Abstract

Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown. Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluorescence in situ hybridization, to show that individual cells of Achromatium oxaliferum, the world’s biggest known freshwater bacterium, harbor genetic diversity typical of whole bacterial communities. The cells contain tens of transposable elements, which likely cause the unprecedented diversity that we observe in the sequence and synteny of genes. Given the high within-cell diversity of the usually conserved 16S ribosomal RNA gene, we suggest that gene conversion occurs in multiple, separated genomic hotspots. The ribosomal RNA distribution inside the cells hints to spatially differential gene expression. We also suggest that intracellular gene transfer may lead to extensive gene reshuffling and increased diversity.

Highlights

  • Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown

  • We find extreme intracellular genetic diversity, and suggest that Achromatium undergoes intracellular gene duplications, re-assortments, and divergence with reduced or minimal gene convergence, leading to genetic diversity typical for populations rather than single cells

  • A light micrograph of a dividing Achromatium cell from Lake Stechlin overlaid with the parallel DNA staining image (Fig. 1, Supplementary Fig. 1) shows that the individual cells contain multiple DNA spots that are not localized in one single area but rather spread across the cell, mostly in between calcium carbonate bodies

Read more

Summary

Introduction

But the genetic and functional diversity resulting from polyploidy is unknown. To confirm the presence and expression of several different rRNA gene alleles in individual cells, two sets of FISH probes were designed: the first based on complete 16S rRNA sequences as assembled from the metagenome, and the second based on the clustering of the V1–V4 amplicons obtained from single cells (Supplementary Fig. 2A). The estimated size of the Achromatium genome based on the 6 single cells and the various metagenomic bins ranges between 3.5 and 12 Mbp (Supplementary Data 1).

Results
Conclusion

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call

Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.