Marine Sediments Illuminate Chlamydiae Diversity and Evolution

Jennah E. Dharamshi, Daniel Tamarit, Laura Eme, Courtney W. Stairs, Joran Martijn, Felix Homa, Steffen L. Jørgensen, Anja Spang, Thijs J.G. Ettema*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies. Dharamshi et al. find abundant, diverse, and active Chlamydiae in deep anoxic marine sediments. Using metagenomics, chlamydial genomes are obtained that form several new clades. Analyses of these genomes provide new insights into the evolution and host association of the Chlamydiae phylum, indicating that some are not symbionts of eukaryotic hosts.

Original languageEnglish
Pages (from-to)1032-1048.e7
JournalCurrent Biology
Volume30
Issue number6
DOIs
Publication statusPublished - 23 Mar 2020
Externally publishedYes

Keywords

  • anoxic marine sediment
  • Chlamydia
  • metagenomics
  • microbe-host association
  • microbial community
  • microbial evolution
  • PVC superphylum
  • symbiosis
  • uncultured microbial diversity

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