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Pandey P, Chiu C, Miao M, Wang Y, Settles M, del Rio NS, Castillo A, Souza A, Pereira R, Jeannotte R. 16S rRNA analysis of diversity of manure microbial community in dairy farm environment. PLoS One 2018; 13:e0190126. [PMID: 29304047 PMCID: PMC5755784 DOI: 10.1371/journal.pone.0190126] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 12/08/2017] [Indexed: 01/01/2023] Open
Abstract
Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.
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Affiliation(s)
- Pramod Pandey
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- * E-mail: (PP); (RJ)
| | - Colleen Chiu
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
| | - Max Miao
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Yi Wang
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
- Department of Biological and Agricultural Engineering, University of California, Davis, California, United States of America
| | - Matthew Settles
- Genome Center Bioinformatics Core, University of California, Davis, California, United States of America
| | - Noelia Silva del Rio
- University of California Cooperative Extension, Veterinary Medicine Teaching and Research Center, Tulare, California, United States of America
| | - Alejandro Castillo
- University of California Cooperative Extension, Merced, California, United States of America
| | - Alex Souza
- University of California Cooperative Extension, Tulare, California, United States of America
| | - Richard Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, United States of America
| | - Richard Jeannotte
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, California, United States of America
- Universidad de Tarapacá, Arica, Chile
- * E-mail: (PP); (RJ)
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Genes Indicative of Zoonotic and Swine Pathogens Are Persistent in Stream Water and Sediment following a Swine Manure Spill. Appl Environ Microbiol 2015; 81:3430-41. [PMID: 25769829 DOI: 10.1128/aem.04195-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/03/2015] [Indexed: 01/31/2023] Open
Abstract
Manure spills into streams are relatively frequent, but no studies have characterized stream contamination with zoonotic and veterinary pathogens, or fecal chemicals, following a spill. We tested stream water and sediment over 25 days and downstream for 7.6 km for the following: fecal indicator bacteria (FIB), the fecal indicator chemicals cholesterol and coprostanol, 20 genes for zoonotic and swine-specific bacterial pathogens by presence/absence PCR for viable cells, one swine-specific Escherichia coli toxin gene (STII gene) by quantitative PCR (qPCR), and nine human and animal viruses by qPCR or reverse transcription-qPCR. Twelve days postspill, and 4.2 km downstream, water concentrations of FIB, cholesterol, and coprostanol were 1 to 2 orders of magnitude greater than those detected before, or above, the spill, and genes indicating viable zoonotic or swine-infectious Escherichia coli were detected in water or sediment. STII gene levels increased from undetectable before or above the spill to 10(5) copies/100 ml of water 12 days postspill. Thirteen of 14 water (8/9 sediment) samples had viable STII-carrying cells postspill. Eighteen days postspill, porcine adenovirus and teschovirus were detected 5.6 km downstream. FIB concentrations (per gram [wet weight]) in sediment were greater than in water, and sediment was a continuous reservoir of genes and chemicals postspill. Constituent concentrations were much lower, and detections less frequent, in a runoff event (200 days postspill) following manure application, although the swine-associated STII and stx2e genes were detected. Manure spills are an underappreciated pathway for livestock-derived contaminants to enter streams, with persistent environmental outcomes and the potential for human and veterinary health consequences.
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Escherichia coli persistence kinetics in dairy manure at moderate, mesophilic, and thermophilic temperatures under aerobic and anaerobic environments. Bioprocess Biosyst Eng 2014; 38:457-67. [DOI: 10.1007/s00449-014-1285-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/06/2014] [Indexed: 10/24/2022]
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Armstrong SD, Smith DR, Owens PR, Joern BC, Huang CH. The development of alum rates to enhance the remediation of phosphorus in fluvial systems following manure spills. JOURNAL OF ENVIRONMENTAL MONITORING : JEM 2012; 14:292-298. [PMID: 22130453 DOI: 10.1039/c1em10484e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Following the remediation of animal manure spills that reach surface waters, contaminated streambed sediments are often left in place and become a source for internal phosphorus (P) loading within the stream in subsequent flow. The objective of this study was to develop treatment rates and combinations of alum and CaCO(3) to mitigate P from contaminated sediments of different particle size distributions following a manure spill. Sediment specific alum and CaCO(3) treatment rates were developed based upon the resultant alum treatment ranges established for each sediment type. Clay loam sediments required 54% more alum to mitigate P desorption relative to sediments that contain at least 60% sand. Amending sediments with the highest rates of alum/alum + CaCO(3), resulted in a 98-100% reduction in P desorption and a similar water column pH for all sediments types. Observations from this study demonstrated the effectiveness of alum/alum + CaCO(3) to increase P retention in sediments following a manure spill.
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Affiliation(s)
- Shalamar D Armstrong
- Department of Agriculture, Illinois State University, Campus Box 5020, Normal, IL 61790-5020, USA.
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