Dr. David S. Holmes

Genomics Sheds Light on the Evolution of Hyper-acidophiles

This presentation explores the evolution and genetic diversity of hyper-acidophilic Bacteria and Archaea (grow at a pH of ≤3). An interactive database of more than 150 publicly available acidophile genomes was constructed and used to identify the lowest pH/highest temperature growth environments occupied by acidophiles and to map onto the Tree of Life the distributions of acidophile phenotypes such as methane/hydrogen/sulfur/iron energy pathways, CO2 fixation and aerobic versus anaerobic metabolisms. Detailed robust and coherent phylogenies were generated from diverse examples of hyper-acidophiles from very different early and late branching microbial lineages distributed around the Tree of Life. Examination of these phylogenies, coupled with comparative genomics identified genes and mechanisms involved in acid resistance and allowed the reconstruction, by inference, of their ancestral evolutionary trajectories, including how acidophilicity can be acquired via recombination and horizontal gene transfer. Surprising, a potential link between the coevolution of acidophilicity and themo-tolerance was discovered.
Genomic sequence-based (e.g. MSLA) and non sequence-based (e.g. ANI) phylogenetic analyses of hyper-acidophiles provided a rich source of data that addresses the fundamental question of whether microbial genetic diversity exists as a continuum or is divided into discrete clusters (species).

Acknowledgements: This work was supported by the Programa de Apoyo a Centros con Financiamiento Basal AFB 170004 to Fundación Ciencia & Vida and Fondecyt 1181717.