Grantee Research Project Results
2022 Progress Report: A comprehensive methodology to track genetically recoded organisms and assess their impacts on freshwater microbial communities
EPA Grant Number: R840203Title: A comprehensive methodology to track genetically recoded organisms and assess their impacts on freshwater microbial communities
Investigators: Konstantinidis, Konstantinos (Kostas) T. , Hatt, Janet K , Vereen, Ethell
Institution: Georgia Institute of Technology - Main Campus (School of Civil & Environmental Engineering)
Current Institution: Georgia Institute of Technology - Main Campus (School of Civil & Environmental Engineering) , Morehouse College
EPA Project Officer: Callan, Richard
Project Period: July 1, 2021 through June 30, 2024
Project Period Covered by this Report: July 1, 2021 through June 30,2022
Project Amount: $759,980
RFA: Assessment Tools for Biotechnology Products (2020) RFA Text | Recipients Lists
Research Category: Chemical Safety for Sustainability , Safer Chemicals
Objective:
The research objectives of the project, as outlined in the original proposal, are:
1. Perform dialysis bag incubations with a synthetic E. coli expressing a recoded enzyme able to degrade benzalkonium chloride disinfectants (BAC) vs. E. coli expressing the wildtype proteins under BAC-supplemented conditions in order to assess the effects of the former on the natural microbial community relative to the latter.
2. Develop biomarkers representing different sources of pollution and synbio organisms by examining large metagenomic/genomic libraries from around the world.
3. Make the underlying gene and genome biomarkers searchable online as part of a “MST webserver” to help users identify the source(s) of pollution in their samples and presence of synbioorganisms by simply uploading their metagenomic dataset(s) to the webserver.
4. Using the best performing biomarkers identified under #2 above, to quantify the relative contributions of different the sources of pollution of impaired creeks in the Atlanta metro area. The overarching hypothesis is that the modified E. coli will not pass BAC-degrading functional genes to indigenous microbes due to inability of these genes to function in non-modified cells.
Progress Summary:
We have performed laboratory incubations using as innocula fecal material from different animal hosts and humans as well as municipal sewage in order to develop our wet-lab and bioinformatics approaches to track released organisms (from the innocula) and develop novel biomarkers for different sources of pollution. This work was published in Water Research in December of 2021 and has already drawn substantial attention based on citations and personal communications. Therefore, we have accomplished Objective #2 above. In addition, we are in the process of making the library of biomarkers of different sources we have developed available online as part of the “MST webserver”. For instance, PhD candidate Blake Lindner presented this work and the prototype of the MST webserver at the Microbe conference of the American Society for Microbiology in June 2022. We are testing the webserver internally at the time of this writing, and we are incorporating the feedback we received during the Microbe meeting. We hope to release the webserver for public use, and publish the corresponding manuscript, later in the fall of 2022. Therefore, we are very close to accomplishing Objective #3 above as well. Finally, we are working closely with our Morehouse College collaborators (Dr. Vereen and his team), and we are characterizing metagenomic samples from several impaired creeks in the Atlanta metro area that the Vereen team has been sampling. We will use these samples to test our Objective #4 above; that is, to use our MST webserver and underlying methodology to quantify the sources of pollution affecting these creeks. Thus, overall, we are making good progress to address all Objectives of our project. There have been no unanticipated delays or changes in the key personnel.
Future Activities:
Our efforts for year 2 will be to perform laboratory incubations with selected SynBio organisms, and release the first version of the MST server and the underlying bioinformatic approaches to track organisms of interest in environmental samples, consistent with the original experimental plan.
Journal Articles on this Report : 2 Displayed | Download in RIS Format
Other project views: | All 4 publications | 4 publications in selected types | All 4 journal articles |
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Type | Citation | ||
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Lindner BG, Suttner B, Zhu KJ, Conrad RE, Rodriguez-R LM, Hatt JK, Brown J, Konstantinidis KT. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms. Water Research 2022;210:117993. |
R840203 (2022) |
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Suttner B, Lindner BG, Kim M, Conrad RE, Rodriguez LM, Orellana LH, Johnston ER, Hatt JK, Zhu KJ, Brown J, Konstantinidis KT. Metagenome-based comparisons of decay rates and host-specificity of fecal microbial communities for improved microbial source tracking. bioRxiv 2021. |
R840203 (2022) |
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Supplemental Keywords:
Recoded genomes, amber mutations, genome detection, bioinformatics, metagenomicsRelevant Websites:
Environmental Microbial Genomics Laboratory Exit
Progress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.