 260 days. All leachate samples were analyzed for the abundance of integrons, sulfonamide resistance (sulR; sul1 and sul2) and beta-lactams resistance (blaR; bla_OXA, bla_CTX-M, and bla_TEM) genes. The enrichment of sulR subtypes was closely associated with the integrons' prevalence during the landfilling process (0.65-0.75 log₁₀(copies/mL)), which can be explained by the multiple linear regression that contained intl1, pH, and nitrogen compounds as variables. The predicted abundance of sulR genes (6.06 ± 0.6 log₁₀(copies/mL)) was statistically the same as the observed value in raw leachates (P = 0.73). The abundance of blaR genes decreased from 5.0 to 2.5 log₁₀(copies/mL) during the experiment (P < 0.001); and a locally weighted regression of blaR genes with integrons, COD and total nitrogen accurately predicted blaR genes abundance in raw leachate (Bootstrap = 10,000, P = 0.67). The partial least squares path modelling (PLS-PM) showed that variations of blaR genes in the lab and raw leachates shared an identical pattern (PLS-PM, Bootstrap = 10,000, P > 0.05), which was influenced by integrons and environmental factors with the coefficients of -0.11 and 0.39, respectively. We believe the validated models are highly useful tools to streamline the strategies for monitoring and prediction of ARGs.

Microbial reduction of nitrate in the presence of zero-valent iron

Microbial reduction of nitrate in the presence of zero-valent iron (ZVI) was evaluated in anoxic shake flasks to assess the feasibility of ZVI-facilitated biological nitrate removal. Nitrate was completely reduced within 3days in the presence of both ZVI and microorganisms (ZVI-M). In contrast, only 75% of the nitrate was reduced in the presence of ZVI but without microbial inoculum. Nitrate removal was affected by ZVI-M flasks initial pH, nitrate concentration and ZVI dosage. Nitrate removal in the inoculated ZVI flasks system could be divided into two phases: adaptation phase and log phase which could be described by first-order kinetic equations. The analysis of bacterial communities in the inoculated flasks in the absence and presence of ZVI, indicated that the addition of ZVI increased the relative abundance of Methylotenera spp., Alcaligenes eutrophus, Pseudomonas spp. which might play an important role in nitrogen removal. The presence of ZVI could enhance biological denitrification through four mechanisms: the biological reduction of nitrate with 1) electrons derived directly from ZVI; 2) with hydrogen released from ZVI; 3) with Fe²⁺ released from ZVI; and 4) with acetate generated by homoacetogens which utilize H₂ released from ZVI.

Metagenomic insights into the effect of oxytetracycline on microbial structures, functions and functional genes in sediment denitrification

Denitrification is an indispensable pathway of nitrogen removal in aquatic ecosystems, and plays an important role in decreasing eutrophication induced by excessive reactive nitrogen pollution. Aquatic environments also suffer from antibiotic pollution due to runoff from farms and sewage systems. The aim of this study was to investigate the effect of oxytetracycline stress on denitrifying functional genes, the microbial community and metabolic pathways in sediments using high-throughput sequencing and metagenomic analysis. The oxytetracycline was observed to significantly inhibit the abundance of nirK and nosZ genes (P < 0.001). KEGG pathway annotation indicated that oxytetracycline treatment decreased the abundance of nitrate reductase, nitrite reductase and N₂O reductase. Functional annotations revealed that oxytetracycline exposure decreased the abundance of the protein metabolism subsystem in the bacterial community. Metagenomic sequencing demonstrated that the abundance of Proteobacteria and Firmicutes increased with oxytetracycline exposure while the Actinobacteria decreased. In sediments, Pseudomonas and Bradyrhizobium were major contributors to denitrification and oxytetracycline exposure resulted in a decreased abundance of Bradyrhizobium. These results indicated that oxytetracycline residues influences the denitrifier community and may heighten occurrence of reactive nitrogen in aquatic ecosystems.

Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River

Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump and the adjoining Duhaney River near Kingston City, Jamaica. We identified no overlap between the microbial communities inhabiting the Riverton City dump leachate and the Duhaney River. Both communities are predicted to degrade aromatic compounds, which are ubiquitous environmental pollutants. Adversely, microbes in both environments are predicted to withstand widely used antibiotics, antiseptics, and metal contamination. The absence of evidence for microbial transfer from the leachate to the river is encouraging; however, the Duhaney River contained several organisms with predicted pathogenic lifestyles, indicating that the river represents a human health risk regardless of impact from the dump.

The Riverton City dump is Jamaica’s largest solid waste disposal site, but it lacks engineered protection for leachate containment and treatment. Shotgun metagenomics was used to survey the microbial communities in the Riverton City dump leachate and in surface waters of the Duhaney River, an urban waterway abutting the dump. The community within the leachate pond was taxonomically distinct from that found in the surface waters of the Duhaney River. Higher microbial diversity was observed within the dump leachate, with members of the Bacteroidetes, Firmicutes, Gammaproteobacteria, Deltaproteobacteria, and Tenericutes being the most abundant, while the river community was dominated by Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The microbial communities exhibit similar functional potential profiles, including chemoorganoheterotrophy as the dominant metabolism, and the potential to degrade aromatic compounds. From reconstruction of metagenome-assembled genomes (MAGs), organisms within both environments are predicted to survive in the presence of multiple antibiotics, antiseptics, biocides, and metals. Strong virulence potential coincided with the most diverse multiple resistance profiles in 1 of 5 leachate MAGs and 5 of 33 river MAGs. Unexpectedly, the microbial resistance profiles were more varied and widespread in the river populations, where we had expected the chemical composition of the leachate to select and enrich for resistance characteristics. This study provides valuable insights into the total functional potential of a landfill leachate microbial community and identifies possible human health hazards within the Duhaney River and Riverton City dump, urban environments with the potential to impact human populations.

IMPORTANCE Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump and the adjoining Duhaney River near Kingston City, Jamaica. We identified no overlap between the microbial communities inhabiting the Riverton City dump leachate and the Duhaney River. Both communities are predicted to degrade aromatic compounds, which are ubiquitous environmental pollutants. Adversely, microbes in both environments are predicted to withstand widely used antibiotics, antiseptics, and metal contamination. The absence of evidence for microbial transfer from the leachate to the river is encouraging; however, the Duhaney River contained several organisms with predicted pathogenic lifestyles, indicating that the river represents a human health risk regardless of impact from the dump.

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N₂O) and dinitrogen (N₂) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N₂O and N₂ production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N₂O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N₂O, but N₂ production was reduced by 84% compared to the control. In parallel with greater N₂O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N₂O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N₂O production due to the inhibitory effects on nosZ-II-carrying communities.

Bioaugmentation with Diaphorobacter polyhydroxybutyrativorans to enhance nitrate removal in a poly (3-hydroxybutyrate-co-3-hydroxyvalerate)-supported denitrification reactor

A newly isolated and identified Diaphorobacter polyhydroxybutyrativorans strain (SL-205) was employed to enhance the denitrification performance of a laboratory-scale solid-phase denitrification (SPD) reactor using poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as a carbon source, and dynamic variations in microbial communities in the reactor were investigated. Results indicated that bioaugmentation with strain SL-205 enabled rapid reactor startup and improved denitrification performance relative to the reactor inoculated with activated sludge. Illumina sequencing revealed that bioaugmentation also significantly increased Proteobacteria abundance along with increased influent nitrate loading. Additionally, two genera of PHBV-degrading denitrifers, Diaphorobacter and Acidovorax, exhibited higher abundance, and elevated expression of denitrification-associated genes (narG, nirK, and nirS) was observed following bioaugmentation relative to the control at influent nitrate loading ranging from 1.28 g N/(L·d) to 1.6 g N/(L·d).

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.

Antibiotic Resistance Genes and Associated Microbial Community Conditions in Aging Landfill Systems

Landfills receive about 350 million tons of municipal solid wastes (MSWs) per year globally, including antibiotics and other coselecting agents that impact antimicrobial resistance (AMR). However, little is known about AMR in landfills, especially as a function of landfill ages. Here we quantified antibiotics, heavy metals, and AMR genes (ARGs) in refuse and leachates from landfills of different age (<3, 10, and >20 years). Antibiotics levels were consistently lower in refuse and leachates from older landfills, whereas ARG levels in leachates significantly increased with landfill age (One-way ANOVA, F = 10.8, P < 0.01). Heavy metals whose contents increased as landfills age (one-way ANOVA, F = 12.3, P < 0.01) were significantly correlated with elevated levels of ARGs (Mantel test, R = 0.66, P < 0.01) in leachates, which implies greater AMR exposure risks around older landfills. To further explain ARGs distributional mechanisms with age, microbial communities, mobile genetic elements (MGEs) and environmental factors were contrasted between refuse and leachate samples. Microbial communities in the refuse were closely correlated with ARG contents (Procrustes test; M² = 0.37, R = 0.86, P < 0.001), whereas ARG in leachates were more associated with MGEs.

On-site removal of antibiotics and antibiotic resistance genes from leachate by aged refuse bioreactor: Effects of microbial community and operational parameters

The abuse of antibiotics has raised the prevalence of antibiotic resistance, which will pose potential risk to human health. Leachate, generated during the landfill treatment of municipal solid waste, is the important hotspot of the antibiotics and antibiotic resistance genes (ARGs), and no effective on-site treatment has been put forward for preventing ARGs dissemination. Herein, the aged refuse bioreactor was employed to remove antibiotics and ARGs from leachate, and the great removal performance was observed. For the detected antibiotics, the total removal efficiency was about 76.75%, and sulfanilamide and macrolide were removed with high efficiencies (>80%). Among the target ARGs, tetracycline and macrolide resistance genes (tetM, tetQ and ermB) were eliminated with 1.2-2.0 orders of magnitude. The occurrences of ARGs did not correlated with water quality parameters such as COD, total nitrogen, ammonia, nitrate and nitrite, but closely linked to the variations of the bacterial community structure. Redundancy analysis (RDA) indicated the significant correlations between four genera and the distribution of ARGs, which implied that these key genera (including potential pathogens) drove the ARGs removal. Furthermore, the hydraulic loading test confirmed that the aged refuse bioreactor was capable of achieving high removal efficiencies even under shock loading for the higher loading was negative for the proliferations of potential ARGs hosts. This study suggested that aged refuse bioreactor could be a promising way for antibiotics and ARGs on-site removal from leachate.