Sustainable farming is an integrated practice of crop and livestock production system (integrated crop-livestock system; ICLS) that aims to reduce the environmental impacts of agricultural practices while maintaining the productivity and profitability. The use of one step's byproducts by another is a crucial component of this practice. The continuity and effectiveness of sustainable farming greatly rely on deep understanding of each component and good management strategy. One essential aspect involved in all farming components is the role of microorganisms in mediating the biological processes therein. Thus, understanding the composition and activities of these communities would open up ways to engineer them and optimize the respective processes for better sustainable farming practices.
The research presented in this dissertation aimed to characterize the microbial metabolism involved in the ICLS with a broader goal of manipulating these systems to improve sustainable agriculture. We focused on two systems that are widely used in the United States, and employed the analysis of 16S rRNA-V4 element for this purpose.
In our first system, we characterized the rumen microbiomes of beef cattle alternately grazing nontoxic MaxQ and toxic KY-31 tall fescue pasture, to understand how these cultivars shape the rumen microbiome and identify microbial species potentially capable of degrading ergot alkaloids for better feed utilization. We found that KY-31 grazing remodeled the rumen microbiome substantially at the cellulolytic and saccharolytic guilds. It suppressed the abundances of Fibrobacter, a major ruminal cellulolytic bacterium, as well as those of Pseudobutyrivibrio and Butyrivibrio, and these losses were compensated by increased occurrences of Eubacterium species. Parts of these new communities lingered once developed, and a different guild composition surfaced upon transfer to MaxQ. We also discovered that most of the observations were not evident at the whole microbiome levels but was identified by analyzing the sessile and planktonic fractions separately. Thus, it showcased the need for analyzing sessile and planktonic segments separately while interrogating a heterogenous microbiome. Finally, we identified several potential ergovaline degrading bacteria such as Paraprevotella and Coprococcus.
In our second system, we studied the microbiome composition and associated transformation pathways mediating nitrogen loss in two dairy manure storage systems, the clay-lined Earthen Pit (EP) and aboveground concrete storage tank (CS) on two commercial dairy farms, to develop strategies to minimize these losses. We first developed a catalog of the archaea and bacteria that were present therein based on the 16S rRNA-V4 amplicons from manure samples collected from several locations and depths of the storages. Then, we inferred the respective metabolic capabilities via PICRUSt2 and literature curation, and developed schemes for nitrogen and carbon transformation pathways operating at various locations of EP and CS. Our results showed that the stored manure microbiome composition was more complex and exhibited more location-to-location variation in EP compared to CS. Further, the inlet and a location with hard surface crust in EP had unique consortia. With regards to nitrogen transformation, the microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to nitrate and further to gaseous compounds such as anammox and autotrophic nitrifiers. However, microbial conversion of nitrate to gaseous N2, NO, and N2O via denitrification and to stable ammonia via dissimilatory nitrite reduction (DNRA) seemed possible. Minor quantity of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. Higher prevalence of nitrate-transforming microbes at the near-surface locations and all depths of the inlet were found as a result of this instance. These findings suggested that ammonia oxidation to nitrate started on the barn floor and as manure is being stored in EP and CS, nitrate was lost to the environment via denitrification. For carbon transformation, hydrogenotrophic Methanocorpusculum species were the primary methane producers, and it exhibited higher abundance in EP. / Doctor of Philosophy / Sustainable farming is an integrated practice of crop and livestock production systems that aims to reduce the environmental impacts of agricultural practices while maintaining the productivity and profitability. The use of one step's byproducts by another such as the utilization of arable land to grow forages for livestock grazing or the use of manure as organic nitrogen amendments for crops is a crucial component of this practice. The continuity and effectiveness of sustainable farming greatly rely on deep understanding of each component and good management strategy. One essential aspect involved in all farming components is the role of microorganisms in mediating the biological processes therein. Thus, understanding the composition and activities of these communities would open up ways to engineer them and optimize the respective processes for a better sustainable farming practice.
The research presented in this dissertation aimed to characterize the microbial metabolism involved in the integrated crop-livestock system with a broader goal of manipulating these to improve sustainable agriculture. We focused on two systems that are widely used in the United States, and employed bioinformatic analysis of a genetic marker for this purpose.
In our first system, we characterized the rumen microbiomes of beef cattle grazing alternately on KY-31 tall fescue, a major grass used in Virginia that carry a toxin-producing fungi, and nontoxic MaxQ tall fescue pasture, to understand how these cultivars shape the rumen microbiome and identify potential microbial species capable of degrading the toxin for better feed utilization. We found that KY-31 grazing remodeled the rumen microbiome substantially, especially affecting microbes responsible for degrading cellulose and starch. Some of these communities lingered once developed, and a different microbial population surfaced upon transfer to MaxQ. Several potential toxin-degrading bacteria were also identified.
In our second system, we studied the microbiome composition and associated transformation pathways mediating nitrogen loss in two dairy manure storage systems, the clay-lined Earthen Pit (EP) and aboveground concrete storage tank (CS), to develop strategies to minimize these losses. We first develop a catalog of the archaea and bacteria that were present in the manure samples collected from several locations and depths of the storages based on a genetic marker. Then, we inferred the respective metabolic capabilities and developed schemes for nitrogen and carbon transformation pathways operating at various locations of EP and CS. Our results showed that the stored manure microbiome exhibited more location-to-location variation in EP compared to CS. Oxygen exposure, continuous addition of fresh manure, and the presence of crust at the storage surface gave rise to these unique populations. With regards to nitrogen transformation, the microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to nitrate and further to gaseous compounds. However, microbial conversion of nitrate to gaseous N2, NO, and N2O seemed possible. These observations showcased that ammonia is stable during storage. Nitrate, on the other hand, can be converted into volatile nitrogen compounds via various processes. Thus, it is imperative to limit the level of nitrate in manure prior to placement in the storage, which is potentially originating from oxidative processes occurring on the barn floor.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/115576 |
| Date | 28 June 2023 |
| Creators | Khairunisa, Bela Haifa |
| Contributors | Genetics, Bioinformatics, and Computational Biology, Mukhopadhyay, Biswarup, Aylward, Frank, Williams, Mark A., Ogejo, Jactone Arogo |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Format | ETD, application/pdf, application/pdf |
| Rights | Creative Commons Attribution-NonCommercial 4.0 International, http://creativecommons.org/licenses/by-nc/4.0/ |
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