Amal Jayakumar
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View article: Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production
Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production Open
Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N 2 O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the amm…
View article: Nutrient management offsets the effect of deoxygenation and warming on nitrous oxide emissions in a large US estuary
Nutrient management offsets the effect of deoxygenation and warming on nitrous oxide emissions in a large US estuary Open
Many estuaries experience eutrophication, deoxygenation and warming, with potential impacts on greenhouse gas emissions. However, the response of N 2 O production to these changes is poorly constrained. Here we applied nitrogen isotope tra…
View article: Determination of site‐specific nitrogen cycle reaction kinetics allows accurate simulation of in situ nitrogen transformation rates in a large North American estuary
Determination of site‐specific nitrogen cycle reaction kinetics allows accurate simulation of in situ nitrogen transformation rates in a large North American estuary Open
Nitrogen (N) bioavailability affects phytoplankton growth and primary production in the aquatic environment. N bioavailability is partly determined by biological N cycling processes that either transform N species or remove fixed N. Reliab…
View article: Aquatic nitrous oxide reductase gene (nosZ) phylogeny and environmental distribution
Aquatic nitrous oxide reductase gene (nosZ) phylogeny and environmental distribution Open
Nitrous oxide (N 2 O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N 2 O originates in aquatic environments. Reduction of N 2 O to dinitrogen gas (N 2 ) requires the nitrous oxide reductase enzy…
View article: Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones
Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones Open
Nitrite is a central molecule in the nitrogen cycle because nitrite oxidation to nitrate (an aerobic process) retains fixed nitrogen in a system and its reduction to dinitrogen gas (anaerobic) reduces the fixed nitrogen inventory. Despite …
View article: Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones
Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones Open
Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechan…
View article: Editorial: Recent developments in oxygen minimum zones biogeochemistry
Editorial: Recent developments in oxygen minimum zones biogeochemistry Open
EDITORIAL article Front. Mar. Sci., 05 December 2023Sec. Marine Biogeochemistry Volume 10 - 2023 | https://doi.org/10.3389/fmars.2023.1333731
View article: Origin, age, and metabolisms of dominant anammox bacteria in the global oxygen deficient zones
Origin, age, and metabolisms of dominant anammox bacteria in the global oxygen deficient zones Open
Anammox bacteria inhabiting oxygen deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss and thus exerting a critical control on the nitrogen budget in the global ocean. However, the diversity, origin, and broad…
View article: Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N <sub>2</sub> fixation
Global oceanic diazotroph database version 2 and elevated estimate of global oceanic N <sub>2</sub> fixation Open
Marine diazotrophs convert dinitrogen (N2) gas into bioavailable nitrogen (N), supporting life in the global ocean. In 2012, the first version of the global oceanic diazotroph database (version 1) was published. Here, we present an updated…
View article: Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones
Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones Open
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3− to N2. This process may be performed entirely by…
View article: Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones
Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones Open
Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO 3 − to N 2 . This process may be performed entirel…
View article: Kinetics of nitrous oxide production from ammonia oxidation in the Eastern Tropical North Pacific
Kinetics of nitrous oxide production from ammonia oxidation in the Eastern Tropical North Pacific Open
Marine oxygen‐deficient zones represent a natural source of nitrous oxide (N 2 O), a potent greenhouse gas and ozone‐depleting agent. To investigate controls on N 2 O production, the responses of ammonia oxidation (AO) to nitrite () and N …
View article: Nitrous Oxide Consumption in Oxygenated and Anoxic Estuarine Waters
Nitrous Oxide Consumption in Oxygenated and Anoxic Estuarine Waters Open
Estuaries emit a large but highly uncertain amount of Nitrous oxide (N 2 O) into the atmosphere. To better understand N 2 O cycling processes in estuaries, we provide the first direct observations of N 2 O consumption in the seasonally ano…
View article: Nitrous oxide consumption in the Chesapeake Bay
Nitrous oxide consumption in the Chesapeake Bay Open
This dataset is associated with Tang, W., Jayakumar, A., Sun, X., Tracey, J. C., Carroll, J., Wallace, E., ... & Ward, B. (2022). Nitrous oxide consumption in oxygenated and anoxic estuarine waters. Geophysical Research Letters, 49(21), e2…
View article: Nitrous oxide production in the Chesapeake Bay
Nitrous oxide production in the Chesapeake Bay Open
This dataset is associated with Tang, W., Tracey, J. C., Carroll, J., Wallace, E., Lee, J. A., Nathan, L., ... & Ward, B. B. (2022). Nitrous oxide production in the Chesapeake Bay. Limnology and Oceanography, 67(9), 2101-2116. https://doi.…
View article: Correction: Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones
Correction: Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones Open
After publication of this article, the authors realized that proteins encoded by the OMZ NOB MAGs were incorrectly annotated as chlorite dismutase (Cld).They are homologs of Cld, and they should be called Cld-like proteins.Key residues for…
View article: Protocols for Assessing Transformation Rates of Nitrous Oxide in the Water Column
Protocols for Assessing Transformation Rates of Nitrous Oxide in the Water Column Open
Nitrous oxide (N 2 O) is a potent greenhouse gas and an ozone destroying substance. Yet, clear step-by-step protocols to measure N 2 O transformation rates in freshwater and marine environments are still lacking, challenging inter-comparab…
View article: Toward resolving disparate accounts of the extent and magnitude of nitrogen fixation in the Eastern Tropical South Pacific oxygen deficient zone
Toward resolving disparate accounts of the extent and magnitude of nitrogen fixation in the Eastern Tropical South Pacific oxygen deficient zone Open
Examination of dinitrogen (N 2 ) fixation in the Eastern Tropical South Pacific oxygen deficient zone has raised questions about the range of diazotrophs in the deep sea and their quantitative importance as a source of new nitrogen globall…
View article: Biological nitrous oxide consumption in oxygenated waters of the high latitude Atlantic Ocean
Biological nitrous oxide consumption in oxygenated waters of the high latitude Atlantic Ocean Open
Nitrous oxide (N 2 O) is important to the global radiative budget of the atmosphere and contributes to the depletion of stratospheric ozone. Globally the ocean represents a large net flux of N 2 O to the atmosphere but the direction of thi…
View article: Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones
Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones Open
Nitrite is a pivotal component of the marine nitrogen cycle. The fate of nitrite determines the loss or retention of fixed nitrogen, an essential nutrient for all organisms. Loss occurs via anaerobic nitrite reduction to gases during denit…
View article: Microbial N2O consumption in and above marine N2O production hotspots
Microbial N2O consumption in and above marine N2O production hotspots Open
The ocean is a net source of N2O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N2O via microbial N2O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expan…
View article: Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans
Diversity and distribution of nitrogen fixation genes in the oxygen minimum zones of the world oceans Open
Diversity and community composition of nitrogen (N) fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives…
View article: Anonymous Referee #2
Anonymous Referee #2 Open
In this study, the authors have reported the diversity and phylogeny of putative diazotrophs in the three major OMZs of the Ocean, including ETNP, ETSP and Arabian Sea.By analysing the clone libraries of nifH gene fragments derived from DN…
View article: Anonymous Referee #1
Anonymous Referee #1 Open
The study of Jayakumar and Ward investigates the microbial nitrogen fixing community in three major oxygen minimum zones in the worlds oceans.They took samples in the ETNP, ETSP and IO where they analysed OTUs using up-to-date DNA / RNA ex…
View article: Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru
Regulation of nitrous oxide production in low-oxygen waters off the coast of Peru Open
Oxygen-deficient zones (ODZs) are major sites of net natural nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contribu…
View article: Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans
Diversity and distribution of Nitrogen Fixation Genes in the Oxygen Minimum Zones of the World Oceans Open
Diversity and community composition of nitrogen fixing microbes in the three main oxygen minimum zones (OMZs) of the world ocean were investigated using operational taxonomic unit (OTU) analysis of nifH clone libraries. Representatives of …
View article: Regulation of nitrous oxide production in low oxygen waters off the coast of Peru
Regulation of nitrous oxide production in low oxygen waters off the coast of Peru Open
Oxygen deficient zones (ODZs) are major sites of net natural nitrous oxide (N2O) production and emissions. In order to understand changes in the magnitude of N2O production in response to global change, knowledge on the individual contribu…
View article: Dinitrogen Fixation Across Physico‐Chemical Gradients of the Eastern Tropical North Pacific Oxygen Deficient Zone
Dinitrogen Fixation Across Physico‐Chemical Gradients of the Eastern Tropical North Pacific Oxygen Deficient Zone Open
The Eastern Tropical North Pacific Ocean hosts one of the world's largest oceanic oxygen deficient zones (ODZs). Hot spots for reactive nitrogen (N r ) removal processes, ODZs generate conditions proposed to promote N r inputs via dinitrog…