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Process studies are designed to improve our understanding of poorly described physical processes that are central to the behavior of the climate system. They typically include coordinated efforts of intensive field campaigns in the atmosphere and/or ocean to collect a carefully planned set of in situ observations. Ideally the observational portion of a process study is paired with numerical modeling efforts that lead to better representation of a poorly simulated or previously neglected physical process in operational and research models. This article provides a framework of best practices to help guide scientists in carrying out more productive, collaborative, and successful process studies. Topics include the planning and implementation of a process study and the associated web of logistical challenges; the development of focused science goals and testable hypotheses; and the importance of assembling an integrated and compatible team with a diversity of social identity, gender, career stage, and scientific background. Guidelines are also provided for scientific data management, dissemination, and stewardship. Above all, developing trust and continual communication within the science team during the field campaign and analysis phase are key for process studies. We consider a successful process study as one that ultimately will improve our quantitative understanding of the mechanisms responsible for climate variability and enhance our ability to represent them in climate models.

Atlantic bluefin tuna (ABT) (Thunnus thynnus) travel long distances to spawn in oligotrophic regions of the Gulf of Mexico (GoM) which suggests these regions offer some unique benefit to offspring survival. To better understand how larval survival varies within the GoM a spatially explicit, Lagrangian, individual-based model was developed that simulates dispersal and mortality of ABT early life stages within realistic predator and prey fields during the spawning periods from 1993 to 2012. The model estimates that starvation is the largest cumulative source of mortality associated with an early critical period. However, elevated predation on older larvae is identified as the main factor limiting survival to late postflexion. As a result, first-feeding larvae have higher survival on the shelf where food is abundant, whereas older larvae have higher survival in the open ocean with fewer predators, making the shelf break an optimal spawning area. The modeling framework developed in this study explicitly simulates both physical and biological factors that impact larval survival and hence could be used to support ecosystem based management efforts for ABT under current and future climate conditions., ECOlogía trófica comparativa de LArvas de aTUN rojo atlántico (Thunnus thynnus) de las áreas de puesta del Medterraneo-NO y el Golfo de México., ECOLATUN, SI

Atlantic Bluefin tuna (ABT) (Thunnus thynnus) travel long distances to spawn in oligotrophic regions of the Gulf of Mexico. To estimate regional larval ABT mortality, we developed a spatially-explicit, Lagrangian, individual-based model that simulates dispersal, growth, and mortality within realistic predator and prey fields during the spawning periods from 1993-2012. Modelled larval ABT experience high mortality in the first week of feeding with an average mortality rate of 0.53 ± 0.26 d−1 prior to postflexion. Survival ranged from 0.12%–0.32% suggesting that recruitment may vary by a factor of 2.7 due to early life stage mortality alone. Starvation is the dominant source of mortality driven by the early critical period; however, survival is ultimately limited by predation on older individuals. As a result, first-feeding larvae survive better in the more food-rich areas on the shelf, while larger larvae survive better in the open ocean with fewer predators, making the shelf break an optimal spawning area. Our findings support the hypothesis that ABT spawn in oligotrophic regions to minimize predation on their larvae. Ocean modeling tools presented in this study may help facilitate an ecosystem-based management approach to improve future stock assessment models by better resolving the stock-recruitment relationship.

Functional ocean biogeography Marine ecosystems are well represented in metagenomic and transcriptomic data. These data are not routinely used to test ecosystem models that explore ocean biogeography or biogeochemistry. Coles et al. built a model in which genes for a range of functions were assigned to different suites of simulated microbes (see the Perspective by Rynearson). Communities emerged from the model with realistic biogeographical and biogeochemical profiles when compared to microbial data collected from the Amazon River plume. However, functional composition trumped the details of taxonomy, and different, coevolving community compositions emerged that provided similar biogeochemical outcomes. Science , this issue p. 1149 ; see also p. 1129

Metatranscriptomics and metagenomics data sets benchmarked with internal standards were used to characterize the expression patterns for biogeochemically relevant bacterial and archaeal genes mediating carbon, nitrogen, phosphorus and sulfur uptake and metabolism through the salinity gradient of the Amazon River Plume. The genes were identified in 48 metatranscriptomic and metagenomic data sets summing to >500 million quality-controlled reads from six locations in the plume ecosystem. The ratio of transcripts per gene copy (a direct measure of expression made possible by internal standard additions) showed that the free-living bacteria and archaea exhibited only small changes in the expression levels of biogeochemically relevant genes through the salinity and nutrient zones of the plume. In contrast, the expression levels of genes in particle-associated cells varied over orders of magnitude among the stations, with the largest differences measured for genes mediating aspects of nitrogen cycling (nifH, amtB and amoA) and phosphorus acquisition (pstC, phoX and phoU). Taxa varied in their baseline gene expression levels and extent of regulation, and most of the spatial variation in the expression level could be attributed to changes in gene regulation after removing the effect of shifting taxonomic composition. We hypothesize that changes in microbial element cycling along the Amazon River Plume are largely driven by shifting activities of particle-associated cells, with most activities peaking in the mesohaline regions where N2 fixation rates are elevated.

Climate change is reshaping the Chesapeake Bay ecosystem and its linked food system. Sea level rise and increased precipitation drive regular flooding events and the erosion of islands and coastal features. This results in the loss of habitat for various species of birds and fishes. Increased temperatures extend the growing season and reduce the incidence of frosts. Rising water temperatures accommodate the immigration of warm-adapted species and endanger populations of cold ones. Increased temperature interacts with cultural eutrophication to extend the duration and extent of seasonal hypoxia. Higher regional temperatures threaten human health, particularly populations of poorer residents that lack refuge from heatwaves and flooding events. Acidification of the Bay, which is linked to climate change agents, endangers species that rely upon calcium carbonate for shell and skeleton. Emission of greenhouse gases (GHGs, primarily CO2, NO2, CH4) from human economic activity drives climate change. The food system accounts for 25–30% of human GHGs emissions. Half of these comes from livestock, which contribute 14.5% of the global anthropogenic GHG load. Eliminating animal-based foods, particularly ruminants (cattle) would facilitate building a sustainable food system with improved health outcomes for the residents of the Chesapeake Bay Region.

As part of the ANACONDAS program, we investigated the role of the Amazon plume in stimulating offshore nitrogen fixation and export production during the river's high-discharge period (May–June 2010). Using the shipboard underway system, we performed high-resolution sampling of over 450,000 km2 of surface waters, characterizing the distribution of nutrients, phytoplankton, particulate organic matter (POM), and stable carbon and nitrogen isotopes of POM in the offshore plume. We found distinct regional variations in diazotroph communities, with the Diatom-Diazotroph Associations (DDA) Hemiaulus hauckii – Richelia intracellularis dominating the low N : P mesohaline waters to the northwest of the plume axis and Trichodesmium spp. primarily occupying oceanic waters to the east. Nutrient availability broadly shaped diazotroph distributions along the salinity gradient, but habitat longevity may also play a role in the finer-scale distributions of communities, particularly of DDAs. H. hauckii and Trichodesmium spp. affected the nitrogen and carbon budgets in fundamentally different ways within the plume-influenced regions, with H. hauckii making much greater contributions to the particulate nitrogen pool and to CO2 drawdown than Trichodesmium spp., leading to much higher export fluxes. Our findings provide an important constraint on the role of the Amazon plume in creating distinct niches and roles for diazotrophs in the nutrient and carbon budgets of the western tropical North Atlantic.

Plankton drive marine food webs and global biogeochemical cycles and are among the most challenging complex systems to model. Systems ecology studies on plankton might strongly profit from omics-based systems biology, which would add another dimension to traditional modelling. However, a deeper and adaptive integration with data-acquisition and data-analysis is required to achieve the goal. A feasible pipeline will integrate traditional and omics observations, over several time scales, in-vitro investigations, high-level computational approaches, such as niche and network modelling, and artificial intelligence methods. This will lead to a deeper understanding of our planet and to provision of knowledge-based directions to stakeholders.

Largely due to size differences, mesozooplankton are important exporters of carbon and prey for larger organisms, while microzooplankton are important recyclers of nutrients, dominant grazers of phytoplankton, and a key link in the microbial loop. We investigated the relative importance of meso- and microzooplankton grazing in the western tropical North Atlantic Ocean (WTNA) and Amazon River plume. Sampling as part of the ANACONDAS project occurred in spring (May–June) 2010 during the peak outflow of the Amazon River and in fall (September–October) 2011 during the plume seasonal retroflection. Mesozooplankton grazing rates decreased with increasing salinity in both seasons, but during the fall both day and nighttime grazing rates were significantly negatively correlated with salinity. Mesozooplankton grazing was highest in plume-influenced surface waters (0–25 m), and usually dominated by smaller size classes (0.2–0.5 mm and 0.5–1.0 mm). Microzooplankton grazing accounted for approximately 68% of bulk phytoplankton growth across all stations. Comparison of meso- and microzooplankton grazing suggests a transition in food web dynamics from a mesozooplankton dominated “export” structure in the plume transitioning to a microzooplankton dominated “retention” structure at mesohaline and oceanic stations above sea surface salinity of 33. Comparison between the seasons suggests a seasonal planktonic succession of low mesozooplankton grazing during the spring peak discharge followed by higher grazing rates and impact by mesozooplankton during the fall retroflection. These results provide important baseline information required for examining effects of climate change on the planktonic food web of the WTNA and for use in biogeochemical models of the region.

The plasticity of nitrogen specific net growth efficiency (NGE) in marine mesozooplankton is currently unresolved, with discordant lines of evidence suggesting that NGE is constant, or that it varies with nitrogen source, food availability, and food quality in marine ecosystems. Specifically, the fate of nitrogen from nitrogen fixation is poorly known. We use 15N : 14N ratios in plankton in combination with hydrological data, nutrient profiles, and nitrogen fixation rate measurements to investigate the relationship between new nitrogen sources and the nitrogen specific NGE in three plankton communities along the outer Amazon River plume. The NGE of small (200–500 μm) mesozooplankton was estimated from the δ15N differences between particulate nitrogen and zooplankton using an open system Rayleigh fractionation model. The transfer efficiency of nitrogen among larger (> 500 μm) mesozooplankton was estimated from the change in δ15N as a function of zooplankton size. The Amazon River was not a significant source of bioavailable nitrogen anywhere in our study region, and subsurface nitrate was the primary new nitrogen source for the outer shelf community, which was dominated by diatoms. N2 fixation was the principal new nitrogen source at sites of high diatom diazotroph association abundance and at oceanic sites dominated by Trichodesmium spp. and Synechococcus spp. Although we found clear spatial differences in food quantity, food quality, and diazotroph inputs into mesozooplankton, our data show no significant differences in mesozooplankton nitrogen transfer efficiency and NGE (for latter, mean ± SD: 59 ± 10%) among sites.

In this paper we examine time-series measurements of near-surface chlorophyll concentration from a mooring that was deployed at 80.5°E on the equator in the Indian Ocean in 2010. These data reveal at least six striking spikes in chlorophyll from October through December, at approximately 2-week intervals, that coincide with the development of the fall Wyrtki jets during the transition between the summer and winter monsoons. Concurrent meteorological and in situ physical measurements from the mooring reveal that the chlorophyll pulses are associated with the intensification of eastward winds at the surface and eastward currents in the mixed layer. These observations are inconsistent with upwelling dynamics as they occur in the Atlantic and Pacific oceans, since eastward winds that force Wyrtki jet intensification should drive downwelling. The chlorophyll spikes could be explained by two alternative mechanisms: (1) turbulent entrainment of nutrients and/or chlorophyll from across the base of the mixed layer by wind stirring or Wyrtki jet-induced shear instability or (2) enhanced southward advection of high chlorophyll concentrations into the equatorial zone. The first mechanism is supported by the phasing and amplitude of the relationship between wind stress and chlorophyll, which suggests that the chlorophyll spikes are the result of turbulent entrainment driven by synoptic zonal wind events. The second mechanism is supported by the observation of eastward flows over the Chagos–Laccadive Ridge, generating high chlorophyll to the north of the equator. Occasional southward advection can then produce the chlorophyll spikes that are observed in the mooring record. Wind-forced biweekly mixed Rossby gravity waves are a ubiquitous feature of the ocean circulation in this region, and we examine the possibility that they may play a role in chlorophyll variability. Statistical analyses and results from the OFAM3 (Ocean Forecasting Australia Model, version 3) eddy-resolving model provide support for both mechanisms. However, the model does not reproduce the observed spikes in chlorophyll. Climatological satellite chlorophyll data show that the elevated chlorophyll concentrations in this region are consistently observed year after year and so are reflective of recurring large-scale wind- and circulation-induced productivity enhancement in the central equatorial Indian Ocean.

We thank the following organizations and programs for financial contributions, support and endorsement: the U.S. National Oceanic and Atmospheric Administration; the U.S. Ocean Carbon and Biogeochemistry program funded by the National Science Foundation and the National Aeronautics and Space Administration; the NASA Physical Oceanography Program; Scripps Institution of Oceanography; and the Indo-US Science and Technology Forum.

The Indonesian throughflow (ITF) is a chokepoint in the upper ocean thermohaline circulation, carrying Pacific waters through the strongly mixed Indonesian Seas and into the Indian Ocean. Yet the influence of the ITF on biogeochemical fluxes into the Indian Ocean is largely unknown. This study determines the first depth- and time-resolved nitrate, phosphate, and silicate fluxes at the three main exit passages of the ITF: Lombok Strait, Ombai Strait, and Timor Passage. Nutrient flux as well as its variability with depth and time differs greatly between the passages. We estimate the effective flux of nutrients into the Indian Ocean by accounting for existing nutrients in the basin and find it largest in the upper 300–400 m. This suggests that the majority of ITF nutrient supply to the Indian Ocean is to thermocline waters, where it is likely to support new production and significantly impact Indian Ocean biogeochemical cycling.

An Advanced Laser Fluorometer (ALF) capable of discriminating several phytoplankton pigment types was utilized in conjunction with microscopic data to map the distribution of phytoplankton communities in the Amazon River plume in May–June-2010, when discharge from the river was at its peak. Cluster analysis and Non-metric Multi-Dimensional Scaling (NMDS) helped distinguish three distinct biological communities that separated largely on the basis of salinity gradients across the plume. These three communities included an ‘‘estuarine type’’ comprised of a high biomass mixed population of diatoms, cryptophytes and green-water Synechococcus spp. located upstream of the plume, a ‘‘mesohaline type’’ made up largely of communities of Diatom-Diazotroph Associations (DDAs) and located in the northwestern region of the plume and an ‘‘oceanic type’’ in the oligotrophic waters outside of the plume made up of Trichodesmium and Synechococcus spp. Although salinity appeared to have a substantial influence on the distribution of different phytoplankton groups, ALF and microscopic measurements examined in the context of the hydro-chemical environment of the river plume, helped establish that the phytoplankton community structure and distribution were strongly controlled by inorganic nitrate plus nitrite (NO3 +N O 2) availability whose concentrations were low throughout the plume. Towards the southern, low-salinity region of the plume, NO3 +N O 2 supplied by the onshore flow of subsurface (80 m depth) water, ensured the continuous sustenance of the mixed phytoplankton bloom. The large drawdown of SiO3 and PO4 associated with this ‘‘estuarine type’’ mixed bloom at a magnitude comparable to that observed for DDAs in the mesohaline waters, leads us to contend that, diatoms, cryptophytes and Synechococcus spp., fueled by the offshore influx of nutrients also play an important role in the cycling of nutrients in the Amazon River plume.

[1] The Amazon River Plume spreads across the tropical North Atlantic creating a barrier to vertical mixing. Here using a 1/6° HYCOM model and data from three research cruises in May–June 2010, September–October 2011, and July 2012, we investigate the pathways and properties of the plume. Four plume pathways for export of freshwater from the western tropical North Atlantic are identified. These consist of direct and indirect pathways to the northwest, and eastward pathways toward the subtropical gyre and toward Africa in the North Equatorial Counter Current. Because of the seasonality and cooccurrence of these pathways, plume characteristics are highly variable. Two pathways export water to the Caribbean, however the time scales associated with those direct and indirect pathways (3 versus 6+ months) differ, leading to different salinity characteristics of the plume water. Models results show that the Amazon river and tropical precipitation have similar magnitude impact on the observed seasonal cycle of freshwater within the western tropical Atlantic and at the 8°N, 38°W PIRATA mooring. Freshwater associated with the Amazon also influences surface salinity in winter as far as 20W in the model. The mean plume salinity minimum leads maximum discharge, highlighting the importance of currents and advection rather than discharge in maintaining plume properties. Plume pathways are tied to the underlying current structure, with the North Equatorial Counter Current jet preventing direct freshwater transport into the southern hemisphere. The plume influences underlying currents as well, generating vertical current shear that leads to enhanced eddy stirring and mixing in the model simulations.

Interannual variability in the abundances of blue crab (Callinectes sapidus) in populations along the U.S. east coast is well documented, but the mechanisms driving these fluctuations remain poorly understood. Using principal component analysis and dynamic factor analysis we quantified the patterns in variability and the degree of synchrony among blue crab populations along the U.S. east coast to gain insight into the mechanisms regulating the dynamics of these populations. We determined that a latitudinal pattern in the variability in abundance among the states existed and that a combination of the Gulf Stream Index, southern winter temperature, and larval mixing in the coastal ocean may be important drivers for the observed fluctuations of blue crab. The blue crab population in the Chesapeake Bay appeared to be an anomaly in that its abundance did not match the latitudinal trend seen in the other states. Understanding the dynamics of blue crab throughout its range may help managers determine which population responses reflect local dynamics and which may reflect shared, regional responses.

[1] We represented mechanistically the process of nitrogen (N) fixation and associated N* anomalies in the Atlantic Ocean using a three-dimensional coupled physical/biogeochemical model. Available direct measurements of N fixation rates in the Atlantic Ocean are compiled, and these, along with observed N* anomalies, constrain the model. The model N fixation rate for the whole Atlantic domain is 2.1 × 1012 molN yr–1. The model-generated N* anomaly shows the observed feature of a subsurface maximum. When plotted on isopycnal surfaces, the model-generated N* anomaly bears little relation to the pattern of N fixation at the surface. However, the highest N fixation rates should be spatially related to N* distribution if particulate export is remineralized at depths in the same region where the N fixation occurred. We performed case studies varying remineralization and advection to clarify the genesis of the N* anomaly and to determine the reasons underlying differences between N* anomalies and N fixation rate patterns. These studies indicated that the difference between these two patterns was created by both horizontal advection of excess N compared to phosphorus (P) and preferential remineralization of P compared to N. N fixation and preferential P remineralization create high N* anomalies both at the surface and in subsurface waters in the tropical Atlantic, which are transported into the northwestern North Atlantic by western boundary currents and subsequently subducted. As a result, the highest N* anomalies are located not in the tropics but in the northwestern North Atlantic.

We all know them: friends, colleagues, and students who left oceanography to pursue other careers. While their talents are certainly highly valued elsewhere, we are often left with lingering concerns that we could have done more to retain them in the field. Losing any oceanographer has an impact. The relatively small number of scientists in this profession leads to close collegial relationships, but the impact is broader than personal connections. Student training requires significant financial and time commitments by the advisor, scholarly institutions, and funding agencies (see sidebar). A recent study revealed that losses in physical oceanography are disproportionately female (Thompson et al., 2011). In a synthesis of the career paths of PhD graduates from six major physical oceanography programs, the authors find that 43% of female PhDs granted between 1980 and 2009 left independent research positions in physical oceanography, compared with 30% of men. Perhaps as a result, women in physical oceanography constitute only 16% of assistant professors and 22% of associate professors (Figure 1) despite healthy enrollment of women in graduate programs across the country. Of those graduates who remained as independent researchers, 73% of men were in tenured or government positions with relatively secure funding, as compared with 57% of women (Thompson et al., 2011). Rather than slowly populating the research field with women, the picture that emerges is one of women leaving the fields of science, engineering, and mathematics at all stages following their PhDs, but particularly at the transition between postdoctoral and full-time positions. This article describes a recent approach to retaining women through the development of mentor groups.

An unnecessary divide separates the marine biogeochemical modeling and omics research communities that impedes the utilization of new omics data in the development and validation of large-scale, three-dimensional, coupled physical–biogeochemical models. To close this gap we have to: (1) bridge the scientific, cultural, and structural divide that separates the marine biogeochemical modeling and omics research communities preventing scientific exchange and collaboration; (2) develop techniques for relating omics data to aspects of our current biogeochemical model structures and functions that allow useful comparisons between the models and the data; and (3) mobilize development of models that are more representative of the diverse microbial community composition and the associated diversity of metabolic functions that exists in marine waters so that this mapping can be realized to a greater degree. An important caveat here is that the latter may lead to the development of increasingly complex models, which creates both computational and validation challenges.

The overarching goal of this study is to simulate subsurface N* (sensu, Gruber and Sarmiento, 1997; GS97) anomaly patterns in the North Atlantic Ocean and determine the basin wide rates of N2-fixation that are required to do so. We present results from a new Atlantic implementation of a coupled physical-biogeochemical model that includes an explicit, dynamic representation of N2-fixation with light, nitrogen, phosphorus and iron limitations, and variable stoichiometric ratios. The model is able to reproduce nitrogen, phosphorus and iron concentration variability to first order. The latter is achieved by incorporating iron deposition directly into the model's detrital iron compartment which allows the model to reproduce sharp near surface gradients in dissolved iron concentration off the west coast of Africa and deep dissolved iron concentrations that have been observed in recent observational studies. The model can reproduce the large scale N* anomaly patterns but requires relatively high rates of surface nitrogen fixation to do so (1.8×1012 moles N yr−1 from 10° N–30° N, 3.4×1012 moles N yr−1 from 25° S–65° N). In the model the surface nitrogen fixation rate patterns are not co-located with subsurface gradients in N*. Rather, the fixed nitrogen is advected away from its source prior to generating a subsurface N* anomaly. Changes in the phosphorus remineralization rate (relative to nitrogen) linearly determine the surface nitrogen fixation rate because they change the degree of phosphorus limitation, which is the dominant limitation in the Atlantic in the model. Phosphorus remineralization rate must be increased by about a factor of 2 (relative to nitrogen) in order to generate subsurface N* anomalies that are comparable to the observations. We conclude that N2-fixation rate estimates for the Atlantic (and globally) may need to be revised upward, which will help resolve imbalances in the global nitrogen budget suggested by Codispoti et al. (2001) and Codispoti (2007).

The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function., Gordon and Betty Moore Foundation (River Ocean Continuum of the Amazon Project. Grants GBMF 2293 and 2928), National Science Foundation (U.S.) (Grant NSF-OCE 0934095)

We investigated expression of genes mediating elemental cycling at the microspatial scale in the ocean's largest river plume using, to our knowledge, the first fully quantitative inventory of genes and transcripts. The bacterial and archaeal communities associated with a phytoplankton bloom in Amazon River Plume waters at the outer continental shelf in June 2010 harbored ∼ 1.0 × 10(13) genes and 4.7 × 10(11) transcripts per liter that mapped to several thousand microbial genomes. Genomes from free-living cells were more abundant than those from particle-associated cells, and they generated more transcripts per liter for carbon fixation, heterotrophy, nitrogen and phosphorus uptake, and iron acquisition, although they had lower expression ratios (transcripts ⋅ gene(-1)) overall. Genomes from particle-associated cells contributed more transcripts for sulfur cycling, aromatic compound degradation, and the synthesis of biologically essential vitamins, with an overall twofold up-regulation of expression compared with free-living cells. Quantitatively, gene regulation differences were more important than genome abundance differences in explaining why microenvironment transcriptomes differed. Taxa contributing genomes to both free-living and particle-associated communities had up to 65% of their expressed genes regulated differently between the two, quantifying the extent of transcriptional plasticity in marine microbes in situ. In response to patchiness in carbon, nutrients, and light at the micrometer scale, Amazon Plume microbes regulated the expression of genes relevant to biogeochemical processes at the ecosystem scale.

International audience; The fresh Amazon/Orinoco plume covers in excess of 106 km2 in late summer–early fall forming a near-surface barrier layer that reduces exchange with the cooler, saltier water below. Barrier layers and higher water turbidity keep SST in the region high and thus are factors in the development of fall season hurricanes. Year to year changes in key properties of salinity and areal coverage may depend on a number of factors including river discharge, ocean rainfall, vertical entrainment rate, and horizontal advection. This study uses new sea surface salinity observations from the Aquarius/SACD and SMOS satellites to show that the plume was 1 psu saltier in early fall 2012 than in the previous fall (despite a stronger Amazon discharge in 2012) and explores the possible causes. The study concludes that the most likely causes of the 2012 salinification are a relative deficit of rainfall over the inflow to the plume region well southeast of the plume in spring and a weaker North Brazil current in spring–summer. The results suggest that tracking spring rainfall can potentially contribute to forecasting the Amazon plume stratification during the fall hurricane season.

The nutrient-rich waters of the Amazon River plume (ARP) support dense blooms of diatom-diazotroph assemblages (DDAs) that introduce large quantities of new nitrogen to the planktonic ecosystem and, unlike other nitrogen-fixers, are likely to directly fuel vertical carbon flux. To investigate the factors controlling DDA blooms, we develop a five phytoplankton (cyanobacteria, diatoms, unicellular microbial diazotrophs, DDAs, and Trichodesmium), two zooplankton model and embed it within a 1/6° resolution physical model of the tropical and subtropical Atlantic. The model generates realistic DDA blooms in the ARP and also exhibits basin-wide primary production, nitrogen fixation, and grazing rates consistent with observed values. By following ARP water parcels with synthetic Lagrangian drifters released at the river mouth we are able to assess the relative impacts of grazing, nutrient supply, and physical forcing on DDA bloom formation. DDA bloom formation is stimulated in the nitrogen-poor and silica-rich water of the ARP by decreases in grazing pressure when mesozooplankton (which co-occur in high densities with coastal diatom blooms) concentrations decrease. Bloom termination is driven primarily by silica limitation of the DDAs. In agreement with in situ data, this net growth niche for DDAs exists in a salinity range from ∼20–34 PSU, although this co-occurrence is coincidental rather than causative. Because net growth rates are relatively modest, bloom formation in ARP water parcels depends critically on the time spent in this ideal habitat, with high DDA biomass only occurring when water parcels spent >23 days in the optimal habitat niche.

A numerical exploration of inertial equilibrium states obtained with a primitive equation ocean model suggests that they can be described using statistical mechanics theory developed in the framework of quasi-geostrophy. The performance of the numerical model is first assessed with respect to the quasi-geostrophic model considering a series of experiments in the quasi-geostrophic range, in a closed basin with flat bottom and varying Rossby numbers. The results show that our model is consistent with the quasi-geostrophic model even in terms of dependence from boundary conditions and eddy viscosity values, and that the free surface contribution is negligible. As in the quasi-geostrophic experiments, a tendency toward Fofonoff flows is observed. This tendency remains in a second series of experiments performed outside the quasi-geostrophic range, namely with flows with higher Rossby numbers and with steep topography, characterized by sloping boundaries with an order one fractional change in the depth. It is only close to the boundaries that ageostrophic effects modify the flows. In conclusion, the fact that statistical mechanics theory, initially developed in the framework of quasi-geostrophy, holds for more realistic flows with steep topography supports development of subgrid scale parameterizations based on statistical mechanics theory, to be used in realistic general circulation models.

Data collected in 1988–1989, as part of the South Atlantic Ventilation Experiment, have been combined with the historical database to study the circulation and water mass variability of the abyssal water in the Argentine Basin. A map of potential temperature at 4000 m used as an indication of geostrophic shear defines a south and western intensified crescent-shaped abyssal recirculation. Within this recirculation, and its northward extension to the Brazil Basin, Antarctic Bottom Water (AABW) properties have undergone two modifications during the 1980s: (1) The water mass cooled (0.05°C) and freshened (0.008 in salinity ratio) on surfaces of constant density. (2) The densest layer of AABW was altered to less dense water through mixing or advection out of the study area. This water mass change does not appear to have affected the flow pattern. Data collected in 1983 and 1988 to the north in the Brazil Basin show penetration of the freshwater mass in the deep western boundary current to between 18°S and 10°S, indicating very rapid propagation of the anomaly from the Argentine Basin into the Brazil Basin as a deep western boundary current. It is suggested that open ocean convective events within the Weddell Sea contributed to the change in AABW documented here.

We present results from a new marine plankton model that combines selective biogeochemical processes with genetic information. The model allows for phytoplankton to adapt to a changing environment by invoking different utilization pathways for acquisition of nutrients (nitrogen and phosphorus) in response to concentration changes. The simulations use simplified environmental conditions represented by a continuously stirred tank reactor, which is populated by 96 different types of phytoplankton that differ in their physiological characteristics and nutrient uptake/metabolism genes. The results show that the simulated phytoplankton community structure is conceptually consistent with observed regional and global phytoplankton biogeography, the genome content from the dominant types of phytoplankton reflects the imposed environmental constraints, and the transcription of the gene clusters is qualitatively simulated according to the environmental changes. The model shows the feasibility of including genomic knowledge into a biogeochemical model and is suited to understanding and predicting changes in marine microbial community structure and function, and to simulating the biological response to rapid environmental changes.

[1] Offshore tropical river plumes are associated with areas of high N2 fixation (diazotrophy) and biological carbon drawdown. Episodic blooms of the diatom Hemiaulus hauckii and its diazotrophic cyanobacterial symbiont Richelia intracellularisare believed to dominate that carbon drawdown, but the mechanism is not well understood. We report primary productivity associated with blooms of these diatom-diazotroph assemblages (DDAs) in the offshore plume of the Amazon River using simultaneous measurements of O2/Ar ratios and the triple-isotope composition of dissolved O2. In these blooms, we observe peaks in net community productivity, but relatively small changes in gross primary productivity, suggesting that DDA blooms increase the ecosystem carbon export ratio more than twofold. These events of enhanced export efficiency lead to biological uptake of dissolved inorganic carbon and silicate, whose longer mixed-layer residence times otherwise obscure the differential impact of DDAs. The shorter-term rate estimates presented here are consistent with the results derived from longer-term geochemical tracers, confirming that DDAs drive a significant biological CO2 pump in tropical oceans.

Many of the anticipated changes (increased streamflow, warmer temperatures, calmer summer winds, and increased depth due to sea-level rise) associated with global climate change would move the Chesapeake Bay ecosystem in the direction of worsening hypoxia (harmful oxygen depletion).

[1] The Amazon River plume is a highly seasonal feature that can reach more than 3000 km across the tropical Atlantic Ocean, and cover ∼2 million km2. Ship observations show that its seasonal presence significantly reduces sea surface salinity and inorganic carbon. In the western tropical North Atlantic during April–May 2003, plume-influenced stations exhibited surface DIC concentrations lowered by as much as 563 μmol C kg−1 (∼28%) and pCO2 as low as 201 μatm. We combine our data with other data sets to understand the annual uptake and seasonal variability of the plume-related CO2 sink. Using flux estimates from all seasons with monthly plume areas determined by satellite, we calculate the annual carbon uptake by the outer plume alone (28 < S < 35) to be 15 ± 6 TgC yr−1. Diazotroph-supported net community production enhanced the air-sea CO2 disequilibrium by 100x and reversed the typical CO2 outgassing from the tropical North Atlantic. The carbon sink in the Amazon plume depends on climate-sensitive conditions that control river hydrology, CO2 solubility, and gas exchange.

[1] We evaluate the relationships of monthly climatological satellite measurements of sea surface height, temperature and chlorophyll-a to climatological subsurface parameters (mixed layer depth, thermocline depth, and Z2N, the 2 μmol NO3 isocline depth) on a global scale to determine the spatial variability and mechanisms underlying their relationships. The goal is to situate satellite surface data in the context of subsurface processes so that ultimately surface variability on longer timescales can be related to physical processes. There are well-defined physical regimes in the tropics (20°S–20°N), where surface and subsurface physical parameters are predominantly positively correlated because of the dominance of baroclinic processes, and the extratropics (20°–60° latitude), where they are negatively correlated, and barotropic processes dominate. The biological regimes differ between these regions. Correlations between surface chlorophyll and subsurface parameters are variable in the tropics, positive at midlatitudes (20°–40° latitude) and negative at high latitudes. We interpret these changing relationships in the context of differing underlying biophysical processes: dynamic uplift causing nutrient entrainment into the euphotic zone in parts of the tropics, seasonal entrainment of nutrients into the euphotic zone at midlatitudes, and seasonal controls on light supply at high latitudes. Together with the physical regimes, these biophysical conceptual models explain the relatively complex, broad-scale relationships between global satellite measurements of sea surface height, temperature, and chlorophyll-a on a climatological seasonal basis.

[1] Climatological satellite observations in the tropical North Atlantic generally show a wintertime surface chlorophyll-a (Chl-a) maximum except over a broad region in the western North Atlantic that has a summer Chl-a maximum. This region also shows decoupling between Chl-a and vertical nutrient flux, based on the positive relationship between sea surface height anomaly (SSH), sea surface temperature, and Chl-a. An analogous summer Chl-a maximum is simulated in a model including a dynamic representation of Trichodesmium and N2-fixation, but not in runs without. These results suggest that the growth is fuelled by N2-fixation. Using the observed summertime increase in Chl-a and the model efficiency for N2-fixation transfer to phytoplankton biomass, we calculate a nitrogen fixation rate of 220 μmol N m−2day−1 in this region. This constitutes the first satellite observation of the effect of nitrogen fixation on Chl-a, and may ultimately provide a means of deriving new global N2-fixation estimates.

[1] In this paper we use a biological-physical model with an explicit representation of Trichodesmium to examine the influence of N2 fixation in the Atlantic. Three solutions are examined, one where the N2 fixation rate has been set to observed levels, one where the rate has been increased to levels comparable to geochemical estimates, and one with no N2 fixation. All solutions are tuned to reproduce satellite surface chlorophyll concentrations, so that differences in the runs are manifested in productivity and export. Model runs with N2 fixation have different phytoplankton production and export distributions than runs without. Over the Atlantic basin the ecosystem “fixes” nitrogen at the rate of 1.47 × 1012 mol N yr−1, when tuned to observed phytoplankton and Trichodesmium biomass. This rate is comparable to the lower range of direct estimates of 1.3–2.2 × 1012mol N yr−1 [Capone et al., 1997; J. N. Galloway et al., manuscript in preparation, 2003; D. Capone et al., New nitrogen input in the tropical North Atlantic Ocean by nitrogen fixation, submitted to Nature, 2004, hereinafter referred to as Capone et al., submitted manuscript, 2004] but less than geochemical indirect estimates over a reduced domain (2.0 × 1012 mol N yr−1 [Gruber and Sarmiento, 1997] versus 0.55 × 1012 mol N yr−1 for the model). The nitrogen from N2 fixation increases new production by 30% and total production by 5%. However, it does not supplement upwelled nitrate sufficiently to bring production and export into line with remote sensing and geochemically derived estimates. Simulations with N2 fixation rates comparable to geochemical estimates show that reasonable phytoplankton concentrations can be maintained if export is increased. Moreover, phytoplankton productivity increases to values approaching remote-sensing-based estimates in the oligotrophic ocean. However, Trichodesmium biomass may be higher than observed.

[1] In this paper we use a coupled, 3-dimensional, biological-physical model, which includes an explicit, dynamic representation of Trichodesmium, to predict the distribution of Trichodesmium and rates of N2-fixation in the tropical and subtropical Atlantic Ocean. It is shown that the model reproduces the approximate observed meridional distribution of Trichodesmium in the Atlantic and elevated concentrations in specific coastal and open ocean regions where this organism is known to occur. The model also appears to reproduce the observed seasonality of Trichodesmium populations at higher latitudes (highest concentrations in summer and fall), but this seasonal cycle may be too pronounced at low latitudes. High and persistent Trichodesmium concentrations and rates of N2-fixation are generated by the model in the Gulf of Guinea off of Africa. This unexpected finding appears to be confirmed by historical measurements. In general, increased Trichodesmium concentrations develop in regions where the mixed layer is relatively thin (resulting in high mean light levels) and dissolved inorganic nitrogen (DIN) concentrations and phytoplankton biomass are low for extended periods of time. The model-predicted Trichodesmium distributions are therefore very sensitive to the fidelity of the physical model's representation of mixed layer depth variability, and upwelling intensity, and the biological model's estimated DIN and phytoplankton concentrations. The model generates a three-step successional sequence where (1) high DIN concentrations due to upwelling and/or mixing stimulate phytoplankton growth, followed by (2) Trichodesmium growth after DIN depletion and phytoplankton decline, followed by (3) enhanced phytoplankton growth due to new nitrogen inputs from N2-fixation. This sequence develops in response to seasonal variations in mixing in the southwestern North Atlantic and in response to upwelling along the coast of Africa and the equator. We interpret this sequence as representing a diatom- Trichodesmium-flagellate succession, which is consistent with observed species successions off of northwest Africa and in the Gulf of Mexico. The results presented in this paper lead us to conclude that our model includes the primary factors that dictate when and where Trichodesmium and N2-fixation occurs in the Atlantic. Moreover, it appears that our model reproduces some of the major effects that diazotrophically-derived inputs of new nitrogen have on the pelagic ecosystem.

The Indian Ocean is a dynamically complex and highly variable system, with circulation features and biogeochemical properties that are unusual in many respects. Yet the Indian Ocean (IO) remains one of the most undersampled and least understood of the world's ocean basins. In this article, we define several outstanding research questions that need to be addressed in the IO related to ocean currents and variability, the controls and fate of primary production, global change and anthropogenic impacts, and the role of higher trophic levels in ecological processes and biogeochemical cycles. We also discuss a unique opportunity that has recently arisen for staging research in the IO.