U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights
Genomic Science Program


Microbes Retain Toxicity Tolerance After They Escape Toxic Elements
Published: February 26, 2019
Posted: November 19, 2019

Groundwater microbes living outside a contaminated area contain mobile genetic elements that give them resistance to heavy metals.

The Science
Bacteria and other microbes contain mobile genetic elements called plasmids that are circular DNA molecules. Plasmids often encode traits that confer some advantage to the harboring microbe such as antibiotic resistance. A team of researchers has developed a method to purify and study plasmids from groundwater microbial communities. Using this method, they discovered several hundred different plasmids in samples from a U.S. Department of Energy site in Tennessee. The most common trait encoded in those plasmids was resistance to toxic metals such as mercury. The team also found that the plasmids were diverse but not as much as the microbial community from which they came.

The Impact
Studying plasmids from microbial communities that live in groundwater is difficult because of the low concentration of cells in those habitats. Researchers knew that heavy metal resistance genes were present in groundwater microbes, but their new method allowed them to prove that these mobile elements harbor metal resistance genes. The method will also facilitate the discovery of new plasmids in other water environments.

Summary
Plasmids are mobile genetic elements that often contain genes that confer important functions to the microbial host. They are composed of circular DNA molecules and are easy to purify. However, plasmid purification methods do not work well if the concentration of cells is low, as is the case in samples of microbial communities from groundwater environments. To solve this problem, a team of researchers developed a method to purify and analyze plasmids from such environments. With this method, the team uncovered over 600 different plasmids that showed an enrichment in metal tolerance genes in addition to antibiotic- and virus-resistance genes. Given that the team did not detect heavy metals in the microbial habitat, they hypothesize that plasmids may represent a mechanism to maintain latent resistance within a microbial community. The discovery of new plasmid genes allowed by this research will provide new possibilities for engineering novel and useful microbial strains.

Contact
Aindrila Mukhopadhyay
Lawrence Berkeley National Laboratory
amukhopadhyay@lbl.gov  

Program Managers
Pablo Rabinowicz
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
Foundational Genomics Research and Biosystems Design
pablo.rabinowicz@science.doe.gov

Todd Anderson
U.S. Department of Energy Office of Science, Office of Biological and Environmental Research
Biological Systems Science Division (SC-23.2)
todd.anderson@science.doe.gov

Funding
This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research.

Publications
Kothari, A., Y. W. Wu, J. M. Chandonia, M. Charrier, L. Rajeev, A. M. Rocha, D. C. Joyner, T. C. Hazen, S. W. Singer, and A. Mukhopadhyay. “Large circular plasmids from groundwater plasmidomes span multiple incompatibility groups and are enriched in multimetal resistance genes.” mBio 10, e02899-18 (2019). [DOI:10.1128/mBio.02899-18]

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Biosystems Design

Division: SC-23.2 Biological Systems Science Division, BER

 

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