New insights into the genomic evolution of cyanobacteria using herbarium exsiccatae

Abstract

ABSTRACT Prokaryotes are the most abundant and diverse inhabitants of the biosphere. However, to directly infer the patterns of their evolutionary history and species diversity requires the study of ancient DNA, which is almost impossible to obtain in free-living prokaryotes. In this paper, we show that cyanobacterial herbarium specimens may serve as a rich source of information to shed light on the genome evolution and species diversity of free-living bacteria. We sequenced two herbarium specimens identified as Nostoc (Cyanobacteria), one of which is over 100 years old. One specimen was identified as N. commune and the second as N. flagelliforme. The two specimens yielded a metagenome composed of six and 11 taxa, respectively. Nostoc was the most abundant in both specimens, with accompanying cyanobacteria and alpha- and beta-proteobacteria. Phylogenomic reconstruction revealed that both Nostoc genomes clustered with a recently sequenced genome of N. flagelliforme CCNUN1. We compared genome properties, including gene composition of N. flagelliforme from the herbarium specimen and N. flagelliforme CCNUN1, both sampled in China. We found a striking difference between the genomes both in gene composition and the presence of genes for secondary metabolites. This poses a potential health risk because N. flagelliforme is consumed in China, and a proper identification of the species strain can be difficult. Furthermore, a surprisingly low frequency of horizontal gene transfer was found within the sequenced Nostoc strains.