Use of commercial organic fertilizer increases the abundance of antibiotic resistance genes and antibiotics in soil

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.

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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 ◽

10.3390/agronomy11071423 ◽

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.

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

The Science of The Total Environment ◽

10.1016/j.scitotenv.2018.08.368 ◽

2019 ◽

Vol 649 ◽

pp. 902-908 ◽

Cited By ~ 22

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

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

Applied and Environmental Microbiology ◽

10.1128/aem.02106-19 ◽

2019 ◽

Vol 86 (2) ◽

Cited By ~ 1

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.

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Antibiotic resistance genes in different animal manures and their derived organic fertilizer

Environmental Sciences Europe ◽

10.1186/s12302-020-00381-y ◽

2020 ◽

Vol 32 (1) ◽

Author(s):

Yan Xu ◽

Houyu Li ◽

Rongguang Shi ◽

Jiapei Lv ◽

Bihan Li ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Organic Fertilizer ◽

Antibiotic Resistance Genes ◽

Animal Manures

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Antibiotic resistance genes in different animal manures and their derived organic fertilizer

10.21203/rs.3.rs-29643/v2 ◽

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 ◽

Antibiotic Resistance Genes ◽

Animal Manure ◽

Procrustes Analysis ◽

Organic Fertilizers ◽

Animal Manures

Abstract Background: The prevalence of antibiotic resistance genes (ARGs) in animal manure poses a threat to environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland and have the potential to cause outbreaks of bacterial resistance in agricultural environments. This study investigated the composition of ARGs in different animal manures and their derived organic fertilizers. Results: The 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 that in animal manure. However, the abundance of Tet K and erm C was higher in animal manure than in organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, and antibiotics was observed by redundancy analysis (RDA). Procrustes analysis revealed a significant correlation between bacterial community structures and ARG abundance (r=0.799, p<0.01). Nonmetric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additionally, the abundance of pathogenic bacteria (especially Actinomadura ) would increase rather than decrease in manure compared to organic fertilizer. Conclusion: The diversity and abundance of most ARGs significantly decreased from animal manure to organic fertilizer. Microorganisms in the prepared organic fertilizer may mainly be inherited from the animal manure. The results also showed that the pathogens in the prepared organic fertilizer would significantly reduce, but would still cause partial pathogen proliferation.

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Association of nanoparticles with extracellular genetic material and implications for the fate of antibiotic resistance genes in environmental systems

10.1021/scimeetings.0c07368 ◽

2020 ◽

Author(s):

Nadrat Chowdhury

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Genetic Material ◽

Antibiotic Resistance Genes ◽

Environmental Systems

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Quintuplex PCR to Detect Antibiotic Resistance Genes in Streptococcus pneumoniae

Journal of Clinical and Health Sciences ◽

10.24191/jchs.v2i1.5861 ◽

2016 ◽

Vol 1 (2) ◽

pp. 22 ◽

Cited By ~ 2

Author(s):

Navindra Kumari Palanisamy ◽

Parasakthi Navaratnam ◽

Shamala Devi Sekaran

Keyword(s):

Antibiotic Resistance ◽

Streptococcus Pneumoniae ◽

Resistance Genes ◽

Bacterial Pathogen ◽

Antibiotic Resistance Genes ◽

Pcr Amplification ◽

Penicillin Resistance ◽

Penicillin Binding Proteins ◽

Efflux Mechanism ◽

Mic Value

Introduction: Streptococcus pneumoniae is an important bacterial pathogen, causing respiratory infection. Penicillin resistance in S. pneumoniae is associated with alterations in the penicillin binding proteins, while resistance to macrolides is conferred either by the modification of the ribosomal target site or efflux mechanism. This study aimed to characterize S. pneumoniae and its antibiotic resistance genes using 2 sets of multiplex PCRs. Methods: A quintuplex and triplex PCR was used to characterize the pbp1A, ermB, gyrA, ply, and the mefE genes. Fifty-eight penicillin sensitive strains (PSSP), 36 penicillin intermediate strains (PISP) and 26 penicillin resistance strains (PRSP) were used. Results: Alteration in pbp1A was only observed in PISP and PRSP strains, while PCR amplification of the ermB or mefE was observed only in strains with reduced susceptibility to erythromycin. The assay was found to be sensitive as simulated blood cultures showed the lowest level of detection to be 10cfu. Conclusions: As predicted, the assay was able to differentiate penicillin susceptible from the non-susceptible strains based on the detection of the pbp1A gene, which correlated with the MIC value of the strains.

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