Reclaiming water, energy and nutrients from livestock wastewater
The goal of this project is to turn livestock wastewater from concentrated animal feeding operations such as swine, poultry, beef, and dairy farms to valuable products including high-quality water fit for irrigation, ammonia gas for energy/fertilizer production and struvite, thereby closing resource cycles in agriculture. The goal will be achieved by pursuing the following interconnected objectives:
Sponsor: United States Department of Agriculture |
References:
Heyang Yuan, Ibrahim M. Abu-Reesh, and Zhen He. "Mathematical modeling assisted investigation of forward osmosis as pretreatment for microbial desalination cells to achieve continuous water desalination and wastewater treatment." Journal of Membrane Science 502 (2016): 116-123.
Heyang Yuan, Ibrahim M. Abu-Reesh, and Zhen He. "Enhancing desalination and wastewater treatment by coupling microbial desalination cells with forward osmosis." Chemical Engineering Journal 270 (2015): 437-443.
Heyang Yuan, Ibrahim M. Abu-Reesh, and Zhen He. "Mathematical modeling assisted investigation of forward osmosis as pretreatment for microbial desalination cells to achieve continuous water desalination and wastewater treatment." Journal of Membrane Science 502 (2016): 116-123.
Heyang Yuan, Ibrahim M. Abu-Reesh, and Zhen He. "Enhancing desalination and wastewater treatment by coupling microbial desalination cells with forward osmosis." Chemical Engineering Journal 270 (2015): 437-443.
Chasing the elusive syntrophic partners in direct interspecies electron transfer
The goal of this project is to gain a mechanistic understanding of the ecophysiology of the electron-donating and -accepting partners in direct interspecies electron transfer (DIET). Our central hypothesis is that DIET and interspecies hydrogen transfer (IHT) play an equally important role in syntrophy-dependent methanogenesis in certain anaerobic environments. The hypothesis is formulated based on prior work and our preliminary study, in which we identified an uncultured Geobacter species Candidatus Geobacter eutrophica. This species was highly abundant in methanogenic bioreactors amended with conductive media and actively expressed genes encoding proteins for extracellular electron transfer and hydrogen metabolism. We will complete the goal and examine the central hypothesis by pursuing the following specific aims :
Sponsor: National Science Foundation |
References:
Heyang Yuan, Xuehao Wang, Tzu-Yu Lin, Jinha Kim, and Wen-Tso Liu , Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Scientific Reports (2021): 11(1): p. 15140.
Jinha Kim, Ran Mei, Fernanda P. Wilson, Heyang Yuan, Benjamin TW Bocher, and Wen-Tso Liu. "Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity." Frontiers in microbiology 11 (2020): 3115.
Heyang Yuan, Xuehao Wang, Tzu-Yu Lin, Jinha Kim, and Wen-Tso Liu , Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Scientific Reports (2021): 11(1): p. 15140.
Jinha Kim, Ran Mei, Fernanda P. Wilson, Heyang Yuan, Benjamin TW Bocher, and Wen-Tso Liu. "Ecogenomics-Based Mass Balance Model Reveals the Effects of Fermentation Conditions on Microbial Activity." Frontiers in microbiology 11 (2020): 3115.
Genomics-enable data-driven and hybrid modeling of engineered bioprocesses
Mechanistic and data-driven models have been developed to provide predictive insights into the design and optimization of engineered bioprocesses. These two modeling strategies can be combined to form hybrid models to address the issues of parameter identifiability and prediction interpretability. Herein, we developed a novel and robust hybrid modeling strategy by incorporating microbial population dynamics into model construction. The hybrid model was constructed using bioelectrochemical systems (BES) as a platform system. We collected 77 samples from 13 publications, in which the BES were operated under diverse conditions. A hybrid model was developed by first building a three-population mechanistic component and subsequently feeding the estimated microbial kinetic parameters into network training. The hybrid model generated a simulated community that shared a Bray-Curtis similarity of 72% with the actual microbial community and an average relative RMSE of 7% for individual taxa. When examined with additional samples that were not included in network training, the hybrid model achieved accurate prediction of current production with a relative error-based RMSE of 0.8 and outperformed the data-driven models. The genomics-enabled hybrid modeling strategy represents a significant step toward robust simulation of a variety of engineered bioprocesses.
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References:
Zhang Cheng, Shiyun Yao, and Heyang Yuan. "Linking Population Dynamics to Microbial Kinetics for Hybrid Modeling of Bioelectrochemical Systems." Water Research (2021): 117418.
Heyang Yuan, Shan Sun, Ibrahim M. Abu-Reesh, Brian D. Badgley, and Zhen He. "Unravelling and reconstructing the nexus of salinity, electricity, and microbial ecology for bioelectrochemical desalination." Environmental science & technology 51, no. 21 (2017): 12672-12682.
Zhang Cheng, Shiyun Yao, and Heyang Yuan. "Linking Population Dynamics to Microbial Kinetics for Hybrid Modeling of Bioelectrochemical Systems." Water Research (2021): 117418.
Heyang Yuan, Shan Sun, Ibrahim M. Abu-Reesh, Brian D. Badgley, and Zhen He. "Unravelling and reconstructing the nexus of salinity, electricity, and microbial ecology for bioelectrochemical desalination." Environmental science & technology 51, no. 21 (2017): 12672-12682.
Fate of antibiotic resistant genes in engineered bioprocesses
Anaerobic biotechnologies can effectively remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), but there is a need to better understand the mechanisms. We use bioelectrochemical systems (BES) as a platform to investigate the fate of a native tetracycline and sulfonamide-resistant Escherichia coli strain and its ARGs. Significant correlations of E. coli vs. current (R2 = 0.73) and ARGs vs. E. coli (R2 ranged from 0.54 to 0.87), and the fact that the BES substrate contained no electron acceptors, implied that the persistence of the E. coli and its ARGs was determined by the availability of indigenous electron acceptors in the BES, i.e., the anode electrode or the electron shuttles generated by the exoelectrogens. Subsequent experiments with pure-culture tetracycline and sulfonamide-resistant E. coli being incubated in a two-chamber MEC and serum bottles demonstrated that the E. coli could survive by respiring anode electrode and/or electron shuttles released by exoelectrogens, and ARGs persisted with their host E. coli.
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References:
Heyang Yuan, Jennifer H. Miller, Ibrahim M. Abu-Reesh, Amy Pruden, and Zhen He. "Effects of electron acceptors on removal of antibiotic resistant Escherichia coli, resistance genes and class 1 integrons under anaerobic conditions." Science of The Total Environment (2016): 569, 1587-1594.
Heyang Yuan, Jennifer H. Miller, Ibrahim M. Abu-Reesh, Amy Pruden, and Zhen He. "Effects of electron acceptors on removal of antibiotic resistant Escherichia coli, resistance genes and class 1 integrons under anaerobic conditions." Science of The Total Environment (2016): 569, 1587-1594.