A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Environmental Microbiome

Research

Pedro J. Cabello-Yeves¹  Jose M. Haro-Moreno²  Francisco Rodriguez-Valera²  M. Pilar Garcillán-Barcia³  Tamara I. Zemskaya⁴  Alexandra Zakharenko⁴ 

[1] Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980, Paterna, Valencia, Spain;Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain;Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Spain;Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia;

关键词: Ca;    Lake Baikal;    Long-read metagenomics;    16S rRNA;   

DOI  :  10.1186/s40793-023-00473-1

 received in 2022-10-26, accepted in 2023-02-21,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundLake Baikal, the world’s deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m.ResultsThe retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria.ConclusionThe recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse “hidden” groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.

【 授权许可】

CC BY   
© The Author(s) 2023

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