Progress 10/01/15 to 09/30/20
Outputs
Target Audience:animal producers, soil microbiologists, waste management experts, veterinarians Changes/Problems:We found the quality of DNA in soils stored under non-optimal conditions is not suitable for high throughput microbiome analyses as we managed to extract very small quantities of DNA from older soils. Antibiotic resistance genes seem difficult to interpret as control soils with no manure amendment had higher levels of genes associated with antibiotic resistance. What opportunities for training and professional development has the project provided?One graduate student completed her doctoral degree working on this project. Several undergraduate students worked on different aspects of the project. How have the results been disseminated to communities of interest?Journal articles and discussions at professional meetings. What do you plan to do during the next reporting period to accomplish the goals?This is the final report for this project.
Impacts
What was accomplished under these goals?
We selected soil samples collected in the years 1999, 2000, 2003,2005, and 2007 to analyze fluctuations in microbial diversity and soil properties due to manure amendment. As samples, when collected, were not intended for microbial analysis and as they were stored between 10-16 years in non-optimal conditions, we could not extract high-quality DNA from most samples. We managed to obtain enough DNA by doing multiple rounds of extractions and pooling samples. V4 region of bacterial 16S rRNA gene was PCR amplified and sequence analyzed using the Illumina HiSeq2500 platform resulting in over 2.2 million 250bp paired-end raw reads. Soil pH, phosphorous, potassium, magnesium, calcium, total nitrogen (TN), and total carbon (TC) were also measured in bovine manure and swine effluent treated soils over the years. Overall, soil P content was significantly affected by treatment and time. Soil pH, Mg, and Ca only significantly changed over time. Both beef manure and swine effluent decreased soil pH over time. Although soil pH is considered one of the most important determinants of soil microbiome, our study did not show pH having a significant influence on soil microbiome. There was no difference between the treatments. Beef manure increased soil P content significantly higher than swine effluent. Most soil properties fluctuated over time without an obvious trend with the exception of Mg., which significantly decreased over time. A total of 30 soil samples representing two treatments, three replicates, and five-time points were sequence analyzed for microbiome analysis. A total of 2,294,735 paired-end raw reads were generated at an average of 76,491±15,173 reads/sample. A total of 29 microbial phyla were identified and they were further classified into 57 classes, 136 orders, 280 families, and 816 genera. The top phyla present in the soil were Actinobacteria, firmicutes, Alphaproteobacteria, and Acidobacteria. Surprisingly, we did not find that these organisms changed significantly and predictably over time. Phylum Actinobacteria was more abundant in swine effluent treated soils in 2000 than in any other soil, whereas Firmicutes were more abundant in bovine manure treated soils in 2003 than in any other treatment. The top four genera in the soils were Gaiella, Solirubroacter, Paenibacillus, and Nitrosphora. Only Nitrosphora significantly changed over treatment. Swine effluent significantly increases the amount of Nitrosphora compared to bovine manure. We found that soil potassium (K) is the key determinant on swine effluent treated soils. Overall, in this study, we found that the soil nutrient content slightly declined over time while no obvious temporal change was observed in the soil microbiome. We also did not find an effect of continuous cultivation on soil microbiome. The core microbiome remained stable in eight years of intensive cultivation. We found that the richness of the soil microbiome slightly decreases over time, indicating an overall decline in microbiome abundance. Total carbon seemed to be the driving force behind soil microbial fluctuations. The core microbiome remained stable over eight years. There was no distinguishable temporal change in the microbiome. We tested the soil samples with a battery of ~20 PCR assays for antibiotic resistance genes. We were only able to detect the presence of four antibiotic resistance genes in the samples we tested. Chlo-Cat (presence of chloramphenicol resistance), Multi-acrD and Multi-mexD (multidrug resistance genes), TetW, TetQ, TetU (tetracycline resistance). These markers were present in bovine manure treated, swine effluence treated, and control (no manure amendment) soils. There was no significant and consistent difference between soil types and the abundance of the markers. There was a slight increase in TetQ marker in control soils.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Spring, S., Premathilake, H., DeSilva, U., Shili, C., Carter, S., Pezeshki, A. 2020. Low Protein High Carbohydrate Diets after Energy Balance, Gut Microbiota Composition and Blood Metabolomics in Young Pigs. Scientific Reports 10(1):3318
- Type:
Journal Articles
Status:
Accepted
Year Published:
2020
Citation:
Hanak, E., DiGirolamo, N., DeSilva, U., Marschang, R., Brandao, J., Desprez, I., Lulich, J. 2020. Composition of Ferret Uroliths in North America and Eurasia: 1054 cases (2010-2018), Journal of American Veterinary Medical Association (JAVMA), in press
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Ramanathan, R., Kiyimba, F., Gonzales, J., Mafi, G., DeSilva, U. 2020. Impact of Up-and Downregulation of metabolites and mitochondrial content on pH and Color of the Longissimus Muscle from Normal-pH and Dark-Cutting Beef. Jour-nal of Agricultural and Food Chemistry 68(27), 7194-7203
- Type:
Journal Articles
Status:
Under Review
Year Published:
2020
Citation:
Ramanathan, R., Kiyimba, F., Gonzalez, J., Mafi, G., DeSilva, U. 2020. Down-regulation of glycolytic metabolites and mitochondrial content differences in dark-cutting beef impact muscle-pH and color
- Type:
Journal Articles
Status:
Under Review
Year Published:
2020
Citation:
Qi, D., Wieneke, X., Xue, P., Li, H., DeSilva, U. 2020. Total nitrogen is the main soil property associated with soil fungal community composition in karst rocky desertification regions in the Wushan County, Chongquin, China.
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Spring, S., Premathilake, H., Bradway, C., Shili, C., DeSilva, U., Carter, S., Pez-eshki, A. 2020. Effect of Very Low-Proten deits Supplemented with Branched-Charin Amino Acids on Energy Balance, Plasma Metabolomics and Fecal Mi-crobiome of Pigs. Scientific Reports, 10(1) 1-16
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Progress 10/01/18 to 09/30/19
Outputs
Target Audience:Animal producers, soil microbiologists, veterinarians, Changes/Problems:Antibiotic resistance genes do not seem to correlate with the fertilizer amendment. What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?Journal articles and presentations at scientific meetings What do you plan to do during the next reporting period to accomplish the goals?publish some of the newer analyses.
Impacts
What was accomplished under these goals?
After analyzing samples spanning 15 years, we sequence analyzed over 4 million bidirectional sequence reads of 16S rDNA fragments, seven soil properties, soil pH and levels of several chemicals were also analyzed. The data shows that soil microbial communities are different under long-term manure amendments. Total carbon seems to be the key driving factor shaping bovine manure treated soil microbiome while potassium is the main determinant of swine effluent treated soils. The core microbiome of Actinobacteria, Firmicutes, Acidobacteria, Proteobacteriaand Chloroflexi, Gemmitmonadetes and Planctomycetes remain stable in non-fertilized soils over a 12-year period. Phyla Actinobacteria and Firmicutes are enriched in bovine manure while Gemmatimonadetes and Nitrospirae respond best to swine effluent treatment.
Publications
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:Animal Scientists, Soil Scientists, Feedlot operators Changes/Problems:Soil Ph seems to be the largest driver of microbial variation. We have been having problems amplifying antibiotic resistant genes What opportunities for training and professional development has the project provided?A graduate student completed her dissertation working on this project. How have the results been disseminated to communities of interest?Journal articles and presentations at professional meetings. What do you plan to do during the next reporting period to accomplish the goals?Further analyze the samples for antibiotic resistance status.
Impacts
What was accomplished under these goals?
We have access to a collection of soil samples from soil that was treated with cattle manure, swine effluent, chemical fertilizer and left untreated for 15 years. Samples were collected every year and were archived. We extracted DNA from samples spanning the whole time period and used 16S rDNA fragment analysis to survey the temporal fluctuation of the microbial community over the 15-r time span. We generated over 4 million bi-directional sequence reads. Seven soil properties, pH, and the levels of several chemicals were measured. Results show that soil microbiome communities are different under long-term manure amendment. Total carbon is the key driving factor shaping bovine manure treated soil microbiome while potassium is the main determinant of swine effluent treated soils. The core microbiome of Actinobacteria, Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, Gemmitmonadetes, and Planctomycetes remain stable in non-fertilized soils over the 12 year period. Phyla Actinobacteria and Firmicutes are enriched in bovine manure while Gemmatimonadetes and Nitrospirae respond best to swine effluent treatment.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Ahlberg, C. M., K. Allwardt, A. Broocks, K. Bruno, L. McPhillips, A. Taylor, C. R. Krehbiel, M. Calvo-Lorenzo, C. J. Richards, S. E. Place, U. DeSilva, D. L. VanOverbeke, R. G. Mateescu, L. A. Kuehn, R. L. Weaber, J. M. Bormann, and M. M. Rolf. 2018a. Test duration for water intake, ADG, and DMI in beef cattle. Journal of animal science 96(8):3043-3054. (Article) doi: 10.1093/jas/sky209
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Ahlberg, C. M., K. Allwardt, A. Broocks, K. Bruno, L. McPhillips, A. Taylor, C. R. Krehbiel, M. S. Calvo-Lorenzo, C. J. Richards, S. E. Place, U. DeSilva, D. L. VanOverbeke, R. G. Mateescu, L. A. Kuehn, R. L. Weaber, J. M. Bormann, and M. M. Rolf. 2018b. Environmental effects on water intake and water intake prediction in growing beef cattle. Journal of animal science 96(10):4368-4384. (Article) doi: 10.1093/jas/sky267
- Type:
Other
Status:
Other
Year Published:
2018
Citation:
Bruno, K., L. J. McPhillips, M. Calvo-Lorenzo, U. deSilva, C. R. krehbiel, M. M. rolf, S. E. place, D. L. Step, R. G. mateescu, D. L. vanoverbeke, and T. C. Husz. 2018. Effect of temperament measures on feedlot cattle performance. Journal of Animal Science 96:18-19. (abstract)
- Type:
Journal Articles
Status:
Awaiting Publication
Year Published:
2018
Citation:
Qi, D., X. Wieneke, J. Tao, X. Zhou, and U. Desilva. 2018. Soil pH is the primary factor correlating with soil microbiome in karst rocky desertification regions in the Wushan County, Chongqing, China. Frontiers in Microbiology 9(MAY)(Article) doi: 10.3389/fmicb.2018.01027
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:animal scientists, soil microbiologists Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A graduate student is being provided professional development and training How have the results been disseminated to communities of interest?Journal articles and presentations at professional meetings. What do you plan to do during the next reporting period to accomplish the goals?Further analyze soils for antibiotic residues
Impacts
What was accomplished under these goals?
Treatment of Agricultural land with animal manure as fertilizer is common practice with large-scale animal industry. This is especially prevalent in geographical areas in the country where high-density animal feeding operations have flourished. This manure contains large number of enteric microorganisms that has been exposed to sub-therapeutic levels of antibiotics and antimicrobials that are commonly used in animal agriculture. It is well-established that manure amendment increases soil quality, productivity and biodiversity. We used samples from a previous study where soil was treated with cattle manure, swine effluent, chemical fertilizer and untreated for 15 years. We extracted DNA from samples spanning 12 years from manure treated soils and from the control, and used 16S rDNA fragment analysis to survey temporal fluctuation in microbial community over 12 year period. Illumina HiSeq platform was used to survey microbiome community by deep sequencing and over 4 million bi-directional sequence reeds were generated. Seven soil properties, pH, total nitrogen, total carbon, potassium, phosphorous, magnesium, and calcium were measured to assess soil quality and fertility. Results show that soil microbiome communities are different under long-term manure amendment. Total carbon is the driving factor shaping bovine manure treated soil microbiome while potassium is the main determinant of swine effluent treated soils. The core microbiome of Actinobacteria, Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, Gemmitmonadetes, and Planctomycetes remain stable in non-fertilized soils over the 12 year period. Phyla Actinobacteria and Firmicutes are entiched in bovine manure while Gemmatimonadetes and Nitrospirae respond best to swine effluent treatment.
Publications
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
U. DeSilva and W.S. Damron. 2017 Biotechnology and Genetic Engineering. In: Introduction to Animal Science: Global, Biological, Social and Industrial Perspectives. W. Stephen Damron. Pearson Education Inc.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Ke YL, Mitacek RM, Abraham A, Mafi GG, VanOverbeke DL, DeSilva U, Rama-nathan R. 2017. Effects of Muscle-Specific Oxidative Stress on Cytochrome c Release and Oxidation Reduction Potential Properties. Journal of Agricultural and Food Chemistry 65: 7749-7755.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Fellow scientsts, undergraduate and graduate students Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A graduate student is being provided professional development and training. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?A major sequencing effort of 16S rDNA fragments from microoranisms from manure amended soil is planned. We will also look for more antibiotic resistant markers.
Impacts
What was accomplished under these goals?
Treatment of agricultural land with animal manure as fertilizer is common practice in states with large-scale animal industry. This is especially prevalent in geographical areas in the country where high-density animal feeding operations have flourished. This manure contains large number of enteric microorganisms that has been exposed to sub-therapeutic levels of antibiotics and antimicrobials that are commonly used in animal agriculture. The long-term effect of continuous treatment of animal manure on agricultural soils or the effect of antibiotic residues and antibiotic resistance bacteria on soil is not very well understood. In a previous study, soil was treated with cattle manure, swine effluent, chemical fertilizer and untreated for 15 years. Each year, soil samples from these plots were collected and archived. We have successfully isolated DNA from these samples, amplified 16S rDNA gene fragments from each year. We have sequence analyzed a cross-section of these samples as a proof-of-concept and have generated over 40,000 sequence reads. They represent ~220 genera of microorganisms that are both reported from animals as well as soil. We have optimized real-time PCR assays for ~25 known antibiotic resistance genes and have tested them on soil samples. Further analysis of these samples are underway.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Roberts SL, Lancaster PA, DeSilva U, Horn GW, Krehbiel CR. 2015. Coordinat-ed gene expression between skeletal muscle and intramuscular adipose tissue in growing beef cattle. Journal of Animal Science 93: 4302-4311.
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Chako, C.Z., Step, D.L., Malayer, J.R., Krehbiel, C.R., DeSilva, U. and Streeter, R.N. 2015 Subacute ruminal acidosis and ruminal lactic acidosis: a review. The Bovine Practitioner 49:2:140-146
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