PhD Student, Freshwater and Marine Science, University of Wisconsin-Madison
I'm a research scientist interested in microbial ecology, biogeochemistry and bioinformatics. My expertise is in aquatic ecology and how we can leverage multidisciplinary approaches to better understand the role of microbes in ecosystems. Beyond research, I served on committee for provincial and national scientific networks, and enjoy teaching and mentoring other scientists through formal and informal workshops, and public outreach events.
Microbes are tiny organisms living all around us -- in our bodies, in terrestrial environments, in aquatic environments, and much more. Not all microbes are bad, in fact, many perform beneficial functions. In ecosystems, for example, microbes regulating global nutrient cycles through their metabolic activities. I aim to research how microbes interact with their environments, and how their metabolic activities influence ecosystem function.
Over the years, I've aimed to develop an expertise in freshwater ecosystems, namely in small wetlands and freshwater lakes. While water covers a major portion of the surface area on earth, only a tiny fraction is readily available as liquid, freshwater. Like in other environments, microbes are responsible for transforming many nutrients and chemicals, contribute to geochemical cycling, and make available otherwise unaccessible compounds to other organisms of the food chain. I aim to understand how microbes specifically transform these compounds at specific interfaces of the lake environment such as chemoclines, oxyclines and thermoclines changes accross the year.
I use a combination of field studies and bioinformatics methods to answer these questions. Bioinformatics is the use of computational methods to access, organize and make available biological data, or to develop and implement novel computational methods to answer biological questions. Most days, I deal with metagenomics and metatranscriptomics datasets. That said, I'm interested in leveragering computational methods to laboratory, analytical techniques, and field work.
DOCTOR OF PHILOSOPHY
I joined the laboratory of Dr. Trina McMahon and Dr. Karthik Anantharaman at the University of Wisconsin Madison as part of the Freshwater and Marine Science program. I'm interested in developping my microbial ecology and bioinformatics skills. My research is about how we can integrate genome-resolved metagenomics and biogeochemistry measurements to better model nutrient dynamics in freshwater lakes, particularly in the hypolimnion (the deeper, colder and often oxygen-free layer of lakes which are seasonally stratified). I'm assoociated with the Department of Bacteriology, the Department of Integrative Biology and the Long-Term Ecological Research network on campus.
MASTER OF SCIENCE IN BIOLOGY DEGREE
I joined the laboratory of Dr. David Walsh at Concordia University to pursue my interest in applying genomic methods to answer ecological questions. I worked on developping methods to analyse metagenomic and metatranscriptomic datasets. As part of my M.Sc. thesis, I worked on the diversity and activity of microbes under ice in seasonally ice-covered lakes. Read my paper here, and my contribution to a colleague's work here.
During that time, I was a trainee in the NSERC-CREATE EcoLac program, a training program in lake and river ecology from 20016 to 2018. During my M.Sc. I served as the elected graduate student representative for Concordia University at the Group for Inter-university Research in Limnology and the Canadian Society of Microbiologists.
I've attended or presented my work at International Society of Microbial Ecology (ISME), the Group for Inter-university Research in Limnology (GRIL), the Canadian Society of Microbiologists (CSM) and the Association for the Sciences of Limnology and Oceanography (ASLO) conferences.
GRADUATE CERTIFICATE IN BIOINFORMATICS
After my undergraduate degree, I did a certificate at McGill University in Bioinformatics. I further developped hands-on skills in programming, structural bioinformatics (e.g. microscopy, imagery, drug discovery through library screenings), functional bioinformatics (clinical data analysis), genomics, and library & information sciences (teaching and understanding how bioinformatics is learnt).
BACHELOR OF SCIENCE HONOURS DEGREE
I did my undergraduate degree at McGill University in Environment, with a concentration in Conservation and Biodiversity. I graduate First Class Honours in the Faculty of Science (Physical Science, Math and Earth Sciences). I did my honours thesis under the supervision of Dr. Martin Lechowicz, on the conservation value of vernal pools in Southern Quebec.
FELLOWSHIPS & AWARDS
2019 Anna Grant Birge Scholarship, Center for Limnology, UW-Madison (Co-applicant on collaborative project with K. Kieft)
2019 National Science and Engineering Council of Canada (NSERC), Alexander Graham Bell CGS-D3 (Accepted PGS-D for taking abroad to UW-Madison)
2019 Capital Exchange Equipment Grant, Center for Limnology, UW-Madison
2018 Chancellor's Award, University of Wisconsin-Madison
2018 Peer-Reviewed Scientific Publication by a Graduate Student Award from GRIL
2018 National Conference Funding for GRIL Student Members
2018 Concordia Graduate Mobility Award, Concordia University
2017 Concordia University Conference and Exposition Award, Concordia University
2017 Fonds Québécois de Recherche en Nature et Technologie (FQRNT) M.Sc. Fellowship
2017 Concordia Graduate Scholarship in Natural Science and Engineering Research
2017 Best Talk by a M.Sc. Student at the GRIL Annual Symposium
2016 Natural Sciences and Engineering Research Council of Canada (NSERC)-CREATE ÉcoLac M.Sc. Scholarship, for 2 years. Honorary in 2017-2018 given FQRNT funding.
2016 Graduate Recruitment Fellowship, Faculty of Arts & Science, Concordia University
2016 First Class Honours, Faculty of Physical, Math and Earth Sciences, McGill University
2015 Quebec Center for Biodiversity Science (QCBS) Biodiversity Science Discovery Award, McGill University
2015 Science Undergraduate Research Awards, Faculty of Science, McGill University
Here is a list of my peer-reviewed publications and pre-prints.
Feel free to contact me for PDFs , if you can't access them online.
Click on logos below to be taken to my personal page on those platforms.
Elizabeth A. McDaniel, Benjamin Peterson, Sarah L.R. Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon. “Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation”. bioRxiv 2020.01.16.909358; DOI: https://doi.org/10.1101/2020.01.16.909358
Patricia Q. Tran, Peter B. McIntyre, Benjamin M. Kraemer, Yvonne M. Vadeboncoeur, Ismael A. Kimirei, Rashid Tamatamah, Katherine D. McMahon, Karthik Anantharaman. “Depth-discrete eco-genomics of Lake Tanganyika reveals roles of diverse microbes, including candidate phyla, in tropical freshwater nutrient cycling”. bioRxiv 834861; DOI: https://doi.org/10.1101/834861
Zhou, Z., Tran P.Q., Kieft K., Anantharaman K.. "Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation" BioRxiv: doi:
Zhou, Z., Tran P.Q., Liu Y., Kieft K., Anantharaman K. "METABOLIC: A scalable high-throughput metabolic and biogeochemical functional trait profiler based on microbial genomes". BioRxiv : doi: Github: https://github.com/AnantharamanLab/METABOLIC
Tran P., Ramachandran A., Khawasik O., Beisner B. E., Rautio M., Huot Y., and Walsh D.A. 2018 “Microbial life under ice: metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes”. Environmental Microbiology. doi:
Colatriano D., Tran P.Q., Guéguen C., Williams W.J., Lovejoy C., and Walsh D.A. 2018 “Genomic evidence for the degradation of terrestrial organic matter by Arctic Ocean Chloroflexi bacteria” Communications Biology. doi:
Below, you will find some pictures from my work (fieldwork, lakes I've worked on, etc.)