Periodic Reporting for period 1 - NITRODEOX (Microbial network controls on N and N2O cycling in an deoxygenating ocean)
Reporting period: 2023-05-01 to 2025-04-30
The decline in oxygen content (deoxygenation) in the ocean is one of the major features of global change and affects biological processes and the biogeochemical cycling of key elements such as nitrogen (N). Oxygen minimum zones (OMZs) are intensifying and expanding their distribution, and many coastal waters such as estuaries and enclosed seas are experiencing seasonal anoxia events. OMZs and coastal waters are ecosystems with global relevance for N processing and hot spots for nitrous oxide (N2O) cycling. N2O is a major ozone-depleting substance and a potent greenhouse gas, and its microbial production depends on N and oxygen availability. So far, many studies have addressed the importance of environmental drivers in N and N2O cycling. However, they are incomplete predictors of ecosystem functioning. Contrarily, little attention has been paid to biotic community associations, despite they can exert selective pressure on marine microbes and affect ecosystem functioning. NITRODEOX aims to investigate the changes in microbial communities caused by ocean deoxygenation, and to assess how these changes affect N cycling and N2O production.
The project aims to:
SO1. To determine the changes in the taxonomic and functional diversity of microbial communities due to marine deoxygenation, with special emphasis on N-processing microorganisms
SO2. To quantify the rate of nitrification, N loss, and N2O production by nitrification and denitrification under changing oxygen conditions
SO3. To integrate taxonomical/functional composition results with N processing rates, and environmental variables to obtain taxonomical/functional association networks, respectively. These networks will be analysed with special emphasis on N-related microorganisms.
SO4. To identify key species and functions in networks affecting N cycling during deoxygenation, and construct metagenome-assembled genomes (MAGs) to investigate their full metabolic potential.
SO5. Model long-term changes in microbial networks and N cycling in OMZs and coastal waters using the global change scenarios for oxygen declining in the ocean
The project aims to:
SO1. To determine the changes in the taxonomic and functional diversity of microbial communities due to marine deoxygenation, with special emphasis on N-processing microorganisms
SO2. To quantify the rate of nitrification, N loss, and N2O production by nitrification and denitrification under changing oxygen conditions
SO3. To integrate taxonomical/functional composition results with N processing rates, and environmental variables to obtain taxonomical/functional association networks, respectively. These networks will be analysed with special emphasis on N-related microorganisms.
SO4. To identify key species and functions in networks affecting N cycling during deoxygenation, and construct metagenome-assembled genomes (MAGs) to investigate their full metabolic potential.
SO5. Model long-term changes in microbial networks and N cycling in OMZs and coastal waters using the global change scenarios for oxygen declining in the ocean
Over the course of the NITRODEOX project, significant progress was made in understanding how ocean deoxygenation affects microbial communities and nitrogen cycling. A central achievement was the successful execution of a 35-day oceanographic campaign in the Eastern Tropical South Pacific (ETSP), aboard the R/V Roger Revelle. This expedition, conducted during a strong El Niño event, provided a unique opportunity to study microbial and biogeochemical dynamics across a gradient of oxygen concentrations, including the core and boundary of the oxygen minimum zone (OMZ).
During the cruise, the fellow and lab colleagues collected approximately 4,000 samples across multiple depths and stations. These samples were used to quantify N2O concentration, and nitrogen transformation rates—particularly nitrification, denitrification, and N2O production. The samples produced during these experiments have been already measured. The fellow is currently working on analyzing these results.
In parallel, hundreds of samples were processed for DNA and RNA extraction, forming the basis for ongoing metagenomic analyses. These analyses aim to characterize microbial taxonomic and functional diversity and to build microbial association networks linked to nitrogen cycling. These analyses are still ongoing.
Training has been a cornerstone of the project. The fellow received hands-on experience in oceanography, bioinformatics, and network inference analysis, supported by expert mentorship and institutional resources. She participated in specialized workshops and seminars, enhancing her skills in metagenomics, data visualization, and scientific communication.
Dissemination activities have included presentations at international conferences (ASLO, ISME), invited talks at leading institutions (WHOI), and outreach events targeting diverse audiences. Two scientific manuscripts are in preparation, based on the ETSP campaign and complementary datasets.
During the cruise, the fellow and lab colleagues collected approximately 4,000 samples across multiple depths and stations. These samples were used to quantify N2O concentration, and nitrogen transformation rates—particularly nitrification, denitrification, and N2O production. The samples produced during these experiments have been already measured. The fellow is currently working on analyzing these results.
In parallel, hundreds of samples were processed for DNA and RNA extraction, forming the basis for ongoing metagenomic analyses. These analyses aim to characterize microbial taxonomic and functional diversity and to build microbial association networks linked to nitrogen cycling. These analyses are still ongoing.
Training has been a cornerstone of the project. The fellow received hands-on experience in oceanography, bioinformatics, and network inference analysis, supported by expert mentorship and institutional resources. She participated in specialized workshops and seminars, enhancing her skills in metagenomics, data visualization, and scientific communication.
Dissemination activities have included presentations at international conferences (ASLO, ISME), invited talks at leading institutions (WHOI), and outreach events targeting diverse audiences. Two scientific manuscripts are in preparation, based on the ETSP campaign and complementary datasets.
NITRODEOX has advanced the scientific frontier by investigating how ocean deoxygenation alters microbial communities and nitrogen cycling, particularly in oxygen minimum zones (OMZs). The project integrates high-resolution biogeochemical measurements with metagenomic analyses to uncover microbial interactions and functional dynamics under low-oxygen conditions.
The project has successfully completed objective SO2, quantifying N2O production rates by nitrification, denitrification, and photochemical processes (photochemodenitrification). These experiments revealed spatial variability in nitrogen transformation processes, and a significant contribution of photochemical N2O production to surface N2O production, contributing novel data to global N2O emission estimates.
Objectives SO1, SO3, and SO4 are currently in progress. Metagenomic datasets from the ETSP cruise and previous campaigns are being analyzed to assess changes in microbial taxonomic and functional diversity (SO1), construct microbial association networks (SO3), and identify key taxa and functions through metagenome-assembled genomes (SO4). These analyses will provide mechanistic understanding of microbial controls on nitrogen cycling under deoxygenation stress.
Objective SO5, focused on modeling long-term changes in microbial networks and nitrogen cycling under global change scenarios, will be addressed during the return phase. Preliminary steps have included reviewing modeling approaches and identifying relevant datasets and collaborators.
The project’s interdisciplinary approach—combining oceanography, molecular biology, and ecological modeling—positions NITRODEOX to deliver high-impact contributions to marine biogeochemistry. The expected outcomes will inform climate models, support sustainable marine management, and enhance our understanding of microbial ecosystem responses to environmental change.
The project has successfully completed objective SO2, quantifying N2O production rates by nitrification, denitrification, and photochemical processes (photochemodenitrification). These experiments revealed spatial variability in nitrogen transformation processes, and a significant contribution of photochemical N2O production to surface N2O production, contributing novel data to global N2O emission estimates.
Objectives SO1, SO3, and SO4 are currently in progress. Metagenomic datasets from the ETSP cruise and previous campaigns are being analyzed to assess changes in microbial taxonomic and functional diversity (SO1), construct microbial association networks (SO3), and identify key taxa and functions through metagenome-assembled genomes (SO4). These analyses will provide mechanistic understanding of microbial controls on nitrogen cycling under deoxygenation stress.
Objective SO5, focused on modeling long-term changes in microbial networks and nitrogen cycling under global change scenarios, will be addressed during the return phase. Preliminary steps have included reviewing modeling approaches and identifying relevant datasets and collaborators.
The project’s interdisciplinary approach—combining oceanography, molecular biology, and ecological modeling—positions NITRODEOX to deliver high-impact contributions to marine biogeochemistry. The expected outcomes will inform climate models, support sustainable marine management, and enhance our understanding of microbial ecosystem responses to environmental change.