June 15, 2020

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Andrea Rocha Coauthored a Paper on Superphylum Patescibacteria in the Journal Microbiome

Andrea Rocha, Ph.D. (Tennessee) coauthored a paper entitled "Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity" that was published in the journal Microbiome in Volume 8, Article 51, on April 6, 2020.

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

Andrea Rocha is a Scientist based in Tennessee with more than 10 years of experience focused on research using an array of geochemical, microbial, computational, and genomics techniques within the areas of environmental microbiology, computational biology, and engineering science. She has proven success in projects, leading multi-disciplinary teams toward project completion, establishing collaborations across organizations and Department of Energy (DOE) National Laboratories. Specific areas of expertise include application of molecular technologies for defining and managing environmental processes; utilization of computational biology tools for characterization of potentially key microbial metabolic processes involved in bioremediation and bioenergy; and implementation of newly developed biotechnology for microbial detection and assessment.

The central purpose of Microbiome is to unite investigators conducting microbiome research in environmental, agricultural, and biomedical arenas. Topics broadly addressing the study of microbial communities, such as, microbial surveys, bioinformatics, meta-omics approaches and community/host interaction modeling will be considered for publication. Through this collection of literature Microbiome hopes to integrate researchers with common scientific objectives across a broad cross-section of sub-disciplines within microbial ecology.

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.

More Information

Learn more about the article: https://doi.org/10.1186/s40168-020-00825-w
Learn more about the journal: https://microbiomejournal.biomedcentral.com/about
For consultation regarding superphylum patescibacteria or groundwater, contact Andrea Rocha at This email address is being protected from spambots. You need JavaScript enabled to view it..
Learn more about Andrea at: https://www.linkedin.com/in/andrea-m-rocha-ph-d-20a81017/