Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

Tian, Renmao; Ning, Daliang; He, Zhili; Zhang, Ping; Spencer, Sarah J; Gao, Shuhong; Shi, Weiling; Wu, Linwei; Zhang, Ya; Yang, Yunfeng; Adams, Benjamin G; Rocha, Andrea M; Detienne, Brittny L; Lowe, Kenneth A; Joyner, Dominique C; Klingeman, Dawn M; Arkin, Adam P; Fields, Matthew W; Hazen, Terry C; Stahl, David A; Alm, Eric J; Zhou, Jizhong

doi:10.1186/s40168-020-00825-w

Title: Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

Journal Article · Mon Apr 06 00:00:00 UTC 2020 · Microbiome

DOI: https://doi.org/10.1186/s40168-020-00825-w · OSTI ID:1631654

Tian, Renmao ^[1]; Ning, Daliang ^[1]; He, Zhili ^[1]; Zhang, Ping ^[1]; Spencer, Sarah J ^[2]; Gao, Shuhong ^[1]; Shi, Weiling ^[1]; Wu, Linwei ^[1]; Zhang, Ya ^[1]; Yang, Yunfeng ^[3]; Adams, Benjamin G ^[4]; Rocha, Andrea M ^[5]; Detienne, Brittny L ^[4]; Lowe, Kenneth A ^[5]; Joyner, Dominique C ^[4]; Klingeman, Dawn M ^[5]; Arkin, Adam P ^[6]; Fields, Matthew W ^[7]; Hazen, Terry C ^[8]; Stahl, David A ^[9] more »

Univ. of Oklahoma, Norman, OK (United States)
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Tsinghua Univ., Beijing (China)
Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Montana State Univ., Bozeman, MT (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Washington, Seattle, WA (United States)
Univ. of Oklahoma, Norman, OK (United States); Tsinghua Univ., Beijing (China); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

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.ResultsHere, 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725

OSTI ID:: 1631654

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 8; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Candidate phylum radiation
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Superphylum Patescibacteria

Additional file 1 of Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.12097230 The current record is supplemented by this text	text	January 2020
Additional file 1 of Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.12097230.v1 The current record is supplemented by this text	text	January 2020
Additional file 1 of Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.12116019 The current record is supplemented by this text	text	January 2020
Additional file 1 of Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.12116019.v1 The current record is supplemented by this text	text	January 2020
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.c.4929912 The current record is supplemented by this collection	collection	January 2020
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.c.4929912.v1 The current record is supplemented by this collection	collection	January 2020
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity Tian, Renmao; Ning, Daliang; He, Zhili https://doi.org/10.6084/m9.figshare.c.4929912.v2 The current record is supplemented by this collection	collection	January 2020