Award: OCE-1924492

Oxygen is declining in parts of the ocean worldwide, creating regions known as oxygen minimum zones (OMZs). These low-oxygen waters are expanding in some areas and have major consequences for marine ecosystems, fisheries, and the ocean’s role in regulating Earth’s chemical balance. Microorganisms dominate these environments and drive the chemical reactions that control how carbon and nitrogen move through the ocean. However, before this project, scientists lacked direct measurements linking these chemical processes to the specific microbes responsible for them.

This project transformed our understanding of how OMZs function by combining advanced oceanographic technology, genomics, and single-cell analysis.During research cruises in oxygen-deficient regions of the Pacific Ocean, we deployed specialized instruments that measure microbial activity directly in the ocean (i.e. in situ). Traditional shipboard experiments can unintentionally introduce oxygen and disturb sensitive microbial communities. By conducting experiments in situ, we were able to quantify critical processes such as nitrogen loss (anammox and denitrification), nitrate and nitrite transformations, and dark carbon fixation while carefully monitoring oxygen at extremely low concentrations. We found that these processes are strongly layered with depth, reflecting subtle changes in oxygen and chemistry. We also discovered that even in the darkest, lowest-oxygen waters, microbes continue to fix carbon, producing organic matter that supports microbial food webs.

To determine which organisms were responsible for these processes, we reconstructed one of the largest genomic datasets ever assembled for oxygen-deficient marine environments. By analyzing more than 200 environmental DNA datasets from 12 low-oxygen regions around the world, we reconstructed more than two thousands microbial genomes. We also generated single-cell genomes from our study site, allowing us to directly connect genetic information to specific environmental conditions. These analyses revealed previously unknown microbial lineages that appear to be uniquely adapted to oxygen-poor waters and showed that many of these microbes possess flexible metabolisms, enabling them to survive in chemically stratified environments. We also uncovered evidence that some of the ocean’s most abundant bacteria exchange genetic material more frequently than previously recognized, providing new insight into how microbial species evolve and maintain diversity in the ocean.

A major innovation of this project was the development of a new method that links microbial identity to activity at the level of individual cells. Using a technique called SIP-Raman-CARD-FISH, we tracked how single microbial cells incorporate labeled forms of carbon and hydrogen into their biomass. We demonstrated that this method can accurately measure microbial growth without introducing technical artifacts. Importantly, we discovered that microbial communities in OMZs are not uniformly active. Instead, individual cells within the same species can show dramatically different activity levels, suggesting complex survival strategies in chemically extreme environments. The analytical tools developed here are broadly applicable to freshwater systems, soils, engineered environments, and even biomedical research.

Beyond its scientific contributions, this project provided extensive training opportunities. US-based and international graduate studends, undergraduates, and visiting scholars gained hands-on experience in oceanographic fieldwork, isotope-based biogeochemistry, molecular biology, and computational genomics. A postdoctoral researcher developed new experimental equipment for low-oxygen rate measurements in collaboration with engineers at WHOI. International teams worked on integrating chemical rate measurements with genomic data, strengthening global scientific collaboration and capacity building.

The results of this project were widely disseminated through peer-reviewed publications in leading journals, presentations at international scientific conferences, and open-access data repositories. Outreach efforts during research cruises included live-streamed educational events, classroom presentations, and public engagement activities focused on ocean deoxygenation and the importance of microscopic life in the ocean. These efforts increased public awareness of how microorganisms regulate the ocean’s carbon and nitrogen cycles.

By directly linking microbial identity to the chemical transformations occurring in expanding low-oxygen regions of the ocean, this project provides essential knowledge for understanding how these regions influence marine ecosystems and global nutrient cycles. The datasets, tools, and methods developed through this award will serve as lasting resources for the scientific community and contribute to a deeper understanding of how the ocean functions under low-oxygen conditions.

 

Last Modified: 02/17/2026
Modified by: Maria Pachiadaki