Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
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document.pdf
Description
Published version
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4.36 MB
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Author(s)
Tian, Renmao
Ning, Daliang
He, Zhili
Zhang, Ping
Spencer, Sarah J.
Gao, Shuhong
Shi, Weiling
Wu, Linwei
Zhang, Ya
Yang, Yunfeng
Date Issued
April 2020
Journal
Microbiome
Publisher
Springer Science and Business Media LLC
Citation
Tian, Renmao et al. "Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity." Microbiome 8, 1 (April 2020): 51 © 2020 The Author(s)
Version
Final published version
Abstract
Background: The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. Results: Here, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group. Conclusions: We found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1186/s40168-020-00825-w
