Comprehensive Comparative Genomics Reveals Over 50 Phyla of Free-living and Pathogenic Bacteria are Associated with Diverse Members of the Amoebozoa

Abstract

The association of bacteria with microbial eukaryotes has been extensively studied. Among these the supergroup Amoebozoa containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria. Amoebozoans not only graze bacteria but also serve as a safe niche for bacterial replication and harbor endosymbiotic bacteria including dangerous human pathogens. Despite their importance, only a few lineages of Amoebozoa have been studied in this regard. Amoebozoa encompasses lineages of extreme diversity in ecology, morphology and evolutionary history. The limited amoebozoans studied are not representative of the high diversity known in the supergroup, and could undermine our understanding of their role as key players in environmental ecosystems and as emerging public health threats. In this research, we conducted a comprehensive genomic and transcriptomic study with expansive taxon sampling by including representatives from the three known clades of the Amoebozoa. We used culture independent whole culture and single cell genomics maintained in our laboratory cultures, and additionally published RNA-Seq data to investigate the association of bacteria with diverse amoebozoans. Relative to current published evidence, we recovered the largest number of bacterial phyla (57) and pathogen genera (49) associated with the Amoebozoa. Using single cell genomics we were able to determine up to 24 potential endobiotic bacterial phyla, some potentially endosymbionts. This includes the majority of multidrug-resistant pathogens designated as major public health threats. Our study demonstrates amoebozoans are associated with many more phylogenetically diverse bacterial phyla than previously recognized. It also shows that all amoebozoans are capable of harboring far more dangerous human pathogens than presently documented, making them of primal public health concern.