The Harke Lab

Research Focus | Team | Featured Collaborators | Featured Publications | Funding Sources | Gallery

From Genomes to Ecosystems: Understanding Microbial Drivers in a Changing Ocean

The Harke Lab, led by Research Scientist Matt Harke, Ph.D., investigates the genetic underpinnings of microbial life to understand how these invisible drivers shape our changing oceans. While Earth harbors an astounding diversity of microbial cells, their functional roles remain a frontier of discovery. By crossing trophic boundaries — from nutrient-poor open oceans to productive coastal estuaries — we identify the drivers of microbial diversity and toxicity. Our focus is to understand how these organisms interact with their environment today to predict the health and resilience of our oceans tomorrow.

Research Focus

We utilize molecular techniques — including metabarcoding, metatranscriptomics, and metagenomics — to measure what organisms are there, what they are doing, how they respond to change, and how that informs ocean health.

Harmful Algal Blooms (HAB) Ecology

We investigate the genetic and environmental drivers of toxic blooms in both freshwater and marine systems. By understanding the transcriptional responses of these organisms to nutrient stress and other triggers, we aim to predict bloom toxicity. A major applied focus of this work is the development of rapid, field-deployable CRISPR-based diagnostic tools to detect toxic species and pathogens in real-time, protecting both public health and aquaculture economies.

Projects:

NOAA MERHAB Project: Rapid Detection of Toxic Algae

This project focuses on employing a novel molecular toolbox for the rapid and sensitive detection of toxic Pseudo-nitzschia species. By developing field-deployable diagnostics, we aim to enhance early warning systems for harmful algal blooms, directly supporting coastal managers in mitigating impacts on shellfish resources.

Project Overview: Employing a Novel Molecular Toolbox for Rapid, Sensitive Detection of Toxic Pseudo-nitzschia Species

Marine Biodiversity

We are documenting the world’s oceans to understand what organisms are present, how that biodiversity is changing, and what that means for a future planet.

Projects:

Stellwagen Bank National Marine Sanctuary eDNA Biodiversity

Leveraging environmental DNA (eDNA), we are assessing ecosystem-wide biodiversity within the Stellwagen Bank National Marine Sanctuary. This work demonstrates how molecular tools can inform management strategies for Marine Protected Areas by providing a comprehensive, non-invasive view of species composition and ecosystem health.

Read the publication: Environmental DNA Documents Ecosystem-Wide Biodiversity Within the Marine Protected Area Stellwagen Bank National Marine Sanctuary

Ocean Biogeochemistry and Microbial Interactions

In the vast open ocean, how do diverse microbes coexist? We use molecular tools to explore how they partition resources and synchronize their metabolic activities. We do this across scales from single organism to whole community.

Projects:

OceanX Partnership

This partnership provides our lab with a global reach to document biodiversity, observe how it is changing, and interpret what those changes mean for ocean health. The collaboration allows us to leverage state-of-the-art technology to test new methods and hypotheses, leading to new discoveries in deep-sea and open-ocean environments.

Meet the Team

Lab Alumni

Sam Major: Research Associate at GMGI, went to Fieldstone Bio

Mia Bender: Marine Molecular Biology Co-op at GMGI, went to Northeastern University as Masters Student

Olivia Simon: OceanX Young Explorers Intern at GMGI, went to Verdantas Flow Labs

Featured Collaborators 

Peter Countway, Ph.D., Bigelow Labs

Kate Hubbard, Ph.D., Florida Fish and Wildlife Conservation Commission

Larissa Frühe, Ph.D., OceanX

Iain Kerr, Ph.D., Ocean Alliance

Dave Wiley, Ph.D., NOAA Stellwagen Bank NMS

Featured Publications

See Dr. Harke’s full list of publications here. 

Panthalil, B., Vogts, A., Benavides, M., Harke, M.J., Hassenrück, C., Subramaniam, A., Montoya, J.P., Voss, M. 2025. Novel pennate diatom symbionts support high N₂ fixation rates. ISME Communications. 5(1), ycaf190. https://doi.org/10.1093/ismeco/ycaf190

Polinski, J.M., Strand, E.L., O’Donnell, T.P., Silva, T.L., Wiley, D.N., & Harke, M.J. 2025. Ecosystem-wide biodiversity with environmental DNA can inform management of Marine Protected Areas. Environmental DNA. 7:3: e70138. doi: 10.1002/edn3.70138

Major, S.R., Polinski, J.M., Penn, K., Rodrigue, M., Harke, M.J. 2025. Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume. Applied and Environmental Microbiology. E02593-24. https://doi.org/10.1128/aem.02593-24.

Pillar, H., Hetherington, E., Levin, L. A., Cimoli, L., Lauderdale, J., Van Der Grient, J., Johannes, K., Heimbach, P., Smith, L., Addey, C. I., Annasawmy, P., Antonio, S., Bax, N., Drake, H. F., Escobar-Briones, E. G., Elser, L. G., Freilich, M., Gallo, N. D., Girard, F., Harke, M. J., Jones, D. O., Joshi, S., Liang, X., Maroni, P. J., Sarti, O., Stefanoudis, P. V., Sulpis, O., Trossman, D. 2024. Future Directions for Deep Ocean Climate Science and Evidence-Based Decision Making. Frontiers in Climate. 6:1445694. doi: 10.3389/fclim.2024.1445694

Polinski, J. M., M. Rodrigue, J. D. Meyer, M. J. Harke. 2023. Drifting in the deep: Metatranscriptomics and metabarcoding reveal sustained metabolic activity and community composition in hydrothermal vent plume microbial communities. Frontiers in Marine Science. 10:1219784. doi: 10.3389/fmars.2023.1219784

Funding Sources

Dalio Philanthropies | OceanX

Danaher Foundation

National Oceanic and Atmospheric Administration

WHOI Sea Grant

Harke Lab Gallery