New globally distributed bacterial phyla within the FCB superphylum

Xianzhe Gong (), Álvaro Rodríguez Río, Le Xu, Zhiyi Chen, Marguerite V. Langwig, Lei Su, Mingxue Sun, Jaime Huerta-Cepas, Valerie Anda () and Brett J. Baker ()
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Xianzhe Gong: Shandong University
Álvaro Rodríguez Río: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)
Le Xu: Shandong University
Zhiyi Chen: Shandong University
Marguerite V. Langwig: University of Texas at Austin
Lei Su: Tongji University
Mingxue Sun: Tongji University
Jaime Huerta-Cepas: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC)
Valerie Anda: University of Texas at Austin
Brett J. Baker: University of Texas at Austin

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: Abstract 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.

Date: 2022
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DOI: 10.1038/s41467-022-34388-1

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