Interior pathways of the North Atlantic meridional overturning circulation

To understand how our global climate will change in response to natural and anthropogenic forcing, it is essential to determine how quickly and by what pathways climate change signals are transported throughout the global ocean, a vast reservoir for heat and carbon dioxide. Labrador Sea Water (LSW), formed by open ocean convection in the subpolar North Atlantic, is a particularly sensitive indicator of climate change on interannual to decadal timescales. Hydrographic observations made anywhere along the western boundary of the North Atlantic reveal a core of LSW at intermediate depths advected southward within the Deep Western Boundary Current (DWBC). These observations have led to the widely held view that the DWBC is the dominant pathway for the export of LSW from its formation site in the northern North Atlantic towards the Equator. Here we show that most of the recently ventilated LSW entering the subtropics follows interior, not DWBC, pathways. The interior pathways are revealed by trajectories of subsurface RAFOS floats released during the period 2003-2005 that recorded once-daily temperature, pressure and acoustically determined position for two years, and by model-simulated 'e-floats' released in the subpolar DWBC. The evidence points to a few specific locations around the Grand Banks where LSW is most often injected into the interior. These results have implications for deep ocean ventilation and suggest that the interior subtropical gyre should not be ignored when considering the Atlantic meridional overturning circulation.Dissertatio

Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein

Cystine-knot miniproteins (knottins) are promising molecular scaffolds for protein engineering applications. Members of the knottin family have multiple loops capable of displaying conformationally constrained polypeptides for molecular recognition. While previous studies have illustrated the potential of engineering knottins with modified loop sequences, a thorough exploration into the tolerated loop lengths and sequence space of a knottin scaffold has not been performed. In this work, we used the Ecballium elaterium trypsin inhibitor II (EETI) as a model member of the knottin family and constructed libraries of EETI loop-substituted variants with diversity in both amino acid sequence and loop length. Using yeast surface display, we isolated properly folded EETI loop-substituted clones and applied sequence analysis tools to assess the tolerated diversity of both amino acid sequence and loop length. In addition, we used covariance analysis to study the relationships between individual positions in the substituted loops, based on the expectation that correlated amino acid substitutions will occur between interacting residue pairs. We then used the results of our sequence and covariance analyses to successfully predict loop sequences that facilitated proper folding of the knottin when substituted into EETI loop 3. The sequence trends we observed in properly folded EETI loop-substituted clones will be useful for guiding future protein engineering efforts with this knottin scaffold. Furthermore, our findings demonstrate that the combination of directed evolution with sequence and covariance analyses can be a powerful tool for rational protein engineering

Modulations of the Chicken Cecal Microbiome and Metagenome in Response to Anticoccidial and Growth Promoter Treatment

With increasing pressures to reduce or eliminate the use of antimicrobials for growth promotion purposes in production animals, there is a growing need to better understand the effects elicited by these agents in order to identify alternative approaches that might be used to maintain animal health. Antibiotic usage at subtherapeutic levels is postulated to confer a number of modulations in the microbes within the gut that ultimately result in growth promotion and reduced occurrence of disease. This study examined the effects of the coccidiostat monensin and the growth promoters virginiamycin and tylosin on the broiler chicken cecal microbiome and metagenome. Using a longitudinal design, cecal contents of commercial chickens were extracted and examined using 16S rRNA and total DNA shotgun metagenomic pyrosequencing. A number of genus-level enrichments and depletions were observed in response to monensin alone, or monensin in combination with virginiamycin or tylosin. Of note, monensin effects included depletions of Roseburia, Lactobacillus and Enterococcus, and enrichments in Coprococcus and Anaerofilum. The most notable effect observed in the monensin/virginiamycin and monensin/tylosin treatments, but not in the monensin-alone treatments, was enrichments in Escherichia coli. Analysis of the metagenomic dataset identified enrichments in transport system genes, type I fimbrial genes, and type IV conjugative secretion system genes. No significant differences were observed with regard to antimicrobial resistance gene counts. Overall, this study provides a more comprehensive glimpse of the chicken cecum microbial community, the modulations of this community in response to growth promoters, and targets for future efforts to mimic these effects using alternative approaches

Mechanisms of decadal variability in the Labrador Sea and the wider North Atlantic in a high-resolution climate model

A necessary step before assessing the performance of decadal predictions is the evaluation of the processes that bring memory to the climate system, both in climate models and observations. These mechanisms are particularly relevant in the North Atlantic, where the ocean circulation, related to both the Subpolar Gyre and the Meridional Overturning Circulation (AMOC), is thought to be important for driving significant heat content anomalies. Recently, a rapid decline in observed densities in the deep Labrador Sea has pointed to an ongoing slowdown of the AMOC strength taking place since the mid 90s, a decline also hinted by in-situ observations from the RAPID array. This study explores the use of Labrador Sea densities as a precursor of the ocean circulation changes, by analysing a 300-year long simulation with the state-of-the-art coupled model HadGEM3-GC2. The major drivers of Labrador Sea density variability are investigated, and are characterised by three major contributions. First, the integrated effect of local surface heat fluxes, mainly driven by year-to-year changes in the North Atlantic Oscillation, which accounts for 62% of the total variance. Additionally, two multidecadal-to-centennial contributions from the Greenland-Scotland Ridge outflows are quantified; the first associated with freshwater exports via the East Greenland Current, and the second with density changes in the Denmark Strait Overflow. Finally, evidence is shown that decadal trends in Labrador Sea densities are followed by important atmospheric impacts. In particular, a negative winter NAO response appears to follow the positive Labrador Sea density trends, and provides a phase reversal mechanism

Atlantic Meridional Overturning Circulation: Observed Transport and Variability

The Atlantic Meridional Overturning Circulation (AMOC) extends from the Southern Ocean to the northern North Atlantic, transporting heat northwards throughout the South and North Atlantic, and sinking carbon and nutrients into the deep ocean. Climate models indicate that changes to the AMOC both herald and drive climate shifts. Intensive trans-basin AMOC observational systems have been put in place to continuously monitor meridional volume transport variability, and in some cases, heat, freshwater and carbon transport. These observational programs have been used to diagnose the magnitude and origins of transport variability, and to investigate impacts of variability on essential climate variables such as sea surface temperature, ocean heat content and coastal sea level. AMOC observing approaches vary between the different systems, ranging from trans-basin arrays (OSNAP, RAPID 26°N, 11°S, SAMBA 34.5°S) to arrays concentrating on western boundaries (e.g., RAPID WAVE, MOVE 16°N). In this paper, we outline the different approaches (aims, strengths and limitations) and summarize the key results to date. We also discuss alternate approaches for capturing AMOC variability including direct estimates (e.g., using sea level, bottom pressure, and hydrography from autonomous profiling floats), indirect estimates applying budgetary approaches, state estimates or ocean reanalyses, and proxies. Based on the existing observations and their results, and the potential of new observational and formal synthesis approaches, we make suggestions as to how to evaluate a comprehensive, future-proof observational network of the AMOC to deepen our understanding of the AMOC and its role in global climate

Interannual to decadal variability in a FESOM model setup, model data comparison of LSW layer thicknesses

The climate in the Atlantic region is essentially influenced by the Atlantic meridional overturning circulation (AMOC) which carries warm waters into northern latitudes and returns cold deep water southward across the equator. In the Labrador Sea basin a major component of the cold limb of the Atlantic meridional overturning circulation (AMOC) is formed. The intermediate water mass that is part of this deep convection process is the Labrador Sea Water (LSW) which can be separated into two different classes: the deep LSW (dLSW) and the less dense upper LSW (uLSW). Both LSW modes are formed by convection, accompanied by a strong surface cooling during winter conditions, which leads to an increase in the near-surface density and to an unstable stratification and a homogenization of the water column. In this study we simulated the deep-water formation in the Labrador Sea using the Finite-Element Sea-Ice Ocean Model (FESOM) in a global model setup with regional focus on the Labrador Sea and Greenland Sea. We evaluated the capability of the model setup to reproduce a realistic deep water formation in the Labrador Sea by analyzing the modeled Labrador Sea hydrography and we compared the modeled and observational derived dLSW and uLSW layer thicknesses for the time interval 1958-2007. It is shown that the model is able to reproduce different phases in the temporal evolution of the potential density, temperature and salinity, which are known in observational data. Based on composite maps of the thermal and haline contributions to the surface density flux we can prove that the central Labrador Sea in the model is dominated by the thermal contributions of the surface density flux, while the haline contributions are limited to the branch of the Labrador Sea Boundary Current system, where they are dominated from the haline contributions of sea ice melting and formation. Our model results feature a shielding of the central Labrador Sea from the haline contributions by the Labrador Sea Boundary Current system. Furthermore we investigated modes of interannual to decadal variability for the period 1958-2004 and attributed the general variability in the model to the atmospheric forcing and to internal modes of the ocean system. Based on a North Atlantic Deep Water (NADW) index defined for a normal and random forced FESOM run, where the interannual to decadal atmospheric variability in the random forced run is replaced by white noise, we identify modes of interannual to quasi-decadal variability of 7yr and 14yr, respectively. The origin of the 14yr variability is attributed to the atmospheric forcing, while the 7yr variability is linked to internal modes of the ocean. To further isolate the horizontal, but also the vertical variability in the model, we apply a principal oscillation pattern analysis in a three dimensional context. Two exceptional stable interannual modes are captured by the POP analysis and their variability is attributed to a propagating Rossby wave structure