SummaryAreas of low oxygen have spread exponentially over the past 40 years, and are cited as a key stressor on coastal ecosystems. The world's second largest coastal hypoxic (≤2 mg of O2 l −1 ) zone occurs annually in the northern Gulf of Mexico. The net effect of hypoxia is the diversion of energy flow away from higher trophic levels to microorganisms. This energy shunt is consequential to the overall productivity of hypoxic water masses and the ecosystem as a whole. In this study, water column samples were collected at 39 sites in the nGOM, 21 of which were hypoxic. Analysis of the microbial community along a hypoxic to oxic dissolved oxygen gradient revealed that the relative abundance (iTag) of Thaumarchaeota species 16S rRNA genes (> 40% of the microbial community in some hypoxic samples), the absolute abundance (quantitative polymerase chain reaction; qPCR) of Thaumarchaeota 16S rRNA genes and archaeal ammonia-monooxygenase gene copy number (qPCR) were significantly higher in hypoxic samples. Spatial interpolation of the microbial and chemical data revealed a continuous, shelfwide band of low dissolved oxygen waters that were dominated by Thaumarchaeota (and Euryarchaeota), amoA genes and high concentrations of phosphate in the nGOM, thus implicating physicochemical forcing on microbial abundance.

The recent trend of global warming has exerted a disproportionately strong influence on the Eurasian land surface, causing a steady decline in snow cover extent over the Himalayan-tibetan plateau region. Here we show that this loss of snow is undermining winter convective mixing and causing stratification of the upper layer of the Arabian Sea at a much faster rate than predicted by global climate models. over the past four decades, the Arabian Sea has also experienced a profound loss of inorganic nitrate. in all probability, this is due to increased denitrification caused by the expansion of the permanent oxygen minimum zone and consequent changes in nutrient stoichiometries. these exceptional changes appear to be creating a niche particularly favorable to the mixotroph, Noctiluca scintillans which has recently replaced diatoms as the dominant winter, bloom forming organism. Although Noctiluca blooms are non-toxic, they can cause fish mortality by exacerbating oxygen deficiency and ammonification of seawater. As a consequence, their continued range expansion represents a significant and growing threat for regional fisheries and the welfare of coastal populations dependent on the Arabian Sea for sustenance. The Arabian Sea (AS) is a unique, low-latitude oceanic ecosystem because it is influenced by monsoonal winds that reverse their direction seasonally 1. These reversing winds cause dynamic shifts in surface currents and alterations in the pycnocline, which help fertilize its normally nutrient-depleted surface layers. However, the mechanisms that drive water-column mixing, the upward transport of nutrients and the consequent upsurge of phytoplankton biomass during the summer (Jun.-Sep.) and the winter (Nov.-Feb.) monsoons are different 2-6. During the summer monsoon, nutrient enrichment is via coastal upwelling, which begins when the adjacent land mass becomes warmer relative to the AS, and low pressure develops over the Arabian Peninsula 3,7,8. During this time of the year, strong topographically-steered southwesterly winds blowing over the AS form a low-level atmospheric jet called the Findlater Jet 9. This jet induces a northeastwardly flow of the surface currents, leading to strong upwelling of deep, nutrient-rich waters, causing large phytoplankton blooms along the coasts of Somalia, Yemen, and Oman 3,5,6,10,11. In contrast, during winter, when the Eurasian continent cools, nutrient enrichment is via deep penetrative convective mixing as a result of excessive heat loss from the AS surface layer caused by cold and dry northeasterly winds blowing from the snow-covered Himalayan-Tibetan Plateau (HTP) 4,5. The erosion of the thermocline, and entrainment of deep (100-150 m) nutrient-rich waters into the surface layer of the AS, begins as early as Dec., and has a major influence on winter phytoplankton blooms observable as far south as 14°N 4,11,12 .

[1] The Navy Coastal Ocean Model (NCOM) is a free-surface, primitive-equation model that is under development at the Naval Research Laboratory (NRL). The NCOM-based model of the Monterey Bay area is evaluated during a series of upwelling and relaxation wind events in August-September of 2000. The model receives open boundary conditions from a regional NCOM implementation of the California Current System and surface fluxes from the Navy Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS TM )(COAMPS is a registered trademark of the Naval Research Laboratory). Issues investigated in this study are: NCOM-based model simulations of upwelling and relaxation events, coupling to COAMPS, use of sigma versus hybrid (sigma-z) vertical grids, and coupling with a larger-scale model on the open boundaries. The NCOM simulations were able to reproduce the observed sequence of the upwelling and relaxation events, which can be attributed, in part, to the good agreement between the observed and COAMPS winds. Comparisons with the mooring observations show that COAMPS overestimates shortwave radiation values, which makes the NCOM modeled SSTs too warm in comparison with observations. The NCOM runs forced with different resolution atmospheric forcing (3 versus 9 km) do not show significant differences in the predicted SSTs and mixed-layer depths at the mooring locations. At the same time, during the extended upwelling event, the model runs forced with 3 and 9 km resolution COAMPS fields show differences in the surface circulation patterns, which are the most distinct in the southern portion of the model domain. The model run with 9-km forcing develops a northward flow along the coast, which is not present in the run with 3-km forcing and in observations (for example, HF radar-derived radials). Comparison of the wind patterns of the 3-and 9-km products shows a weakening of the 9-km wind stress along the southern coast of the NCOM model domain, which is responsible for the development of the artificial northward flow in the NCOM run with 9-km forcing.

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[1] This paper introduces and evaluates a new atmospheric model reanalysis product for the U.S. west coast from the Navy's operational Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS 2 ) implemented on a triply nested 81/27/9 km grid. Wind measurements from Monterey Bay Aquarium Research Institute (MBARI) moorings are used to evaluate a two year time series of the model output from October 1998 to October 2000. The model accurately reproduced both the landward decrease in the large-scale wind field and the shoreward intensification of the diurnal cycle during the summer season. This new reanalysis product will be required for accurate high resolution (km) coastal (0 -10 km) simulations of the U.S. west coast by ocean models.INDEX TERMS: 3337

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Observations show significant differences in circulation patterns of upwelling and relaxation events that occurred in the Monterey Bay during two Autonomous Ocean Sampling Network field experiments in August 2003 and 2006. During the 2003 experiment, circulation exhibited more typical patterns associated with upwelling/relaxation: the development of the southward flowing jet and pair of cyclonic (inside of the bay) and anticyclonic (outside of the bay) circulations during upwelling and the development of the northward flow along the coast during relaxation of winds. During the upwelling event of 2006, the southward flow was weaker and shallower than in 2003. The second relaxation event of 2006 was significantly different from the first relaxation event of 2006 and the relaxation event of 2003: a southward flow was present along the entrance to the bay and this southward flow penetrated into the subsurface up to around 50 m at the mooring location. Two reasons for the observed differences in upwelling and relaxation events of 2003 and 2006 are identified in the paper: weaker winds in August 2006 than in August 2003 and strong positive sea surface height anomalies propagating poleward along the coast during 2006. The 2003 field program included an extensive sampling of the bay and surrounding areas with a fleet of underwater gliders, while during 2006 program, the extensive sampling was conducted in the area of upwelling center to the north of the Monterey Bay. During the 2003 field program, the Monterey Bay model was able to reproduce observed surface and subsurface features with assimilation of glider observations. However, during the 2006 field program, the assimilation of glider data from the upwelling center to the north of the Monterey Bay had minimal impact on model simulations of observed features to the south of the upwelling center.