Annual Review of Marine Science - Volume 6, 2014

André Morel (1933–2012) was a prominent pioneer of modern optical oceanography, enabling significant advances in this field. Through his forward thinking and research over more than 40 years, he made key contributions that this field needed to grow and to reach its current status. This article first summarizes his career and then successively covers different aspects of optical oceanography where he made significant contributions, from fundamental work on optical properties of water and particles to global oceanographic applications using satellite ocean color observations. At the end, we share our views on André's legacy to our research field and scientific community.

The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter.

Submarine canyons are morphological incisions into continental margins that act as major conduits of sediment from shallow- to deep-sea regions. However, the exact mechanisms involved in sediment transfer within submarine canyons are still a subject of investigation. Several studies have provided direct information about contemporary sedimentary processes in submarine canyons that suggests different modes of transport and various triggering mechanisms. Storm-induced turbidity currents and enhanced off-shelf advection, hyperpycnal flows and failures of recently deposited fluvial sediments, dense shelf-water cascading, canyon-flank failures, and trawling-induced resuspension largely dominate present-day sediment transfer through canyons. Additionally, internal waves periodically resuspend ephemeral deposits within canyons and contribute to dispersing particles or retaining and accumulating them in specific regions. These transport processes commonly deposit sediments in the upper- and middle-canyon reaches for decades or centuries before being completely or partially flushed farther down-canyon by large sediment failures.

Much of the year-to-year climate variability on the Earth is associated with El Niño and the Southern Oscillation (ENSO). This variability is generated primarily by a coupled ocean-atmosphere instability near the eastern edge of the western equatorial Pacific warm pool. Here, I discuss the physics of this variability, including its phase locking to the seasonal cycle. ENSO growth typically occurs from April/May to November, and by July the perturbation is usually strong enough that it persists to the beginning of the following year, when ENSO events usually end. Consequently, predicting ENSO is easy from July to February but is more challenging across the April/May transition to the next event. I discuss precursors of this transition and recent results from dynamical and statistical models used for ENSO forecasting.

Nearly all operational models of upper-ocean mixing assume that the turbulence responsible for this mixing is driven by the atmospheric fluxes of momentum, heat, and moisture and the shear imposed by the ocean circulation. This idealization is supported by historical measurements of dissipation rate within the boundary layer. Detailed measurements made recently by many investigators and supported by theoretical and numerical results have found significant deviations from this classical view attributable to the influence of surface waves. Although a review of these measurements finds strong support for the influence of waves—and, in particular, for the predictions of large-eddy simulations, including the Craik-Leibovich vortex force—there are insufficient data to give definitive support to a new paradigm.

Very-low-frequency sounds between 1 and 100 Hz propagate large distances in the ocean sound channel. Weather conditions, earthquakes, marine mammals, and anthropogenic activities influence sound levels in this band. Weather-related sounds result from interactions between waves, bubbles entrained by breaking waves, and the deformation of sea ice. Earthquakes generate sound in geologically active regions, and earthquake T waves propagate throughout the oceans. Blue and fin whales generate long bouts of sounds near 20 Hz that can dominate regional ambient noise levels seasonally. Anthropogenic sound sources include ship propellers, energy extraction, and seismic air guns and have been growing steadily. The increasing availability of long-term records of ocean sound will provide new opportunities for a deeper understanding of natural and anthropogenic sound sources and potential interactions between them.

Most benthic invertebrates broadcast their gametes into the sea, whereupon successful fertilization relies on the complex interaction between the physics of the surrounding fluid flow and the biological properties and behavior of eggs and sperm. We present a holistic overview of the impact of instantaneous flow processes on fertilization across a range of scales. At large scales, transport and stirring by the flow control the distribution of gametes. Although mean dilution of gametes by turbulence is deleterious to fertilization, a variety of instantaneous flow phenomena can aggregate gametes before dilution occurs. We argue that these instantaneous flow processes are key to fertilization efficiency. At small scales, sperm motility and taxis enhance contact rates between sperm and chemoattractant-releasing eggs. We argue that sperm motility is a biological adaptation that replaces molecular diffusion in conventional mixing processes and enables gametes to bridge the gap that remains after aggregation by the flow.

Nutrient and light conditions control phytoplankton division rates in the surface ocean and, it is commonly believed, dictate when and where high concentrations, or blooms, of plankton occur. Yet after a century of investigation, rates of phytoplankton biomass accumulation show no correlation with cell division rates. Consequently, factors controlling plankton blooms remain highly controversial. In this review, we endorse the view that blooms are not governed by abiotic factors controlling cell division, but rather reflect subtle ecosystem imbalances instigated by climate forcings or food-web shifts. The annual global procession of ocean plankton blooms thus represents a report on the recent history of predator-prey interactions modulated by physical processes that, almost coincidentally, also control surface nutrient inputs.

Mangroves are ecologically and economically important forests of the tropics. They are highly productive ecosystems with rates of primary production equal to those of tropical humid evergreen forests and coral reefs. Although mangroves occupy only 0.5% of the global coastal area, they contribute 10–15% (24 Tg C y⁻¹) to coastal sediment carbon storage and export 10–11% of the particulate terrestrial carbon to the ocean. Their disproportionate contribution to carbon sequestration is now perceived as a means for conservation and restoration and a way to help ameliorate greenhouse gas emissions. Of immediate concern are potential carbon losses to deforestation (90–970 Tg C y⁻¹) that are greater than these ecosystems' rates of carbon storage. Large reservoirs of dissolved inorganic carbon in deep soils, pumped via subsurface pathways to adjacent waterways, are a large loss of carbon, at a potential rate up to 40% of annual primary production. Patterns of carbon allocation and rates of carbon flux in mangrove forests are nearly identical to those of other tropical forests.

Multiple natural and anthropogenic processes alter the carbonate chemistry of the coastal zone in ways that either exacerbate or mitigate ocean acidification effects. Freshwater inputs and multiple acid-base reactions change carbonate chemistry conditions, sometimes synergistically. The shallow nature of these systems results in strong benthic-pelagic coupling, and marine invertebrates at different life history stages rely on both benthic and pelagic habitats. Carbonate chemistry in coastal systems can be highly variable, responding to processes with temporal modes ranging from seconds to centuries. Identifying scales of variability relevant to levels of biological organization requires a fuller characterization of both the frequency and magnitude domains of processes contributing to or reducing acidification in pelagic and benthic habitats. We review the processes that contribute to coastal acidification with attention to timescales of variability and habitats relevant to marine bivalves.

Infectious diseases are common in marine environments, but the effects of a changing climate on marine pathogens are not well understood. Here we review current knowledge about how the climate drives host-pathogen interactions and infectious disease outbreaks. Climate-related impacts on marine diseases are being documented in corals, shellfish, finfish, and humans; these impacts are less clearly linked for other organisms. Oceans and people are inextricably linked, and marine diseases can both directly and indirectly affect human health, livelihoods, and well-being. We recommend an adaptive management approach to better increase the resilience of ocean systems vulnerable to marine diseases in a changing climate. Land-based management methods of quarantining, culling, and vaccinating are not successful in the ocean; therefore, forecasting conditions that lead to outbreaks and designing tools/approaches to influence these conditions may be the best way to manage marine disease.

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

The soluble B vitamins (B1, B7, and B12) have long been recognized as playing a central metabolic role in marine phytoplankton and bacteria; however, the importance of these organic external metabolites in marine ecology has been largely disregarded, as most research has focused on inorganic nutrients and trace metals. Using recently available genomic data combined with culture-based surveys of vitamin auxotrophy (i.e., vitamin requirements), we show that this auxotrophy is widespread in the marine environment and occurs in both autotrophs and heterotrophs residing in oligotrophic and eutrophic environments. Our analysis shows that vitamins originate from the activities of some bacteria and algae and that taxonomic changes observed in marine phytoplankton communities could be the result of their specific vitamin requirements and/or vitamin availability. Dissolved vitamin concentration measurements show that large areas of the world ocean are devoid of B vitamins, suggesting that vitamin limitation could be important for the efficiency of carbon and nitrogen fixation in those regions.

Camouflage is exceptionally challenging in pelagic environments because of their featureless nature. Thus, it is perhaps no surprise that pelagic species have evolved highly sophisticated cryptic strategies, three of which—transparency, mirrors, and counterillumination—are rare or absent in other habitats. Pelagic visual systems are equally complex, and several visual capabilities, including UV and polarization sensitivity and intraocular filters, are thought to facilitate detection of camouflaged animals. This article reviews the optical nature of the pelagic realm and both the camouflage and camouflage-breaking strategies of its inhabitants, focusing primarily on underlying principles and what remains to be discovered. A theme throughout is that far more is known about the structures of the optical and visual systems involved than about their function, an imbalance that is due primarily to the rarity of observations of undisturbed behavior.

The potential for antagonistic coevolution between marine viruses and their (primarily bacterial) hosts is well documented, but our understanding of the consequences of this rapid evolution is in its infancy. Acquisition of resistance against co-occurring viruses and the subsequent evolution of virus host range in response have implications for bacterial mortality rates as well as for community composition and diversity. Drawing on examples from a range of environments, we consider the potential dynamics, underlying genetic mechanisms and fitness costs, and ecological impacts of virus-host coevolution in marine waters. Given that much of our knowledge is derived from laboratory experiments, we also discuss potential challenges and approaches in scaling up to diverse, complex networks of virus-host interactions. Finally, we note that a variety of novel approaches for characterizing virus-host interactions offer new hope for a mechanistic understanding of antagonistic coevolution in marine plankton.

Tropical marginal seas (TMSs) are natural subregions of tropical oceans containing biodiverse ecosystems with conspicuous, valued, and vulnerable biodiversity assets. They are focal points for global marine conservation because they occur in regions where human populations are rapidly expanding. Our review of 11 TMSs focuses on three key ecosystems—coral reefs and emergent atolls, deep benthic systems, and pelagic biomes—and synthesizes, illustrates, and contrasts knowledge of biodiversity, ecosystem function, interaction between adjacent habitats, and anthropogenic pressures. TMSs vary in the extent that they have been subject to human influence—from the nearly pristine Coral Sea to the heavily exploited South China and Caribbean Seas—but we predict that they will all be similarly complex to manage because most span multiple national jurisdictions. We conclude that developing a structured process to identify ecologically and biologically significant areas that uses a set of globally agreed criteria is a tractable first step toward effective multinational and transboundary ecosystem management of TMSs.

Polar sea ice is one of the largest ecosystems on Earth. The liquid brine fraction of the ice matrix is home to a diverse array of organisms, ranging from tiny archaea to larger fish and invertebrates. These organisms can tolerate high brine salinity and low temperature but do best when conditions are milder. Thriving ice algal communities, generally dominated by diatoms, live at the ice/water interface and in recently flooded surface and interior layers, especially during spring, when temperatures begin to rise. Although protists dominate the sea ice biomass, heterotrophic bacteria are also abundant. The sea ice ecosystem provides food for a host of animals, with crustaceans being the most conspicuous. Uneaten organic matter from the ice sinks through the water column and feeds benthic ecosystems. As sea ice extent declines, ice algae likely contribute a shrinking fraction of the total amount of organic matter produced in polar waters.

The continental shelf of the Ross Sea exhibits substantial variations in physical forcing, ice cover, and biological processes on a variety of time and space scales. Its circulation is characterized by advective inputs from the east and exchanges with off-shelf regions via the troughs along the northern portions. Phytoplankton biomass is greater there than anywhere else in the Antarctic, although nitrate is rarely reduced to levels below 10 μmol L⁻¹. Overall growth is regulated by irradiance (via ice at the surface and by the depths of the mixed layers) and iron concentrations. Apex predators reach exceptional abundances, and the world's largest colonies of Adélie and emperor penguins are found there. Krill are represented by two species (Euphausia superba near the shelf break and Euphausia crystallorophias throughout the continental shelf region). Equally important and poorly known is the Antarctic silverfish (Pleuragramma antarcticum), which is also consumed by most upper-trophic-level predators. Future changes in the Ross Sea environment will have profound and unpredictable effects on the food web.