I had the opportunity to work at the Agricultural Systems and Microbial Genomics Laboratory at New Bolton Center, School of Veterinary Medicine, UPenn for 10 weeks during the summer of 2019. The objectives of my project are: (i) to gain a better understanding of the interactions between bacteria and methanogenic archaea across anoxic environments such as the rumen and anaerobic digester, (ii) determine to what extent methanogenic archaea may be inhibited by feeding Asparagopsis Taxiformis (AT), a seaweed (marine algae) to dairy cows and (iii) investigate the effect of methanogen inhibition on bacterial populations in the rumen.
For objective (i), throughout the summer, I read literature describing the fermentation processes in the rumen and anaerobic digester, the microbial ecology and the role of bacteria and archaea in digestion of biomass in these environments. I also read about the different types of anaerobic digesters and other differences in anaerobic digestion in the rumen and anaerobic digester.
For objectives (ii) and (iii), I was trained to extract genomic DNA from rumen samples using the RBB+C protocol. The genomic DNA was then PCR-amplified for V1-V2 region of the 16S rDNA bacterial gene. I also used qPCR for quantitative analysis of specific bacterial populations.
Besides doing wet lab experiments, I also learned bioinformatics, which is used to statistically validate bacteria and archaea data from different treatments. In the bioinformatics sessions held, I learned about QIIME and about how specific R code is used to handle the data obtained from QIIME. Also, over the summer, there were journal clubs organized where each summer student presented their work and discussed relevant papers. This was interesting as it helped me to connect all the different projects in the lab and see how they fit in the bigger picture.
Throughout my time working in the lab, I had frequent discussions with Dr. Pitta about the direction of the project and its future potential. She introduced me to the concept of applying the interactions between bacteria and archaea to anaerobic digesters for improving their yield of biogas, a clean and renewable source of energy. Through these productive discussions, I learnt about both a crosstalk between microbes in an ecosystem and of the possibility of communication between microbiomes of different host/habitat. For the first time, I realized that such communications are necessary for transfer of genetic elements between microbiota. Quorum Sensing, for example, allows bacteria to communicate in an ecosystem and may facilitate transfer of antimicrobial resistance genes
Through this experience, I was able to develop a new interest in anaerobic digesters and correlate microbiology to this. I want to expand my knowledge of bioinformatics in the future. I want to further explore and connect the rumen and anaerobic digesters, and also understand their similarities and differences. Thus, through this experience, I will be able to supplement my chemical engineering knowledge with knowledge of microbiology, which will allow me to develop an interdisciplinary approach to solving problems such as climate change, clean energy production and exploitation of microbial processes.