scholarly journals Manure Application Did Not Enrich Antibiotic Resistance Genes in Root Endophytic Bacterial Microbiota of Cherry Radish Plants

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Yu-Jing Zhang ◽  
Hang-Wei Hu ◽  
Qing-Lin Chen ◽  
Hui Yan ◽  
Jun-Tao Wang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Structural Equation ◽  
Organic Fertilizer ◽  
Antibiotic Resistance Genes ◽  
Pot Experiment ◽  
Equation Modeling ◽  
Manure Application ◽  
Edible Part ◽  
Bacterial Microbiota

ABSTRACT Growing evidence suggests that livestock manure used as organic fertilizer in agriculture may lead to the potential propagation of antibiotic resistance genes (ARGs) from “farm to fork.” However, little is known about the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes (including rhizosphere, endosphere, and phyllosphere), which hampers our ability to assess the dissemination of antibiotic resistance in the soil-plant system. Here, we constructed a pot experiment to explore the effects of poultry and cattle manure applications on the shifts in the resistome in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected among all the samples. Rhizosphere and phyllosphere microbiomes harbored significantly higher diversity and abundance of ARGs than did root endophytic microbiomes of cherry radish. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere but not in the endophytes of the root, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications and clustered separately according to different sample types and treatments. Structural equation modeling revealed that bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. Taken together, we provide evidence that enrichment of the resistome in the rhizosphere and phyllosphere of cherry radish is more obvious than with the endosphere after manure application, suggesting that manure amendment might not enhance the dissemination of ARGs into the root of vegetables in the pot experiment. IMPORTANCE Our study provides important evidence that manure application increased the occurrence of ARGs in the rhizosphere and phyllosphere of cherry radish, compared with that in the endophytic bacterial microbiota of root, which is the edible part of cherry radish. Our findings suggest that although manure amendment is a significant route of ARGs entering agricultural soils, these manure-derived ARGs may be at low risk of migrating into the endophytes of root vegetables.

scholarly journals Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ishi Keenum ◽  
Robert K. Williams ◽  
Partha Ray ◽  
Emily D. Garner ◽  
Katharine F. Knowlton ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Land Application ◽  
Multidimensional Analysis ◽  
Small Scale ◽  
Antibiotic Administration ◽  
Metagenomic Sequencing ◽  
Combined Effects ◽  
Bacterial Microbiota

Abstract Background Research is needed to delineate the relative and combined effects of different antibiotic administration and manure management practices in either amplifying or attenuating the potential for antibiotic resistance to spread. Here, we carried out a comprehensive parallel examination of the effects of small-scale (> 55 °C × 3 days) static and turned composting of manures from dairy and beef cattle collected during standard antibiotic administration (cephapirin/pirlimycin or sulfamethazine/chlortetracycline/tylosin, respectively), versus from untreated cattle, on “resistomes” (total antibiotic resistance genes (ARGs) determined via shotgun metagenomic sequencing), bacterial microbiota, and indicator ARGs enumerated via quantitative polymerase chain reaction. To gain insight into the role of the thermophilic phase, compost was also externally heated to > 55 °C × 15 days. Results Progression of composting with time and succession of the corresponding bacterial microbiota was the overarching driver of the resistome composition (ANOSIM; R = 0.424, p = 0.001, respectively) in all composts at the small-scale. Reduction in relative abundance (16S rRNA gene normalized) of total ARGs in finished compost (day 42) versus day 0 was noted across all conditions (ANOSIM; R = 0.728, p = 0.001), except when externally heated. Sul1, intI1, beta-lactam ARGs, and plasmid-associated genes increased in all finished composts as compared with the initial condition. External heating more effectively reduced certain clinically relevant ARGs (blaOXA, blaCARB), fecal coliforms, and resistome risk scores, which take into account putative pathogen annotations. When manure was collected during antibiotic administration, taxonomic composition of the compost was distinct according to nonmetric multidimensional analysis and tet(W) decayed faster in the dairy manure with antibiotic condition and slower in the beef manure with antibiotic condition. Conclusions This comprehensive, integrated study revealed that composting had a dominant effect on corresponding resistome composition, while little difference was noted as a function of collecting manure during antibiotic administration. Reduction in total ARGs, tet(W), and resistome risk suggested that composting reduced some potential for antibiotic resistance to spread, but the increase and persistence of other indicators of antibiotic resistance were concerning. Results indicate that composting guidelines intended for pathogen reduction do not necessarily provide a comprehensive barrier to ARGs or their mobility prior to land application and additional mitigation measures should be considered.

scholarly journals Antibiotic Resistance Genes in Different Animal Manure and their Derived Organic Fertilizer

2020 ◽  
Author(s):  
Yan Xu ◽  
Houyu Li ◽  
Rongguang Shi ◽  
Jiapei Lv ◽  
Bihan Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Organic Fertilizer ◽  
Poultry Manure ◽  
Antibiotic Resistance Genes ◽  
Animal Manure ◽  
Procrustes Analysis ◽  
Organic Fertilizers

Abstract Background: The prevalence of antibiotic resistance genes (ARGs) in animal manure poses threats to the environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland, which would cause the potential outbreak of bacterial resistance in agricultural environment. This study investigated the composition of ARGs in different animal manure and their derived organic fertilizers. Results: Results showed that the abundance of several ARGs, such as sul 2, Tet B-01, Tet G-01 and Tet M-01 in organic fertilizer samples was 12%~96% lower than in animal manure. However, there was an increasing of Tet K and erm C abundance from animal manure to the organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, antibiotics was observed by Redundancy analysis (RDA). Procrustes analysis revealed the significant correlation between bacterial community structures and the ARGs abundance (r=0.799, p<0.01). Non-metric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additional, pathogenic bacteria (especially Actinomadura ) would proliferate rather than decrease from manure to organic fertilizer. Conclusion: Overall, this research suggests that the composting treatment of manure could effectively reduce these ARGs and pathogens,even cause partial ARGs and pathogens proliferation. It also shows that the microorganism might significantly influence ARGs profiles in composting.

scholarly journals Impact of Long-Term Manure and Sewage Sludge Application to Soil as Organic Fertilizer on the Incidence of Pathogenic Microorganisms and Antibiotic Resistance Genes

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1423
Author(s):  
Hana Stiborova ◽  
Martina Kracmarova ◽  
Tereza Vesela ◽  
Marta Biesiekierska ◽  
Jindrich Cerny ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Sewage Sludge ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Agricultural Soils ◽  
Organic Fertilizer ◽  
Antibiotic Resistance Genes ◽  
Thermophilic Conditions ◽  
Repeated Applications

The reuse of stabilized (under thermophilic conditions) sewage sludge and manure on agricultural soils is a common practice. The aim of this study was to evaluate the risks associated with their repeated applications on the spread of pathogenic bacteria and antibiotic resistance genes (ARGs) that encode resistance to tetracycline (tetA and tetW), sulphonamide (sul1 and sul2), erythromycin (ermB), vancomycin (vanA) and integron genetic element (intI1). The trial fields has been regularly fertilized every 3rd year since 1996 with manure (MF; 330 kg N/ha) and sewage sludge (SF; 330 kg N/ha and SF3; 990 kg N/ha). Unfertilized soil (CF) served as a control. Samples were collected at different time points: (i) right before fertilization (which was also 3 years after the last fertilization), (ii) 5 months after fertilization, and (iii) 11 months after fertilization. The relative abundance of amplicon sequence variants (ASVs) assigned to potentially pathogenic bacteria was low (0.3% and 0.25% in sludge and manure, respectively), and no association with the application of these fertilizers was found. On the other hand, our data indicate that an increased relative abundance of the ARGs sul1 and tetW was significantly associated with these fertilizer applications, and sul1 was increased in all treatments regardless of the time. It is suggested that sul1 should be monitored in organically fertilized soils to prevent its spread and possible further accumulation in crops.

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer

2019 ◽  
Vol 649 ◽  
pp. 902-908 ◽  
Author(s):  
Xue Zhou ◽  
Min Qiao ◽  
Jian-Qiang Su ◽  
Yin Wang ◽  
Zhi-Hong Cao ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Organic Fertilizer ◽  
Antibiotic Resistance Genes ◽  
Pig Manure

Impact of liquid hog manure applications on antibiotic resistance genes concentration in soil and drainage water in field crops

2020 ◽  
Vol 66 (10) ◽  
pp. 549-561
Author(s):  
Élodie Larouche ◽  
Mylène Généreux ◽  
Marie-Ève Tremblay ◽  
Mohamed Rhouma ◽  
Marc-Olivier Gasser ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Water Samples ◽  
Antibiotic Resistance Genes ◽  
Drainage Water ◽  
Manure Application ◽  
Tillage Practices ◽  
Hog Manure ◽  
The Impact ◽  
Soil And Water

Agricultural practices such as manure applications could contribute to the spread of antibiotic resistance genes (ARGs) within the environment. Our objective was to assess the impact of certain fertilization methods (mineral or manure) and tillage practices (reduced or conventional) on the presence of ARGs and bacteria in soil and drainage water under wheat and grain corn crops. Targeted ARGs tet(T), sul1, and blaCTX-M-1 in liquid hog manure, soil, and water samples were quantified by qPCR. Conventional PCR was used to detect mcr-1 and mcr-2. ARGs in control plots were detected despite the absence of manure, representing an environmental reservoir of resistant microorganisms. The manure application rate higher than 39 m3/ha increased tet(T) and sul1 gene concentrations in soil for more than 180 days. Tillage practices had no impact on ARG concentrations in soil and water samples. The blaCTX-M-1 gene was only detected in seven water samples in 2016, but no link was established with the treatments. The mcr-1 and mcr-2 genes were not detected in all tested samples. This study demonstrated that tet(T) and sul1 gene concentrations increased in soil after liquid hog manure application as well as in drainage water in the next weeks.

Effect of Manure Application on Abundance of Antibiotic Resistance Genes and Their Attenuation Rates in Soil: Field-Scale Mass Balance Approach

2014 ◽  
Vol 48 (5) ◽  
pp. 2643-2650 ◽  
Author(s):  
Nicole Fahrenfeld ◽  
Katharine Knowlton ◽  
Leigh Anne Krometis ◽  
W. Cully Hession ◽  
Kang Xia ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mass Balance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Field Scale ◽  
Manure Application ◽  
Balance Approach ◽  
Mass Balance Approach
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