Annual Review of Marine Science - Volume 5, 2013

Paraphrasing Pasteur, in scientific work Fortuna favors only the prepared mind. This is illustrated by my career after an incidental escape from the former German East Prussia just ahead of the Red Army, my switch in Kiel from zoology to oceanography, and my learning of a vacancy in Seattle. Treated here are the accidental discovery of upwelling during the southwest monsoon along India's west coast, studies of benthic polychaetous annelids in the Oregonian zoogeographic province, the discovery of phytoplankton blooms and an absence of upwelling during the northeast monsoon in the northern Arabian Sea, and an ocean-wide description of the seasonality of satellite-derived chlorophyll. My admonition is that grazing rather than cell division rate regulates the abundance and size composition of phytoplankton and affects the dynamics of the understudied zooplankton. I end with a pessimistic view about predicting the vertical flux of particulate organic matter from the euphotic layer with an accuracy useful for deep-sea carbon budgets.

Regional sea level changes can deviate substantially from those of the global mean, can vary on a broad range of timescales, and in some regions can even lead to a reversal of long-term global mean sea level trends. The underlying causes are associated with dynamic variations in the ocean circulation as part of climate modes of variability and with an isostatic adjustment of Earth's crust to past and ongoing changes in polar ice masses and continental water storage. Relative to the coastline, sea level is also affected by processes such as earthquakes and anthropogenically induced subsidence. Present-day regional sea level changes appear to be caused primarily by natural climate variability. However, the imprint of anthropogenic effects on regional sea level—whether due to changes in the atmospheric forcing or to mass variations in the system—will grow with time as climate change progresses, and toward the end of the twenty-first century, regional sea level patterns will be a superposition of climate variability modes and natural and anthropogenically induced static sea level patterns. Attribution and predictions of ongoing and future sea level changes require an expanded and sustained climate observing system.

Taiwan's unique setting allows it to release disproportionately large quantities of fluvial sediment into diverse dispersal systems around the island. Earthquakes, lithology, topography, cyclone-induced rainfall, and human disturbance play major roles in the catchment dynamics. Deep landslides dominate the sediment-removal process on land, giving fluvial sediment distinct geochemical signals. Extreme conditions in river runoff, sediment load, nearshore waves and currents, and the formation of gravity flows during typhoon events can be observed within short distances. Segregation of fresh biomass and clastic sediment occurs during the marine transport process, yet turbidity currents in the Gaoping Submarine Canyon carry woody debris. Strong currents in the slope and back-arc basin of the Okinawa Trough disperse fine-grained sediments rapidly and widely. Temporal deposition and remobilization may occur when the shallow Taiwan Strait acts as a receptacle. Taiwan can therefore serve as a demonstration of the episodic aspect of the source-to-sink pathway to both the coastal and deep-ocean environments.

It is increasingly important to understand and predict how marine environments respond to changes in climate and sea level and to variability in sediment flux from rivers. The dynamics of these factors occur over several orders of temporal magnitude and, under favorable geologic conditions, contribute to long-lived sediment accumulation. Thus, stratigraphic successions along continental margins are archives of these environmental changes and can be used to reconstruct land-ocean linkages, which provide important context for shorter-term and future modifications to this critical zone. Here, we discuss an integrated approach to the analysis of deep-time sediment archives (>10⁶ years) that considers the entire system, from eroding catchments where sediment is produced to subsiding basins where sediment accumulates. This holistic approach is presented within the framework of fundamental concepts about sedimentary-basin analysis and stratigraphic characterization through a combination of foundational literature and studies that represent the state of the art.

The shallow waters of the nearshore ocean are popular, dynamic, and often hostile. Prediction in this domain is usually limited less by our understanding of the physics or by the power of our models than by the availability of input data, such as bathymetry and wave conditions. It is a challenge for traditional in situ instruments to provide these inputs with the appropriate temporal or spatial density or at reasonable logistical or financial costs. Remote sensing provides an attractive alternative. We discuss the range of different sensors that are available and the differing physical manifestations of their interactions with the ocean surface. We then present existing algorithms by which the most important geophysical variables can be estimated from remote sensing measurements. Future directions and opportunities will depend on expected developments in sensors and platforms and on improving processing algorithms, including data assimilation formalisms.

This article reviews the discovery, development, and use of high-frequency (HF) radio wave backscatter in oceanography. HF radars, as the instruments are commonly called, remotely measure ocean surface currents by exploiting a Bragg resonant backscatter phenomenon. Electromagnetic waves in the HF band (3–30 MHz) have wavelengths that are commensurate with wind-driven gravity waves on the ocean surface; the ocean waves whose wavelengths are exactly half as long as those of the broadcast radio waves are responsible for the resonant backscatter. Networks of HF radar systems are capable of mapping surface currents hourly out to ranges approaching 200 km with a horizontal resolution of a few kilometers. Such information has many uses, including search and rescue support and oil-spill mitigation in real time and larval population connectivity assessment when viewed over many years. Today, HF radar networks form the backbone of many ocean observing systems, and the data are assimilated into ocean circulation models.

Lagrangian motion in geophysical fluids may be strongly influenced by coherent structures that support distinct regimes in a given flow. The problems of identifying and demarcating Lagrangian regime boundaries associated with dynamical coherent structures in a given velocity field can be studied using approaches originally developed in the context of the abstract geometric theory of ordinary differential equations. An essential insight is that when coherent structures exist in a flow, Lagrangian regime boundaries may often be indicated as material curves on which the Lagrangian-mean principal-axis strain is large. This insight is the foundation of many numerical techniques for identifying such features in complex observed or numerically simulated ocean flows. The basic theoretical ideas are illustrated with a simple, kinematic traveling-wave model. The corresponding numerical algorithms for identifying candidate Lagrangian regime boundaries and lines of principal Lagrangian strain (also called Lagrangian coherent structures) are divided into parcel and bundle schemes; the latter include the finite-time and finite-size Lyapunov exponent/Lagrangian strain (FTLE/FTLS and FSLE/FSLS) metrics. Some aspects and results of oceanographic studies based on these approaches are reviewed, and the results are discussed in the context of oceanographic observations of dynamical coherent structures.

Because the initial phase of barrier reef evolution is often buried under more recent phases of coralgal growth, the origins of modern barrier reefs have remained elusive. Direct observations on the nature of the substrate on top of which barrier reefs have developed are lacking, and simple questions about whether the substrate contributes to their overall linear morphology have remained unanswered. We present here a review dedicated to late-Quaternary shelf-edge deposition in tropical mixed siliciclastic-carbonate systems. These modern analogs are used to develop a quantitative understanding of shelf-edge barrier reef formation during different segments of relatively well-established sea-level cycles. The onset of rapid sea-level rise during early deglaciations, when siliciclastics were deposited along newly formed coasts at up-dip positions, provided opportune time windows for coralgal communities to establish themselves on top of maximum lowstand siliciclastic coastal deposits, such as beach ridges and lowstand shelf-edge deltas.

Trace metals are required for numerous processes in phytoplankton and can influence the growth and structure of natural phytoplankton communities. The metal contents of phytoplankton reflect biochemical demands as well as environmental availability and influence the distribution of metals in the ocean. Metal quotas of natural populations can be assessed from analyses of individual cells or bulk particle assemblages or inferred from ratios of dissolved metals and macronutrients in the water column. Here, we review the available data from these approaches for temperate, equatorial, and Antarctic waters in the Pacific and Atlantic Oceans. The data show a generalized metal abundance ranking of Fe≈Zn>Mn≈Ni≈Cu≫Co≈Cd; however, there are notable differences between taxa and regions that inform our understanding of ocean metal biogeochemistry. Differences in the quotas estimated by the various techniques also provide information on metal behavior. Therefore, valuable information is lost when a single metal stoichiometry is assumed for all phytoplankton.

Iron is essential for all life, but it is particularly important to photoautotrophs because of the many iron-dependent electron transport components in photosynthetic membranes. Since the proliferation of oxygenic photosynthesis in the Archean ocean, iron has been a scarce commodity, and it is now recognized as a limiting resource for phytoplankton over broad expanses of the open ocean and even in some coastal/continental shelf waters. Iron stress does not impair photochemical or carbon fixation efficiencies, and in this respect it resembles the highly tuned photosynthetic systems of steady-state macronutrient-limited phytoplankton. However, iron stress does present unique photophysiological challenges, and phytoplankton have responded to these challenges through major architectural changes in photosynthetic membranes. These evolved responses include overexpression of photosynthetic pigments and iron-economic pathways for ATP synthesis, and they result in diagnostic fluorescence properties that allow a broad appraisal of iron stress in the field and even the detection of iron stress from space.

The use of clean sampling and incubation methods and the development of biomass-independent techniques for estimating the rates of growth and grazing mortality of phytoplankton in the ocean have resulted in estimates of phytoplankton growth rates that are approximately twice those reported prior to roughly 1980. Light-saturated growth rates in tropical and subtropical latitudes correspond to a doubling time of roughly 1 day. The results of mesoscale nutrient-enrichment experiments and comparison of growth rates with estimates of strictly temperature-limited rates indicate that light-saturated growth rates are no more than 50% of nutrient-saturated values, a conclusion consistent with the resiliency of food webs to perturbations. Phytoplankton growth rates in the euphotic zone of the ocean appear to be controlled largely by the grazing activities of micro- and mesozooplankton and the recycling of nutrients associated with the catabolism of consumed prey.

Global warming and its disproportionate impact on polar regions have led to increased iceberg populations. Southern Ocean studies in the northwest Weddell Sea have verified substantial delivery of terrestrial material accompanied by increased primary production and faunal abundance associated with free-drifting icebergs. It is hypothesized that input and utilization of macro- and micronutrients are promoted by conditions unique to free-drifting icebergs, leading to increased production, grazing, and export of organic carbon. In Arctic regions, increased freshwater input from meltwater acts to stratify and stabilize the upper water column. As has been observed in the Southern Ocean, Arctic-region icebergs should drive turbulent upwelling and reduce stratification, potentially leading to increased nitrate delivery to the local ecosystem. Increasing populations of icebergs in polar regions can potentially be important in mediating the drawdown and sequestration of CO2 and can thus impact the oceanic carbon cycle.

Lake Michigan, a 58,000-km² freshwater inland sea, is large enough to have persistent basin-scale circulation yet small enough to enable development of approximately balanced budgets for water, energy, and elements including carbon and silicon. Introduction of nonindigenous species—whether through invasion, intentional stocking, or accidental transplantation—has transformed the lake's ecosystem function and habitat structure. Of the 79 nonindigenous species known to have established reproductive populations in the lake, only a few have brought considerable ecological pressure to bear. Four of these were chosen for this review to exemplify top-down (sea lamprey, Petromyzon marinus), middle-out (alewife, Alosa pseudoharengus), and bottom-up (the dreissenid zebra and quagga mussels, Dreissena polymorpha and Dreissena rostriformis bugensis, respectively) transformations of Lake Michigan ecology, habitability, and ultimately physical environment. Lampreys attacked and extirpated indigenous lake trout, the top predator. Alewives outcompeted native planktivorous fish and curtailed invertebrate populations. Dreissenid mussels—especially quagga mussels, which have had a much greater impact than the preceding zebra mussels—moved ecosystem metabolism basin-wide from water column to bottom dominance and engineered structures throughout the lake. Each of these nonindigenous species exerted devastating effects on commercial and sport fisheries through ecosystem structure modification.

The persistence of carbonate structures on coral reefs is essential in providing habitats for a large number of species and maintaining the extraordinary biodiversity associated with these ecosystems. As a consequence of ocean acidification (OA), the ability of marine calcifiers to produce calcium carbonate (CaCO3) and their rate of CaCO3 production could decrease while rates of bioerosion and CaCO3 dissolution could increase, resulting in a transition from a condition of net accretion to one of net erosion. This would have negative consequences for the role and function of coral reefs and the eco-services they provide to dependent human communities. In this article, we review estimates of bioerosion, CaCO3 dissolution, and net ecosystem calcification (NEC) and how these processes will change in response to OA. Furthermore, we critically evaluate the observed relationships between NEC and seawater aragonite saturation state (Ωa). Finally, we propose that standardized NEC rates combined with observed changes in the ratios of dissolved inorganic carbon to total alkalinity owing to net reef metabolism may provide a biogeochemical tool to monitor the effects of OA in coral reef environments.

Predicting the response of the biota to global change remains a formidable endeavor. Zooplankton face challenges related to global warming, ocean acidification, the proliferation of toxic algal blooms, and increasing pollution, eutrophication, and hypoxia. They can respond to these changes by phenotypic plasticity or genetic adaptation. Using the concept of the evolution of reaction norms, I address how adaptive responses can be unequivocally discerned from phenotypic plasticity. To date, relatively few zooplankton studies have been designed for such a purpose. As case studies, I review the evidence for zooplankton adaptation to toxic algal blooms, hypoxia, and climate change. Predicting the response of zooplankton to global change requires new information to determine (a) the trade-offs and costs of adaptation, (b) the rates of evolution versus environmental change, (c) the consequences of adaptation to stochastic or cyclic (toxic algal blooms, coastal hypoxia) versus directional (temperature, acidification, open ocean hypoxia) environmental change, and (d) the interaction of selective pressures, and evolutionary and ecological processes, in promoting or hindering adaptation.

Ecological resilience to climate change is a combination of resistance to increasingly frequent and severe disturbances, capacity for recovery and self-organization, and ability to adapt to new conditions. Here, we focus on three broad categories of ecological properties that underlie resilience: diversity, connectivity, and adaptive capacity. Diversity increases the variety of responses to disturbance and the likelihood that species can compensate for one another. Connectivity among species, populations, and ecosystems enhances capacity for recovery by providing sources of propagules, nutrients, and biological legacies. Adaptive capacity includes a combination of phenotypic plasticity, species range shifts, and microevolution. We discuss empirical evidence for how these ecological and evolutionary mechanisms contribute to the resilience of coastal marine ecosystems following climate change–related disturbances, and how resource managers can apply this information to sustain these systems and the ecosystem services they provide.

Long-term declines in oxygen concentrations are evident throughout much of the ocean interior and are particularly acute in midwater oxygen minimum zones (OMZs). These regions are defined by extremely low oxygen concentrations (<20–45 μmol kg⁻¹), cover wide expanses of the ocean, and are associated with productive oceanic and coastal regions. OMZs have expanded over the past 50 years, and this expansion is predicted to continue as the climate warms worldwide. Shoaling of the upper boundaries of the OMZs accompanies OMZ expansion, and decreased oxygen at shallower depths can affect all marine organisms through multiple direct and indirect mechanisms. Effects include altered microbial processes that produce and consume key nutrients and gases, changes in predator-prey dynamics, and shifts in the abundance and accessibility of commercially fished species. Although many species will be negatively affected by these effects, others may expand their range or exploit new niches. OMZ shoaling is thus likely to have major and far-reaching consequences.

Marine dissolved organic carbon (DOC) exhibits a spectrum of reactivity, from very fast turnover of the most bioavailable forms in the surface ocean to long-lived materials circulating within the ocean abyss. These disparate reactivities group DOC by fractions with distinctive functions in the cycling of carbon, ranging from support of the microbial loop to involvement in the biological pump to a hypothesized major source/sink of atmospheric CO2 driving paleoclimate variability. Here, the major fractions constituting the global ocean's recalcitrant DOC pool are quantitatively and qualitatively characterized with reference to their roles in carbon biogeochemistry. A nomenclature for the fractions is proposed based on those roles.

Chromophoric dissolved organic matter (CDOM) is a ubiquitous component of the open ocean dissolved matter pool, and is important owing to its influence on the optical properties of the water column, its role in photochemistry and photobiology, and its utility as a tracer of deep ocean biogeochemical processes and circulation. In this review, we discuss the global distribution and dynamics of CDOM in the ocean, concentrating on developments in the past 10 years and restricting our discussion to open ocean and deep ocean (below the main thermocline) environments. CDOM has been demonstrated to exert primary control on ocean color by its absorption of light energy, which matches or exceeds that of phytoplankton pigments in most cases. This has important implications for assessing the ocean biosphere via ocean color–based remote sensing and the evaluation of ocean photochemical and photobiological processes. The general distribution of CDOM in the global ocean is controlled by a balance between production (primarily microbial remineralization of organic matter) and photolysis, with vertical ventilation circulation playing an important role in transporting CDOM to and from intermediate water masses. Significant decadal-scale fluctuations in the abundance of global surface ocean CDOM have been observed using remote sensing, indicating a potentially important role for CDOM in ocean-climate connections through its impact on photochemistry and photobiology.