Browsing by Author "Khairunisa, Bela Haifa"

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    Evolving understanding of rumen methanogen ecophysiology
    Khairunisa, Bela Haifa; Heryakusuma, Christian; Ike, Kelechi; Mukhopadhyay, Biswarup; Susanti, Dwi (Frontiers, 2023-11-06)
    Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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    Microbiome Metabolism in the Rumen of Bovine Grazing Toxic Tall Fescue and in Stored Dairy Manure
    Khairunisa, Bela Haifa (Virginia Tech, 2023-06-28)
    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.
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    Nutritional Evaluation of Black Soldier Fly Frass as an Ingredient in Florida Pompano (Trachinotus carolinus L.) Diets
    Banavar, Amiti; Amirkolaei, Samad Keramat; Duscher, Lexi; Khairunisa, Bela Haifa; Mukhopadhyay, Biswarup; Schwarz, Michael; Urick, Steve; Ovissipour, Reza (MDPI, 2022-09-14)
    The aquaculture industry is in need of sustainable fish feed to reduce the use of expensive and environmentally invasive wild-caught fish currently fed to many carnivorous species. The black soldier fly (BSF) has become a popular sustainable alternative protein source; however, the nutritional waste byproduct of BSF, frass, has not been extensively studied as a feed replacement in carnivorous species. This study evaluates the potential of BSF frass on the growth, body composition, and intestinal microbiome of the Florida pompano, Trachinotus carolinus. Four experimental diets were formulated containing different levels of frass, replacing plant-based carbohydrate sources. As a result of this study, the frass did not improve the growth performance, resulting in a lower specific growth rate and higher feed conversion rate. While the frass diets did not alter the body composition, the visceral somatic index (VSI) significantly increased compared to the control diet and the hepatosomatic index (HIS) was lowered. The microbiome analysis showed high variation among the diets, with the control diet having the most distinct consortia, which may have been driven by the increased levels of starch compared to frass diets. This study indicates that BSF frass may not be a suitable feed replacement for carnivorous pompano; however, frass could still potentially be a replacement feed for herbivore or detritivore fish and should be further studied.