Effect of Different Growth Conditions on Cell Growth Using Biphenyl as a Sole Carbon Source by the Bacteria Isolated from Soil Samples Collected from San Jacinto River, Texas
Based on the initial assessment in 2012, the EPA Superfund site - San Jacinto River Waste Pit had suffered from inadequate waste treatment, resulting in the accumulation of highly toxic PCBs/Biphenyl. Following Hurricane Harvey in 2017, concerns were raised about the potential for contamination spreading to other regions. Initial suspected the pollutants could be carried downstream from the SJRWP, with Terrace River Park identified as one of the two major sites potentially affected. It was hypothesized that if there is significant biphenyl deposition at the collection site of Terrace River Park, then it is expected to find biphenyl-degrading activity in the microbial population sites. As part of this assessment, seven unidentified bacteria were isolated from Terrace River Park. This master thesis first assesses the biphenyl degradation capacity of seven unidentified bacterial strains; the strains were cultured in a carbon-deficient medium with biphenyl as the sole carbon source. Among these strains, FR CSM SOY, identified as Escherichia Coli demonstrated higher cell density growth, and was further monitored by GC-MS for canonical degradation intermediates. Based on the preliminary data, FR CSM SOY could be a putative biphenyl degrader. It was further hypothesized that if FR CSM SOY can produce some downstream metabolites when exposed to biphenyl as its sole carbon source, then it possesses functional biphenyl degradation pathway. To evaluate the second hypothesis, whole genome sequencing and annotation was performed to determine whether or not FR CSM SOY harbors any known bph genes to break down biphenyl. Bioinformatic tools such as BUSCO, BRAKER, PROKKA, RAST, Roary, KEGG Map, and ghostKoala were employed to investigate and verify the presence of pathways potentially capable of producing novel biphenyl’s derived secondary metabolite. Annotation results revealed an unconfirmed dioxygenase gene in FR CSM SOY. However, GC-MS data shown the strain was unable to convert biphenyl into known degradation derivative. Moreover, FR CSM SOY strain does not possess any homolog of biphenyl dioxygenase genes such as bphA-C, although it does encode a homolog of bphD (Denome SA. et al, 1993).
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