New globally distributed bacterial phyla within the FCB superphylum

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Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.

This work was funded by the Simons Foundation (Award number 687165) to B.J.B. This work was also supported by National Natural Science Foundation of China (Grant numbers 91951202, 42006134, and 42072333), National Key Research and Development Program of China (grant number 2018YFA0605800), State Key Laboratory of Marine Geology, Tongji University (grant number MGK202009) and Shandong University Foundation for Future Scholar Plan, and China Scholarship Council to X.G.; the “la Caixa” Foundation (ID 100010434, fellowship code LCF/BQ/DI18/11660009) to Á.R.R.; the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 713673; National Program for Fostering Excellence in Scientific and Technical Research (grant PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE to J.H.-C.

Peer reviewed