Aquatic Microbial Dynamics Lab

Research

We use mathematical models to study how aquatic microorganisms grow, interact, and die. Our work spans ocean and freshwater systems, focusing on the ecological and biogeochemical consequences of microbial processes at the scale of individual cells through to the global ocean.

A central theme is understanding mortality in microbial communities. This includes losses due to viruses, grazers, pathogenic bacteria, and oxidative stress. We work closely with lab and field scientists to inform model development.

Publications

Microbial Primer: Bayesian learning of traits from microbial time series data

Dey R, Beach R, Hambrick KM, Sgouralis I, Frémont P, Demory D, Carr E, Beckett SJ, Weitz JS, Talmy D

Microbiology 2026
Acclimation temperature influences phage susceptibility in a toxin-producing strain of Microcystis aeruginosa

Hambrick KM, Smith LE, Martin RM, Wei B, Dey R, Boyer GL, Weitz JS, Talmy D, Wilhelm SW, Zinser ER

Microbiology Spectrum 2026
Resource competition modeling suggests hydrogen peroxide determines competitive outcomes among oligotrophic cyanobacteria

McCullough DK, Talmy D

ISME Communications 2026
Coexistence of photosynthetic marine microorganisms, viruses and grazers: towards integration in ocean ecosystem models

Frémont P, Beckett SJ, Demory D, Carr E, Follett CL, Lindell D, Talmy D, Dutkiewicz S, Weitz JS

Environmental Microbiology 2026
Quantification of the coupled dynamics of marine microbes and reactive oxygen species in laboratory batch culture experiments

McCullough DK, Bowden EC, Calfee BC, Gilchrist MA, Zinser ER, Talmy D

Microbiology Spectrum 2026
Viruses in multi-scale ocean models: challenges and opportunities

Talmy D, Howard-Varona C, Eveillard D, Covert M, Sullivan MB

Frontiers in Marine Science 2025
Quantitative assessment of biological dynamics with aggregate data

McCoy S, McBride D, McCullough DK, Calfee BC, Zinser ER, Talmy D, Sgouralis I

Bulletin of Mathematical Biology 2025
Coastal bacteria and protists assimilate viral carbon and nitrogen

Martínez Martínez J, Talmy D, Kimbrel JA, Weber PK, Mayali X

The ISME Journal 2024 10 citations
Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction

Lennon JT, Abramoff RZ, Allison SD, et al.

mBio 2024 36 citations
Killing the predator: impacts of top-predator mortality on global ocean ecosystem structure

Talmy D, Carr E, Rajakaruna H, Våge S, Omta AW

Biogeosciences 2024
Prioritization of the concepts and skills in quantitative education for graduate students in biomedical science

Gross LJ, McCord RP, LoRe S, Ganusov VV, Hong T, Strickland C, Talmy D, von Arnim AG, Wiggins G

PLOS ONE 2023
Trophic model closure influences ecosystem response to enrichment

Omta AW, Heiny EA, Rajakaruna H, Talmy D, Follows MJ

Ecological Modelling 2023
A model of algal–virus population dynamics reveals underlying controls on material transfer

Hinson A, Papoulis S, Fiet L, Knight M, Cho P, Szeltner B, Sgouralis I, Talmy D

Limnology and Oceanography 2023 13 citations
Life, death, and cyanobacteria biogeography

Talmy D

Nature Microbiology (News & Views) 2022
Linear scaling between microbial predator and prey densities in the global ocean

Rajakaruna H, Carr E, Omta AW, Talmy D

Environmental Microbiology 2022
The diel cycle of surface ocean elemental stoichiometry has implications for ocean productivity

Garcia NS, Talmy D, Fu WW, Larkin AA, Lee J, Martiny AC

Global Biogeochemical Cycles 2022 11 citations
Marine phytoplankton resilience may moderate oligotrophic ecosystem responses and biogeochemical feedbacks to climate change

Martiny AC, Hagstrom GI, DeVries T, Letscher RT, Britten GL, Garcia CA, et al.

Limnology and Oceanography 2022 48 citations
Open ocean particle flux variability from surface to seafloor

Cael BB, Bisson K, Conte M, Duret MT, Follett CL, Henson SA, Honda MC, et al.

Geophysical Research Letters 2021 19 citations
Nutrient loading and viral memory drive accumulation of restriction modification systems in bloom-forming cyanobacteria

Papoulis SE, Wilhelm SW, Talmy D, Zinser ER

mBio 2021 14 citations
Quantifying nutrient throughput and DOM production by algae in continuous culture

Omta AW, Talmy D, Sher D, Finkel ZV, Irwin AJ, Inomura K, Follows MJ

Journal of Theoretical Biology 2020
The “Neglected Viruses” of Taihu: abundant transcripts for viruses infecting eukaryotes and their potential role in phytoplankton succession

Pound HL, Gann ER, Tang X, Krausfeldt LE, Huff M, Staton ME, Talmy D, Wilhelm SW

Frontiers in Microbiology 2020 25 citations
A mechanistic model of macromolecular allocation, elemental stoichiometry, and growth rate in phytoplankton

Inomura K, Omta AW, Talmy D, Bragg J, Deutsch C, Follows MJ

Frontiers in Microbiology 2020 76 citations
An empirical model of carbon flow through marine viruses and microzooplankton grazers

Talmy D, Beckett SJ, Taniguchi DAA, Brussaard CPD, Weitz JS, Follows MJ

Environmental Microbiology 2019 40 citations
Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology

Nissimov JI, Talmy D, Haramaty L, Fredricks HF, Zelzion E, Knowles B, et al.

Environmental Microbiology 2019 23 citations
Contrasting controls on microzooplankton grazing and viral infection of microbial prey

Talmy D, Beckett SJ, Zhang AB, Taniguchi DAA, Weitz JS, Follows MJ

Frontiers in Marine Science 2019 30 citations
Light regulation of coccolithophore host–virus interactions

Thamatrakoln K, Talmy D, Haramaty L, Maniscalco C, Latham JR, et al.

New Phytologist 2019 41 citations
Extracting phytoplankton physiological traits from batch and chemostat culture data

Omta AW, Talmy D, Sher D, Finkel ZV, Irwin AJ, Follows MJ

Limnology and Oceanography: Methods 2017 16 citations
Diatom growth responses to photoperiod and light are predictable from diel reductant generation

Li G, Talmy D, Campbell DA

Journal of Phycology 2017 41 citations
Diel variability in the elemental composition of the marine cyanobacterium Synechococcus

Lopez JS, Garcia NS, Talmy D, Martiny AC

Journal of Plankton Research 2016 43 citations
Quantifying tradeoffs for marine viruses

Record NR, Talmy D, Våge S

Frontiers in Marine Science 2016 47 citations
Microzooplankton regulation of surface ocean POC:PON ratios

Talmy D, Martiny AC, Hill CN, Hickman AE, Follows MJ

Global Biogeochemical Cycles 2016 34 citations
Flexible C:N ratio enhances metabolism of large phytoplankton when resource supply is intermittent

Talmy D, Blackford J, Hardman-Mountford NJ, Polimene L, Follows MJ, Geider RJ

Biogeosciences 2014 62 citations
An optimality model of photoadaptation in contrasting aquatic light regimes

Talmy D, Blackford J, Hardman-Mountford NJ, Dumbrell AJ, Geider RJ

Limnology and Oceanography 2013 62 citations

Lab Members

Postdoctoral Researchers

Dr. Harshana Rajakaruna (2020–2022)

Now Systems Biology Modeler, Meharry Medical College
Dr. Spiro Papoulis (2020–2021)

Now Senior Scientist, Montage Bio
Dr. Audra Hinson (2018–2020)

Now Program Officer, Environmental Protection and Stewardship, Gulf Research Program, The National Academies of Sciences, Engineering, and Medicine

Graduate Students

Jackson Page-Roth

Microbiology Master’s Student, University of Tennessee (present)
Katie McCullough (2018–2024)

Microbiology PhD

Doctoral thesis: Modeling the impact of reactive oxygen species on ocean microbial community dynamics

Now Adjunct Professor, Pellissippi State Community College and South College
Kyla Linn (2018–2022)

Genome Science and Technology MS

Master’s thesis: Ecological controls on successional patterns in bloom forming cyanobacteria

Now Biology Teacher, Los Alamos Public Schools
Max Showalter (2019–2021)

Astrobiology Program, University of Washington

Thesis chapter: Modeling virus-host dynamics in sea ice brines

Now Policy Analyst, Washington State Department of Natural Resources

Undergraduates

Francesca Ravelli (2024–2025) — Math Honors Thesis
Emily Landolt (2023) — NSF Research Experience for Undergraduates
Kamryn Henderson (2021) — National Summer Undergraduate Research Project
Umang Joshi, Stephanie Westaway, Michael Lin (2020) — NIMBioS Research Experience for Undergraduates
Lucas Fiet, Margie Knight, Priscilla Cho (2019) — NIMBioS Research Experience for Undergraduates
Aaron Lin (2019) — NSF Research Experience for Undergraduates
Maitraya Ghatak (2018–2019) — Undergraduate Research in Microbiology
Brielle Shortreed (2018) — NSF Research Experience for Undergraduates

Lab Staff

Eric Carr (2020–present)

Technical Professional

Contact

Department of Microbiology
University of Tennessee, Knoxville
dtalmy@utk.edu

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