PATRICIA TRAN

PhD Candidate in Freshwater and Marine Sciences at the University of Wisconsin-Madison

ptran5 {at} wisc {dot} edu

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. I particularly care about teaching and actively am mentoring the next generation of scientists.

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MY RESEARCH

Lake and Mountainous Landscape

MICROBIAL ECOLOGY

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.

 
Calm Lake

AQUATIC ECOSYSTEMS

Over the years, I developed 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.

Circuit Board

BIOINFORMATICS

I use a combination of field studies, laboratory experiments 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. I'm interested in leveraging computational methods to laboratory, analytical techniques, and field work in order to gain a more hollistic understanding of the world around us. 

CV

Education

DOCTOR OF PHILOSOPHY, Department of Integrative Biology

(2018-Current) University of Wisconsin-Madison, Wisconsin, USA

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. My research is about concerns microbial ecology and metabolism in anoxic zones of freshwater lakes. Specifically -- 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 associated with the Department of Bacteriology, the Department of Integrative Biology and the Long-Term Ecological Research network on campus. I've taken courses in lake modelling, statistics for molecular biology, teaching in the college classroom (Science and Engineering), and Improv to improve science communication and teaching,

MASTER OF SCIENCE, Department of Biology

(2016-2018) Concordia University, Montreal, QC, Canada

I joined the lab of Dr. David Walsh to pursue my M.Sc. degree. With the aim to find a lab where I could combine both my interests in ecology and bioinformatics, I worked on under-ice microbial ecology and winter limnology. During my M.Sc. I was part of the NSERC-CREATE EcoLac training program. Additionally, I served as a graduate student representative for the Inter-university Research Group in Limnology (GRIL) and the Canadian Society of Microbiologists (CSM). I presented and attended a number of scientific conferences (GRIL, ISME 2016 in Montreal, CSM 2017 in Waterloo, the Association for the Sciences of Limnology and Oceanography (ASLO) 2018 in Victoria, BC). I had the chance to publish 2 peer-reviewed articles, and won the "best talk" award at GRIL2017. 

GRADUATE CERTIFICATE in BIOINFORMATICS

(2016) McGill University, Montreal, QC, Canada

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, McGill School of Environment, Faculty of Science

(2013-2015) McGill University, Montreal, QC, Canada

I received 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

2020

Anna Grant Birge Scholarship, Center for Limnology, UW-Madison

2019

US DoE Joint Genome Institute Community Science Project New Investigator with PI Anantharaman

Anna  Grant Birge Scholarship, Center for Limnology, UW-Madison (Co-applicant on collaborative project with K. Kieft)

Natural Science and Engineering Council of Canada (NSERC), Alexander Graham Bell CGS-D3 (Accepted PGS-D for taking abroad to UW-Madison)

Capital Exchange Equipment Grant, Center for Limnology, UW-Madison 

2018

Chancellor's Award, University of Wisconsin-Madison 
Peer-Reviewed Scientific Publication by a Graduate Student Award from GRIL 
National Conference Funding for GRIL Student Members 
Concordia Graduate Mobility Award, Concordia University 

2017

Concordia University Conference and Exposition Award, Concordia University

Fonds Québécois de Recherche en Nature et Technologie (FQRNT) M.Sc. Fellowship Concordia

Graduate Scholarship in Natural Science and Engineering Research 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.

Graduate Recruitment Fellowship, Faculty of Arts & Science, Concordia University 

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 
Science Undergraduate Research Awards, Faculty of Science, McGill University 

 

PUBLICATIONS

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.

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Peer-reviewed

  1. Benjamin D. Peterson, Elizabeth A. McDaniel, Anna G. Schmidt, Ryan F. Lepak, Patricia Q. Tran, Robert A. Marick, Jacob M. Ogorek, John F. DeWild, David P. Krabbenhoft, Katherine D. McMahon. “Mercury methylation trait dispersed across diverse anaerobic microbial guilds in a eutrophic sulfate-enriched lake”. Environmental Science and Technology. 2020. DOI: https://doi.org/10.1021/acs.est.0c05435 

  2. Elizabeth A. McDaniel, Benjamin D. Peterson, Sarah L. R. Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon.  "Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms". mSystems Aug 2020, 5 (4) e00299-20; DOI: 10.1128/mSystems.00299-2

  3. Zhou, Z., Tran, P.Q., Kieft, K. et al. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J (2020). https://doi.org/10.1038/s41396-020-0669-4

  4. 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: https://doi.org/10.1111/1462-2920.14283

  5. 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: https://doi.org/10.1038/s42003-018-0086-7

Pre-Prints

  1. Patricia Q. Tran, Bachand, S.C., 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  (In Review)

  2. 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: https://doi.org/10.1101/761643 Github: https://github.com/AnantharamanLab/METABOLIC (Submitted)

 

GALLERY

Below, you will find some pictures from my work (fieldwork, lakes I've worked on, etc.)

Lake Croche

Lake Croche (2017)

A bouy on Lake Croche (Quebec, Canada) takes environmental data continously. Lake Croche is part of the GLEON network.

Winter Sampling on Lake Mendota

Winter Sampling on Lake Mendota (2018)

Here, I am taking a water sample to bring back to the lab to analyse the microbial community under ice in freshwater lakes.

Sunset Mendota

Sunset Mendota (2018)

Sunset on Lake Mendota

Fieldwork at Sapelo Island, GA (2018)

Fieldwork at Sapelo Island, GA (2018)

Frozen Assets Festival (2019)

Frozen Assets Festival (2019)

A group of us at Water@UW volunteering at Frozen Assets, a annual fundraiser to support the Clean Lakes Alliance

24 Heures de Sciences (2017)

24 Heures de Sciences (2017)

Science outreach event at Parc Lafontaine, Montreal, Canada.

 

CONTACT ME

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Patricia Tran

Microbial Sciences Building

University of Wisconsin-Madison

Madison, WI, USA.

Email: ptran5 [at] wisc [dot] edu

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Calm Sea