Abstract:
What a strain is and how many strains make up a natural bacterial population
remain elusive concepts despite their apparent importance for assessing the
role of intra-population diversity in disease emergence or response to environmental
perturbations. To advance these concepts, we sequenced 138 randomly
selected Salinibacter ruber isolates from two solar salterns and assessed
these genomes against companion short-read metagenomes from the same
samples. The distribution of genome-aggregate average nucleotide identity
(ANI) values among these isolates revealed a bimodal distribution, with fourfold
lower occurrence of values between 99.2% and 99.8% relative to
ANI >99.8% or <99.2%, revealing a natural “gap” in the sequence space within
species. Accordingly, we used this ANI gap to define genomovars and a higher
ANI value of >99.99% and shared gene-content >99.0% to define strains. Using
these thresholds and extrapolating from how many metagenomic reads each
genomovar uniquely recruited, we estimated that –although our 138 isolates
represented about 80% of the Sal. ruber population– the total population in
one saltern pond is composed of 5,500 to 11,000 genomovars, the great
majority of which appear to be rare in-situ. These data also revealed that the
most frequently recovered isolate in lab media was often not the most abundant
genomovar in-situ, suggesting that cultivation biases are significant, even
in cases that cultivation procedures are thought to be robust. The methodology
and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.
