Achromatium: A giant bacterium with split personality
Achromatium is large and hyperpolyploid. Single cells contain ca. 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Using single-cell genomics, metagenomics, single-cell amplicon sequencing and fluorescence in-situ hybridization, we showed that individual cells of Achromatium harbor genetic diversity typical of multi-species populations. Furhermore, we show that these cells contain and express tens of transposable elements, which likely contribute the unprecedented diversity we observe in sequence and synteny of genes. We propose that the multiple chromosomes of Achromatium do not represent copies of its genome and making it the only known “heterozygous” bacterium. Most proteins are, however, under conservation pressure. Thus, given the high single-cell diversity of functional genes and the usually conserved 16S rRNA gene, we suggest that gene conversion is limited to chromosomal clusters formed by the large calcite bodies in the cell. We further suggest that upon cell division, these clusters are shuffled resulting in two daughter cells different from each other as well as from the mother cell. Surveying all publicly available sediment sequence archives, we show Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. While saline and freshwater Achromatium spp. are to a certain extent phylogenetically separated, the genus Achromatiumcontains a globally identical, complete functional inventory regardless of habitat. Thus, Achromatiumspp. cells from differing ecosystems (e.g. freshwater vs. saline) are, unexpectedly, equally functionally equipped, but differ in gene expression patterns by transcribing only relevant genes. We suggest environmental adaptation occurs by increasing the copy number of relevant genes across the cell’s hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium, and its genomic features, reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.
Host: Hans-Peter Grossart