Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR

作者：Maria‐Cecilia Chiriac, Paul‐Adrian Bulzu, Adrian‐Ștefan Andrei, Yusuke Okazaki, Shin‐ichi Nakano, Markus Haber, Vinicius Kavagutti, Paul Layoun, Rohit Ghai, Michaela M. Salcher · 发表于：Microbiome · 年份：2022 · DOI：10.1186/s40168-022-01274-3 · 被引用次数：101 · 研究领域：Microbial Community Ecology and Physiology、Genomics and Phylogenetic Studies、Protist diversity and phylogeny

Abstract Background The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples. Results A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02–14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineage...