Dataset Information

Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management.

ABSTRACT: The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best management practices (rotationally grazed with a riparian (RBR) area and a fenced riparian buffer strip (RBS), which excluded cattle grazing and poultry litter applications) relative to standard pasture management (continuously grazed (CG) and hayed (H)) minimize the presence and amount of AMR genes. Quantitative PCR (Q-PCR) was performed to enumerate four AMR genes (ermB, sulI, intlI, and blactx-m-32 ) in soil, cattle manure, and poultry litter environments. Six soil samples were additionally subjected to metagenomic sequencing and resistance genes were identified from assembled sequences. Following 14-years of continuous management, ermB, sulI, and intlI genes in soil were greatest (P < 0.05) in samples collected under long-term continuous grazing (relative to conservation best management practices), under suggesting overgrazing and continuous cattle manure deposition may increase AMR gene presence. In general, AMR gene prevalence increased downslope, suggesting potential lateral movement and accumulation based on landscape position. Poultry litter had lower abundance of AMR genes (ermB, sulI, and intlI) relative to cattle manure. Long-term applications of poultry litter increased the abundance of sulI and intlI genes in soil (P < 0.05). Similarly, metagenomic shotgun sequencing revealed a greater total number of AMR genes under long-term CG, while fewer AMR genes were found in H (no cattle manure) and RBS (no animal manure or poultry litter). Results indicate long-term conservation pasture management practices (e.g., RBS and RBR) and select animal manure (poultry litter inputs) may minimize the presence and abundance of AMR genes in grassland soils.

SUBMITTER: Yang Y

PROVIDER: S-EPMC7646296 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management.

Yang Yichao Y Ashworth Amanda J AJ DeBruyn Jennifer M JM Durso Lisa M LM Savin Mary M Cook Kim K Moore Philip A PA Owens Phillip R PR

PeerJ 20201103

The persistence of antimicrobial resistant (AMR) genes in the soil-environment is a concern, yet practices that mitigate AMR are poorly understood, especially in grasslands. Animal manures are widely deposited on grasslands, which are the largest agricultural land-use in the United States. These nutrient-rich manures may contain AMR genes. The aim of this study was to enumerate AMR genes in grassland soils following 14-years of poultry litter and cattle manure deposition and evaluate if best man ...[more]

PMID: 33194426

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Project description:Runoff from land-applied manure and poultry litter is one mechanism by which manure-borne bacteria are transported over large distances in the environment. There is a global concern that antimicrobial resistant (AMR) genes may be transmitted through the food chain from animal manures to soil to surface water. However, details are lacking on the ecology of AMR genes in water runoff as well as how conservation management practices may affect the runoff microbiome or minimize the movement of AMR genes. The aim of this study was to identify microbial community structure and diversity in water runoff following 14-years of poultry litter and cattle manure deposition and to evaluate the amount of AMR genes under five conventional and conservation pasture management strategies. Since 2004, all watersheds received annual poultry litter at a rate of 5.6 Mg ha-1 and were consistently managed. Surface runoff samples were collected from each watershed from 2018 to 2019, characterized using Illumina 16S rRNA gene amplicon sequencing and enumerated for four AMR-associated genes (ermB, sulI, intlI, and blactx-m-32 ) using quantitative PCR. Overall, long-term pasture management influenced water microbial community structure, with effects differing by year (p < 0.05). Bacterial richness (Chao1 index) was influenced by pasture management, with the lowest richness occurring in the control (nearby non-agricultural water source) and the greatest under fields that were hayed (no cattle presence). Runoff bacterial richness in watersheds increased following poultry litter applications, indicating poultry litter is a possible source of bacteria and altered runoff community structure. The blactx-m-32 gene was not detected in any surface water sample. The remaining three AMR genes were absent in the non-agricultural control, but present in agricultural samples. However, there was no impact (p > 0.05) from pasture management on the abundance of these genes, indicating both conventional and conservation practices have similar ecologies for these targets; however, there was a greater detection of sulI genes from runoff in continuously grazed systems in 2019, with hay being lowest in 2019. Results illustrate that the edge of field buffer strips may increase bacterial richness in water runoff, but these changes in richness do not greatly impact target AMR genes in the United States largest land-use category.

Project description:Soil microorganisms are important for maintaining soil health, decomposing organic matter, and recycling nutrients in pasture systems. However, the impact of long-term conservation pasture management on soil microbial communities remains unclear. Therefore, soil microbiome responses to conservation pasture management is an important component of soil health, especially in the largest agricultural land-use in the US. The aim of this study was to identify soil microbiome community differences following 13-years of pasture management (hayed (no cattle), continuously grazed, rotationally grazed with a fenced, un-grazed and unfertilized buffer strip, and a control (no poultry litter or cattle manure inputs)). Since 2004, all pastures (excluding the control) received annual poultry litter at a rate of 5.6 Mg ha-1. Soil samples were collected at a 0-15 cm depth from 2016-2017 either pre or post poultry litter applications, and bacterial communities were characterized using Illumina 16S rRNA gene amplicon sequencing. Overall, pasture management influenced soil microbial community structure, and effects were different by year (P < 0.05). Soils receiving no poultry litter or cattle manure had the lowest richness (Chao). Continuously grazed systems had greater (P < 0.05) soil community richness, which corresponded with greater soil pH and nutrients. Consequently, continuously grazed systems may increase soil diversity, owing to continuous nutrient-rich manure deposition; however, this management strategy may adversely affect aboveground plant communities and water quality. These results suggest conservation pasture management (e.g., rotationally grazed systems) may not improve microbial diversity, albeit, buffer strips were reduced nutrients and bacterial movement as evident by low diversity and fertility in these areas compared to areas with manure or poultry litter inputs. Overall, animal inputs (litter or manure) increased soil microbiome diversity and may be a mechanism for improved soil health.

Project description:The study is focused on impact of manure application, rice varieties and water management on greenhouse gas (GHG) emissions from paddy rice soil in pot experiment. The objectives of this study were a) to assess the effect of different types of manure amendments and rice varieties on greenhouse gas emissions and b) to determine the optimum manure application rate to increase rice yield while mitigating GHG emissions under alternate wetting and drying irrigation in paddy rice production. The first pot experiment was conducted at the Department of Agronomy, Yezin Agricultural University, Myanmar, in the wet season from June to October 2016. Two different organic manures (compost and cow dung) and control (no manure), and two rice varieties; Manawthukha (135 days) and IR-50 (115 days), were tested. The results showed that cumulative CH4 emission from Manawthukha (1.084 g CH4 kg-1 soil) was significantly higher than that from IR-50 (0.683 g CH4 kg-1 soil) (P<0.0046) with yield increase (P<0.0164) because of the longer growth duration of the former. In contrast, higher cumulative nitrous oxide emissions were found for IR-50 (2.644 mg N2O kg-1 soil) than for Manawthukha (2.585 mg N2O kg-1 soil). However, IR-50 showed less global warming potential (GWP) than Manawthukha (P<0.0050). Although not significant, the numerically lowest CH4 and N2O emissions were observed in the cow dung manure treatment (0.808 g CH4 kg-1 soil, 2.135 mg N2O kg-1 soil) compared to those of the control and compost. To determine the effect of water management and organic manures on greenhouse gas emissions, second pot experiments were conducted in Madaya township during the dry and wet seasons from February to October 2017. Two water management practices {continuous flooding (CF) and alternate wetting and drying (AWD)} and four cow dung manure rates {(1) 0 (2) 2.5 t ha-1 (3) 5 t ha-1 (4) 7.5 t ha-1} were tested. The different cow dung manure rates did not significantly affect grain yield or greenhouse gas emissions in this experiment. Across the manure treatments, AWD irrigation significantly reduced CH4 emissions by 70% during the dry season and 66% during the wet season. Although a relative increase in N2O emissions under AWD was observed in both rice seasons, the global warming potential was significantly reduced in AWD compared to CF in both seasons (P<0.0002, P<0.0000) according to reduced emission in CH4. Therefore, AWD is the effective mitigation practice for reducing GWP without compromising rice yield while manure amendment had no significant effect on GHG emission from paddy rice field. Besides, AWD saved water about 10% in dry season and 19% in wet season.

Dataset Information

Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management.

Publications

Antimicrobial resistant gene prevalence in soils due to animal manure deposition and long-term pasture management.

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