Pangenomics reveals alternative environmental lifestyles among chlamydiae

Stephan Köstlbacher, Astrid Collingro, Tamara Halter, Frederik Schulz, Sean P. Jungbluth and Matthias Horn ()
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Stephan Köstlbacher: University of Vienna
Astrid Collingro: University of Vienna
Tamara Halter: University of Vienna
Frederik Schulz: DOE Joint Genome Institute
Sean P. Jungbluth: DOE Joint Genome Institute
Matthias Horn: University of Vienna

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

Date: 2021
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DOI: 10.1038/s41467-021-24294-3

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