Nutrient management offsets the effect of deoxygenation and warming on nitrous oxide emissions in a large US estuary.

Many estuaries experience eutrophication, deoxygenation and warming, with potential impacts on greenhouse gas emissions. However, the response of NO production to these changes is poorly constrained. Here we applied nitrogen isotope tracer incubations to measure NO production under experimentally manipulated changes in oxygen and temperature in the Chesapeake Bay-the largest estuary in the United States.

Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones.

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 its acknowledged requirement for oxygen, nitrite oxidation is observed in oxygen-depleted layers of the ocean's oxygen minimum zones (OMZs), challenging the current understanding of OMZ nitrogen cycling. Previous attempts to determine whether nitrite-oxidizing bacteria in the anoxic layer differ from known nitrite oxidizers in the open ocean were limited by cultivation difficulties and sequencing depth.

Aquatic nitrous oxide reductase gene () phylogeny and environmental distribution.

Nitrous oxide (NO) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric NO originates in aquatic environments. Reduction of NO to dinitrogen gas (N) requires the nitrous oxide reductase enzyme, which is encoded by the gene .

Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones.

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 mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the genus, which represent most, if not all, of the anammox bacteria in the global ODZs.

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences.

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia.

Particle-associated denitrification is the primary source of NO in oxic coastal waters.

The heavily human-perturbed coastal oceans are hotspots of nitrous oxide (NO) emission to the atmosphere. The processes underpinning the NO flux, however, remain poorly understood, leading to large uncertainties in assessing global NO budgets. Using a suite of nitrogen isotope labeling experiments, we show that multiple processes contribute to NO production throughout the estuarine-coastal gradient, sustaining intensive NO flux to the atmosphere.

Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones.

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 to N. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas NO. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions.

Pathways of NO production by marine ammonia-oxidizing archaea determined from dual-isotope labeling.

The ocean is a net source of the greenhouse gas and ozone-depleting substance, nitrous oxide (NO), to the atmosphere. Most of that NO is produced as a trace side product during ammonia oxidation, primarily by ammonia-oxidizing archaea (AOA), which numerically dominate the ammonia-oxidizing community in most marine environments. The pathways to NO production and their kinetics, however, are not completely understood.

Evaluation of Genomic Sequence-Based Growth Rate Methods for Synchronized Cultures.

Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in and . We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized cultures under different light intensities and temperatures.

Long-Term Fertilization Alters Nitrous Oxide Cycling Dynamics in Salt Marsh Sediments.

Salt marsh sediments are known hotspots for nitrogen cycling, including the production and consumption of nitrous oxide (NO), a potent greenhouse gas and ozone-depleting agent. Coastal eutrophication, particularly elevated nitrogen loading from the application of fertilizers, is accelerating nitrogen cycling processes in salt marsh sediments. Here, we examine the impact of long-term fertilization on nitrogen cycling processes with a focus on NO dynamics in a New England salt marsh.

Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone.

Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ.

Microbial niche differentiation explains nitrite oxidation in marine oxygen minimum zones.

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 denitrification and anammox, while retention occurs via nitrite oxidation to nitrate.

Microbial NO consumption in and above marine NO production hotspots.

The ocean is a net source of NO, a potent greenhouse gas and ozone-depleting agent. However, the removal of NO via microbial NO consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand NO consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic seawater for the first time.

Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for Nitrogen Budgets and Dynamics.

Nitrogen (N) is used in many of life's fundamental biomolecules, and it is also a participant in environmental redox chemistry. Biogeochemical processes control the amount and form of N available to organisms ("fixed" N). These interacting processes result in N acting as the proximate limiting nutrient in most surface environments.

Amperometric sensor for nanomolar nitrous oxide analysis.

Nitrous oxide is an important greenhouse gas and there is a need for sensitive techniques to study its distribution in the environment at concentrations near equilibrium with the atmosphere (9.6 nM in water at 20 °C). Here we present an electrochemical sensor that can quantify NO in the nanomolar range.

The Discovery of Twenty-Eight New Encapsulin Sequences, Including Three in Anammox Bacteria.

Many prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in "Candidatus Scalindua rubra" and "Candidatus Scalindua sp.

Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones.

Oxygen minimum zones (OMZs) are marine regions where O is undetectable at intermediate depths. Within OMZs, the oxygen-depleted zone (ODZ) induces anaerobic microbial processes that lead to fixed nitrogen loss via denitrification and anammox. Surprisingly, nitrite oxidation is also detected in ODZs, although all known marine nitrite oxidizers (mainly Nitrospina) are aerobes.

Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle.

Understanding the interactions between microbial communities and their environment sufficiently to predict diversity on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. However, modeling microbial communities is problematic, because (i) communities are complex, (ii) most descriptions are qualitative, and (iii) quantitative understanding of the way communities interact with their surroundings remains incomplete. One approach to overcoming such complications is the integration of partial qualitative and quantitative descriptions into more complex networks.

Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas.

nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary.

Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages.

Biological nitrogen fixation in the oxygen-minimum region of the eastern tropical North Pacific ocean.

Biological nitrogen fixation (BNF) was investigated above and within the oxygen-depleted waters of the oxygen-minimum zone of the Eastern Tropical North Pacific Ocean. BNF rates were estimated using an isotope tracer method that overcame the uncertainty of the conventional bubble method by directly measuring the tracer enrichment during the incubations. Highest rates of BNF (~4 nM day) occurred in coastal surface waters and lowest detectable rates (~0.

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific.

The ozone-depleting and greenhouse gas, nitrous oxide (NO), is mainly consumed by the microbially mediated anaerobic process, denitrification. NO consumption is the last step in canonical denitrification, and is also the least O tolerant step. Community composition of total and active NO consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase () genes using a functional gene microarray.