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Genomic insights into versatile lifestyle of three new bacterial candidate phyla

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Abstract

Metagenomic explorations of the Earth’s biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (91951102, 31800105, 31970105, 32061133009), the Innovation Team Project of Universities in Guangdong Province (2020KCXTD023), the Scientific Research Foundation of Third Institute of Oceanography, MNR (2019022), and the Science and Technology Innovation Committee of Shenzhen (JCYJ20190808152403587, JCYJ20180305163524811, JCYJ20200109105010363). We thank the crew and scientific team of R/V Xiangyanghong 09, the pilots and the supporting team of Jiaolong manned submersible in 37th and 38th Dayang Cruise for the sampling, and Ms. Wan Liu for the genome submission to eLMSG.

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Authors and Affiliations

  1. Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China

    Xinxu Zhang, Zongbao Liu, Jie Pan, Yuhan Huang, Mingwei Cai & Meng Li

  2. Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China

    Xinxu Zhang, Zongbao Liu, Jie Pan, Yuhan Huang, Mingwei Cai & Meng Li

  3. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China

    Wei Xu & Zhuhua Luo

  4. School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, 210044, China

    Zhuhua Luo

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  1. Xinxu Zhang
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Zhang, X., Liu, Z., Xu, W. et al. Genomic insights into versatile lifestyle of three new bacterial candidate phyla. Sci. China Life Sci. 65, 1547–1562 (2022). https://doi.org/10.1007/s11427-021-2037-x

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