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Hartfiel LM, Hoover NL, Hall SJ, Isenhart TM, Gomes CL, Soupir ML. Extreme low-flow conditions in a dual-chamber denitrification bioreactor contribute to pollution swapping with low landscape-scale impact. Sci Total Environ 2023; 877:162837. [PMID: 36924958 DOI: 10.1016/j.scitotenv.2023.162837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 05/06/2023]
Abstract
Denitrification bioreactors are an effective edge-of-field conservation practice for nitrate (NO3) reduction from subsurface drainage. However, these systems may produce other pollutants and greenhouse gases during NO3 removal. Here a dual-chamber woodchip bioreactor system experiencing extreme low-flow conditions was monitored for its spatiotemporal NO3 and total organic carbon dynamics in the drainage water. Near complete removal of NO3 was observed in both bioreactor chambers in the first two years of monitoring (2019-2020) and in the third year of monitoring in chamber A, with significant (p < 0.01) reduction of the NO3-N each year in both chambers with 8.6-11.4 mg NO3-N L-1 removed on average. Based on the NO3 removal observed, spatial monitoring of sulfate (SO4), dissolved methane (CH4), and dissolved nitrous oxide (N2O) gases was added in the third year of monitoring (2021). In 2021, chambers A and B had median hydraulic residence times (HRTs) of 64 h and 39 h, respectively, due to varying elevations of the chambers, with drought conditions making the differences more pronounced. In 2021, significant production of dissolved CH4 was observed at rates of 0.54 g CH4-C m-3 d-1 and 0.07 g CH4-C m-3 d-1 in chambers A and B, respectively. In chamber A, significant removal (p < 0.01) of SO4 (0.23 g SO4 m-3 d-1) and dissolved N2O (0.21 mg N2O-N m-2 d-1) were observed, whereas chamber B produced N2O (0.36 mg N2O-N m-2 d-1). Considering the carbon dioxide equivalents (CO2e) on an annual basis, chamber A had loads (~12,000 kg CO2e ha-1 y-1) greater than comparable poorly drained agricultural soils; however, the landscape-scale impact was small (<1 % change in CO2e) when expressed over the drainage area treated by the bioreactor. Under low-flow conditions, pollution swapping in woodchip bioreactors can be reduced at HRTs <50 h and NO3 concentrations >2 mg N L-1.
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Affiliation(s)
- Lindsey M Hartfiel
- UW Discovery Farms, University of Wisconsin-Madison, Division of Extension, Madison, WI, United States.
| | - Natasha L Hoover
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Steven J Hall
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Thomas M Isenhart
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, United States
| | - Carmen L Gomes
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Liao C, Santoscoy MC, Craft J, Anderson C, Soupir ML, Jarboe LR. Allelic variation of Escherichia coli outer membrane protein A: Impact on cell surface properties, stress tolerance and allele distribution. PLoS One 2022; 17:e0276046. [PMID: 36227900 PMCID: PMC9560509 DOI: 10.1371/journal.pone.0276046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Outer membrane protein A (OmpA) is one of the most abundant outer membrane proteins of Gram-negative bacteria and is known to have patterns of sequence variations at certain amino acids-allelic variation-in Escherichia coli. Here we subjected seven exemplar OmpA alleles expressed in a K-12 (MG1655) ΔompA background to further characterization. These alleles were observed to significantly impact cell surface charge (zeta potential), cell surface hydrophobicity, biofilm formation, sensitivity to killing by neutrophil elastase, and specific growth rate at 42°C and in the presence of acetate, demonstrating that OmpA is an attractive target for engineering cell surface properties and industrial phenotypes. It was also observed that cell surface charge and biofilm formation both significantly correlate with cell surface hydrophobicity, a cell property that is increasingly intriguing for bioproduction. While there was poor alignment between the observed experimental values relative to the known sequence variation, differences in hydrophobicity and biofilm formation did correspond to the identity of residue 203 (N vs T), located within the proposed dimerization domain. The relative abundance of the (I, δ) allele was increased in extraintestinal pathogenic E. coli (ExPEC) isolates relative to environmental isolates, with a corresponding decrease in (I, α) alleles in ExPEC relative to environmental isolates. The (I, α) and (I, δ) alleles differ at positions 203 and 251. Variations in distribution were also observed among ExPEC types and phylotypes. Thus, OmpA allelic variation and its influence on OmpA function warrant further investigation.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
| | - Miguel C. Santoscoy
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
| | - Julia Craft
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Chiron Anderson
- Department of Chemical and Biological Engineering, Biological Materials and Processes (BioMAP) NSF REU Program, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa United States of America
- * E-mail:
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Schaefer A, Lee J, Soupir ML, Moorman TB, Howe A. Comparison of microbial communities in replicated woodchip bioreactors. J Environ Qual 2022; 51:205-215. [PMID: 34965312 DOI: 10.1002/jeq2.20320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Denitrification in woodchip bioreactors is a microbial process, but the effects of variations in bioreactors operation on microbial community structure are not well understood. Here, our goals were to understand hydraulic retention time (HRT) as a factor that influences woodchip bioreactor microbial community variation and structure in replicated field bioreactors and to evaluate relationships between microbial community membership and marker genes for denitrification. We used a combination of quantitative polymerase chain reaction of nirS, nirK, nosZI, and nosZII and 16S rRNA amplicon sequencing to characterize the microbial communities of nine pilot-scale woodchip bioreactors located at Iowa State University. Our results showed dynamic microbial communities but with persistent taxa between two sampling years and three HRTs. Similarities between functional gene copy numbers across sampling year and HRT indicate that the potential for denitrification is conserved despite differences in the microbial communities. These results are evidence that there are specific and persistent taxa within replicated bioreactors. Woodchip bioreactor microbial community membership is recommended to be the focus of future studies to better understand the relationship between microbial community functions and bioreactor management.
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Affiliation(s)
- Abby Schaefer
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Jaejin Lee
- Genomics and Environmental Research in Microbial Systems Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3346 Elings Hall, Ames, IA, 50011, USA
| | - Michelle L Soupir
- Water Quality Research Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3358 Elings Hall, Ames, IA, 50011, USA
| | - Thomas B Moorman
- USDA-ARS, National Laboratory for Agriculture and the Environment, 2110 University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Genomics and Environmental Research in Microbial Systems Laboratory, Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 3346 Elings Hall, Ames, IA, 50011, USA
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Hartfiel LM, Schaefer A, Howe AC, Soupir ML. Denitrifying bioreactor microbiome: Understanding pollution swapping and potential for improved performance. J Environ Qual 2022; 51:1-18. [PMID: 34699064 DOI: 10.1002/jeq2.20302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Denitrifying woodchip bioreactors are a best management practice to reduce nitrate-nitrogen (NO3 -N) loading to surface waters from agricultural subsurface drainage. Their effectiveness has been proven in many studies, although variable results with respect to performance indicators have been observed. This paper serves the purpose of synthesizing the current state of the science in terms of the microbial community, its impact on the consistency of bioreactor performance, and its role in the production of potential harmful by-products including greenhouse gases, sulfate reduction, and methylmercury. Microbial processes other than denitrification have been observed in these bioreactor systems, including dissimilatory nitrate reduction to ammonia (DNRA) and anaerobic ammonium oxidation (anammox). Specific gene targets for denitrification, DNRA, anammox, and the production of harmful by-products are identified from bioreactor studies and other environmentally relevant systems for application in bioreactor studies. Lastly, cellulose depletion has been observed over time via increasing ligno-cellulose indices, therefore, the microbial metabolism of cellulose is an important function for bioreactor performance and management. Future work should draw from the knowledge of soil and wetland ecology to inform the study of bioreactor microbiomes.
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Affiliation(s)
- Lindsey M Hartfiel
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Abby Schaefer
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Adina C Howe
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
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Howe AC, Soupir ML. Antimicrobial resistance in integrated agroecosystems: State of the science and future opportunities. J Environ Qual 2021; 50:1255-1265. [PMID: 34528726 DOI: 10.1002/jeq2.20289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
As the Journal of Environmental Quality (JEQ) celebrates 50 years of publication, the division of environmental microbiology is one of the newest additions to the journal. During this time, significant advances in understanding of the interconnected microbial community and impact of the microbiome on natural and designed environmental systems have occurred. In this review, we highlight the intractable challenge of antimicrobial resistance (AMR) on humans, animals, and the environment, with particular emphasis on the role of integrated agroecosystems and by highlighting contributions published in JEQ. From early studies of phenotypic resistance of indicator organisms in waters systems to current calls for integrating AMR assessment across "One Health," publications in JEQ have advanced our understanding of AMR. As we reflect on the state of the science, we emphasize future opportunities. First, integration of phenotypic and molecular tools for assessing environmental spread of AMR and human health risk continues to be an urgent research need for a one health approach to AMR. Second, monitoring AMR levels in manure is recommended to understand inputs and potential spread through agroecosystems. Third, baseline knowledge of AMR levels is important to realize the impact of manure inputs on water quality and public health risk; this can be achieved through background monitoring or identifying the source-related genes or organisms. And finally, conservation practices designed to meet nutrient reduction goals should be explored for AMR reduction potential.
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Affiliation(s)
- Adina C Howe
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., Ames, IA, 50011, USA
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Alt LM, Iverson AN, Soupir ML, Moorman TB, Howe A. Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure. J Environ Qual 2021; 50:911-922. [PMID: 33982299 DOI: 10.1002/jeq2.20240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.
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Affiliation(s)
- Laura M Alt
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Alyssa N Iverson
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
| | - Thomas B Moorman
- National Lab. for Agriculture and the Environment, USDA-ARS, 1015 N University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Dep. of Agricultural and Biosystems Engineering, IA State Univ., Elings Hall, 605 Bissell Rd., Ames, IA, 50011, USA
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Neher TP, Ma L, Moorman TB, Howe A, Soupir ML. Seasonal variations in export of antibiotic resistance genes and bacteria in runoff from an agricultural watershed in Iowa. Sci Total Environ 2020; 738:140224. [PMID: 32806354 DOI: 10.1016/j.scitotenv.2020.140224] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Seasonal variations of antimicrobial resistance (AMR) indicators in runoff water can help improve our understanding of AMR sources and transport within an agricultural watershed. This study aimed to monitor multiple areas throughout the Black Hawk Lake (BHL) watershed (5324 ha) in central Iowa during 2017 and 2018 that consists of both swine and cattle feeding operations as well as known areas with manure application. The measured indicators included plate counts for fecal indicator bacteria (FIB) E. coli, Enterococcus, antibiotic resistant fecal indicator bacteria (ARBs) tylosin resistant Enterococcus, tetracycline resistant Enterococcus, and antibiotic resistance genes (ARGs): ermB, ermF (macrolide), tetA, tetM, tetO, tetW (tetracycline), sul1, sul2 (sulfonamide), aadA2 (aminoglycoside), vgaA, and vgaB (pleuromutilin). Both the plate count and the ARG analyses showed seasonal trends. Plate counts were significantly greater during the growing season, while the ARGs were greater in the pre-planting and post-harvest seasons (Wilcoxon Rank-Sum Test p < 0.05). The ermB gene concentration was significantly correlated (p < 0.05) with E. coli and Enterococcus concentrations in 2017, suggesting a potential use of this ARG as an indicator of environmental AMR and human health risk. Flow rate was not a significant contributor to annual variations in bacteria and AMR indicators. Based on observed seasonal patterns, we concluded that manure application was the likely contributor to elevated ARG indicators observed in the BHL watershed, while the driver of elevated ARB indictors in the growing season can only be speculated. Understanding AMR export patterns in agricultural watersheds provides public health officials knowledge of seasonal periods of higher AMR load to recreational waters.
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Affiliation(s)
- Timothy P Neher
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States.
| | - Lanying Ma
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, IA, United States
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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Palmer JA, Law JY, Soupir ML. Spatial and temporal distribution of E. coli contamination on three inland lake and recreational beach systems in the upper Midwestern United States. Sci Total Environ 2020; 722:137846. [PMID: 32197161 DOI: 10.1016/j.scitotenv.2020.137846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/14/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Swimming advisories are commonly posted at public beaches across the United States every year. In Iowa, weekly monitoring of public swimming areas at state and county beaches have resulted in the impairment of numerous lakes for fecal indicator bacteria (FIB) contamination, as detected by E. coli. An extensive study was established to assess the relationships between E. coli contamination of nearshore beach water environments, open lake conditions and beach sands in three recreational beach/lake systems currently impaired for FIB contamination across Iowa. A transect/grab sample based sampling design was implemented across the systems with collections spanning from April through October of 2015 and 2016. Collections of E. coli along water transects identified strong near to far shore gradients of decreasing concentrations in all systems. Results indicate that concentrations of E. coli observed in swimming waters consistently disassociate with concentrations in the broader lake environment. Swimming water E. coli concentrations correlated with elevated beach sand E. coli, samples collected from beach sands uncovered concentrations up to 86,500 times higher than adjacent swimming waters. Results from this study indicate that foreshore beach sands and other beach proximate FIB sources serve as the major contributing source for swimming zone advisories. The current methodology used by state and federal officials includes impairing entire lake waterbodies for FIB contamination of the swimming area. These impairment listings do not accurately reflect the condition(s) of the larger lake environment outside the swimming area and fail to account for beach proximate conditions in the assessment process. Further, this approach provides potentially misleading information to the public and may undermine implementation strategies deployed by resource managers aimed at addressing FIB contamination at recreational swimming areas. Views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the Iowa Department of Natural Resources.
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Affiliation(s)
- Jason A Palmer
- Iowa Department of Natural Resources, 502 E 9th Street, Des Moines, IA 50319, USA.
| | - Ji-Yeow Law
- Department of Agriculture and Biosystems Engineering, Iowa State University, 3358 Elings Hall, Bissell Rd, Ames, IA 50011, USA.
| | - Michelle L Soupir
- Department of Agriculture and Biosystems Engineering, Iowa State University, 3358 Elings Hall, Bissell Rd, Ames, IA 50011, USA.
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Neher TP, Ma L, Moorman TB, Howe AC, Soupir ML. Catchment-scale export of antibiotic resistance genes and bacteria from an agricultural watershed in central Iowa. PLoS One 2020; 15:e0227136. [PMID: 31923233 PMCID: PMC6953785 DOI: 10.1371/journal.pone.0227136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/12/2019] [Indexed: 01/20/2023] Open
Abstract
Antibiotics are administered to livestock in animal feeding operations (AFOs) for the control, prevention, and treatment of disease. Manure from antibiotic treated livestock contains unmetabolized antibiotics that provide selective pressure on bacteria, facilitating the expression of anti-microbial resistance (AMR). Manure application on row crops is an agronomic practice used by growers to meet crop nutrient needs; however, it can be a source of AMR to the soil and water environment. This study in central Iowa aims to directly compare AMR indicators in outlet runoff from two adjacent (221 to 229 ha) manured and non-manured catchments (manure comparison), and among three catchments (600 to 804 ha) with manure influence, no known manure application (control), and urban influences (mixed land use comparison). Monitored AMR indicators included antibiotic resistance genes (ARGs) ermB, ermF (macrolide), tetA, tetM, tetO, tetW (tetracycline), sul1, sul2 (sulfonamide), aadA2 (aminoglycoside), vgaA, and vgaB (pleuromutilin), and tylosin and tetracycline resistant enterococci bacteria. Results of the manure comparison showed significantly higher (p<0.05) tetracycline and tylosin resistant bacteria from the catchment with manure application in 2017, but no differences in 2018, possibly due to changes in antibiotic use resulting from the Veterinary Feed Directive. Moreover, the ARG analysis indicated a larger diversity of ARGs at the manure amended catchment. The mixed land use comparison showed the manure amended catchment had significantly higher (p<0.05) tetracycline resistant bacteria in 2017 and significantly higher tylosin resistant bacteria in 2017 and 2018 than the urban influenced catchment. The urban influenced catchment had significantly higher ermB concentrations in both sampling years, however the manure applied catchment runoff consisted of higher relative abundance of total ARGs. Additionally, both catchments showed higher AMR indicators compared to the control catchment. This study identifies four ARGs that might be specific to AMR as a result of agricultural sources (tetM, tetW, sul1, sul2) and optimal for use in watershed scale monitoring studies for tracking resistance in the environment.
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Affiliation(s)
- Timothy P. Neher
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| | - Lanying Ma
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Thomas B. Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, Ames, Iowa, United States of America
| | - Adina C. Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
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Dougherty BW, Pederson CH, Mallarino AP, Andersen DS, Soupir ML, Kanwar RS, Helmers MJ. Midwestern cropping system effects on drainage water quality and crop yields. J Environ Qual 2020; 49:38-49. [PMID: 33016359 DOI: 10.1002/jeq2.20007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 10/29/2019] [Accepted: 11/11/2019] [Indexed: 06/11/2023]
Abstract
Grain producers are challenged to maximize crop production while utilizing nutrients efficiently and minimizing negative impacts on water quality. There is a particular concern about nutrient export to the Gulf of Mexico via loss from subsurface drainage systems. The objective of this study was to investigate the effects of crop rotation, tillage, crop residue removal, swine manure applications, and cereal rye (Secale cereale L.) cover crops on nitrate-N (NO3 -N) and total reactive phosphorus (TRP) loss via subsurface drainage. The study was evaluated from 2008 through 2015 using 36 0.4-ha plots outfitted with a subsurface drainage water quality monitoring system. Results showed that when swine manure was applied before both corn (Zea mays L.) and soybean [Glycine max (L.) Merr.], drainage water had significantly higher 8-yr-average flow-weighted NO3 -N concentrations compared with swine manure applied before corn only in a corn-soybean rotation. The lowest NO3 -N loss was 15.2 kg N ha-1 yr-1 from a no-till corn-soybean treatment with rye cover crop and spring application of urea-ammonium nitrate (UAN) to corn. The highest NO3 -N loss was 29.5 kg N ha-1 yr-1 from swine manure applied to both corn and soybean. A rye cover crop reduced NO3 -N loss, whereas tillage and residue management had little impact on NO3 -N loss. Losses of TRP averaged <32 g P ha-1 yr-1 from all treatments. Corn yield was negatively affected by both no-till management and cereal rye cover crops. Results showed that cropping management affected N leaching but impacts on P leaching were minimal.
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Affiliation(s)
- Brian W Dougherty
- Iowa State Univ. Extension and Outreach, 14858 West Ridge Lane, Suite 2, Dubuque, IA, 52003
| | - Carl H Pederson
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, 605 Bissell Rd, Ames, IA, 50011
| | - Antonio P Mallarino
- Dep. of Agronomy, Iowa State Univ., 3216 Agronomy Hall, 716 Farm House Ln., Ames, IA, 50011
| | - Daniel S Andersen
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, 605 Bissell Rd, Ames, IA, 50011
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, 605 Bissell Rd, Ames, IA, 50011
| | - Ramesh S Kanwar
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, 605 Bissell Rd, Ames, IA, 50011
| | - Matthew J Helmers
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, 605 Bissell Rd, Ames, IA, 50011
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Hoover NL, Law JY, Long LAM, Kanwar RS, Soupir ML. Long-term impact of poultry manure on crop yield, soil and water quality, and crop revenue. J Environ Manage 2019; 252:109582. [PMID: 31614262 DOI: 10.1016/j.jenvman.2019.109582] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 05/15/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
A long-term poultry manure fertilizer study was initiated in 1998 and continued until 2009 under corn-soybean (CS) rotation. To match changing landscape trends, the plots were switched to continuous corn (CC) from 2010 to 2017. In both CS and CC phases, poultry manure (PM) was applied at the crop rotation recommended agronomic N rate and either half (CC phase) or double (CS phase) the recommended rate. Urea-ammonium nitrate (UAN) was applied to comparison plots at the crop recommended application rate (168 kg N ha-1 and 224 kg N ha-1 for the CS and CC phases, respectively) throughout the study. The objectives of this study include evaluation of the economic benefits of long-term PM application at various rates (PM2, PM, and PM0.5), and the impact of poultry manure application on soil health and nutrient levels, crop yield, and drainage water quality. Lower NO3-N concentrations were reported in drainage from PM treated plots when compared to UAN fertilizer applied at the same agronomic rate. Of the parameters tested for soil health analysis after twenty years of repeat application, particulate organic matter (POM) present was significantly greater in the PM treated soils (6.1-6.7 g kg soil-1) when compared to UAN plots (4.6 g kg soil-1), showing potential for stabilized soil particles, increased infiltration and water-holding capacity. The results show a consistent positive impact of manure application on corn and soybean yields when compared to yields observed in UAN treated plots. During the CS phase, we estimated the same average revenue per dollar spent for PM and UAN treatments, while the average return rate for PM2 was 1% lower; during CC phase,15% increased return rates were observed when PM0.5 and PM were compared against the UAN treatment. When managed properly, PM application to cropland is a sustainable option for diversifying agroecosystems, improving soil health and improving farm economics.
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Affiliation(s)
- Natasha L Hoover
- Department of Agricultural and Biosystems Engineering, 3350 Elings Hall, Iowa State University, Ames, IA, 50011, USA.
| | - Ji Yeow Law
- Department of Agricultural and Biosystems Engineering, 3324 Elings Hall, Iowa State University, Ames, IA, 50011, USA.
| | - Leigh Ann M Long
- Department of Agricultural and Biosystems Engineering, 3350 Elings Hall, Iowa State University, Ames, IA, 50011, USA.
| | - Ramesh S Kanwar
- Department of Agricultural and Biosystems Engineering, 2212 NSRIC, Iowa State University, Ames, IA, 50011, USA.
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, 3358 Elings Hall, Iowa State University, Ames, IA, 50011, USA.
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Smith SD, Colgan P, Yang F, Rieke EL, Soupir ML, Moorman TB, Allen HK, Howe A. Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems. PLoS One 2019; 14:e0222470. [PMID: 31527917 PMCID: PMC6748443 DOI: 10.1371/journal.pone.0222470] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023] Open
Abstract
Manure from animals that have been treated with antibiotics is often used to fertilize agricultural soils and its application has previously been shown to enrich for genes associated with antibiotic resistance in agroecosystems. To investigate the magnitude of this effect, we designed a column experiment simulating manure-treated agricultural soil that utilizes artificial subsurface drainage to determine the duration and extent which this type of manure fertilization impacts the set of genes associated with antibiotic resistance in drainage water. We classified ARGs in manure-treated drainage effluent water by its source of origin. Overall, we found that 61% and 7% of the total abundance of ARGs found in drainage water samples could be attributed to manure enrichment and manure addition, respectively. Among these ARGs, we identified 75 genes unique to manure that persisted in both soil and drainage water throughout a drainage season typical of the Upper Midwestern United States. While most of these genes gradually decreased in abundance over time, the IS6100-associated tet(33) gene accrued. These results demonstrate the influence of manure applications on the composition of the resistome observed in agricultural drainage water and highlight the importance of anthropogenic ARGs in the environment.
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Affiliation(s)
- Schuyler D. Smith
- Bioinformatics and Computational Biology Department, Iowa State University, Ames, Iowa, United States of America
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Phillip Colgan
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Elizabeth L. Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Thomas B. Moorman
- United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Heather K. Allen
- United States Department of Agriculture, Agricultural Research Service, Ames, Iowa, United States of America
| | - Adina Howe
- Bioinformatics and Computational Biology Department, Iowa State University, Ames, Iowa, United States of America
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
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13
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Davis MP, Martin EA, Moorman TB, Isenhart TM, Soupir ML. Nitrous oxide and methane production from denitrifying woodchip bioreactors at three hydraulic residence times. J Environ Manage 2019; 242:290-297. [PMID: 31054393 DOI: 10.1016/j.jenvman.2019.04.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 04/10/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
Denitrifying bioreactors remove nitrate (NO3-) from agricultural drainage and are slated to be an integral part of nitrogen reduction strategies in the Mississippi River Basin. However, incomplete denitrification can result in nitrous oxide (N2O) production and anaerobic conditions within bioreactors may be conducive to methane (CH4) production via methanogenesis. Greenhouse gas production has the potential to trade excess NO3- in surface water with excess greenhouses gases in the atmosphere. Our study examined N2O and CH4 production from pilot scale (6.38 m3) bioreactors across three hydraulic residence times (HRTs), 2, 8, and 16 h. Production was measured from both the surface of the bioreactors and dissolved in the bioreactor effluent. Nitrous oxide and CH4 was produced across all HRTs, with the majority dissolved in the effluent. Nitrous oxide production was significantly greater (P < 0.05) from 2 h HRTs (478.43 mg N2O m-3 day-1) than from 8 (29.95 mg N2O m-3 day-1) and 16 (36.61 mg N2O m-3 day-1) hour HRTs. Methane production was significantly less (P < 0.05) from 2 h HRTs (0.51 g C m3 day-1) compared to 8 (1.50 g C m3 day-1) and 16 (1.69 g C m3 day-1) hour HRTs. The 2 h HRTs had significantly greater (P = 0.05) impacts to climate change compared to 8 and 16 h HRTs. Results from this study suggest managing HRTs between 6 and 8 h in field bioreactors could minimize total greenhouse gas production and maximize NO3- removal.
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Affiliation(s)
- Morgan P Davis
- Dep. of Agronomy, Iowa State Univ., 2104 Agronomy Hall, Ames, IA, 50011, USA.
| | - Emily A Martin
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, Ames, IA, 50011, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 1015 N. University Blvd., Ames, IA, 50011, USA
| | - Thomas M Isenhart
- Dep. of Natural Resource Ecology and Management, Iowa State Univ., 339 Science Hall II, USA
| | - Michelle L Soupir
- Dep. of Agricultural and Biosystems Engineering, Iowa State Univ., 1340 Elings Hall, Ames, IA, 50011, USA
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14
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Martin EA, Davis MP, Moorman TB, Isenhart TM, Soupir ML. Impact of hydraulic residence time on nitrate removal in pilot-scale woodchip bioreactors. J Environ Manage 2019; 237:424-432. [PMID: 30822646 DOI: 10.1016/j.jenvman.2019.01.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/17/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Nitrate (NO3-N) export from row crop agricultural systems with subsurface tile drainage continues to be a major water quality concern. Woodchip bioreactors are an effective edge-of-field practice designed to remove NO3-N from tile drainage. The NO3-N removal rate of woodchip bioreactors can be impacted by several factors, including hydraulic residence time (HRT). This study examined the impact of three HRTs, 2 h, 8 h, and 16 h, on NO3-N removal in a set of nine pilot-scale woodchip bioreactors in Central Iowa. NO3-N concentration reduction from the inlet to the outlet was significantly different for all HRTs (p < 0.05). The 16 h HRT removed the most NO3-N by concentration (7.5 mg L-1) and had the highest removal efficiency at 53.8%. The 8 h HRT removed an average of 5.5 mg L-1 NO3-N with a removal efficiency of 32.1%. The 2 h HRT removed an average of 1.3 mg L-1 NO3-N with a removal efficiency of 9.0%. The 2 h HRT had the highest NO3-N mass removal rate (MRR) at 9.0 g m-3 day-1, followed by the 8 h HRT at 8.5 g m-3 day-1, and the 16 h HRT at 7.4 g m-3 day-1, all of which were statistically different (p < 0.05). Significant explanatory variables for removal efficiency were HRT (p < 0.001) and influent NO3-N concentration (p < 0.001), (R2 = 0.80), with HRT accounting for 93% contribution. When paired with results from a companion study, the ideal HRT for the bioreactors was 8 h to achieve maximum NO3-N removal while reducing the impact from greenhouse gas emissions.
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Affiliation(s)
- E A Martin
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA.
| | - M P Davis
- Iowa State University, Dept. of Agronomy, 2104 Agronomy Hall, Ames, IA 5001, USA.
| | - T B Moorman
- USDA-ARS National Laboratory for Agriculture and the Environment, 2110 University Boulevard, Ames, IA 50011, USA.
| | - T M Isenhart
- Iowa State University, Dept. of Natural Resource Ecology and Management, 334 Science II, Ames, IA 50011, USA.
| | - M L Soupir
- Iowa State University, Water Quality Research Lab, Dept. of Agricultural and Biosystems Engineering, 3358 Elings Hall, USA.
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15
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Choi J, Rieke EL, Moorman TB, Soupir ML, Allen HK, Smith SD, Howe A. Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance. FEMS Microbiol Ecol 2019; 94:4810543. [PMID: 29346541 PMCID: PMC5939627 DOI: 10.1093/femsec/fiy006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 12/29/2022] Open
Abstract
Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%–85% of the erm gene diversity in the manures analyzed.
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Affiliation(s)
- Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Elizabeth L Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Blvd, Ames, IA 50011, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
| | - Heather K Allen
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, IA, 50010, USA
| | - Schuyler D Smith
- Department of Bioinformatics and Computational Biology, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1201 Sukup Hall, Ames, IA 50011, USA
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Brendel CE, Soupir ML, Long LAM, Helmers MJ, Ikenberry CD, Kaleita AL. Catchment-scale Phosphorus Export through Surface and Drainage Pathways. J Environ Qual 2019; 48:117-126. [PMID: 30640359 DOI: 10.2134/jeq2018.07.0265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The site-specific nature of P fate and transport in drained areas exemplifies the need for additional data to guide implementation of conservation practices at the catchment scale. Total P (TP), dissolved reactive P (DRP), and total suspended solids (TSS) were monitored at five sites-two streams, two tile outlets, and a grassed waterway-in three agricultural subwatersheds (221.2-822.5 ha) draining to Black Hawk Lake in western Iowa. Median TP concentrations ranged from 0.034 to 1.490 and 0.008 to 0.055 mg P L for event and baseflow samples, respectively. The majority of P and TSS export occurred during precipitation events and high-flow conditions with greater than 75% of DRP, 66% of TP, and 59% of TSS export occurring during the top 25% of flows from all sites. In one subwatershed, a single event (annual recurrence interval < 1 yr) was responsible for 46.6, 84.0, and 81.0% of the annual export of TP, DRP, and TSS, respectively, indicating that frequent, small storms have the potential to result in extreme losses. Isolated monitoring of surface and drainage transport pathways indicated significant P and TSS losses occurring through drainage; over the 2-yr study period, the drainage pathway was responsible for 69.8, 59.2, and 82.6% of the cumulative TP, DRP, and TSS export, respectively. Finally, the results provided evidence that particulate P losses in drainage were greater than dissolved P losses. Understanding relationships between flow, precipitation, transport pathway, and P fraction at the catchment scale is needed for effective conservation practice implementation.
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17
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Rieke EL, Soupir ML, Moorman TB, Yang F, Howe AC. Temporal Dynamics of Bacterial Communities in Soil and Leachate Water After Swine Manure Application. Front Microbiol 2018; 9:3197. [PMID: 30627124 PMCID: PMC6309816 DOI: 10.3389/fmicb.2018.03197] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/10/2018] [Indexed: 11/17/2022] Open
Abstract
Application of swine manure to agricultural land allows recycling of plant nutrients, but excess nitrate, phosphorus and fecal bacteria impact surface and drainage water quality. While agronomic and water quality impacts are well studied, little is known about the impact of swine manure slurry on soil microbial communities. We applied swine manure to intact soil columns collected from plots maintained under chisel plow or no-till with corn and soybean rotation. Targeted 16S-rRNA gene sequencing was used to characterize and to identify shifts in bacterial communities in soil over 108 days after swine manure application. In addition, six simulated rainfalls were applied during this time. Drainage water from the columns and surface soil were sampled, and DNA was extracted and sequenced. Unique DNA sequences (OTU) associated with 12 orders of bacteria were responsible for the majority of OTUs stimulated by manure application. Proteobacteria were most prevalent, followed by Bacteroidetes, Firmicutes, Actinobacteria, and Spirochaetes. While the majority of the 12 orders decreased after day 59, relative abundances of genes associated with Rhizobiales and Actinomycetales in soil increased. Bacterial orders which were stimulated by manure application in soil had varied responses in drainage waters over the course of the experiment. We also identified a “manure-specific core” of five genera who comprised 13% of the manure community and were not significantly abundant in non-manured control soils. Of these five genera, Clostridium sensu stricto was the only genus which did not return to pre-manure relative abundance in soil by day 108. Our results show that enrichment responses after manure amendment could result from displacement of native soil bacteria by manure-borne bacteria during the application process or growth of native bacteria using manure-derived available nutrients.
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Affiliation(s)
- Elizabeth L Rieke
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Michelle L Soupir
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, United States Department of Agriculture-Agricultural Research Service, Ames, IA, United States
| | - Fan Yang
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Adina C Howe
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
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18
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Pandey P, Soupir ML, Wang Y, Cao W, Biswas S, Vaddella V, Atwill R, Merwade V, Pasternack G. Water and Sediment Microbial Quality of Mountain and Agricultural Streams. J Environ Qual 2018; 47:985-996. [PMID: 30272806 DOI: 10.2134/jeq2017.12.0483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Increased public health risk caused by pathogen contamination in streams is a serious issue, and mitigating the risk requires improvement in existing microbial monitoring of streams. To improve understanding of microbial contamination in streams, we monitored in stream water columns and streambed sediment. Two distinct streams and their subwatersheds were studied: (i) a mountain stream (Merced River, California), which represents pristine and wild conditions, and (ii) an agricultural stream (Squaw Creek, Iowa), which represents an agricultural setting (i.e., crop, manure application, cattle access). Stream water column and sediment samples were collected in multiple locations in the Merced River and Squaw Creek watersheds. Compared with the mountain stream, water column concentrations in the agricultural stream were considerably higher. In both mountain and agricultural streams, concentrations in bed sediment were higher than the water column, and principal component analysis indicates that land use affected water column levels significantly ( < 0.05). The cluster analysis showed grouping of subwatersheds for each basin, indicating unique land use features of each watershed. In general, water column levels in the mountain stream were lower than the USEPA's existing water quality criteria for bacteria. However, the levels in the agricultural stream exceeded the USEPA's microbial water quality criteria by several fold, which substantiated that increased agricultural activities, use of animal waste as fertilizers, and combined effect of rainfall and temperature may act as potential determining factors behind the elevated levels in agriculture streams.
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19
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Rieke EL, Moorman TB, Soupir ML, Yang F, Howe A. Assessing Pathogen Presence in an Intensively Tile Drained, Agricultural Watershed. J Environ Qual 2018; 47:1033-1042. [PMID: 30272801 DOI: 10.2134/jeq2017.12.0500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Increases in swine production and concomitant manure application provide beneficial nutrients for crops but also include the potential to spread pathogenic bacteria in the environment. While manure is known to contain a variety of pathogens, little is known regarding the long-term effect of manure application on fate and transport of this diverse set of pathogens into surrounding waterways. We report on the use of 16S-rRNA gene sequencing to detect pathogen-containing genera in the agriculturally dominated South Fork Iowa River watershed, home to approximately 840,000 swine in the 76,000-ha basin. DNA was extracted from monthly grab samples collected from three surface water sites and two main artificial drainage outlets. DNA sequences from water samples were matched with sequences from genera known to contain pathogens using targeted 16S rRNA amplicon sequencing. The specific genera known to contain pathogens were quantified by combining percentage of genera sequence matches with 16S rRNA gene quantitative polymerase chain reaction results. Specifically, abundances of , , and significantly increased in surface water after typical fall manure application. Additionally, the likely transport pathways for specific genera known to contain pathogens were identified. Surface water concentrations were influenced mainly by artificial drainage, whereas was primarily transported to surface waters by runoff events. The results of this study will help us to understand environmental pathways that may be useful for mitigation of the diverse set of pathogenic genera transported in agroecosystems and the capability of manure application to alter existing microbial community structures.
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20
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Pandey PK, Biswas S, Vaddella VK, Soupir ML. Correction to: Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures under aerobic and anaerobic environments. Bioprocess Biosyst Eng 2018; 41:887. [PMID: 29633026 DOI: 10.1007/s00449-018-1936-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures.
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Affiliation(s)
- Pramod K Pandey
- Department of Population Health and Reproduction, Veterinary Medicine Extension, University of California, Davis, CA, USA.
| | - Sagor Biswas
- Department of Population Health and Reproduction, Veterinary Medicine Extension, University of California, Davis, CA, USA
| | - Venkata K Vaddella
- Department of Population Health and Reproduction, Veterinary Medicine Extension, University of California, Davis, CA, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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21
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Washington MT, Moorman TB, Soupir ML, Shelley M, Morrow AJ. Monitoring tylosin and sulfamethazine in a tile-drained agricultural watershed using polar organic chemical integrative sampler (POCIS). Sci Total Environ 2018; 612:358-367. [PMID: 28854391 DOI: 10.1016/j.scitotenv.2017.08.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
This study evaluated the influence of temporal variation on the occurrence, fate, and transport of tylosin (TYL) and sulfamethazine (SMZ); antibiotics commonly used in swine production. Atrazine (ATZ) was used as a reference analyte to indicate the agricultural origin of the antibiotics. We also assessed the impact of season and hydrology on antibiotic concentrations. A reconnaissance study of the South Fork watershed of the Iowa River (SFIR), was conducted from 2013 to 2015. Tile drain effluent and surface water were monitored using polar organic integrative sampler (POCIS) technology. Approximately 169 animal feeding operations (AFOs) exist in SFIR, with 153 of them being swine facilities. All analytes were detected, and detection frequencies ranged from 69 to 100% showing the persistence in the watershed. Antibiotics were detected at a higher frequency using POCIS compared to grab samples. We observed statistically significant seasonal trends for SMZ and ATZ concentrations during growing and harvest seasons. Time weighted average (TWA) concentrations quantified from the POCIS were 1.87ngL-1 (SMZ), 0.30ngL-1 (TYL), and 754.2ngL-1 (ATZ) in the watershed. SMZ and TYL concentrations were lower than the minimum inhibitory concentrations (MIC) for E. coli. All analytes were detected in tile drain effluent, confirming tile drainage as a pathway for antibiotic transport. Our results identify the episodic occurrence of antibiotics, and highlights the importance identifying seasonal fate and occurrence of these analytes.
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Affiliation(s)
- Maurice T Washington
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1340 Elings Hall, 605 Bissell Road Ames, Iowa, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Boulevard Ames Iowa, 50011, USA.
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, 1340 Elings Hall, 605 Bissell Road Ames, Iowa, USA
| | - Mack Shelley
- Department of Political Science and Department of Statistics, 503 Ross Hall, Iowa State University, Ames, Iowa, USA
| | - Amy J Morrow
- National Laboratory for Agriculture and the Environment, USDA-ARS, 2110 University Boulevard Ames Iowa, 50011, USA
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22
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Rieke EL, Moorman TB, Douglass EL, Soupir ML. Seasonal variation of macrolide resistance gene abundances in the South Fork Iowa River Watershed. Sci Total Environ 2018; 610-611:1173-1179. [PMID: 28847138 DOI: 10.1016/j.scitotenv.2017.08.116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/11/2017] [Accepted: 08/12/2017] [Indexed: 06/07/2023]
Abstract
The Midwestern United States is dominated by agricultural production with high concentrations of swine, leading to application of swine manure onto lands with artificial subsurface drainage. Previous reports have indicated elevated levels of antibiotic resistance genes (ARGs) in surface water and groundwater around confined animal feeding operations which administer antimicrobials. While previous studies have examined the occurrence of ARGs around confined swine feeding operations, little information is known how their transport from tile-drained fields receiving swine manure application impacts downstream environments. To further our knowledge in this area, water samples were collected from five locations in the agriculturally dominated South Fork Iowa River Watershed with approximately 840,000 swine present in the 76,000ha basin. Samples were collected monthly from three stream sites and two main artificial subsurface drainage outlets. Samples were analyzed for macrolide resistance genes ermB, ermF and 16S rRNAgene abundance using qPCR. Abundance of erm genes ranged from below limits of quantification to >107 copies 100mL-1 water. Eighty-nine percent of stream water samples contained one of these two ARGs. Results indicate significantly more ermB and ermF in main drainage outlets than stream samples when normalized by 16S rRNA abundance (p<0.0001). Both artificial drainage locations revealed temporal trends for ermB and ermF abundance when normalized to 16S rRNA abundance. The higher resistance gene concentrations identified in artificial drainage samples occurring mid-Spring and late-Fall are likely due to manure application.
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Affiliation(s)
- Elizabeth Luby Rieke
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA.
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, Ames, IA, USA
| | - Elizabeth L Douglass
- National Laboratory for Agriculture and the Environment, USDA-ARS, Ames, IA, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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Hice SA, Santoscoy MC, Soupir ML, Cademartiri R. Distinguishing between metabolically active and dormant bacteria on paper. Appl Microbiol Biotechnol 2017; 102:367-375. [DOI: 10.1007/s00253-017-8604-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/21/2022]
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Liang X, Liao C, Soupir ML, Jarboe LR, Thompson ML, Dixon PM. Escherichia coli attachment to model particulates: The effects of bacterial cell characteristics and particulate properties. PLoS One 2017; 12:e0184664. [PMID: 28910343 PMCID: PMC5599003 DOI: 10.1371/journal.pone.0184664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/28/2017] [Indexed: 11/18/2022] Open
Abstract
E. coli bacteria move in streams freely in a planktonic state or attached to suspended particulates. Attachment is a dynamic process, and the fraction of attached microorganisms is thought to be affected by both bacterial characteristics and particulate properties. In this study, we investigated how the properties of cell surfaces and stream particulates influence attachment. Attachment assays were conducted for 77 E. coli strains and three model particulates (ferrihydrite, Ca-montmorillonite, or corn stover) under environmentally relevant conditions. Surface area, particle size distribution, and total carbon content were determined for each type of particulate. Among the three particulates, attachment fractions to corn stover were significantly larger than the attachments to 2-line ferrihydrite (p-value = 0.0036) and Ca-montmorillonite (p-value = 0.022). Furthermore, attachment to Ca-montmorillonite and corn stover was successfully modeled by a Generalized Additive Model (GAM) using cell characteristics as predictor variables. The natural logarithm of the net charge on the bacterial surface had a significant, positive, and linear impact on the attachment of E. coli bacteria to Ca-montmorillonite (p-value = 0.013), but it did not significantly impact the attachment to corn stover (p-value = 0.36). The large diversities in cell characteristics among 77 E. coli strains, particulate properties, and attachment fractions clearly demonstrated the inadequacy of using a static parameter or linear coefficient to predict the attachment behavior of E. coli in stream water quality models.
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Affiliation(s)
- Xiao Liang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Chunyu Liao
- Department of Microbiology, Iowa State University, Ames, Iowa, United States of America
| | - Michelle L. Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| | - Laura R. Jarboe
- Department of Microbiology, Iowa State University, Ames, Iowa, United States of America
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Michael L. Thompson
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Philip M. Dixon
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
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Liao C, Liang X, Yang F, Soupir ML, Howe AC, Thompson ML, Jarboe LR. Allelic Variation in Outer Membrane Protein A and Its Influence on Attachment of Escherichia coli to Corn Stover. Front Microbiol 2017; 8:708. [PMID: 28515712 PMCID: PMC5413513 DOI: 10.3389/fmicb.2017.00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 04/05/2017] [Indexed: 01/16/2023] Open
Abstract
Understanding the genetic factors that govern microbe-sediment interactions in aquatic environments is important for water quality management and reduction of waterborne disease outbreaks. Although chemical properties of bacteria have been identified that contribute to initiation of attachment, the outer membrane proteins that contribute to these chemical properties still remain unclear. In this study we explored the attachment of 78 Escherichia coli environmental isolates to corn stover, a representative agricultural residue. Outer membrane proteome analysis led to the observation of amino acid variations, some of which had not been previously described, in outer membrane protein A (OmpA) at 10 distinct locations, including each of the four extracellular loops, three of the eight transmembrane segments, the proline-rich linker and the dimerization domain. Some of the polymorphisms within loops 1, 2, and 3 were found to significantly co-occur. Grouping of sequences according to the outer loop polymorphisms revealed five distinct patterns that each occur in at least 5% of our isolates. The two most common patterns, I and II, are encoded by 33.3 and 20.5% of these isolates and differ at each of the four loops. Statistically significant differences in attachment to corn stover were observed among isolates expressing different versions of OmpA and when different versions of OmpA were expressed in the same genetic background. Most notable was the increased corn stover attachment associated with a loop 3 sequence of SNFDGKN relative to the standard SNVYGKN sequence. These results provide further insight into the allelic variation of OmpA and implicate OmpA in contributing to attachment to corn stover.
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Affiliation(s)
- Chunyu Liao
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA
| | - Xiao Liang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Fan Yang
- Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Michelle L Soupir
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | - Adina C Howe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Agricultural and Biosystems Engineering, Iowa State UniversityAmes, IA, USA
| | | | - Laura R Jarboe
- Interdepartmental Microbiology Program, Iowa State UniversityAmes, IA, USA.,Department of Chemical and Biological Engineering, Iowa State UniversityAmes, IA, USA
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Liang X, Liao C, Thompson ML, Soupir ML, Jarboe LR, Dixon PM. E. coli Surface Properties Differ between Stream Water and Sediment Environments. Front Microbiol 2016; 7:1732. [PMID: 27847507 PMCID: PMC5088573 DOI: 10.3389/fmicb.2016.01732] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
The importance of E. coli as an indicator organism in fresh water has led to numerous studies focusing on cell properties and transport behavior. However, previous studies have been unable to assess if differences in E. coli cell surface properties and genomic variation are associated with different environmental habitats. In this study, we investigated the variation in characteristics of E. coli obtained from stream water and stream bottom sediments. Cell properties were measured for 77 genomically different E. coli strains (44 strains isolated from sediments and 33 strains isolated from water) under common stream conditions in the Upper Midwestern United States: pH 8.0, ionic strength 10 mM and 22°C. Measured cell properties include hydrophobicity, zeta potential, net charge, total acidity, and extracellular polymeric substance (EPS) composition. Our results indicate that stream sediment E. coli had significantly greater hydrophobicity, greater EPS protein content and EPS sugar content, less negative net charge, and higher point of zero charge than stream water E. coli. A significant positive correlation was observed between hydrophobicity and EPS protein for stream sediment E. coli but not for stream water E. coli. Additionally, E. coli surviving in the same habitat tended to have significantly larger (GTG)5 genome similarity. After accounting for the intrinsic impact from the genome, environmental habitat was determined to be a factor influencing some cell surface properties, such as hydrophobicity. The diversity of cell properties and its resulting impact on particle interactions should be considered for environmental fate and transport modeling of aquatic indicator organisms such as E. coli.
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Affiliation(s)
- Xiao Liang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames IA, USA
| | - Chunyu Liao
- Department of Microbiology, Iowa State University, Ames IA, USA
| | | | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames IA, USA
| | - Laura R Jarboe
- Department of Microbiology, Iowa State University, AmesIA, USA; Department of Chemical and Biological Engineering, Iowa State University, AmesIA, USA
| | - Philip M Dixon
- Department of Statistics, Iowa State University, Ames IA, USA
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Hoover NL, Bhandari A, Soupir ML, Moorman TB. Woodchip Denitrification Bioreactors: Impact of Temperature and Hydraulic Retention Time on Nitrate Removal. J Environ Qual 2016; 45:803-812. [PMID: 27136145 DOI: 10.2134/jeq2015.03.0161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Woodchip denitrification bioreactors, a relatively new technology for edge-of-field treatment of subsurface agricultural drainage water, have shown potential for nitrate removal. However, few studies have evaluated the performance of these reactors under varied controlled conditions including initial woodchip age and a range of hydraulic retention times (HRTs) and temperatures similar to the field. This study investigated (i) the release of total organic C (TOC) during reactor start up for fresh and weathered woodchips, (ii) nitrate (NO-N) removal at HRTs ranging from 2 to 24 h, (iii) nitrate removal at influent NO-N concentrations of 10, 30, and 50 mg L, and (iv) NO-N removal at 10, 15, and 20°C. Greater TOC was released during bioreactor operation with fresh woodchips, whereas organic C release was low when the columns were packed with naturally weathered woodchips. Nitrate-N concentration reductions increased from 8 to 55% as HRT increased. Nitrate removal on a mass basis (g NO-N m d) did not follow the same trend, with relatively consistent mass removal measured as HRT increased from 1.7 to 21.2 h. Comparison of mean NO-N load reduction for various influent NO-N concentrations showed lower reduction at an influent concentration of 10 mg L and higher NO-N reductions at influent concentrations of 30 and 50 mg L. Nitrate-N removal showed a stepped increase with temperature. Temperature coefficient () factors calculated from NO-N removal rates ranged from 2.2 to 2.9.
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Luby EM, Moorman TB, Soupir ML. Fate and transport of tylosin-resistant bacteria and macrolide resistance genes in artificially drained agricultural fields receiving swine manure. Sci Total Environ 2016; 550:1126-1133. [PMID: 26874610 DOI: 10.1016/j.scitotenv.2016.01.132] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Application of manure from swine treated with antibiotics introduces antibiotics and antibiotic resistance genes to soil with the potential for further movement in drainage water, which may contribute to the increase in antibiotic resistance in non-agricultural settings. We compared losses of antibiotic-resistant Enterococcus and macrolide-resistance (erm and msrA) genes in water draining from plots with or without swine manure application under chisel plow and no till conditions. Concentrations of ermB, ermC and ermF were all >10(9)copies g(-1) in manure from tylosin-treated swine, and application of this manure resulted in short-term increases in the abundance of these genes in soil. Abundances of ermB, ermC and ermF in manured soil returned to levels identified in non-manured control plots by the spring following manure application. Tillage practices yielded no significant differences (p>0.10) in enterococci or erm gene concentrations in drainage water and were therefore combined for further analysis. While enterococci and tylosin-resistant enterococci concentrations in drainage water showed no effects of manure application, ermB and ermF concentrations in drainage water from manured plots were significantly higher (p<0.01) than concentrations coming from non-manured plots. ErmB and ermF were detected in 78% and 44%, respectively, of water samples draining from plots receiving manure. Although ermC had the highest concentrations of the three genes in drainage water, there was no effect of manure application on ermC abundance. MsrA was not detected in manure, soil or water. This study is the first to report significant increases in abundance of resistance genes in waters draining from agricultural land due to manure application.
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Affiliation(s)
- Elizabeth M Luby
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
| | - Thomas B Moorman
- National Laboratory for Agriculture and the Environment, USDA-ARS, Ames, IA, USA
| | - Michelle L Soupir
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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Hruby CE, Soupir ML, Moorman TB, Shelley M, Kanwar RS. Effects of tillage and poultry manure application rates on Salmonella and fecal indicator bacteria concentrations in tiles draining Des Moines Lobe soils. J Environ Manage 2016; 171:60-69. [PMID: 26874615 DOI: 10.1016/j.jenvman.2016.01.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/28/2016] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Application of poultry manure (PM) to cropland as fertilizer is a common practice in artificially drained regions of the Upper Midwest United States. Tile-waters have the potential to contribute pathogenic bacteria to downstream waters. This 3-year study (2010-2012) was designed to evaluate the impacts of manure management and tillage practices on bacteria losses to drainage tiles under a wide range of field conditions. PM was applied annually in spring, prior to planting corn, at application rates ranging from 5 to 40 kg/ha to achieve target rates of 112 and 224 kg/ha nitrogen (PM1 and PM2). Control plots received no manure (PM0). Each treatment was replicated on three chisel-plowed (CP) plots and one no-till (NT) plot. Tile-water grab samples were collected weekly when tiles were flowing beginning 30 days before manure application to 100 days post application, and additional grab samples were obtained to target the full spectrum of flow conditions. Manure and tile-water samples were analyzed for the pathogen, Salmonella spp. (SALM), and fecal indicator bacteria (FIB), Escherichia coli (EC), and enterococci (ENT). All three bacterial genera were detected more frequently, and at significantly higher concentrations, in tile-waters draining NT plots compared to CP plots. Transport of bacteria to NT tiles was most likely facilitated by macropores, which were significantly more numerous above tiles in NT plots in 2012 as determined by smoke-testing. While post-manure samples contained higher concentrations of bacteria than pre-manure samples, significant differences were not seen between low (PM1) and high (PM2) rates of PM application. The highest concentrations were observed under the NT PM2 plot in 2010 (6.6 × 10(3) cfu/100 mL EC, 6.6 × 10(5) cfu/100 mL ENT, and 2.8 × 10(3) cfu/100 mL SALM). Individual and 30-day geometric mean ENT concentrations correlated more strongly to SALM than EC; however, SALM were present in samples with little or no FIB.
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Affiliation(s)
- C E Hruby
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | - M L Soupir
- Department of Agricultural and Biosystems Engineering, 3358 Elings Hall, Iowa State University, Ames, IA 50011, USA.
| | - T B Moorman
- National Laboratory for Agriculture and the Environment, USDA ARS, 2110 University Boulevard, Ames, IA 50011, USA
| | - M Shelley
- Departments of Statistics and Political Science, 509 Ross Hall, Iowa State University, Ames, IA 50011, USA
| | - R S Kanwar
- Department of Agricultural and Biosystems Engineering, 4358 Elings Hall, Iowa State University, Ames, IA 50011, USA
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Zwonitzer MR, Soupir ML, Jarboe LR, Smith DR. Quantifying Attachment and Antibiotic Resistance of from Conventional and Organic Swine Manure. J Environ Qual 2016; 45:609-617. [PMID: 27065408 DOI: 10.2134/jeq2015.05.0245] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Broad-spectrum antibiotics are often administered to swine, contributing to the occurrence of antibiotic-resistant bacteria in their manure. During land application, the bacteria in swine manure preferentially attach to particles in the soil, affecting their transport in overland flow. However, a quantitative understanding of these attachment mechanisms is lacking, and their relationship to antibiotic resistance is unknown. The objective of this study is to examine the relationships between antibiotic resistance and attachment to very fine silica sand in collected from swine manure. A total of 556 isolates were collected from six farms, two organic and four conventional (antibiotics fed prophylactically). Antibiotic resistance was quantified using 13 antibiotics at three minimum inhibitory concentrations: resistant, intermediate, and susceptible. Of the 556 isolates used in the antibiotic resistance assays, 491 were subjected to an attachment assay. Results show that isolates from conventional systems were significantly more resistant to amoxicillin, ampicillin, chlortetracycline, erythromycin, kanamycin, neomycin, streptomycin, tetracycline, and tylosin ( < 0.001). Results also indicate that isolated from conventional systems attached to very fine silica sand at significantly higher levels than those from organic systems ( < 0.001). Statistical analysis showed that a significant relationship did not exist between antibiotic resistance levels and attachment in from conventional systems but did for organic systems ( < 0.001). Better quantification of these relationships is critical to understanding the behavior of in the environment and preventing exposure of human populations to antibiotic-resistant bacteria.
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Pandey PK, Pasternack GB, Majumder M, Soupir ML, Kaiser MS. A neighborhood statistics model for predicting stream pathogen indicator levels. Environ Monit Assess 2015; 187:124. [PMID: 25694031 DOI: 10.1007/s10661-014-4228-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Because elevated levels of water-borne Escherichia coli in streams are a leading cause of water quality impairments in the U.S., water-quality managers need tools for predicting aqueous E. coli levels. Presently, E. coli levels may be predicted using complex mechanistic models that have a high degree of unchecked uncertainty or simpler statistical models. To assess spatio-temporal patterns of instream E. coli levels, herein we measured E. coli, a pathogen indicator, at 16 sites (at four different times) within the Squaw Creek watershed, Iowa, and subsequently, the Markov Random Field model was exploited to develop a neighborhood statistics model for predicting instream E. coli levels. Two observed covariates, local water temperature (degrees Celsius) and mean cross-sectional depth (meters), were used as inputs to the model. Predictions of E. coli levels in the water column were compared with independent observational data collected from 16 in-stream locations. The results revealed that spatio-temporal averages of predicted and observed E. coli levels were extremely close. Approximately 66 % of individual predicted E. coli concentrations were within a factor of 2 of the observed values. In only one event, the difference between prediction and observation was beyond one order of magnitude. The mean of all predicted values at 16 locations was approximately 1 % higher than the mean of the observed values. The approach presented here will be useful while assessing instream contaminations such as pathogen/pathogen indicator levels at the watershed scale.
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Affiliation(s)
- Pramod K Pandey
- Department of Population Health and Reproduction, University of California, Davis, CA, 95616, USA,
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Liang X, Soupir ML, Rigby S, Jarboe LR, Zhang W. Flow cytometry is a promising and rapid method for differentiating between freely suspended Escherichia coli and E. coli attached to clay particles. J Appl Microbiol 2014; 117:1730-9. [PMID: 25284438 DOI: 10.1111/jam.12660] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 11/27/2022]
Abstract
AIM A standard procedure does not exist to distinguish between attached and unattached micro-organisms. In this study, we compared two methods to quantify between Escherichia coli attached to clay particles and E. coli freely suspended in solution: flow cytometry (attachment assay and viability assay) and settling (or centrifugation followed by settling). METHODS AND RESULTS Methods were tested using three environmental strains collected from swine facilities (A, B and C) and one purchased modified pathogenic strain (ATCC 43888); four clay particles: Hectorite, Kaolinite, Ca-Montmorillonite, Montmorillonite K-10; and a range of surface area ratios (particle surface area to E. coli surface area). When comparing the two methods, the per cent attached obtained from the flow cytometry was lower, but not significantly different from the per cent attached obtained from the settling method for all conditions except when the particle was Hectorite or Montmorillonite K-10; when the strain was C; and when the surface area ratio was below 100. Differences between the methods are likely because traditional culture-based methods cannot detect the viable but nonculturable (VBNC) population, whereas flow cytometry can detect the fraction of VBNC with intact membranes. CONCLUSION Our results indicate that flow cytometry is a rapid and culture-independent method for differentiating between attached and unattached micro-organisms. SIGNIFICANCE AND IMPACT OF THE STUDY Flow cytometry is useful for laboratory-based studies of micro-organism-particle interactions.
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Affiliation(s)
- X Liang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, USA
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Ikenberry CD, Soupir ML, Schilling KE, Jones CS, Seeman A. Nitrate-nitrogen export: magnitude and patterns from drainage districts to downstream river basins. J Environ Qual 2014; 43:2024-2033. [PMID: 25602219 DOI: 10.2134/jeq2014.05.0242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Alteration of the prairie pothole ecosystem through installation of subsurface tile drains has enabled the U.S. Corn Belt to become one of the most agriculturally productive areas in the world but has also led to increased nitrogen losses to surface water. The literature contains numerous field plot studies but few in-depth studies of nitrate exports from small, tile-drained catchments representative of agricultural drainage districts. The objectives of this study were to quantify hydrology and nitrate-nitrogen (NO-N) export patterns from three tile-drained catchments and the downstream river over a 5-yr period, compare results to prior plot-, field-, and watershed-scale studies, and discuss implications for water quality improvement in these landscapes. The tile-drained catchments had an annual average water yield of 247 mm yr, a flow-weighted NO-N concentration of 17.1 mg L, and an average NO-N loss of nearly 40 kg ha yr. Overall, water yields were consistent with prior tile drainage studies in Iowa and the upper Midwest, but associated NO-N concentrations and losses were among the highest reported for plot studies and higher than those found in small watersheds. More than 97% of the nitrate export occurs during the highest 50% of flows, at both the small catchment and river basin scale. Findings solidified the importance of working at the drainage district scale to achieve nitrate reductions necessary to meet water quality goals. They also point to the need for implementing strategies that address both hydrology and nitrogen supply in tile-drained landscapes.
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Garder JL, Moorman TB, Soupir ML. Transport and persistence of tylosin-resistant enterococci, genes, and tylosin in soil and drainage water from fields receiving Swine manure. J Environ Qual 2014; 43:1484-1493. [PMID: 25603096 DOI: 10.2134/jeq2013.09.0379] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Land application of manure from tylosin-treated swine introduces tylosin, tylosin-resistant enterococci, and erythromycin resistant rRNA methylase () genes, which confer resistance to tylosin. This study documents the persistence and transport of tylosin-resistant enterococci, genes, and tylosin in tile-drained chisel plow and no-till agricultural fields treated with liquid swine manure in alternating years. Between 70 and 100% of the enterococci in manure were resistant to tylosin and B concentrations exceeded 10 copies g manure, while the mean F concentrations exceeded 10 copies g manure (T was not detected). The mean concentration of tylosin was 73 ng g manure. Soil collected from the manure injection band closely following application contained >10 copies g soil of both B and F in 2010 and >10 copies g soil after the 2011 application compared to 3 × 10 to 3 × 10 copies g soil in the no-manure control plots. Gene abundances declined over the subsequent 2-yr period to levels similar to those in the no-manure controls. Concentrations of enterococci in tile water were low, while tylosin-resistant enterococci were rarely detected. In approximately 75% of tile water samples, B was detected, and F was detected in 30% of tile water samples, but levels of these genes were not elevated due to manure application, and no difference was found between tillage practices. These results show that tylosin usage increased the short-term occurrence of tylosin-resistant enterococci, genes, and tylosin in soils but had minimal effect on tile drainage water quality in years of average to below average precipitation.
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Pandey PK, Kass PH, Soupir ML, Biswas S, Singh VP. Contamination of water resources by pathogenic bacteria. AMB Express 2014; 4:51. [PMID: 25006540 PMCID: PMC4077002 DOI: 10.1186/s13568-014-0051-x] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 05/27/2014] [Indexed: 01/22/2023] Open
Abstract
Water-borne pathogen contamination in water resources and related diseases are a major water quality concern throughout the world. Increasing interest in controlling water-borne pathogens in water resources evidenced by a large number of recent publications clearly attests to the need for studies that synthesize knowledge from multiple fields covering comparative aspects of pathogen contamination, and unify them in a single place in order to present and address the problem as a whole. Providing a broader perceptive of pathogen contamination in freshwater (rivers, lakes, reservoirs, groundwater) and saline water (estuaries and coastal waters) resources, this review paper attempts to develop the first comprehensive single source of existing information on pathogen contamination in multiple types of water resources. In addition, a comprehensive discussion describes the challenges associated with using indicator organisms. Potential impacts of water resources development on pathogen contamination as well as challenges that lie ahead for addressing pathogen contamination are also discussed.
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Abstract
Fecal deposits by grazing animals on pasturelands have the potential to leach nutrients to runoff during rainfall events. Unlike croplands, grazing systems such as pasturelands or rangelands have little opportunity to ameliorate nutrient runoff through in-field or edge-of-field management practices. Thus, we investigated the amounts and concentrations of nutrients in overland flow from simulated grazing lands. Two grazing management scenarios were simulated: continuous grazing represented by two sparsely vegetated (SV) plots and rotational grazing represented by two densely vegetated (DV) plots. In addition, there were two control plots. The plots were treated with standard cowpats and rainfall was simulated until overland flow at the edge of the plots reached steady-state. Higher runoff was observed from DV plots (9.97 mm) than SV plots (7.05 mm), but the average total suspended solids concentration in runoff from SV plots was approximately 17 times the concentration observed in runoff from the DV plots. The average total phosphorus (TP) concentrations were highest in plots simulating continuous grazing (5.91 mg L(-1)). In both DV and SV plots at least 83% of the TP was found to be in the dissolved form. The average total Kjeldhal nitrogen (TKN) and total nitrogen concentrations observed in runoff samples from SV plots were 1.25 and 1.46 mg L(-1), respectively. Organic nitrogen comprised 95% of the TKN observed in runoff samples from SV plots. The SV plots have relatively higher loads for those nutrients in the particle associated form compared to DV plots, whereas DV plots had higher loads for those nutrients in the dissolved form. Grazing lands without any additional manure applications were found to release nutrients in high levels and vegetation did not show any effect on removing dissolved nutrients from runoff. These results are useful to inform selection of appropriate management practices to reduce nutrient transport to surface waters in watersheds dominated by grazed lands.
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Affiliation(s)
- Rohith K Gali
- Agricultural & Biosystems Engineering, Iowa State University, Ames, IA, USA
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Pandey PK, Soupir ML, Rehmann CR. A model for predicting resuspension of Escherichia coli from streambed sediments. Water Res 2012; 46:115-126. [PMID: 22082528 DOI: 10.1016/j.watres.2011.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 10/14/2011] [Accepted: 10/16/2011] [Indexed: 05/27/2023]
Abstract
To improve the modeling of water quality in watersheds, a model is developed to predict resuspension of Escherichia coli from sediment beds in streams. The resuspension rate is expressed as the product of the concentration of E. coli attached to sediment particles and an erosion rate adapted from work on sediment transport. The model uses parameter values mostly taken from previous work, and it accounts for properties of the flow through the bottom shear stress and properties of the sediment through the critical shear stresses for cohesive and non-cohesive sediment. Predictions were compared to resuspension rates inferred from a steady mass balance applied to measurements at sixteen locations in a watershed. The model's predictions matched the inferred rates well, especially when the diameter of particles to which E. coli attach was allowed to depend on the bottom shear stress. The model's sensitivity to the parameters depends on the contributions of particle packing and binding effects of clay to the critical shear stress. For the current data set, the uncertainty in the predictions is controlled by the concentration of E. coli attached to sediment particles and the slope used to estimate the bottom shear stress.
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Affiliation(s)
- Pramod K Pandey
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
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Pandey PK, Soupir ML. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures. AMB Express 2011; 1:18. [PMID: 21906374 PMCID: PMC3222320 DOI: 10.1186/2191-0855-1-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 07/15/2011] [Indexed: 11/17/2022] Open
Abstract
Batch anaerobic digestion experiments using dairy manure as feedstocks were performed at moderate (25°C), mesophilic (37°C), and thermophilic (52.5°C) temperatures to understand E. coli, an indicator organism for pathogens, inactivation in dairy manure. Incubation periods at 25, 37, and 52.5°C, were 61, 41, and 28 days respectively. Results were used to develop models for predicting E. coli inactivation and survival in anaerobic digestion. For modeling we used the decay of E. coli at each temperature to calculate the first-order inactivation rate coefficients, and these rates were used to formulate the time - temperature - E. coli survival relationships. We found the inactivation rate coefficient at 52.5°C was 17 and 15 times larger than the inactivation rate coefficients at 25 and 37°C, respectively. Decimal reduction times (D10; time to achieve one log removal) at 25, 37, and 52.5°C, were 9 -10, 7 - 8 days, and < 1 day, respectively. The Arrhenius correlation between inactivation rate coefficients and temperatures over the range 25 -52.5°C was developed to understand the impacts of temperature on E. coli inactivation rate. Using this correlation, the time - temperature - E. coli survival relationships were derived. Besides E. coli inactivation, impacts of temperature on biogas production, methane content, pH change, ORP, and solid reduction were also studied. At higher temperatures, biogas production and methane content was greater than that at low temperatures. While at thermophilic temperature pH was increased, at mesophilic and moderate temperatures pH were reduced over the incubation period. These results can be used to understand pathogen inactivation during anaerobic digestion of dairy manure, and impacts of temperatures on performance of anaerobic digesters treating dairy manure.
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Affiliation(s)
- Pramod K Pandey
- Agricultural and Biosystems Engineering Department, Iowa State University, Ames, 50011, USA
| | - Michelle L Soupir
- Agricultural and Biosystems Engineering Department, Iowa State University, Ames, 50011, USA
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Abstract
Association of Escherichia coli and enterococci with particulates present in runoff from erodible soils has important implications for modeling the fate and transport of bacteria from agricultural sources and in the selection of management practices to reduce bacterial movement to surface waters. Three soils with different textures were collected from the Ap horizon (silty loam, silty clay loam, and loamy fine sand), placed in portable box plots, treated with standard cowpats, and placed under a rainfall simulator. Rainfall was applied to the plots until saturation-excess flow occurred for 30 min, and samples were collected 10, 20, and 30 min after initiation of the runoff event. The attachment of E. coli and enterococci to particles present in runoff was determined by a screen filtration and centrifugation procedure. Percentage of E. coli and enterococci attached to particulates in runoff ranged from 28 to 49%, with few statistically significant differences in attachment among the three soils. Similar partitioning release patterns were observed between E. coli and enterococci from the silty loam (r = 0.57) and silty clay loam soils (r = 0.60). At least 60% of all attached E. coli and enterococci were associated particles within an 8- to 62-microm particle size category. The results indicate that the majority of fecal bacteria attach to and are transported with manure colloids in sediment-laden flow regardless of the soil texture.
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Affiliation(s)
- Michelle L Soupir
- Agricultural &Biosystems Engineering, Iowa State University, Ames, IA 50011, USA.
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40
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Rehmann CR, Soupir ML. Importance of interactions between the water column and the sediment for microbial concentrations in streams. Water Res 2009; 43:4579-4589. [PMID: 19615712 DOI: 10.1016/j.watres.2009.06.049] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 06/19/2009] [Accepted: 06/22/2009] [Indexed: 05/28/2023]
Abstract
The effect of interactions between the sediment and water column on concentrations of microbes in streams is quantified with a one-dimensional, steady state model. The effects of nine main parameters describing the flow, sediment transport, and microbial growth and decay are encapsulated in two dimensionless parameters: the Damköhler number Da, or the ratio of the time scales of advection and net growth, and the sediment interaction parameter S, or the ratio of the amount of microbes lost or gained in the sediment and the amount of microbes lost or gained in the water column. Applications of the model illustrate the importance of the sediment and identify parameters that require further study. The model predicts the field measurements of Jamieson et al. (2005b) within a factor of 2 in two of three cases, while concentrations predicted by ignoring the sediment exceed the measured values. In general, the effects of ignoring interactions with the sediment depend on Da and S. The loading predicted to meet water quality standards when the sediment is considered can be either greater than or less than the loading predicted when it is not considered. The applications of the model and an analysis of uncertainty suggest that further work on the settling velocity, attached fraction, resuspension rate, and net growth rate in the sediment would help to improve predictions of the fate and transport of microbes.
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Affiliation(s)
- Chris R Rehmann
- Department of Civil, Construction, and Environmental Engineering, Iowa State University, Ames, IA 50011, USA.
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41
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Soupir ML, Mostaghimi S, Yagow ER. Nutrient transport from livestock manure applied to pastureland using phosphorus-based management strategies. J Environ Qual 2006; 35:1269-78. [PMID: 16825446 DOI: 10.2134/jeq2005.0314] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Land applications of manure from confined animal systems and direct deposit by grazing animals are both major sources of nutrients in streams. The objectives of this study were to determine the effects of P-based manure applications on total suspended solids (TSS) and nutrient losses from dairy manures and poultry litter surface applied to pasturelands and to compare the nutrient losses transported to the edge of the field during overland flow events. Two sets of plots were established: one set for the study of in-field release and another set for the study of edge-of-the-field nutrient transport. Release plots were constructed at three pastureland sites (previous poultry litter applications, previous liquid dairy manure application, and no prior manure application) and received four manure treatments (turkey [Meleagris gallopavo] litter, liquid dairy manure, standard cowpies, and none). Pasture plots with a history of previous manure applications released higher concentrations of TSS and higher percentages of total P (TP) in the particulate form. Transport plots were developed on pasture with no prior manure application. The average flow-weighted TP concentrations were highest in runoff samples from the plots treated with cowpies (1.57 mg L(-1)). Reducing excess P in dairy cow diets and surface applying manure to the land using P-based management practices did not increase N concentrations in runoff. This study found that nutrients are most transportable from cowpies; thus a buffer zone between pastureland and streams or other appropriate management practices are necessary to reduce nutrient losses to waterbodies.
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Affiliation(s)
- M L Soupir
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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