Showing papers in "Annual Review of Marine Science in 2012"

Climate Change Impacts on Marine Ecosystems

Abstract: In marine ecosystems, rising atmospheric CO2 and climate change are associated with concurrent shifts in temperature, circulation, stratification, nutrient input, oxygen content, and ocean acidification, with potentially wideranging biological effects. Population-level shifts are occurring because of physiological intolerance to new environments, altered dispersal patterns, and changes in species interactions. Together with local climate-driven invasion and extinction, these processes result in altered community structure and diversity, including possible emergence of novel ecosystems. Impacts are particularly striking for the poles and the tropics, because of the sensitivity of polar ecosystems to sea-ice retreat and poleward species migrations as well as the sensitivity of coral-algal symbiosis to minor increases in temperature. Midlatitude upwelling systems, like the California Current, exhibit strong linkages between climate and species distributions, phenology, and demography. Aggregated effects may modify energy and material flows as well as biogeochemical cycles, eventually impacting the overall ecosystem functioning and services upon which people and societies depend.

Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management.

Abstract: The public health, tourism, fisheries, and ecosystem impacts from harmful algal blooms (HABs) have all increased over the past few decades. This has led to heightened scientific and regulatory attention, and the development of many new technologies and approaches for research and management. This, in turn, is leading to significant paradigm shifts with regard to, e.g., our interpretation of the phytoplankton species concept (strain variation), the dogma of their apparent cosmopolitanism, the role of bacteria and zooplankton grazing in HABs, and our approaches to investigating the ecological and genetic basis for the production of toxins and allelochemicals. Increasingly, eutrophication and climate change are viewed and managed as multifactorial environmental stressors that will further challenge managers of coastal resources and those responsible for protecting human health. Here we review HAB science with an eye toward new concepts and approaches, emphasizing, where possible, the unexpected yet promising new directions that research has taken in this diverse field.

The rare bacterial biosphere.

Abstract: All communities are dominated by a few species that account for most of the biomass and carbon cycling. On the other hand, a large number of species are represented by only a few individuals. In the case of bacteria, these rare species were until recently invisible. Owing to their low numbers, conventional molecular techniques could not retrieve them. Isolation in pure culture was the only way to identify some of them, but current culturing techniques are unable to isolate most of the bacteria in nature. The recent development of fast and cheap high-throughput sequencing has begun to allow access to the rare species. In the case of bacteria, the exploration of this rare biosphere has several points of interest. First, it will eventually produce a reasonable estimate of the total number of bacterial taxa in the oceans; right now, we do not even know the right order of magnitude. Second, it will answer the question of whether “everything is everywhere.” Third, it will require hypothesizing and testing the e...

The fate of terrestrial organic carbon in the marine environment.

Abstract: Understanding the fate of terrestrial organic carbon (Corg) delivered to oceans by rivers is critical for constraining models of biogeochemical cycling and Earth surface evolution. Corg fate is dependent on both intrinsic characteristics (molecular structure, matrix) and the environmental conditions to which fluvial Corg is subjected. Three distinct patterns are evident on continental margins supplied by rivers: (a) high-energy, mobile muds with enhanced oxygen exposure and efficient metabolite exchange have very low preservation of both terrestrial and marine Corg (e.g., Amazon subaqueous delta); (b) low-energy facies with extreme accumulation have high Corg preservation (e.g., Ganges-Brahmaputra); and (c) small, mountainous river systems that sustain average accumulation rates but deliver a large fraction of low-reactivity, fossil Corg in episodic events have the highest preservation efficiencies. The global patterns of terrestrial Corg preservation reflect broadly different roles for passive and active margin systems in the sedimentary Corg cycle.

Marine viruses: truth or dare.

Abstract: Over the past two decades, marine virology has progressed from a curiosity to an intensely studied topic of critical importance to oceanography. At concentrations of approximately 10 million viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans. The majority of these viruses are phages (viruses that infect bacteria). Through lysing their bacterial hosts, marine phages control bacterial abundance, affect community composition, and impact global biogeochemical cycles. In addition, phages influence their hosts through selection for resistance, horizontal gene transfer, and manipulation of bacterial metabolism. Recent work has also demonstrated that marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions. This review is structured as a scientific “truth or dare,” revealing several well-established “truths” about marine viruses and presenting a few “dares” for the research community to undertake in future studies.

Jellyfish and Ctenophore Blooms Coincide with Human Proliferations and Environmental Perturbations

Abstract: Human populations have been concentrated along and exploiting the coastal zones for millennia. Of regions with the highest human impacts on the oceans (Halpern et al. 2008), 6 of the top 10 have recently experienced blooms or problems with jellies. I review the time lines of human population growth and their effects on the coastal environment. I explore evidence suggesting that human activities—specifically, seafood harvest, eutrophication, hard substrate additions, transport of nonindigenous species, aquaculture, and climate change—may benefit jelly populations. Direct evidence is lacking for most of these factors; however, numerous correlations show abundant jellies in areas with warm temperatures and low forage fish populations. Jelly populations fluctuate in ∼10- and ∼20-year cycles in concert with solar and climate cycles. Global warming will provide a rising baseline against which climate cycles will cause fluctuations in jelly populations. The probable acceleration of anthropogenic effects may lead...

The Physiology of Global Change: Linking Patterns to Mechanisms

Abstract: Global change includes alterations in ocean temperature, oxygen availability, salinity, and pH, abiotic variables with strong and interacting influences on the physiology of all taxa. Physiological stresses resulting from changes in these four variables may cause broad biogeographic shifts as well as localized changes in distribution in mosaic habitats. To elucidate these causal linkages, I address the following questions: What types of physiological limitations can alter species' distributions and, in cases of extreme stress, cause extinctions? Which species are most threatened by these physiological challenges—and why? How do contents of genomes establish capacities to respond to global change, notably in the case of species that have evolved in highly stable habitats? How fully can phenotypic acclimatization offset abiotic stress? Can physiological measurements, including new molecular (“-omic”) approaches, provide indices of the degree of sublethal stress an organism experiences? And can physiological...

Shifting patterns of life in the Pacific Arctic and Sub-Arctic seas

Abstract: Recent changes in the timing of sea ice formation and retreat, along with increasing seawater temperatures, are driving shifts in marine species composition that may signal marine ecosystem reorganization in the Pacific Arctic sector. Interannual variability in seasonal sea ice retreat in the northern Bering Sea has been observed over the past decade; north of the Bering Strait, the Chukchi Sea ecosystem has had consistent earlier spring sea ice retreat and later fall sea ice formation. The latitudinal gradient in sea ice persistence, water column chlorophyll, and carbon export to the sediments has a direct impact on ecosystem structure in this Arctic/sub-Arctic complex. Large-scale decadal patterns in the benthic biological system are driven by sea ice extent, hydrographic forcing, and export production that influences benthic processes. Shifts in species composition and northward faunal range expansions indicate a changing system. The shifting patterns of life and change in key biological processes have...

Marine Fungi: Their Ecology and Molecular Diversity

Abstract: Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

Marine protistan diversity.

Abstract: Protists have fascinated microbiologists since their discovery nearly 350 years ago. These single-celled, eukaryotic species span an incredible range of sizes, forms, and functions and, despite their generally diminutive size, constitute much of the genetic diversity within the domain Eukarya. Protists in marine ecosystems play fundamental ecological roles as primary producers, consumers, decomposers, and trophic links in aquatic food webs. Much of our knowledge regarding the diversity and ecological activities of these species has been obtained during the past half century, and only within the past few decades have hypotheses depicting the evolutionary relationships among the major clades of protists attained some degree of consensus. This recent progress is attributable to the development of genetic approaches, which have revealed an unexpectedly large diversity of protists, including cryptic species and previously undescribed clades of protists. New genetic tools now exist for identifying protistan species of interest and for reexamining long-standing debates regarding the biogeography of protists. Studies of protistan diversity provide insight regarding how species richness and community composition contribute to ecosystem function. These activities support the development of predictive models that describe how microbial communities will respond to natural or anthropogenically mediated changes in environmental conditions.

Thin Phytoplankton Layers: Characteristics, Mechanisms, and Consequences

Abstract: For over four decades, aggregations of phytoplankton known as thin layers have been observed to harbor large amounts of photosynthetic cells within narrow horizontal bands. Field observations have revealed complex linkages among thin phytoplankton layers, the physical environment, cell behavior, and higher trophic levels. Several mechanisms have been proposed to explain layer formation and persistence, in the face of the homogenizing effect of turbulent dispersion. The challenge ahead is to connect mechanistic hypotheses with field observations to gain better insight on the phenomena that shape layer dynamics. Only through a mechanistic understanding of the relevant biological and physical processes can we begin to predict the effect of thin layers on the ecology of phytoplankton and higher organisms.

The Wind- and Wave-Driven Inner-Shelf Circulation

Abstract: The inner continental shelf, which spans water depths of a few meters to tens of meters, is a dynamically defined region that lies between the surf zone (where waves break) and the middle continental shelf (where the along-shelf circulation is usually in geostrophic balance). Many types of forcing that are often neglected over the deeper shelf—such as tides, buoyant plumes, surface gravity waves, and cross-shelf wind stress—drive substantial circulations over the inner shelf. Cross-shelf circulation over the inner shelf has ecological and geophysical consequences: It connects the shore to the open ocean by transporting pollutants, larvae, phytoplankton, nutrients, and sediment. This review of circulation and momentum balances over the inner continental shelf contrasts prior studies, which focused mainly on the roles of alongshelf wind and pressure gradients, with recent understanding of the dominant roles of cross-shelf wind and surface gravity waves.

Understanding continental margin biodiversity: a new imperative.

Abstract: Until recently, the deep continental margins (200–4,000 m) were perceived as monotonous mud slopes of limited ecological or environmental concern. Progress in seafloor mapping and direct observation now reveals unexpected heterogeneity, with a mosaic of habitats and ecosystems linked to geomorphological, geochemical, and hydrographic features that influence biotic diversity. Interactions among water masses, terrestrial inputs, sediment diagenesis, and tectonic activity create a multitude of ecological settings supporting distinct communities that populate canyons and seamounts, high-stress oxygen minimum zones, and methane seeps, as well as vast reefs of cold corals and sponges. This high regional biodiversity is fundamental to the production of valuable fisheries, energy, and mineral resources, and performs critical ecological services (nutrient cycling, carbon sequestration, nursery and habitat support). It is under significant threat from climate change and human resource extraction activities. Serious...

Genomic Insights into Bacterial DMSP Transformations

Abstract: Genomic and functional genomic methods applied to both model organisms and natural communities have rapidly advanced understanding of bacterial dimethylsulfoniopropionate (DMSP) degradation in the ocean. The genes for the two main pathways in bacterial degradation, routing DMSP to distinctly different biogeochemical fates, have recently been identified. The genes dmdA, -B, -C, and -D mediate the demethylation of DMSP and facilitate retention of carbon and sulfur in the marine microbial food web. The genes dddD, -L, -P, -Q, -W, and -Y mediate the cleavage of DMSP to dimethylsulfide (DMS), with important consequences for ocean-atmosphere sulfur flux. In ocean metagenomes, sufficient copies of these genes are present for ∼60% of surface ocean bacterial cells to directly participate in DMSP degradation. The factors that regulate these two competing pathways remain elusive, but gene transcription analyses of natural bacterioplankton communities are making headway in unraveling the intricacies of bacterial DMSP...

Nutrient Ratios as a Tracer and Driver of Ocean Biogeochemistry

Abstract: Microbial life in the ocean contains immense taxonomic and physiological diversity, yet its collective activity yields global cycles of the major biolimiting elements N and P that are tightly linked. Moreover, the availability of N and P in seawater is closely matched to the metabolic demands of “average” plankton, as if plankton composition and the oceanic nutrient reservoirs were mutually influenced. These simple observations have broad implications for the function of nutrient cycles within the Earth system, which can operate either as a biological homeostat that buffers ocean fertility against large changes or as an amplifier of climate perturbations, by alleviating or exacerbating the nutrient limitation of biological productivity and ocean C storage. A mechanistic understanding of these observations and dynamics must draw upon diverse fields, from physiology and evolution to physical oceanography and paleoceanography, and must account for processes spanning a wide range of spatial and temporal scales. Here we summarize this understanding from the perspective of the nutrient distributions themselves and their changes over time. We offer a synthesis view in which ocean circulation communicates the resource constraints of stoichiometrically distinct planktonic biomes across large spatial scales, allowing geochemical constancy to emerge from rich biological diversity.

Overturning in the North Atlantic.

Abstract: The global overturning of ocean waters involves the equatorward transport of cold, deep waters and the poleward transport of warm, near-surface waters. Such movement creates a net poleward transport of heat that, in partnership with the atmosphere, establishes the global and regional climates. Although oceanographers have long assumed that a reduction in deep water formation at high latitudes in the North Atlantic translates into a slowing of the ocean's overturning and hence in Earth's climate, observational and modeling studies over the past decade have called this assumed linkage into question. The observational basis for linking water mass formation with the ocean's meridional overturning is reviewed herein. Understanding this linkage is crucial to efforts aimed at predicting the consequences of the warming and freshening of high-latitude surface waters to the climate system.

Plankton and Particle Size and Packaging: From Determining Optical Properties to Driving the Biological Pump

Abstract: Understanding pelagic ecology and quantifying energy fluxes through the trophic web and from the surface to the deep ocean requires the ability to detect and identify all organisms and particles in situ and in a synoptic manner. An idealized sensor should observe both the very small living or dead particles such as picoplankton and detritus, respectively, and the large particles such as aggregates and meso- to macroplankton. Such an instrument would reveal an astonishing amount and diversity of living and nonliving particles present in a parcel of water. Unfortunately such sensors do not exist. However, complex interactions constrain the space, temporal, and size distributions of these objects in such ways that general rules can be inferred from the measurement of their optical properties. Recent technological developments allow for the in situ measurement of the optical properties and size distributions of particles and plankton in a way such that synoptic surveys are possible. This review deals with particle and plankton size distributions (PSDs) as well as how particles’ geometry and nature affect their optical properties. Finally, we propose the integration of the PSD into size-structured mathematical models of biogeochemical fluxes.

Benthic Foraminiferal Biogeography: Controls on Global Distribution Patterns in Deep-Water Settings

Abstract: Benthic foraminifera, shell-bearing protists, are familiar from geological studies. Although many species are well known, undescribed single-chambered forms are common in the deep sea. Coastal and sublittoral species often have restricted distributions, but wide ranges are more frequent among deep-water species, particularly at abyssal depths. This probably reflects the transport of tiny propagules by currents across ocean basins that present few insurmountable barriers to dispersal, combined with slow rates of evolution. Undersampling of the vast deep-sea habitat, however, makes it very difficult to establish the ranges of less common foraminiferal species, and endemism may be more prevalent than currently realized. On continental slopes, some species have restricted distributions, but wide-ranging bathyal species that exhibit considerable morphological variation are more common. This may be linked to the greater heterogeneity of continental slopes compared with oceans basins. Improved knowledge of deep-sea foraminiferal biogeography requires sound morphology-based taxonomy combined with molecular genetic studies.

Serpentinite Mud Volcanism: Observations, Processes, and Implications

Abstract: Large serpentinite mud volcanoes form on the overriding plate of the Mariana subduction zone. Fluids from the descending plate hydrate (serpentinize) the forearc mantle and enable serpentinite muds to rise along faults to the seafloor. The seamounts are direct windows into subduction processes at depths far too deep to be accessed by any known technology. Fluid compositions vary with distance from the trench, signaling changes in chemical reactions as temperature and pressure increase. The parageneses of rocks in the mudflows permits us to constrain the physical conditions of the decollement region. If eruptive episodes are related to seismicity, seafloor observatories at these seamounts hold the potential to capture a subduction event and trace the effects of eruption on the biological communities that the slab fluids support, such as extremophile Archaea. The microorganisms that inhabit this high-pH, extreme environment support their growth by utilizing chemical constituents present in the slab fluids. ...

A Conversation with Karl K. Turekian

Abstract: Editors' NoteEach year, the editorial board invites a distinguished member of the oceanographic community to contribute a prefatory chapter; this year, we were delighted when Karl Turekian, Sterling Professor of Geology and Geophysics at Yale, accepted our invitation. Over the course of a long and productive career, Dr. Turekian has pursued his interests in marine and atmospheric geochemistry by using natural radioactive and radiogenic isotopes to study Earth's evolution and the impacts of global change. He has also directed both the Center for the Study of Global Change at Yale and the Yale Institute for Biospheric Studies. In this interview, conducted by his former student Kirk Cochran, Dr. Turekian tells the story of his early career and discusses some of the major scientific challenges and opportunities faced along the way. His personal account of the rise of geochemistry is a charming story of how chance events and personalities impact scientific careers. His technical insight into the future of this...