Annual Review of Marine Science - Volume 7, 2015

This is a personal review of how one can apply the principles of physical chemistry to study the ocean and other natural waters. Physical chemistry is the study of chemical thermodynamics, kinetics, and molecular structure. My long-term interest in the chemistry of seawater is an extension of my early work on water and the interactions that occur in aqueous electrolyte solutions, which I began as part of my PhD research on the thermodynamics of organic acids in water. Over the years, I have attempted to apply the tools of physical chemistry to elucidate the structures of seawater, brines, lakes, and rivers. I have developed and continue to work on ionic interaction models that can be applied to all natural waters. Here, I reflect on how my students, postdocs, research assistants, and scientific colleagues have influenced my life, my career, and the field of marine physical chemistry. My hope was and is to use these tools to understand the molecular structures of natural waters.

This article reviews the past 15 years of developments in regional ocean data assimilation. A variety of scientific, management, and safety-related objectives motivate marine scientists to characterize many ocean environments, including coastal regions. As in weather prediction, the accurate representation of physical, chemical, and/or biological properties in the ocean is challenging. Models and observations alone provide imperfect representations of the ocean state, but together they can offer improved estimates. Variational and sequential methods are among the most widely used in regional ocean systems, and there have been exciting recent advances in ensemble and four-dimensional variational approaches. These techniques are increasingly being tested and adapted for biogeochemical applications.

Although the oceans play a fundamental role in shaping the distribution and function of coral reefs worldwide, a modern understanding of the complex interactions between ocean and reef processes is still only emerging. These dynamics are especially challenging owing to both the broad range of spatial scales (less than a meter to hundreds of kilometers) and the complex physical and biological feedbacks involved. Here, we review recent advances in our understanding of these processes, ranging from the small-scale mechanics of flow around coral communities and their influence on nutrient exchange to larger, reef-scale patterns of wave- and tide-driven circulation and their effects on reef water quality and perceived rates of metabolism. We also examine regional-scale drivers of reefs such as coastal upwelling, internal waves, and extreme disturbances such as cyclones. Our goal is to show how a wide range of ocean-driven processes ultimately shape the growth and metabolism of coral reefs.

We present a review of the processes, morphology, and stratigraphy of the Ganges-Brahmaputra-Meghna delta (GBMD), including insights gained from detailed elevation data. The review shows that the GBMD is best characterized as a composite system, with different regions having morphologic and stratigraphic attributes of an upland fluvial fan delta; a lowland, backwater-reach delta; a downdrift tidal delta plain; and an offshore subaqueous-delta clinoform. These distinct areas of upland and lowland fluvial reaches and tidal dominance vary in time and space, and we distinguish late-Holocene phases of delta construction, maintenance, and decline similar to delta-lobe cycling in other systems. The overall stability of the GBMD landform, relative to many deltas, reflects the efficient, widespread dispersal of sediment by the large monsoon discharge and high-energy tides that affect this region. However, we do identify portions of the delta that are in decline and losing elevation relative to sea level owing to insufficient sediment delivery. These areas, some of which are well inland of the coast, represent those most at risk to the continued effect of sea-level rise.

Rapid mass loss from the Greenland Ice Sheet has sparked interest in its glacial fjords for two main reasons: Increased submarine melting of glaciers terminating in fjords is a plausible trigger for glacier retreat, and the anomalous freshwater discharged from Greenland is transformed by fjord processes before being released into the large-scale ocean. Knowledge of the fjords' dynamics is thus key to understanding ice sheet variability and its impact on climate. Although Greenland's fjords share some commonalities with other fjords, their deep sills and deeply grounded glaciers, the presence of Atlantic and Polar Waters on the continental shelves outside the fjords' mouths, and the seasonal discharge at depth of large amounts of surface melt make them unique systems that do not fit existing paradigms. Major gaps in understanding include the interaction of the buoyancy-driven circulation (forced by the glacier) and shelf-driven circulation, and the dynamics in the near-ice zone. These must be addressed before appropriate forcing conditions can be supplied to ice sheet and ocean/climate models.

The Gulf Stream carries the warm, poleward return flow of the wind-driven North Atlantic subtropical gyre and the Atlantic Meridional Overturning Circulation. This northward flow drives a significant meridional heat transport. Various lines of evidence suggest that Gulf Stream heat transport profoundly influences the climate of the entire Northern Hemisphere and, thus, Europe's climate on timescales of decades and longer. The Gulf Stream's influence is mediated through feedback processes between the ocean, atmosphere, and cryosphere. This review synthesizes paleoclimate archives, model simulations, and the instrumental record, which collectively suggest that decadal and longer-scale variability of the Gulf Stream's heat transport manifests in changes in European temperature, precipitation, and storminess. Given that anthropogenic climate change is projected to weaken the Atlantic Meridional Overturning Circulation, associated changes in European climate are expected. However, large uncertainty in the magnitude of the anticipated weakening undermines the predictability of the future climate in Europe.

Mounting evidence indicates that spatial interactions are important in structuring coastal ecosystems. Until recently, however, most of this work has been focused on seemingly exceptional systems that are characterized by regular, self-organized patterns. In this review, we document that interactions that operate at long distances, beyond the direct neighborhood of individual organisms, are more common and have much more far-reaching implications for coastal ecosystems than was previously realized. We review studies from a variety of ecosystem types—including cobble beaches, mussel beds, coral reefs, seagrass meadows, and mangrove forests—that reveal a startling interplay of positive and negative interactions between habitats across distances of up to a kilometer. In addition to classical feeding relations, alterations of physical conditions constitute an important part of these long-distance interactions. This entanglement of habitats has crucial implications for how humans manage coastal ecosystems, and evaluations of anthropogenic impact should explicitly address long-distance and system-wide effects before we deem these human activities to be causing little harm.

Marine particles are a main vector by which the biological carbon pump in the ocean transfers carbon from the atmosphere to the deep ocean. Marine particles exist in a continuous spectrum of sizes, but they can be functionally grouped into a small, suspended class (which constitutes most of the total particle mass) and a large, sinking class (which contributes most of the particle flux). These two classes are connected by aggregation and disaggregation processes. The interplay of processes that create, aggregate, and destroy marine particles determines the strength and transfer efficiency of the biological pump. Measurements of radiocarbon, barium, and organic biomarkers on suspended and sinking particles have provided qualitative insights into particle dynamics, and measurements of thorium isotopes have provided quantitative estimates of rates. Here, we review what has been learned so far about particle dynamics in the ocean from chemical measurements on suspended and sinking particles. We then discuss future directions for this approach.

Most of the carbon fixed in primary production is rapidly cycled and remin-eralized, leaving behind various forms of organic carbon that contribute to a vast reservoir of nonliving organic matter in seawater. Most of this carbon resides in dissolved molecules of varying bioavailability and reactivity, and aspects of the cycling of this carbon remain an enigma. The size-reactivity continuum model provides a conceptual framework for understanding the mechanisms governing the formation and mineralization of this carbon. In the seawater bioassay experiments that served as the original basis for this model, investigators observed that larger size classes of organic matter were more bioavailable and more rapidly remineralized by microbes than were smaller size classes. Studies of the chemical composition and radiocarbon content of marine organic matter have further indicated that the complexity and age of organic matter increase with decreasing molecular size. Biodegradation processes appear to shape the size distribution of organic matter and the nature of the small dissolved molecules that persist in the ocean.

The phenomenon of subsurface chlorophyll maximum layers (SCMLs) is not a unique ecological response to environmental conditions; rather, a broad range of interacting processes can contribute to the formation of persistent layers of elevated chlorophyll a concentration (Chl) that are nearly ubiquitous in stratified surface waters. Mechanisms that contribute to the formation and maintenance of the SCMLs include a local maximum in phytoplankton growth rate near the nutricline, photoacclimation of pigment content that leads to elevated Chl relative to phytoplankton biomass at depth, and a range of physiologically influenced swimming behaviors in motile phytoplankton and buoyancy control in diatoms and cyanobacteria that can lead to aggregations of phytoplankton in layers, subject to grazing and physical control. A postulated typical stable water structure characterizes consistent patterns in vertical profiles of Chl, phytoplankton biomass, nutrients, and light across a trophic gradient structured by the vertical flux of nutrients and characterized by the average daily irradiance at the nutricline. Hypothetical predictions can be tested using a nascent biogeochemical global ocean observing system. Partial results to date are generally consistent with predictions based on current knowledge, which has strong roots in research from the twentieth century.

Phytoplankton size structure controls the trophic organization of planktonic communities and their ability to export biogenic materials toward the ocean's interior. Our understanding of the mechanisms that drive the variability in phytoplankton size structure has been shaped by the assumption that the pace of metabolism decreases allometrically with increasing cell size. However, recent field and laboratory evidence indicates that biomass-specific production and growth rates are similar in both small and large cells but peak at intermediate cell sizes. The maximum nutrient uptake rate scales isometrically with cell volume and superisometrically with the minimum nutrient quota. The unimodal size scaling of phytoplankton growth arises from ataxonomic, size-dependent trade-off processes related to nutrient requirement, acquisition, and use. The superior ability of intermediate-size cells to exploit high nutrient concentrations explains their biomass dominance during blooms. Biogeographic patterns in phytoplankton size structure and growth rate are independent of temperature and driven mainly by changes in resource supply.

Phytoplankton physiology is dynamic and highly responsive to the environment. Phytoplankton acclimate to changing environmental conditions by a complex reallocation of carbon and energy through metabolic pathways to optimize growth. Considering the tremendous diversity of phytoplankton, it is not surprising that different phytoplankton taxa use different strategies to partition carbon and energy resources. It has therefore been satisfying to discover that general principles of energetic stoichiometry appear to govern these complex processes and can be broadly applied to interpret phytoplankton distributions, productivity, and food web dynamics. The expectation of future changes in aquatic environments brought on by climate change warrants gathering knowledge about underlying patterns of photosynthetic energy allocation and their impacts on community structure and ecosystem productivity.

The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools—such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization—have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.

Marine scientists have long been interested in the interactions of marine phytoplankton with their chemical environments. Nutrient availability clearly controls carbon fixation on a global scale, but the interactions between phytoplankton and nutrients are complex and include both short-term responses (seconds to minutes) and longer-term evolutionary adaptations. This review outlines how genomics and functional genomics approaches are providing a better understanding of these complex interactions, especially for cyanobacteria and diatoms, for which the genome sequences of multiple model organisms are available. Transporters and related genes are emerging as the most likely candidates for biomarkers in stress-specific studies, but other genes are also possible candidates. One surprise has been the important role of horizontal gene transfer in mediating chemical-biological interactions.

Planktonic, prokaryotic, and eukaryotic photoautotrophs (phytoplankton) share a diverse and ancient evolutionary history, during which time they have played key roles in regulating marine food webs, biogeochemical cycles, and Earth's climate. Because phytoplankton represent the basis of marine ecosystems, the manner in which they die critically determines the flow and fate of photosynthetically fixed organic matter (and associated elements), ultimately constraining upper-ocean biogeochemistry. Programmed cell death (PCD) and associated pathway genes, which are triggered by a variety of nutrient stressors and are employed by parasitic viruses, play an integral role in determining the cell fate of diverse photoautotrophs in the modern ocean. Indeed, these multifaceted death pathways continue to shape the success and evolutionary trajectory of diverse phytoplankton lineages at sea. Research over the past two decades has employed physiological, biochemical, and genetic techniques to provide a novel, comprehensive, mechanistic understanding of the factors controlling this key process. Here, I discuss the current understanding of the genetics, activation, and regulation of PCD pathways in marine model systems; how PCD evolved in unicellular photoautotrophs; how it mechanistically interfaces with viral infection pathways; how stress signals are sensed and transduced into cellular responses; and how novel molecular and biochemical tools are revealing the impact of PCD genes on the fate of natural phytoplankton assemblages.

The Deepwater Horizon oil spill in the northern Gulf of Mexico represents the largest marine accidental oil spill in history. It is distinguished from past spills in that it occurred at the greatest depth (1,500 m), the amount of hydrocarbon gas (mostly methane) lost was equivalent to the mass of crude oil released, and dispersants were used for the first time in the deep sea in an attempt to remediate the spill. The spill is also unique in that it has been characterized with an unprecedented level of resolution using next-generation sequencing technologies, especially for the ubiquitous hydrocarbon-degrading microbial communities that appeared largely to consume the gases and to degrade a significant fraction of the petroleum. Results have shown an unexpectedly rapid response of deep-sea Gammaproteobacteria to oil and gas and documented a distinct succession correlated with the control of the oil flow and well shut-in. Similar successional events, also involving Gammaproteobacteria, have been observed in nearshore systems as well.

Fixed nitrogen limits primary productivity in many parts of the global ocean, and it consequently plays a role in controlling the carbon dioxide content of the atmosphere. The concentration of fixed nitrogen is determined by the balance between two processes: the fixation of nitrogen gas into organic forms by diazotrophs, and the reconversion of fixed nitrogen to nitrogen gas by denitrifying organisms. However, current sedimentary denitrification rates are poorly constrained, especially in permeable sediments, which cover the majority of the continental margin. Also, anammox has recently been shown to be an additional pathway for the loss of fixed nitrogen in sediments. This article briefly reviews sedimentary fixed nitrogen loss by sedimentary denitrification and anammox, including in sediments in contact with oxygen-deficient zones. A simple extrapolation of existing rate measurements to the global sedimentary denitrification rate yields a value smaller than many existing measurement-based estimates but still larger than the rate of water column denitrification.

The discovery of electric currents in marine sediments arose from a simple observation that conventional biogeochemistry could not explain: Sulfide oxidation in one place is closely coupled to oxygen reduction in another place, centimeters away. After experiments demonstrated that this resulted from electric coupling, the conductors were found to be long, multicellular, filamentous bacteria, now known as cable bacteria. The spatial separation of oxidation and reduction processes by these bacteria represents a shortcut in the conventional cascade of redox processes and may drive most of the oxygen consumption. In addition, it implies a separation of strong proton generators and consumers and the formation of measurable electric fields, which have several effects on mineral development and ion migration. This article reviews the work on electric currents and cable bacteria published through April 2014, with an emphasis on general trends, thought-provoking consequences, and new questions to address.

Mussels form dense aggregations that dominate temperate rocky shores, and they are key aquaculture species worldwide. Coastal environments are dynamic across a broad range of spatial and temporal scales, and their changing abiotic conditions affect mussel populations in a variety of ways, including altering their investments in structures, physiological processes, growth, and reproduction. Here, we describe four categories of ecomechanical models (biochemical, mechanical, energetic, and population) that we have developed to describe specific aspects of mussel biology, ranging from byssal attachment to energetics, population growth, and fitness. This review highlights how recent advances in these mechanistic models now allow us to link them together across molecular, material, organismal, and population scales of organization. This integrated ecomechanical approach provides explicit and sometimes novel predictions about how natural and farmed mussel populations will fare in changing climatic conditions.