Annual Review of Marine Science - Volume 3, 2011

Ocean history is largely read from deep-sea sediments, using microscopic fossils, notably foraminifers. Ice age fluctuations in the ocean's sediments provided for a new geologic understanding of climate change. The discovery of rapid decay of ice masses at the end of glacial periods was especially important, yielding rates of sea level rise reaching values of 1 to 2 m per century for millennia. Thanks to deep-ocean drilling, the overall planetary cooling trend in the Cenozoic was recognized as occurring in three large steps. The first step is at the Eocene–Oligocene boundary and is marked by a great change in sedimentation patterns; the second is in the middle Miocene, associated with a major pulse in the buildup of Antarctic ice masses and the intensification of upwelling regimes; and the third is within the late Pliocene and led into the northern ice ages. Evolution in the sea is linked to these various steps.

Many of the largest earthquakes are generated at subduction zones or other plate boundary fault systems near enough to the coast that marine environments may record evidence of them. During and shortly after large earthquakes in the coastal and marine environments, a spectrum of evidence may be left behind, mirroring onshore paleoseismic evidence. Shaking or displacement of the seafloor can trigger processes such as turbidity currents, submarine landslides, tsunami (which may be recorded both onshore and offshore), and soft-sediment deformation. Marine sites may also share evidence of fault scarps, colluvial wedges, offset features, and liquefaction or fluid expulsion with their onshore counterparts. This article reviews the use of submarine turbidite deposits for paleoseismology, focuses on the dating and correlation techniques used to establish stratigraphic continuity of marine deposits, and outlines criteria for distinguishing earthquake deposits and the strategies used to acquire suitable samples and data for marine paleoseismology.

Restoration of river deltas involves diverting sediment and water from major channels into adjoining drowned areas, where the sediment can build new land and provide a platform for regenerating wetland ecosystems. Except for local engineered structures at the points of diversion, restoration mainly relies on natural delta-building processes. Present understanding of such processes is sufficient to provide a basis for determining the feasibility of restoration projects through quantitative estimates of land-building rates and sustainable wetland area under different scenarios of sediment supply, subsidence, and sea-level rise. We are not yet to the point of being able to predict the evolution of a restored delta in detail. Predictions of delta evolution are based on field studies of active deltas, deltas in mine-tailings ponds, experimental deltas, and countless natural experiments contained in the stratigraphic record. These studies provide input for a variety of mechanistic delta models, ranging from radially averaged formulations to more detailed models that can resolve channels, topography, and ecosystem processes. Especially exciting areas for future research include understanding the mechanisms by which deltaic channel networks self-organize, grow, and distribute sediment and nutrients over the delta surface and coupling these to ecosystem processes, especially the interplay of topography, network geometry, and ecosystem dynamics.

Continental margin systems are important contributors to global nutrient and carbon budgets. Effort is needed to quantify this contribution and how it will be modified under changing patterns of climate and land use. Coupled models will be used to provide projections of future states of continental margin systems. Thus, it is appropriate to consider the limitations that impede the development of realistic models. Here, we provide an overview of the current state of modeling carbon cycling on continental margins as well as the processes and issues that provide the next challenges to such models. Our overview is done within the context of a coupled circulation-biogeochemical model developed for the northeastern North American continental shelf region. Particular choices of forcing and initial fields and process parameterizations are used to illustrate the consequences for simulated distributions, as revealed by comparisons to observations using quantitative statistical metrics.

Estuaries are a major boundary in the land-ocean interaction zone where organic carbon (OC) and nutrients are being processed, resulting in a high water-to-air carbon dioxide (CO2) flux (∼0.25 Pg C y⁻¹). The continental shelves, however, take up CO2 (∼0.25 Pg C y⁻¹) from the atmosphere, accounting for approximately 17% of open ocean CO2 uptake (1.5 Pg C y⁻¹). It is demonstrated here that CO2 release in estuaries is largely supported by microbial decomposition of highly productive intertidal marsh biomass. It appears that riverine OC, however, would bypass the estuarine zone, because of short river-transit times, and contribute to carbon cycling in the ocean margins and interiors. Low-latitude ocean margins release CO2 because they receive two-thirds of the terrestrial OC. Because of recent CO2 increase in the atmosphere, CO2 releases from low latitudes have become weaker and CO2 uptake by mid- and high-latitude shelves has become stronger, thus leading to more dissolved inorganic carbon export to the ocean.

Our knowledge of physical, chemical, geological and biological processes affecting methane in the ocean and in underlying sediments is expanding at a rapid pace. On first inspection, marine methane biogeochemistry appears simple: Methane distribution in sediment is set by the deposition pattern of organic material, and the balance of sources and sinks keeps its concentration low in most waters. However, recent research reveals that methane is affected by complex biogeochemical processes whose interactions are understood only at a superficial level. Such processes span the deep-subsurface, near subsurface, and ocean waters, and relate primarily to the production, consumption, and transport of methane. The purpose of this synthesis is to examine select processes within the framework of methane biogeochemistry, to formulate hypotheses on how they might operate and interact with one another, and to consider their controls.

An advantage of using chlorofluorocarbons (CFCs) and sulfur hexafluoride (SF6) as tracers of ocean circulation is that the time-dependent source functions permit calculation of rates for ocean processes. These compounds are also sensitive indicators highlighting interior ocean regions where surface-derived anomalies can be transported on timescales of decades. Significant applications for CFCs have been for the deep limb of the Atlantic meridional overturning circulation, upper ocean ventilation, and biogeochemical rates, including apparent oxygen utilization rates and anthropogenic CO2 inventories. Although CFCs have started to decrease in the atmosphere, SF6 continues to increase. There are benefits to measuring both CFCs and SF6: A large global CFC data set exists; CFCs are still increasing in older waters; SF6 expands estimates of age; and calculations of anthropogenic CO2 inventory are enhanced. Thus, the outlook for using CFCs as tracers for oceanic processes, and in particular in concert with SF6, remains very positive.

The marine nitrogen (N) cycle controls the productivity of the oceans. This cycle is driven by complex biogeochemical transformations, including nitrogen fixation, denitrification, and assimilation and anaerobic ammonia oxidation, mediated by microorganisms. New processes and organisms continue to be discovered, complicating the already complex picture of oceanic N cycling. Genomics research has uncovered the diversity of nitrogen metabolism strategies in phytoplankton and bacterioplankton. The elemental ratios of nutrients in biological material are more flexible than previously believed, with implications for vertical export of carbon and associated nutrients to the deep ocean. Estimates of nitrogen fixation and denitrification continue to be modified, and anaerobic ammonia oxidation has been identified as a new process involved in denitrification in oxygen minimum zones. The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change.

Marine photosynthetic plankton are responsible for approximately 50 petagrams (10¹⁵) of carbon per year of net primary production, an amount equivalent to that on land. This primary production supports essentially all life in the oceans and profoundly affects global biogeochemical cycles and climate. This review discusses the general distribution of primary production in the sea, the processes that regulate this distribution, and how marine primary production is sensitive to climate variability and change. Statistical modes of ocean variability and their characteristic interannual to multi-decadal timescales over the last century are described. Recent in situ and satellite time-series of primary production can be clearly linked to interannual ocean variability. Global marine primary production appears to have increased over the past several decades in association with multi-decadal variations. A paleoclimate record extends discussion to the centennial scale, providing contrasting insights into how marine primary production might vary in the future.

Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. Here, we review the recent discoveries in the field of autotrophic carbon fixation, including the biochemistry and evolution of the different pathways, as well as their ecological relevance in various oceanic ecosystems.

The accumulation of inorganic carbon from seawater by eukaryotic marine phytoplankton is limited by the diffusion of carbon dioxide (CO2) in water and the dehydration kinetics of bicarbonate to CO2 and by ribulose-1,5-bisphosphate carboxylase/oxygenase's (RubisCO) low affinity for its inorganic carbon substrate, CO2. Nearly all marine phytoplankton have adapted to these limitations and evolved inorganic carbon (or CO2) concentrating mechanisms (CCMs) to support photosynthetic carbon fixation at the concentrations of CO2 present in ocean surface waters (<10–30 μM). The biophysics and biochemistry of CCMs vary within and among the three dominant groups of eukaryotic marine phytoplankton and may involve the activity of external or intracellular carbonic anhydrase, HCO3⁻ transport, and perhaps a C4 carbon pump. In general, coccolithophores have low-efficiency CCMs, and diatoms and the haptophyte genus Phaeocystis have high-efficiency CCMs. Dinoflagellates appear to possess moderately efficient CCMs, which may be necessitated by the very low CO2 affinity of their form II RubisCO. The energetic and nutrient costs of CCMs may modulate how variable CO2 affects primary production, element composition, and species composition of phytoplankton in the ocean.

Oxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration. Conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss. N-loss in OMZs is attributable to anammox and heterotrophic denitrification, whereas nitrate reduction to nitrite along with dissimilatory nitrate reduction to ammonium are major remineralization pathways. Despite virtually anoxic conditions, nitrification also occurs in OMZs, converting remineralized ammonium to N-oxides. The concurrence of all these processes provides a direct channel from organic N to the ultimate N-loss, whereas most individual processes are likely controlled by organic matter. Many microorganisms inhabiting the OMZs are capable of multiple functions in the N- and other elemental cycles. Their versatile metabolic potentials versus actual activities present a challenge to ecophysiological and biogeochemical measurements. These challenges need to be tackled before we can realistically predict how N-cycling in OMZs, and thus oceanic N-balance, will respond to future global perturbations.

Metagenomics literally means “beyond the genome.” Marine microbial metagenomic databases presently comprise ∼400 billion base pairs of DNA, only ∼3% of that found in 1 ml of seawater. Very soon a trillion-base-pair sequence run will be feasible, so it is time to reflect on what we have learned from metagenomics. We review the impact of metagenomics on our understanding of marine microbial communities. We consider the studies facilitated by data generated through the Global Ocean Sampling expedition, as well as the revolution wrought at the individual laboratory level through next generation sequencing technologies. We review recent studies and discoveries since 2008, provide a discussion of bioinformatic analyses, including conceptual pipelines and sequence annotation and predict the future of metagenomics, with suggestions of collaborative community studies tailored toward answering some of the fundamental questions in marine microbial ecology.

Environmental proteomics, the study of changes in the abundance of proteins and their post-translational modifications, has become a powerful tool for generating hypotheses regarding how the environment affects the biology of marine organisms. Proteomics discovers hitherto unknown cellular effects of environmental stressors such as changes in thermal, osmotic, and anaerobic conditions. Proteomic analyses have advanced the characterization of the biological effects of pollutants and identified comprehensive and pollutant-specific sets of biomarkers, especially those highlighting post-translational modifications. Proteomic analyses of infected organisms have highlighted the broader changes occurring during immune responses and how the same pathways are attenuated during the maintenance of symbiotic relationships. Finally, proteomic changes occurring during the early life stages of marine organisms emphasize the importance of signaling events during development in a rapidly changing environment. Changes in proteins functioning in energy metabolism, cytoskeleton, protein stabilization and turnover, oxidative stress, and signaling are common responses to environmental change.

Extracellular enzymes initiate microbial remineralization of organic matter by hydrolyzing substrates to sizes sufficiently small to be transported across cell membranes. As much of marine primary productivity is processed by heterotrophic microbes, the substrate specificities of extracellular enzymes, the rates at which they function in seawater and sediments, and factors controlling their production, distribution, and active lifetimes, are central to carbon cycling in marine systems. In this review, these topics are considered from biochemical, microbial/molecular biological, and geochemical perspectives. Our understanding of the capabilities and limitations of heterotrophic microbial communities has been greatly advanced in recent years, in part through genetic and genomic approaches. New methods to measure enzyme activities in the field are needed to keep pace with these advances and to pursue intriguing evidence that patterns of enzyme activities in different environments are linked to differences in microbial community composition that may profoundly affect the marine carbon cycle.

Biogeochemical cycles in the ocean are mediated by complex and diverse microbial communities. Over the past decade, marine ecosystem and biogeochemistry models have begun to address some of this diversity by resolving several groups of (mostly autotrophic) plankton, differentiated by biogeochemical function. Here, we review recent model approaches that are rooted in the notion that an even richer diversity is fundamental to the organization of marine microbial communities. These models begin to resolve, and address the significance of, diversity within functional groups. Seeded with diverse populations spanning prescribed regions of trait space, these simulations self-select community structure according to relative fitness in the virtual environment. Such models are suited to considering ecological questions, such as the regulation of patterns of biodiversity, and to simulating the response to changing environments. A key issue for all such models is the constraint of viable trait space and trade-offs. Size-structuring and mechanistic descriptions of energy and resource allocation at the individual level can rationalize these constraints.

Communities of microorganisms form thin coats across solid surfaces in the sea. Larvae of many marine invertebrates use biofilm components as cues to appropriate settlement sites. Research on the tube-dwelling polychaete worm Hydroides elegans, a globally common member of biofouling communities, is described to exemplify approaches to understanding biofilm bacteria as a source of settlement cues and larvae as bearers of receptors for bacterial cues. The association of species of the bacterial genus Pseudoalteromonas with larval settlement in many phyla is described, and the question of whether cues are soluble or surface-bound is reviewed, concluding that most evidence points to surface-bound cues. Seemingly contradictory data for stimulation of barnacle settlement are discussed; possibly both explanations are true. Paleontological evidence reveals a relationship between metazoans and biofilms very early in metazoan evolution, and thus the receptors for bacterial cues of invertebrate larvae are very old and possibly unique. Finally, despite more than 60 years of intense investigation, we still know very little about either the bacterial ligands that stimulate larval settlement or the cellular basis of their detection by larvae.

More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ∼648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

Local adaptation in the sea was regarded historically as a rare phenomenon that was limited to a handful of species with exceptionally low dispersal potential. However, a growing body of experimental studies indicates that adaptive differentiation occurs in numerous marine invertebrates in response to selection imposed by strong gradients (and more complex mosaics) of abiotic and biotic conditions. Moreover, a surprisingly high proportion of the marine invertebrates known or suspected of exhibiting local adaptation are species with planktonic dispersal. Adaptive divergence among populations can occur over a range of spatial scales, including those that are fine-grained (i.e., meters to kilometers), reflecting a balance between scales of gene flow and selection. Addressing the causes and consequences of adaptive genetic differentiation among invertebrate populations promises to advance community ecology, climate change research, and the effective management of marine ecosystems.