Marine Sediments Illuminate Chlamydiae Diversity and Evolution

• Published in: Current Biology
• Main Authors: Dharamshi, Jennah, Tamarit, Daniel, Eme, Laura, Stairs, Courtney, Martijn, Joran, Homa, Felix, Jørgensen, Steffen, Spang, Anja, Ettema, Thijs J.G.
• Other Authors: Uppsala University, Wageningen University and Research Wageningen (WUR), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), University of Bergen (UiB), Royal Netherlands Institute for Sea Research (NIOZ), European Project: 625521,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IEF,ENIGMAARCHAEA(2014), European Project: 704263,H2020,H2020-MSCA-IF-2015,Gap2bridge
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2020
• Subjects: [SDV]Life Sciences [q-bio]; [SDV.BBM]Life Sciences [q-bio]/Biochemistry; Molecular Biology; Arctic
• Online Access: https://hal.science/hal-03368662; https://doi.org/10.1016/j.cub.2020.02.016

International audience 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.