A model‐based insight into the coupling of nitrogen and sulfur cycles in a coastal upwelling system

Azhar, Muchamad Al; Canfield, Donald E.; Fennel, Katja; Thamdrup, Bo; Bjerrum, Christian J.

doi:10.1002/2012jg002271

Cited by 28 publications

(34 citation statements)

References 63 publications

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“…under anaerobic conditions can use nitrate as the terminal electron acceptor rather than oxygen (Visscher and Taylor, 1993). For example, the oxidation of sulfur and thiosulfate can be linked to nitrate and nitrite reduction in both cultivars (Aminuddin and Nicholas, 1973) as well as in oceanic oxygen minimum zones (Azhar et al, 2014), suggesting that in the thrombolite-forming mats the sulfur and nitrogen cycle are closely coupled.…”

Section: Network Analysis Of Metabolic Pathwaysmentioning

confidence: 99%

A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles

Louyakis

Gourlé

Casaburi

et al. 2017

Environmental Microbiology

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Microbialites are one of the oldest known ecosystems on Earth and the coordinated metabolisms and activities of these mineral-depositing communities have had a profound impact on the habitability of the planet. Despite efforts to understand the diversity and metabolic potential of these systems, there has not been a systematic molecular analysis of the transcriptional changes that occur within a living microbialite over time. In this study, we generated metatranscriptomic libraries from actively growing thrombolites, a type of microbialite, throughout diel and seasonal cycles and observed dynamic shifts in the population and metabolic transcriptional activity. The most transcribed genes in all seasons were associated with photosynthesis, but only transcripts associated with photosystem II exhibited diel cycling. Photosystem I transcripts were constitutively expressed at all time points including midnight and sunrise. Transcripts associated with nitrogen fixation, methanogenesis and dissimilatory sulfate reduction exhibited diel cycling, and variability between seasons. Networking analysis of the metatranscriptomes showed correlated expression patterns helping to elucidate how metabolic interactions are coordinated within the thrombolite community. These findings have identified distinctive temporal patterns within the thrombolites and will serve an important foundation to understand the mechanisms by which these communities form and respond to changes in their environment.

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Section: Network Analysis Of Metabolic Pathwaysmentioning

confidence: 99%

A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles

Louyakis

Gourlé

Casaburi

et al. 2017

Environmental Microbiology

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“…MOM was operated using CORE-II forcing data (Large and Yeager, 2009) from 1950 to 2008. We also used data from the Surface Ocean CO 2 Atlas (SOCAT) (Bakker et al, 2016) from the analysis period to verify the CO 2 airsea gas flux in TOPAZ. The time periods for which SOCAT observational data exist for point 102 are April 2001, January 2005, November 2008, and December 2008.…”

Section: Methodsmentioning

confidence: 99%

A single-column ocean biogeochemistry model (GOTM–TOPAZ) version 1.0

et al. 2019

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Abstract. Recently, Earth system models (ESMs) have begun to consider the marine ecosystem to reduce errors in climate simulations. However, many models are unable to fully represent the ocean-biology-induced climate feedback, which is due in part to significant bias in the simulated biogeochemical properties. Therefore, we developed the Generic Ocean Turbulence Model–Tracers of Phytoplankton with Allometric Zooplankton (GOTM–TOPAZ), a single-column ocean biogeochemistry model that can be used to improve ocean biogeochemical processes in ESMs. This model was developed by combining GOTM, a single-column model that can simulate the physical environment of the ocean, and TOPAZ, a biogeochemical module. Here, the original form of TOPAZ has been modified and modularized to allow easy coupling with other physical ocean models. To demonstrate interactions between ocean physics and biogeochemical processes, the model was designed to allow ocean temperature to change due to absorption of visible light by chlorophyll in phytoplankton. We also added a module to reproduce upwelling and the air–sea gas transfer process for oxygen and carbon dioxide, which are of particular importance for marine ecosystems. The simulated variables (e.g., chlorophyll, oxygen, nitrogen, phosphorus, silicon) of GOTM–TOPAZ were evaluated by comparison against observations. The temporal variability in the observed upper-ocean (0–20 m) chlorophyll is well captured by the GOTM–TOPAZ with a correlation coefficient of 0.53 at point 107 in the Sea of Japan. The surface correlation coefficients among GOTM–TOPAZ oxygen, nitrogen, phosphorus, and silicon are 0.47, 0.31, 0.16, and 0.19, respectively. We compared the GOTM–TOPAZ simulations with those from MOM–TOPAZ and found that GOTM–TOPAZ showed relatively lower correlations, which is most likely due to the limitations of the single-column model. Results also indicate that source–sink terms may contribute to the biases in the surface layer (<60 m), while initial values are important for realistic simulations in the deep sea (>250 m). Despite this limitation, we argue that our GOTM–TOPAZ model is a good starting point for further investigation of key biogeochemical processes and is also useful to couple complex biogeochemical processes with various oceanic global circulation models.

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“…This study employed version 3.6 of ROMS (Shchepetkin & McWilliams, , ; Song & Haidvogel, ), with additional modifications to biogeochemistry that are detailed in Al Azhar et al (). ROMS is a terrain‐following, primitive equation regional ocean model.…”

Section: Methodsmentioning

confidence: 99%

Tracking the Paleocene‐Eocene Thermal Maximum in the North Atlantic: A Shelf‐to‐Basin Analysis With a Regional Ocean Model

Hantsoo

Kump

Haupt

et al. 2018

Paleoceanog and Paleoclimatol

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The Paleocene‐Eocene Thermal Maximum (PETM), a transient greenhouse climate interval spurred by a large release of carbon to the ocean‐atmosphere approximately 56 million years ago, provides a geological point of comparison for potential effects of anthropogenic carbon emission. Geochemical proxies and fossil assemblages offer insight into the continental shelf response to the PETM, but global ocean‐atmosphere models cannot resolve shelf processes at sufficient resolution for model‐data comparisons. We present high‐resolution simulations of the pre‐PETM and PETM North Atlantic basin using the Regional Ocean Modeling System (ROMS), including a resolved continental shelf along the eastern margin of North America in the Salisbury Embayment. ROMS' high‐resolution, terrain‐following coordinate system permits greater vertical resolution and eddy resolution along continental margins while also capturing open‐ocean processes. We find that during the PETM, benthic oxygen concentration ([O2]) in the Salisbury Embayment decreases 18% to an average state of year‐round mild hypoxia, while average benthic calcite saturation (Ω) declines from 4.4 to 2.3. These benthic decreases are driven largely by enhanced benthic oxic respiration, which occurs despite no increase in shelf productivity. Instead, increased respiration stems from less vigorous off‐shelf transport of organic matter due to (a) weakened along‐shelf water currents and (b) weakened coastal upwelling that forces productivity closer to the shelf seafloor. Model results do not include riverine inputs, which would have further lowered benthic [O2] and Ω. Our data suggest lowered benthic calcite saturation and mild hypoxia as an upper bound on the oxygenation state of the Salisbury Embayment seafloor during the PETM.

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A model‐based insight into the coupling of nitrogen and sulfur cycles in a coastal upwelling system

Cited by 28 publications

References 63 publications

A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles

A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles

A single-column ocean biogeochemistry model (GOTM–TOPAZ) version 1.0

Tracking the Paleocene‐Eocene Thermal Maximum in the North Atlantic: A Shelf‐to‐Basin Analysis With a Regional Ocean Model

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