People

Stewart lab members

Stewart lab members

Frank Stewart

Associate Professor

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1242
frank.stewart@biology.gatech.edu
Personal Webpage, Curriculum Vitae


Post-Docs

Anthony Bertagnolli

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1120

My primary research interests surround the impact of lithotrophic microbes on oceanic and atmospheric chemistry. I’m specifically interested in the diversity, activity, and abundance of microorganisms involved in methane and ammonia oxidation and how these organisms are impacted by dissolved oxygen. To understand these populations, a combination of culture independent molecular approaches, culture dependent enrichment approaches, and process based rate estimates will be applied to water-column and sediment samples from differing oxygen minimum zone regimes.

 

Andrew Burns

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1120
andrew.burns@biology.gatech.edu

My personal interests lie in regulation of metabolism both within a single organism as well as through competition/interaction between organisms within a community. My current work uses meta-omic and culture-based approaches to study microbial communities that mediate coupled metal and sulfur transformations in aquatic sediments.

 

bombay

Nastassia Patin

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
email will update soon

I received my Ph.D. from Scripps Institution of Oceanography at UC San Diego, where I studied the chemical ecology of marine actinomycete bacteria. I am broadly interested in understanding the chemical interactions of marine microbial communities using a combination of meta-omic and culture-dependent techniques. As a postdoc in the Stewart Lab I am spearheading a project on the role of fish microbiota in degrading seaweed. I will also be exploring other marine microbial community dynamics, with a focus on host-microbe relationships and inter-species interactions.

Zoe Pratte

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
zoe.pratte@biology.gatech.edu

I received my Ph.D. from Florida International University, examining bleaching and disease susceptibilities of two closely related brain corals. For my Ph.D. investigations, I used a combination of microscopy, coral transcriptomics, and bacterial 16S rRNA metagenomics. In this lab, I plan to continue my work with bacterial metagenomics, exploring how gut microbiome communities differ in diversity and function among species and families of marine fish. Future investigations will elucidate how differences in fish microbiome communities affect the ecological behavior and health of fishes.

Neha Sarode

Dept. of Organismic and Evolutionary Biology, Harvard (current residence)
Biological Laboratories Building, 3103
nehasarode@fas.harvard.edu
http://girguislab.oeb.harvard.edu/people/neha-sarode

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
neha.sarode@biology.gatech.edu

The primary focus of my work is in line with our lab’s main interest, i.e. OMZ microbial ecology. My last project (manuscript in prep) was a collaborative effort with members of the Thamdrup lab (U. Southern Denmark), on metagenomics and biogeochemical analysis of nitrite accumulation in the Gulf of Mexico seasonal hypoxic zone.
Ongoing projects I am involved in are: (a) a meta-omic analysis of diversity and gene transcription in chemoautotrophic symbionts of the hydrothermal vent snail Ifremeria nautilei (in collaboration with the Girguis lab, Harvard); (b) a survey of coral-associated microbial diversity in response to coral-seaweed interactions (in collaboration with the Hay lab, Georgia Tech).


Graduate Students

Cory Padilla

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1122
cpadilla7@gatech.edu

I am interested in how oceanographic redox gradients affect microbial ecology, diversity, and metabolism. My dissertation research focuses on detecting and characterizing a recently reported metabolic pathway, nitrite-dependent anaerobic oxidation of methane (AOM), in permanent marine oxygen minimum zones (OMZ). The candidate bacterial clade NC10 is thought to utilize nitrite reduction to anaerobically oxidize methane, but has thus far been characterized primarily from freshwater sediments. My work explores the genetic diversity and activity of NC10-like bacteria in OMZs. This research combines functional gene surveys (PCR and qPCR), transcriptomics, environmental chemical measurements (collaborator P. Girguis, Harvard), and isotopic rate analysis (collaborators B. Thamdrup & L. Bristow, U. Southern Denmark). I am also using experimental incubations to enrich for nitrite-dependent AOM bacteria from OMZs and to characterize OMZ microbial transcription in response to methane stimulation. I am also interested in optimizing sample collection techniques. Work in this area includes testing a prototype auto-sampler for the in situ preservation of marine microbial RNA and exploring the effect of filtration methods on community composition estimates.

D Josh Parris

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1122
darren.parris@biology.gatech.edu

I am broadly interested in how the microbiome of eukaryotes influences host behavior, ecology, and health. Currently, I am using amplicon sequencing and metagenomics to characterize the diversity and function of bacteria in the gut of reef fishes. I plan to expand this work to targeted experimental systems as a means of understanding the role that gut microorganisms play in fish behavior and health. This work involves a collaboration with the lab of Dr. Danielle Dixson (Georgia Tech).

Piyush Ranjan

School of Biology, Georgia Institute of Technology
Environmental Science & Technology (ES&T) 1124
piyuranjan@gatech.edu

I have a developing research interest in microbial symbiosis. I am primarily interested in questions of how diverse microbial populations can co-exist within a host environment and how they interact with the host at functional and behavioral levels to affect host fitness. To this direction, I am involved in a project focusing on improving our understanding of the microbial diversity associated with a host-symbiont system in the deep sea hydrothermal vent snail Ifremeria nautilei. This work uses a combination of experimental, bioinformatics, metagenomic and metatranscriptomic analyses and is being done in collaboration with Dr. Pete Girguis (Harvard University). I am also involved in the analysis of single-cell genomes from free-living microbial populations in a marine OMZ.


Undergraduate Students

Rebecca Hollman

Georgia Tech undergrad researcher (beginning summer 2016), project: "Phylogenetic and diet determinants of microbiome diversity in diverse reef fish of Moorea" (supervised by Dr. Zoe Pratte)


Collaborators

 

Name

Affiliation

Project

 
Georgia Tech

Biodiversity of Iron-Respiring Microorganisms (NSF Dimensions)

 
University of Delaware

Reef fish microbiomes (Simons Foundation)

 
Georgia Tech

The Summer Workshop in Marine Science (SWiMS)

 

Georgia Tech

Novel processes of anaerobic microbial methane oxidation (NSF BIO OCE, NASA)

 

Harvard University

OMZ methane cycling, deep-sea symbiont transcriptomics, in situ RNA sampler instrumentation

 

Georgia Tech

Reef coral-microbiome-algae interactions

 

Georgia Tech

Single-cell genomics of OMZ bacteria (DOE CSP)

 

Georgia Tech

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)

 

University of Connecticut

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)

 

Roger Williams University

Microbiomes of facultatively symbiotic corals

 

Georgia Tech

Biodiversity of Iron-Respiring Microorganisms (NSF Dimensions)

 

U. Southern Denmark

OMZ microbial biogeochemistry and novel processes of anaerobic methane oxidation (NSF BIO OCE, ERC)

 

DOE Joint Genome Institute

Single-cell genomics of OMZ bacteria (DOE CSP)

 

Georgia State

Computational analysis of metabolic pathway activity from RNA-seq data (NSF ABI)


Lab Alumni

 

Postdocs/Research Scientists

 
 

Jieying Wu

Postdoc (2014-2016), Georgia Tech, project: "Metagenomic and genomic analysis of novel anaerobic bacteria from marine environments"

 

Sherry Seston

Visiting Professor (2013), Alverno College, project: "Comparative metatranscriptomic analysis of Ifremeria nautilei endosymbionts in multiple individuals under different electron donating conditions"

 

Alejandro Caro-Quintero

Postdoc (2013), Georgia Tech, project: "Metagenomics of the Gulf of Mexico hypoxic zone"

 

Graduate students

 
 

Sangita Ganesh

Ph.D., 2016, School of Biological Sciences (in lab 2011-2016), thesis: "Environmental niche partitioning of microbial community genomic diversity, gene expression, and metabolism in a marine oxygen minimum zone", current: genomics researcher at Radiant Genomics

 

Undergraduates

 
 

Max Beecroft

Georgia Tech undergrad (in lab 2016), independent research: "Cichlid gut microbiome not dependent on diet"

 

Michael Morgan

Georgia Tech undergrad (in lab 2014-2016), independent research: "Determinants of gut microbiome diversity in reef fish"

 

Shelby Gantt

Georgia Tech undergrad (in lab 2014-2016), BIOL 4690 manuscript (2016): "Effects on the Pocillopora verrucosa microbiome when in contact with macroalgae under ocean acidification"

 

Natalie Moise

Georgia Tech undergrad - Sustainable Aquatics internship program, BIOL 4690 manuscript (2015): "Gut microbiome diversity shifts during development in the clownfish Amphiprion ocellaris"

 

Alex Huhman

Georgia Tech undergrad (in lab 2014-2015), BIOL 4690 manuscript (2015): "Variation in the gut microbiota diversity across subregions of the lionfish gastrointestinal tract"

 

Ben Stone

ACE REU undergrad (2015), Bowdoin College, project: "Quantitative gene analysis indicates dominance of SAR11 narG in a marine oxygen minimum zone"

 

Catherine Benson

ACE REU undergrad (2014), Middlebury College, project: "Methane cycling microorganisms in the Eastern Tropical North Pacific oxygen minimum zone"

 

Jack Cartee

Georgia Tech undergrad, senior thesis (2014): "Significant changes in microbial community composition in the Gulf of Mexico 'dead zone' over a diel cycle"

 

Abigail Shockey

Georgia Tech undergrad, senior thesis (2014): "The effects of variation in electron donor concentration and species on deep-sea endosymbiont community composition and gene expression"

 

Niko Alexandre

ACE REU undergrad (2012), Vassar College, project: "Effects of salinity changes on coastal water column microbial communities"

 

Sarah York

ACE REU undergrad (2011), U. Miami, project: "Development of new water contamination assessment tests for Escherichia coli"