The role of a changing Arctic Ocean and climate for the biogeochemical cycling of dimethyl sulphide and carbon monoxide

Dimethyl sulphide (DMS) and carbon monoxide(CO) are climate-relevant trace gases that play key roles in the radiative budget of the Arctic atmosphere. Under global warming, Arctic sea ice retreats at an unprecedented rate, altering light penetration and biological communities, and potentially affect DMS and CO cycling in the Arctic Ocean. This could have socio-economic implications in and beyond the Arctic region. However, little is known about CO production pathways and emissions in this region and the future development of DMS and CO cycling. Here we summarize the current understanding and assess potential future changes of DMS and CO cycling in relation to changes in sea ice coverage, light penetration, bacterial and microalgal communities, pH and physical properties. We suggest that production of DMS and CO might increase with ice melting, increasing light availability and shifting phytoplankton community. Among others, policy measures should facilitate large scale process studies, coordinated long term observations and modelling efforts to improve our current understanding of the cycling and emissions of DMS and CO in the Arctic Ocean and of global consequences

Nitrous oxide and methane in a changing Arctic Ocean

Human activities are changing the Arctic environment at an unprecedented rate resulting in rapid warming, freshening, sea ice retreat and ocean acidification of the Arctic Ocean. Trace gases such as nitrous oxide (N2O) and methane (CH4) play important roles in both the atmospheric reactivity and radiative budget of the Arctic and thus have a high potential to influence the region’s climate. However, little is known about how these rapid physical and chemical changes will impact the emissions of major climate-relevant trace gases from the Arctic Ocean. The combined consequences of these stressors present a complex combination of environmental changes which might impact on trace gas production and their subsequent release to the Arctic atmosphere. Here we present our current understanding of nitrous oxide and methane cycling in the Arctic Ocean and its relevance for regional and global atmosphere and climate and offer our thoughts on how this might change over the coming decades

Reproducible and relocatable regional ocean modelling: fundamentals and practices

In response to an increasing demand for bespoke or tailored regional ocean modelling configurations, we outline fundamental principles and practices that can expedite the process to generate new configurations. The paper develops the principle of reproducibility and advocates adherence by presenting benefits to the community and user. The elements of this principle are reproducible workflows and standardised assessment, with additional effort over existing working practices being balanced against the added value generated. The paper then decomposes the complex build process, for a new regional ocean configuration, into stages and presents guidance, advice and insight for each component. This advice is compiled from across the NEMO (Nucleus for European Modelling of the Ocean) user community and sets out principles and practises that encompass regional ocean modelling with any model. With detailed and region-specific worked examples in Sects. 3 and 4, the linked companion repositories and DOIs all target NEMOv4. The aim of this review and perspective paper is to broaden the user community skill base and to accelerate development of new configurations in order to increase the time available for exploiting the configurations

Comparing benthic biogeochemistry at a sandy and a muddy site in the Celtic Sea using a model and observations

Results from a 1D setup of the European Regional Seas Ecosystem Model (ERSEM) biogeochemical model were compared with new observations collected under the UK Shelf Seas Biogeochemistry (SSB) programme to assess model performance and clarify elements of shelf-sea benthic biogeochemistry and carbon cycling. Observations from two contrasting sites (muddy and sandy) in the Celtic Sea in otherwise comparable hydrographic conditions were considered, with the focus on the benthic system. A standard model parameterisation with site-specific light and nutrient adjustments was used, along with modifications to the within-seabed diffusivity to accommodate the modelling of permeable (sandy) sediments. Differences between modelled and observed quantities of organic carbon in the bed were interpreted to suggest that a large part (>90%) of the observed benthic organic carbon is biologically relatively inactive. Evidence on the rate at which this inactive fraction is produced will constitute important information to quantify offshore carbon sequestration. Total oxygen uptake and oxic layer depths were within the range of the measured values. Modelled depth average pore water concentrations of ammonium, phosphate and silicate were typically 5–20% of observed values at the muddy site due to an underestimate of concentrations associated with the deeper sediment layers. Model agreement for these nutrients was better at the sandy site, which had lower pore water concentrations, especially deeper in the sediment. Comparison of pore water nitrate with observations had added uncertainty, as the results from process studies at the sites indicated the dominance of the anammox pathway for nitrogen removal; a pathway that is not included in the model. Macrofaunal biomasses were overestimated, although a model run with increased macrofaunal background mortality rates decreased macrofaunal biomass and improved agreement with observations. The decrease in macrofaunal biomass was compensated by an increase in meiofaunal biomass such that total oxygen demand remained within the observed range. The permeable sediment modification reproduced some of the observed behaviour of oxygen penetration depth at the sandy site. It is suggested that future development in ERSEM benthic modelling should focus on: (1) mixing and degradation rates of benthic organic matter, (2) validation of benthic faunal biomass against large scale spatial datasets, (3) incorporation of anammox in the benthic nitrogen cycle, and (4) further developments to represent permeable sediment processes

Association of bronchopulmonary sequestration with expression of the homeobox protein Hoxb-5.

Bronchopulmonary sequestration (BPS) is caused by the abnormal development of an accessory lung diverticulum from the foregut very early in embryogenesis. The developmental abnormalities seen with BPS suggest that this anomaly is caused by abnormal expression of homeobox genes, which control axial identity and organ-specific patterning during embryogenesis. The authors previously have shown that the homeobox gene Hoxb-5 is necessary for normal airway branching during lung development. The authors now report that BPS is associated with aberrant developmental expression of Hoxb-5 protein, suggesting that this Hox gene is involved in the development of BPS

Expression of Hoxb-5 during human lung development and in congenital lung malformations.

BACKGROUND: We have previously shown that the Hox gene Hoxb-5 is necessary for normal mouse lung branching morphogenesis. Abnormal Hoxb-5 regulation causes specific alterations in airway branching. We hypothesized that Hoxb-5 is similarly involved in human lung branching morphogenesis, and is abnormally expressed in bronchopulmonary sequestration (BPS) and congenital cystic adenomatoid malformation (CCAM), both of which are congenital lung malformations with abnormal airway development. METHODS: The temporal, spatial, and cellular expression of the Hoxb-5 protein was evaluated in normal human lung and BPS and CCAM tissue using Western blot analysis and immunocytochemistry. RESULTS: The expression of Hoxb-5 during human lung development showed strong similarities to that during mouse lung development. Western blots showed high Hoxb-5 protein levels in the pseudoglandular period (PSG), decreased but sustained levels in the canalicular period (CAN), and negligible levels during the alveolar period (ALV). Immunocytochemistry showed Hoxb-5 protein expression in mesenchymal cells around branching airways in the pseuodglandular period, subepithelial fibroblast localization (especially at airway branch points) in the CAN and minimal expression in the ALV. In BPS and CCAM tissue, Hoxb-5 protein levels were increased compared to age- and developmentally-matched lung tissue, and were more similar to the PSG and CAN with Hoxb-5-positive cells in mesenchyme surrounding abnormally branched airways. CONCLUSIONS: Hoxb-5 expression during human lung branching morphogenesis, which is similar to that observed in mouse lung development, indicates that it plays a role in controlling airway patterning. This notion is supported by results from BPS and CCAM tissue, in which Hoxb-5 is maintained in a manner typical of an earlier developmental stage and is associated with development of abnormal lung tissue