不同生物炭对猪粪堆肥过程中抗生素及抗生素抗性基因的削减规律研究

为探讨不同类型生物炭对猪粪堆肥过程中抗生素和抗生素抗性基因(ARGs)的削减规律,分别将玉米秸秆生物炭、竹炭和猪粪生物炭添加到猪粪中进行好氧堆肥,解析不同类型生物炭添加对猪粪堆肥过程中抗生素浓度和ARGs丰度的影响.研究发现,添加竹炭堆肥对抗生素的平均去除率最高(97％),其中对四环素类抗生素的去除率高达98％;添加玉...     

Abundance and removal of antibiotic resistance genes (ARGs) in the rearing environments of intensive shrimp aquaculture in South China

Although research regarding antibiotic resistance genes (ARGs) in aquaculture environments has gained increasing scientific interest, further studies are required to understand the abundances and removal mechanisms of ARGs during the entire rearing period of shrimp aquaculture. Thus, in this study, abundances, distributions and removal rates of ARGs in different environmental compartments of intensive shrimp farms in South China were investigated during the entire rearing period. The results indicated that sul1 and cmlA were the predominant ARGs in the water and sediment samples. Additionally, the total abundance of ARGs was higher in shrimp pond water than in the source water and farm effluent. Moreover, sediment samples indicated significantly higher ARG abundances than water samples from the shrimp ponds (P?<?0.05). Environmental factors were found to significantly affect the distribution of ARGs in shrimp rearing environments. Furthermore, stable ponds aided the removal of ARGs from shrimp pond water. This study accounted for temporal variations in ARG abundances as well as removal of ARGs in different environmental compartments during the entire shrimp rearing period. However, additional research is required to optimize the water treatment process for removal of ARGs from the aquaculture.     

High-throughput analysis of the effects of different fish culture methods on antibiotic resistance gene abundances in a lake

Freshwater lakes are important reservoirs for antibiotic resistance genes (ARGs). In this study, we determined the ARG profiles in water samples from Ying Lake, China, using high-throughput quantitative PCR. The high prevalence of ARGs suggested significant pollution with ARGs in the study area, where the ARG diversity and abundance were greater in an area with box-type fish farming than an area with fenced fish farming. Network analysis indicated the widespread co-occurrence of ARGs and mobile genetic elements. cphA-01, blalMP02, and blaCMY202 were identified as adequate indicator genes for estimating the total ARG abundances. Redundancy analysis indicated that changes in the microbial communities caused by variations in the physicochemical parameters with different fish culture methods mainly determined the ARGs in the lake system. Thus, analyzing the factors that affect ARGs provided novel insights into the mechanisms responsible for the maintenance and propagation of ARGs in a lake.

     

Fate of antimicrobial resistance genes in response to application of poultry and swine manure in simulated manure-soil microcosms and manure-pond microcosms

This study aimed to determine the occurrence, abundance, and fate of nine important antimicrobial resistance genes (ARGs) (sul1, sul2, tetB, tetM, ermB, ermF, fexA, cfr, and Intl1) in the simulated soil and pond microcosms following poultry and swine manure application. Absolute quantitative PCR method was used to determine the gene copies. The results were modeled as a logarithmic regression (N?=?mlnt?+?b) to explore the fate of target genes. Genes sul1, Intl1, sul2, and tetM had the highest abundance following the application of the two manure types. The logarithmic regression model fitted the results well (R ² values up to 0.99). The reduction rate of all genes (except for the genes fexA and cfr) in manure-pond microcosms was faster than those in manure-soil microcosms. Importantly, sul1, intl1, sul2, and tetM had the lowest reduction rates in all the samples and the low reduction rates of tetM was the first time to be reported. These results indicated that ARG management should focus on using technologies for the ARG elimination before the manure applications rather than waiting for subsequent attenuation in soil or water, particularly the ARGs (such as sul1, intl1, sul2, and tetM investigated in this study) that had high abundance and low reduction rate in the soil and water after application of manure.     

人工湿地中抗生素抗性大肠杆菌和抗性基因的去除与分布

抗生素的滥用导致抗生素抗性菌和抗性基因随生活污水和养殖废水的排放在环境中肆意散播,其去除及环境行为越来越受到关注。采用K-B纸片法测定了9套不同工艺构型模拟人工湿地中大肠杆菌对7种抗生素的抗性率,并应用多重PCR检测磺胺类sul1、2、3与四环素tetA、B、C、D抗性基因,探究人工湿地对抗性菌的去除效率及抗性菌、抗性基因的分布规律。结果显示,人工湿地能有效去除污水中70%左右的抗性大肠杆菌,有效降低了细菌抗性的传播风险;共计分离出535株大肠肝菌中有378株对一种以上抗生素有抗性性,以四环素、磺胺类和氨苄西林抗性率最高,达到25%以上,其他4种抗性率较低,不足20%;2种抗性基因的检出率都在70%以上;对不同采样点大肠杆菌的抗性性及抗性基因的比较发现,各部分大肠杆菌的抗性水平、多重抗性指数(MRI)以及抗性基因(sul、tet)检出率和组合数表现出:基质≥出水>进水,推测抗性菌被湿地基质截留,在基质生物膜上发生抗性基因的重组,并释放抗性菌,提高了出水中抗性水平和抗性基因检出率。     

Removal of tetracyclines,sulfonamides, and quinolones by industrial-scale composting and anaerobic digestion processes

This study evaluated and compared the removal of antibiotics by industrial-scale composting and anaerobic digestion at different seasons. Twenty compounds belonged to three classes of widely used veterinary antibiotics (i.e., tetracyclines, sulfonamides, and quinolones) were investigated. Results show that of the three groups of antibiotics, tetracyclines were dominant in swine feces and poorly removed by anaerobic digestion with significant accumulation in biosolids, particularly in winter. Compared to that in winter, a much more effective removal (>?97%) by anaerobic digestion was observed for sulfonamides in summer. By contrast, quinolones were the least abundant antibiotics in swine feces and exhibited a higher removal by anaerobic digestion in winter than in summer. The overall removal of antibiotics by aerobic composting could be more than 90% in either winter or summer. Nevertheless, compost products from livestock farms in Beijing contained much higher antibiotics than commercial organic fertilizers. Thus, industrial composting standards should be strictly applied to livestock farms to further remove antibiotics and produce high quality organic fertilizer.     

Antibiotic resistance genes in an urban river as impacted by bacterial community and physicochemical parameters

Antibiotic resistance genes (ARGs) in urban rivers are a serious public health concern in regions with poorly planned, rapid development. To gain insights into the predominant factors affecting the fate of ARGs in a highly polluted urban river in eastern China, a total of 285 ARGs, microbial communities, and 20 physicochemical parameters were analyzed for 17 sites. A total of 258 unique ARGs were detected using high-throughput qPCR, and the absolute abundance of total ARGs was positively correlated with total organic carbon and total dissolved nitrogen concentrations (P < 0.01). ARG abundance and diversity were greatly altered by microbial community structure. Variation partitioning analysis showed that the combined effects of multiple factors contributed to the profile and dissemination of ARGs, and variation of microbial communities was the major factor affecting the distribution of ARGs. The disparate distribution of some bacteria, including Bacteroides from mammalian gastrointestinal flora, Burkholderia from zoonotic infectious diseases, and Zoogloea from wastewater treatment, indicates that the urban river was strongly influenced by point-source pollution. Results imply that microbial community shifts caused by changes in water quality may lead to the spread of ARGs, and point-source pollution in urban rivers requires greater attention to control the transfer of ARGs between environmental bacteria and pathogens.

     

The addition of modified attapulgite reduces the emission of nitrous oxide and ammonia from aerobically composted chicken manure

The acceleration of the composting process and the improvement of compost quality have been explored by evaluating the efficacy of various additives, inoculating with specific microorganisms and the application of various biosurfactants. The magnesium-aluminum silicate attapulgite is a low-cost potential composting additive, but its effects on aerobic composting are unknown. This study investigated the effects of attapulgite application on compost production and quality during the aerobic composting of chicken manure. Addition of attapulgite significantly increased the temperature (p < 0.05) while it reduced compost total organic carbon (TOC) and seed germination indices (GIs) throughout the process. Its addition enhanced nitrate concentrations, promoted organic matter degradation, increased seed germination indices, and accelerated the composting process. Interestingly, attapulgite addition did not increase the population of ammonia-oxidizing bacteria. These results suggest that attapulgite is a good additive for the composting industry.

Implications: We investigated the addition of two forms of attapulgite during aerobic composting of chicken manure to determine their effects under strict composting environmental parameter control. Our results provides primary evidence that attapulgite may have potential for application in the composting industry.

All treatments showed no increase within the first 15 days. However, emissions increased for all treatments within 15–45 days, reaching approximately 6300, 2000, and 4000 mg/m² from the control, artifactitious attapulgite, and raw attapulgite treatments, respectively.     

Contamination of antibiotic resistance genes (ARGs) in a typical marine aquaculture farm: source tracking of ARGs in reared aquatic organisms

Abstract

Although the prevalence and concentrations of antibiotic resistance genes (ARGs) in aquaculture is receiving increasing scientific interest, there is little understanding of the direct sources and dissemination pathways of ARGs in marine aquaculture-reared organisms. This study investigated the dynamics of ARGs and the bacterial community throughout the rearing period in a typical marine aquaculture farm in South China. The results demonstrated that sul1 and qnrD were predominant in the sediment, and qnrD and qnrA were predominant in the intestinal tracts of shrimps. Network analysis showed that the chemical oxygen demand, total organic carbon, dissolved organic carbon, suspended solids, and total phosphorus were positively correlated with the predominant ARGs. The results of the network and source tracking analyses indicate that environmental factors and the bacterial community may drive the dissemination of ARGs dissemination in the environment and in shrimp reared by marine aquaculture, and sediment is the most direct and important medium in this dissemination. These results aid in improving our understanding of the sources, level, and dissemination of ARGs in marine aquaculture.     

Diversity of antibiotic resistance genes and encoding ribosomal protection proteins gene in livestock waste polluted environment

The rapid development and increase of antibiotic resistance are global phenomena resulting from the extensive use of antibiotics in human clinics and animal feeding operations. Antibiotics can promote the occurrence of antibiotic resistance genes (ARGs), which can be transferred horizontally to humans and animals through water and the food chain. In this study, the presence and abundance of ARGs in livestock waste was monitored by quantitative PCR. A diverse set of bacteria and tetracycline resistance genes encoding ribosomal protection proteins (RPPs) from three livestock farms and a river were analyzed through denaturing gradient gel electrophoresis (DGGE). The abundance of sul(I) was 10³ to 10⁵ orders of magnitude higher than that of sul(II). Among 11 tet-ARGs, the most abundant was tet(O). The results regarding bacterial diversity indicated that the presence of antibiotics might have an evident impact on bacterial diversity at every site, particularly at the investigated swine producer. The effect of livestock waste on the bacterial diversity of soil was stronger than that of water. Furthermore, a sequencing analysis showed that tet(M) exhibited two genotypes, while the other RPPs-encoding genes exhibited at least three genotypes. This study showed that various ARGs and RPPs-encoding genes are particularly widespread among livestock.     

Detection of Escherichia coli in a cattle manure composting process by selective cultivation and colony polymerase chain reaction

Livestock manure is suitable for use as a composting material. However, various intestinal microbes, such as Escherichia coli, are significant components of such manures. Thus, it is desirable that the level of intestinal microbes, and particularly opportunistic pathogens, in compost is inspected and counted regularly. The sensitivity and specificity of detection of E. coli in compost have been improved by selective cultivation followed by colony polymerase chain reaction (PCR) using the ECO primer. Indeed, the sensitivity of this method is higher than that of DNA extraction from compost and PCR. In this study, changes in numbers of E. coli present in a field-scale composting process over time was assessed using selective cultivation and colony PCR. Numbers of ECO-positive colonies after 24 h decreased, with a concomitant rise in compost temperature. ECO-positive colonies were not detected from 33 to 48 h. However, ECO-positive colony numbers increased beginning on day 4 and continuing until day 42. Thus, it seems likely that the high temperatures reached during the composting process did not affect E. coli numbers in the final compost. Additionally, selective cultivation followed by colony PCR using specific primers is an appropriate method of determining levels of cultivable pathogens in composted materials.     

Dynamics of antibiotic resistance genes and microbial community in shortcut nitrification–denitrification process under antibiotic stresses

In this study, the performance of shortcut nitrification–denitrification (SCND) at different TC and SD stress conditions (0 μg/L, 1–97 days; 100 μg/L, 98–138 days; 500 μg/L, 139–175 days) was investigated. Higher level antibiotic stress (500 μg/L) led to the serious deterioration of nitrogen removal, and denitrification was more sensitive to antibiotic stress than nitrification. The dynamics of antibiotic resistance genes (ARGs) and microbial community were revealed by quantitative real-time PCR and 16S rDNA high-throughput sequencing, respectively. Tet-genes (tetA, tetQ, tetW), sul-genes (sulI, sulII), and mobile genetic element (intI1) in activated sludge increased by 1.2?~?2.5 logs with long-term exposure of antibiotic stress, and sulI, tetA, tetQ, and tetW were significantly positively correlated with intI1. Long-term antibiotics stress caused the decrease of most denitrifiers, and five genera were identified as the potential host of ARGs. The key impact factors of SCND drove the dynamics of ARGs and microbial community. Except for sulII gene, DO and FA were significantly positively correlated with ARGs, while FNA, NAR, and NO₂^?-N showed opposite effects to ARGs. Overall, maintaining relative lower DO, higher FNA, NAR, and NO₂^?-N conditions are not only benefit to the stable operation of SCND, but may also conducive to the control of ARG dissemination. This study provides theoretical basis on the control of ARGs in the SCND process.

     

Dynamics of copper and tetracyclines during composting of water hyacinth biomass amended with peat or pig manure

Composting is one of the post-treatment methods for phytoremediation plants. Due to a high potential of water hyacinth to accumulate pollutants, the physicochemical parameters, microbial activity as well as fates of copper (Cu) and tetracyclines (TCs) were investigated for the different amended water hyacinth biomass harvested from intensive livestock and poultry wastewater, including unamended water hyacinth (W), water hyacinth amended with peat (WP), and water hyacinth amended with pig manure (WPM) during the composting process. Pig manure application accelerated the composting process as evidenced by an increase of temperature, electrical conductivity (EC), NH₄-N, as well as functional diversity of microbial communities compared to W and WP treatments. Composting process was slowed down by high Cu, but not by TCs. The addition of peat significantly increased the residual fraction of Cu, while pig manure addition increased available Cu concentration in the final compost. Cu could be effectively transformed into low available (oxidizable) and residual fractions after fermentation. In contrast, less than 0.5% of initial concentrations of TCs were determined at the end of 60-day composting for all treatments in the final composts. The dissipation of TCs was accelerated by the high Cu concentration during composting. Therefore, composting is an effective method for the post-treatment and resource utilization of phytoremediation plants containing Cu and/or TCs.     

The Fate of the Recombinant DNA in Corn During Composting

Abstract

In order to make regulations that safeguard food and the environment, an understanding of the fate of transgenes from genetically modified (GM) plants is of crucial importance. A compost experiment including mature transgenic corn plants and seeds of event Bt 176 (Zea mays L.) was conducted to trace the fate of the transgene cryIA(b) during the period of composting. In bin 1, shredded corn plants including seeds were composted above a layer of cow manure and samples from the corn layer were collected at intervals during a 12-month period. The samples were tested for the transgene persistence and microbial counts and also the compost was monitored for temperature. In bin 2, piles of corn seeds, surrounded by sheep manure and straw, were composted for 12 months. A method combining nested polymerase chain reaction (PCR) and southern hybridization was developed for detection of the transgene in compost. The detection sensitivity was 200 copies of the transgene per gram of dry composted corn material. Composting commenced on day 0, and the transgene was detected in specimens from bin 1 on days 0 and 7 but not on day 14 or thereafter. The transgene in corn seeds was not detectable after 12 months of composting in bin 2. Temperatures in both bins rose to about 50°C within 2 weeks and remained above that temperature for about 3 months, even when the ambient temperature dropped below ?20°C. Extracts from compost were inoculated onto culture plates and then were incubated at 23 to 55°C. Within the first 2 weeks of composting in bin 1, the counts of bacteria incubated at 55°C increased from 3.5 to 7.5 log ₁₀, whereas those incubated at 23°C remained at about 7.5 log ₁₀. The counts of fungi incubated at 45°C increased slightly from 2.5 to 3.1 log₁₀, but those incubated at 23°C decreased from 6.3 to 3.0 log ₁₀. The rapid degradation of the transgene during composting of Bt corn plants suggested that the composting process could be used for safe disposal of transgenic plant wastes.     

Effects of different ratios of pig manure to fungus residue on physicochemical parameters during composting

This study examined physicochemical parameters to assess their effectiveness as stability and maturity indicators during the process of composting pig manure and fungus residue at different ratios. The results showed that composting mixtures with all ratios of pig manure to fungus residue maintained a temperature exceeding 50 °C for more than 10 days during composting and met the requirement for pathogen destruction. The treatment containing mainly pig manure showed higher nitrogen loss and a shorter thermophilic phase and maturity time than the treatment containing mainly fungus residue. The germination index (GI) values indicated that compost maturity was achieved in the final compost with initial ratios of pig manure to fungus residue of 9:1–7:3 (GIs of 101.4%, 91.2%, and 81.3%); the ratio of 6:4 did not reach compost maturity (GI of 63.8%) and had an inhibitory effect on seed germination. The results of this study suggest that a ratio of pig manure to fungus residue of approximately 8:2 can be considered suitable for the efficient and quality composting of pig manure and fungus residue.

Implications: Co-composting of pig manure and edible fungi residue with appropriate proportion can effectively reduce the risk of environmental pollution caused by agricultural wastes, as well as achieve a safer and high-quality organic fertilizer, which can be used to improve physical and chemical properties of the soil, increase crop yields, and promote agricultural sustainable development. Therefore, technique of co-composting of pig manure and edible fungi residue has a wide prospect of application in practical production all over the world.     

Development of functional composts using spent coffee grounds,poultry manure and biochar through microbial bioaugmentation

Spent coffee grounds (SCG), poultry manure, and agricultural waste-derived biochar were used to manufacture functional composts through microbial bioaugmentation. The highest yield of tomato stalk-based biochar (40.7%) was obtained at 450°C with a surface area of 2.35 m² g^?1. Four pilot-scale composting reactors were established to perform composting for 45 days. The ratios of NH₄⁺–N/NO₃^?–N, which served as an indicator of compost maturity, indicate rapid, and successful composting via microbial bioaugmentation and biochar amendment. Moreover, germination indices for radish also increased by 14–34% through augmentation and biochar amendment. Microbial diversity was also enhanced in the augmented and biochar-amended composts by 7.1–8.9%, where two species of Sphingobacteriaceae were dominant (29–43%). The scavenging activities of 2,2-diphenyl-1-picrylhydrazyl (DPPH) were enhanced by 14.1% and 8.6% in the fruits of pepper plants grown in the presence of the TR-2 (augmentation applied only) and TR-3 (both augmentation and biochar amendment applied) composts, respectively. Total phenolic content was also enhanced by 68% in the fruits of the crops grown in TR-3. Moreover, the other compost, TR-L (augmentation applied only), boosted DPPH scavenging activity by 111% in leeks compared with commercial organic fertilizer, while TR-3 increased the phenolic content by 44.8%. Composting facilitated by microbial augmentation and biochar amendment shortened the composting time and enhanced the quality of the functional compost. These results indicate that functional compost has great potential to compete with commercially available organic fertilizers and that the novel composting technology could significantly contribute to the eco-friendly recycling of organic wastes such as spent coffee grounds, poultry manure, and agricultural wastes.     

Antibiotic resistance and virulence factors of Escherichia coli from eagles and goshawks

One of the major global problems in medicine is microbial resistance to antibiotics (antimicrobial resistance) and this has become an increasingly frequent research topic. This study focuses on antimicrobial resistance, phylogenetic and genetic characterization of Escherichia coli from wild birds: ten isolates from eagles (Aquila chrysaetos), nine from goshawks (Accipiter gentilis) and 24 from broilers in the Slovak Republic. Twenty-two strains with presence of int1 gene were selected and examined for the presence or absence of transposon gene (tn3), genes of antibiotic resistance and virulence factors. We detected sequence type (ST) in eagles ST 442 with genes iss, papC, iutA, cvaC, tsh, fyuA, iroN, kps, feoB, sitA, irp2, ireA for virulence factors and tetA, sul1, sul2, dfrA, aadA for antibiotic resistance; in goshawks ST 1011 with iss, papC, fyuA, iroN, feoB, sitA and qnrS1, tetA, sul1, sul2, dfrA, aadA, respectively. These ST types have been found in humans too and should be evaluated further for possible zoonotic potential and transfer of resistance genes from the environment.     

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.

     

The fate of recombinant plasmids during composting of organic wastes

Composting was investigated as a means for safe disposal of organic waste containing bacteria that carry transgenes in recombinant plasmids. To generate model recombinant plasmids, a mobile IncQ plasmid, RSF1010, and a non-mobile plasmid, pGFP, were genetically modified to carry a DNA segment encoding both green fluorescent protein and kanamycin resistance and were designated as RSF1010-GFPK and pGFPK. Escherichia coli (E. coli) C600 harboring these plasmids were inoculated into chicken manure specimens that were placed in compost at 20 and 60 cm from the bottom of a 1.0-m high compost bin. Control specimens were held at ambient temperature. By day 10, compost temperatures at the lower and upper levels of the bin had reached 45.3 and 61.5°C, respectively, and at both levels the target E. coli had been inactivated and the plasmids had lost their capacity to be transformed or mobilized. Furthermore, based on real time Polymerase chain reaction (PCR), the transgene fragments along with the host chromosomal DNA fragment from specimens at the upper level had been degraded beyond the detection limit. However, at the lower level where temperatures remained below 48°C these fragment persisted to day 21. At ambient temperatures (0–8°C), the E. coli, plasmids and the transgene fragments persisted in manure specimens throughout the 21 day test period. The study showed the potential for composting as a safe procedure for disposal of bacteria carrying transgenes in recombinant plasmids.     

Dynamics of oxytetracycline and resistance genes in soil under long-term intensive compost fertilization in Northern China

In the present study, we explored the dynamics of antibiotics (ciprofloxacin, norfloxacin, enrofloxacin, and oxytetracycline), tetracycline resistance genes (TRGs), and bacterial communities over 2013–2015 in soils fertilized conventionally or with two levels (82.5 and 165 t/ha) of compost for 12 years. In the soil receiving 165 t/ha of compost, only oxytetracycline was 46% higher than that in the conventionally fertilized soil. Transient enrichment of both tetM (20% to 9-fold) and tetK (25% to 67-fold) was observed in multiple instances immediately after the application of compost. The majority of genera which positively correlated with tetM or tetK were affiliated to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The structural equation model analysis indicated that fertilization regimes directly affected the bacterial composition and antibiotics and had an indirect effect on the abundance of tetK and tetM via these antibiotics. In summary, this study shed light into the complex interactions between fertilization, antibiotics, and antibiotic resistance pollution in greenhouse soil.