Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes
Yusuke Okazaki, Shin‐ichi Nakano, Atsushi Toyoda, Hideyuki Tamaki
Abstract
Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.