Morphological changes and genome evolution in Raphidiopsis raciborskii CS-506 after 23 years in living culture

Abstract

ABSTRACT Microscopic organisms maintained in long-term living monocultures undergo evolution, adapting to the stable laboratory environment. Culture adaptation can result in isolates no longer being representative of their native environmental niche. This study characterized the morphology and compared the full genomes of four daughter cultures of the toxic cyanobacterium Raphidiopsis raciborskii CS-506 maintained in living culture for 23 years. The four daughter cultures were split from the parent culture between 2 and 10 years ago. The morphotypes of two cultures had changed from coiled to straight (CS-506A, B), while CS-506C, D had smaller cells and shorter coiled trichomes. The toxin cell quota had increased for cultures CS-506A-C but decreased in CS-506D compared to 2012 measurements. Culture CS-506C was unable to produce heterocysts or fix atmospheric nitrogen. The core genome, comprising 78% of all genes and all primary metabolic functions, was unchanged. The variable genome, ~12%, showed difference in gene presence/absence, and ~1% of each genome was unique proteins, with evidence of horizontal gene transfer from contaminating bacteria and multiple gene loss events, and an overall strategy of genome reduction. The changes in morphology, nitrogen fixation and toxin cell quota were not supported by identifiable genome changes, with 100% synteny across nifHDK and cyr gene clusters. The results suggest that R. raciborskii CS-506 has a stable core genome, heritable phenotypes, and a variable genome generated through horizontal gene transfer and gene loss.