Mechanisms driving genome reduction of a novel Roseobacter lineage

• Published in: The ISME Journal 2021-12, Vol.15 (12), p.3576-3586
• Main Authors: Feng, Xiaoyuan, Chu, Xiao, Qian, Yang, Henson, Michael W., Lanclos, V. Celeste, Qin, Fang, Barnes, Shelby, Zhao, Yanlin, Thrash, J. Cameron, Luo, Haiwei
• Format: Article
• Language: English
• Subjects: 631/326/41/2529; 631/326/41/2535; Bacterioplankton; Biomedical and Life Sciences; Carbon cycle; Chlorophyll; Chlorophyll A; Clusters; Ecology; Evolutionary Biology; Gene expression; Genome, Bacterial - genetics; Genomes; Life Sciences; Metabolites; Metagenomics; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Phylogeny; Phytoplankton; Plankton; Pseudogenes; Reduction; Roseobacter - genetics; Seawater; Sulfur; Symbiosis; Vitamin B12
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/s41396-021-01036-3

Summary Members of the marine Roseobacter group are key players in the global carbon and sulfur cycles. While over 300 species have been described, only 2% possess reduced genomes (mostly 3–3.5 Mbp) compared to an average roseobacter (>4 Mbp). These taxonomic minorities are phylogenetically diverse but form a Pelagic Roseobacter Cluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novel Roseobacter lineage which we named ‘CHUG’. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members are globally distributed and active in marine pelagic environments. CHUG members possess some of the smallest genomes (~2.6 Mb) among all known roseobacters, but they do not exhibit canonical features of typical bacterioplankton lineages theorized to have undergone genome streamlining processes, like higher coding density, fewer paralogues and rarer pseudogenes. While CHUG members form a genome content cluster with traditional PRC members, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their relative gene expression levels are correlated with chlorophyll a concentration across the global samples. CHUG members cannot utilize most phytoplankton-derived metabolites or synthesize vitamin B 12 , a key metabolite mediating the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection owing to lifestyle shift is likely an important driver of genome reduction in CHUG.