State-of-the-art Approaches for Sequencing, Assembling and Annotating Naphthenic Acid Degrading Bacterial Metagenomes
Abstract
Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I characterize the metagenomes of novel NA-degrading bacterial communities seeded in NA-enriched granulated activated carbon (GAC) filters. I demonstrate methods that maximize the throughput of extraction, sequencing, and annotation of novel metagenomes - producing 72 MAGs and other 5432 circular contigs - 226 of which were putative phages. I also include state-of-the-art protein structure prediction and structure homology search tools, which greatly enrich annotations of novel sequences that are below the threshold for homology finding by sequence alone. Overall, these approaches unveiled a diverse and constantly changing consortium of novel bacteria and many potential NA-degrading genes.