Authors:

Simon H. Kissel

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About Paper:

Aquatic bacteria aid in the cycling of nutrients and removal of pollutants in freshwater ecosystems and are critical to lake stability. Current methods of taxonomic classification rely on core functional genes to identify bacteria. However, the resulting observed changes in abundance and diversity of taxa mask phenomena like horizontal gene transfer, changes in gene copy number, and overall gene family presence. To better understand the relationship between traditional taxonomy, functional categorization, and niche occupancy, we use two decades of publicly available metagenome assembled genome (MAG) data from Lake Mendota in Madison, WI. Through a combinatorial approach of pangenome analysis and Topological Data Analysis (TDA), we look at the presence and absence of gene families in 10 large clusters of MAGs sharing Average Nucleotide Identity (ANI) of 98.5%. We compare the clusters based on two main distinctions: class delineation (Cyanobacteria, Bacteroidia, Planctomycetia, Alphaproteobacteria) and plasticity (open or closed pangenome). Preliminary findings indicate that clusters fall on a continuum of plasticity with a strongly conserved core gene section. Most interestingly, specific motility and phage related genes, which are expected to correspond to horizontal gene transfer, show differential presence patterns across open and closed pangenome clusters. TDA further indicates complicated dynamics in bacteria diversity through the presence of 1-dimensional holes in the data, possibly suggesting new interpretations of phylogenetic relatedness. Together, these results demonstrate that genetically identified clusters have different patterns in functional adaptability indicating a need for revision in the current taxonomy model. Future efforts will be needed to validate these data across a broader array of environments and with more accurate sequencing techniques.

Source:

Northwestern University

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Co-authors:

Simon H. Kissel