April 16, 2019

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Andrea Rocha Coauthors Paper on Groundwater Plasmidomes in the Journal mBio

Andrea Rocha, Ph.D. (Tennessee) coauthored a paper entitled "Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes" that was published in the journal mBio in Volume 10, Issue 1 on April 3, 2019.

Her coauthors were Ankita Kothari, Yu-Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Dominique C. Joyner, Terry C. Hazen, Steven W. Singer, and Aindril Mukhopadhyaya.

Andrea is a Senior Staff 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.

mBio is American Society for Microbiology (ASM's) first broad-scope, online-only, open access journal. mBio offers review and publication of research in microbiology and allied fields.

The American Society for Microbiology is the oldest and largest single life science membership organization in the world. Membership has grown from 59 scientists in 1899 to more than 39,000 members today, with more than one third located outside the United States. The members represent 26 disciplines of microbiological specialization plus a division for microbiology educators.


Naturally occurring plasmids constitute a major category of mobile genetic elements responsible for harboring and transferring genes important in survival and fitness. A targeted evaluation of plasmidomes can reveal unique adaptations required by microbial communities. We developed a model system to optimize plasmid DNA isolation procedures targeted to groundwater samples which are typically characterized by low cell density (and likely variations in the plasmid size and copy numbers). The optimized method resulted in successful identification of several hundred circular plasmids, including some large plasmids (11 plasmids more than 50 kb in size, with the largest being 1.7 Mb in size). Several interesting observations were made from the analysis of plasmid DNA isolated in this study. The plasmid pool (plasmidome) was more conserved than the corresponding microbiome distribution (16S rRNA based). The circular plasmids were diverse as represented by the presence of seven plasmid incompatibility groups. The genes carried on these groundwater plasmids were highly enriched in metal resistance. Results from this study confirmed that traits such as metal, antibiotic, and phage resistance along with toxin-antitoxin systems are encoded on abundant circular plasmids, all of which could confer novel and advantageous traits to their hosts. This study confirms the ecological role of the plasmidome in maintaining the latent capacity of a microbiome, enabling rapid adaptation to environmental stresses.

More Information

Read the article: https://mbio.asm.org/content/10/1/e02899-18
Learn more about ASM: https://www.asm.org/
For consultation regarding groundwater plasmidomes, 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/