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Abstract. As a key biogeochemical pathway in the marine nitrogen cycle, nitrification (ammonia oxidation and nitrite oxidation) converts the most reduced form of nitrogen – ammonium–ammonia (NH4+–NH3) – into the oxidized species nitrite (NO2-) and nitrate (NO3-). In the ocean, these processes are mainly performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). By transforming nitrogen speciation and providing substrates for nitrogen removal, nitrification affects microbial community structure; marine productivity (including chemoautotrophic carbon fixation); and the production of a powerful greenhouse gas, nitrous oxide (N2O). Nitrification is hypothesized to be regulated by temperature, oxygen, light, substrate concentration, substrate flux, pH and other environmental factors. Although the number of field observations from various oceanic regions has increased considerably over the last few decades, a global synthesis is lacking, and understanding how environmental factors control nitrification remains elusive. Therefore, we have compiled a database of nitrification rates and nitrifier abundance in the global ocean from published literature and unpublished datasets. This database includes 2393 and 1006 measurements of ammonia oxidation and nitrite oxidation rates and 2242 and 631 quantifications of ammonia oxidizers and nitrite oxidizers, respectively. This community effort confirms and enhances our understanding of the spatial distribution of nitrification and nitrifiers and their corresponding drivers such as the important role of substrate concentration in controlling nitrification rates and nitrifier abundance. Some conundrums are also revealed, including the inconsistent observations of light limitation and high rates of nitrite oxidation reported from anoxic waters. This database can be used to constrain the distribution of marine nitrification, to evaluate and improve biogeochemical models of nitrification, and to quantify the impact of nitrification on ecosystem functions like marine productivity and N2O production. This database additionally sets a baseline for comparison with future observations and guides future exploration (e.g., measurements in the poorly sampled regions such as the Indian Ocean and method comparison and/or standardization). The database is publicly available at the Zenodo repository: https://doi.org/10.5281/zenodo.8355912 (Tang et al., 2023).
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Controls on nitrite oxidation in the upper Southern Ocean: insights from winter kinetics experiments in the Indian sector
Abstract. Across the Southern Ocean in winter, nitrification is the dominantmixed-layer nitrogen cycle process, with some of the nitrate producedtherefrom persisting to fuel productivity during the subsequent growingseason. Because this nitrate constitutes a regenerated rather than a newnutrient source to phytoplankton, it will not support the net removal ofatmospheric CO2. To better understand the controls on Southern Oceannitrification, we conducted nitrite oxidation kinetics experiments insurface waters across the western Indian sector in winter. While allexperiments (seven in total) yielded a Michaelis–Menten relationship withsubstrate concentration, the nitrite oxidation rates only increasedsubstantially once the nitrite concentration exceeded 115±2.3 to245±18 nM, suggesting that nitrite-oxidizing bacteria (NOB) require aminimum (i.e., “threshold”) nitrite concentration to produce nitrate. Thehalf-saturation constant for nitrite oxidation ranged from 134±8 to403±24 nM, indicating a relatively high affinity of Southern OceanNOB for nitrite, in contrast to results from culture experiments. Despitethe high affinity of NOB for nitrite, its concentration rarely declinesbelow 150 nM in the Southern Ocean's mixed layer, regardless of season. Inthe upper mixed layer, we measured ammonium oxidation rates that were two-to seven-fold higher than the coincident rates of nitrite oxidation,indicating that nitrite oxidation is the rate-limiting step fornitrification in the winter Southern Ocean. The decoupling of ammonium andnitrite oxidation, combined with a possible nitrite concentration thresholdfor NOB, may explain the non-zero nitrite that persists throughout theSouthern Ocean's mixed layer year-round. Additionally, nitrite oxidation maybe limited by dissolved iron, the availability of which is low across theupper Southern Ocean. Our findings have implications for understanding thecontrols on nitrification and ammonium and nitrite distributions, both inthe Southern Ocean and elsewhere.
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- Award ID(s):
- 1946516
- PAR ID:
- 10485856
- Publisher / Repository:
- Copernicus Publications
- Date Published:
- Journal Name:
- Biogeosciences
- Volume:
- 19
- Issue:
- 14
- ISSN:
- 1726-4189
- Page Range / eLocation ID:
- 3425 to 3444
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some cores are significantly higher than the theoretical ratio range predicted from physiological traits of AOA and NOB characterized under realistic ocean conditions, indicating that some NOBs are yet to be discovered. Here we report a bacterial phylumCandidatusNitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments.Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilus) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) additionally appears in anoxic sediments. CountingCa. Nitrosediminicolota as a nitrite-oxidizer helps to resolve the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert controls on the nitrite budget.more » « less
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null (Ed.)Abstract Nitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N 2 O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N 2 O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N 2 O yields between 0.18 and 0.41 ng N 2 O–N per µg NO x –N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.more » « less
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Abstract Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia‐oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite‐oxidizing bacteria (NOB)Nitrotogadominate at depth in the summer, the ammonia‐oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.more » « less
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.5194/bg-19-3425-2022
