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Showing papers by "Woods Hole Oceanographic Institution published in 2016"


Journal ArticleDOI
University of East Anglia1, University of Oslo2, Commonwealth Scientific and Industrial Research Organisation3, University of Exeter4, Oak Ridge National Laboratory5, National Oceanic and Atmospheric Administration6, Woods Hole Research Center7, University of California, San Diego8, Karlsruhe Institute of Technology9, Cooperative Institute for Marine and Atmospheric Studies10, Centre national de la recherche scientifique11, University of Maryland, College Park12, National Institute of Water and Atmospheric Research13, Woods Hole Oceanographic Institution14, Flanders Marine Institute15, Alfred Wegener Institute for Polar and Marine Research16, Netherlands Environmental Assessment Agency17, University of Illinois at Urbana–Champaign18, Leibniz Institute of Marine Sciences19, Max Planck Society20, University of Paris21, Hobart Corporation22, Oeschger Centre for Climate Change Research23, University of Bern24, National Center for Atmospheric Research25, University of Miami26, Council of Scientific and Industrial Research27, University of Colorado Boulder28, National Institute for Environmental Studies29, Joint Institute for the Study of the Atmosphere and Ocean30, Geophysical Institute, University of Bergen31, Montana State University32, Goddard Space Flight Center33, University of New Hampshire34, Bjerknes Centre for Climate Research35, Imperial College London36, Lamont–Doherty Earth Observatory37, Auburn University38, Wageningen University and Research Centre39, VU University Amsterdam40, Met Office41
TL;DR: In this article, the authors quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community.
Abstract: . Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere – the “global carbon budget” – is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates and consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models. We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2006–2015), EFF was 9.3 ± 0.5 GtC yr−1, ELUC 1.0 ± 0.5 GtC yr−1, GATM 4.5 ± 0.1 GtC yr−1, SOCEAN 2.6 ± 0.5 GtC yr−1, and SLAND 3.1 ± 0.9 GtC yr−1. For year 2015 alone, the growth in EFF was approximately zero and emissions remained at 9.9 ± 0.5 GtC yr−1, showing a slowdown in growth of these emissions compared to the average growth of 1.8 % yr−1 that took place during 2006–2015. Also, for 2015, ELUC was 1.3 ± 0.5 GtC yr−1, GATM was 6.3 ± 0.2 GtC yr−1, SOCEAN was 3.0 ± 0.5 GtC yr−1, and SLAND was 1.9 ± 0.9 GtC yr−1. GATM was higher in 2015 compared to the past decade (2006–2015), reflecting a smaller SLAND for that year. The global atmospheric CO2 concentration reached 399.4 ± 0.1 ppm averaged over 2015. For 2016, preliminary data indicate the continuation of low growth in EFF with +0.2 % (range of −1.0 to +1.8 %) based on national emissions projections for China and USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. In spite of the low growth of EFF in 2016, the growth rate in atmospheric CO2 concentration is expected to be relatively high because of the persistence of the smaller residual terrestrial sink (SLAND) in response to El Nino conditions of 2015–2016. From this projection of EFF and assumed constant ELUC for 2016, cumulative emissions of CO2 will reach 565 ± 55 GtC (2075 ± 205 GtCO2) for 1870–2016, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quere et al., 2015b, a, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center ( doi:10.3334/CDIAC/GCP_2016 ).

1,224 citations


Journal ArticleDOI
25 Feb 2016
TL;DR: Modification of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi with nonaquatic samples demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types.
Abstract: Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of data sets amplified with varied primers requires attention. Here, we examined the performance of modified 16S rRNA gene and internal transcribed spacer (ITS) primers for archaea/bacteria and fungi, respectively, with nonaquatic samples. We moved primer bar codes to the 5' end, allowing for a range of different 3' primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4 and 5 of the 16S rRNA gene. We additionally demonstrated that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and clade SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies. IMPORTANCE We continue to uncover a wealth of information connecting microbes in important ways to human and environmental ecology. As our scientific knowledge and technical abilities improve, the tools used for microbiome surveys can be modified to improve the accuracy of our techniques, ensuring that we can continue to identify groundbreaking connections between microbes and the ecosystems they populate, from ice caps to the human body. It is important to confirm that modifications to these tools do not cause new, detrimental biases that would inhibit the field rather than continue to move it forward. We therefore demonstrated that two recently modified primer pairs that target taxonomically discriminatory regions of bacterial and fungal genomic DNA do not introduce new biases when used on a variety of sample types, from soil to human skin. This confirms the utility of these primers for maintaining currently recommended microbiome research techniques as the state of the art.

1,222 citations


Journal ArticleDOI
TL;DR: The discovery of a distinctive, multigenus consortium in the microbiome of supragingival dental plaque illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms.
Abstract: The spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. Although the revolution in DNA sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria. The consortium ranges in size from a few tens to a few hundreds of microns in radius and is spatially differentiated. Within the structure, individual taxa are localized at the micron scale in ways suggestive of their functional niche in the consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend to be near each other. Based on our observations and the literature, we propose a model for plaque microbiome development and maintenance consistent with known metabolic, adherence, and environmental considerations. The consortium illustrates how complex structural organization can emerge from the micron-scale interactions of its constituent organisms. The understanding that plaque community organization is an emergent phenomenon offers a perspective that is general in nature and applicable to other microbiomes.

613 citations


Journal ArticleDOI
TL;DR: An exhaustive review and reanalysis of geological, paleontological, and molecular records converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma.
Abstract: The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas. To bring clarity to the question of when the Isthmus of Panama formed, we provide an exhaustive review and reanalysis of geological, paleontological, and molecular records. These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

595 citations


Journal ArticleDOI
TL;DR: The ephemeral nature of mesoscale features in the ocean makes it difficult to elucidate the attendant mechanisms of physical-biological-biogeochemical interaction, requiring the use of multidisciplinary approaches involving in situ observations, remote sensing, and modeling.
Abstract: Mesoscale phenomena are ubiquitous and highly energetic features of ocean circulation. Their influence on biological and biogeochemical processes varies widely, stemming not only from advective transport but also from the generation of variations in the environment that affect biological and chemical rates. The ephemeral nature of mesoscale features in the ocean makes it difficult to elucidate the attendant mechanisms of physical-biological-biogeochemical interaction, necessitating the use of multidisciplinary approaches involving in situ observations, remote sensing, and modeling. All three aspects are woven through this review in an attempt to synthesize current understanding of the topic, with particular emphasis on novel developments in recent years.

392 citations


Journal ArticleDOI
TL;DR: This is the first, to the authors' knowledge, estimate of global sea-level (GSL) change over the last ∼3,000 years that is based upon statistical synthesis of a global database of regional sea- level reconstructions, and indicates that, without global warming, GSL in the 20th century very likely would have risen by between −3 cm and +7 cm, rather than the ∼14 cm observed.
Abstract: We assess the relationship between temperature and global sea-level (GSL) variability over the Common Era through a statistical metaanalysis of proxy relative sea-level reconstructions and tide-gauge data. GSL rose at 0.1 ± 0.1 mm/y (2σ) over 0-700 CE. A GSL fall of 0.2 ± 0.2 mm/y over 1000-1400 CE is associated with ∼ 0.2 °C global mean cooling. A significant GSL acceleration began in the 19th century and yielded a 20th century rise that is extremely likely (probability [Formula: see text]) faster than during any of the previous 27 centuries. A semiempirical model calibrated against the GSL reconstruction indicates that, in the absence of anthropogenic climate change, it is extremely likely ([Formula: see text]) that 20th century GSL would have risen by less than 51% of the observed [Formula: see text] cm. The new semiempirical model largely reconciles previous differences between semiempirical 21st century GSL projections and the process model-based projections summarized in the Intergovernmental Panel on Climate Change's Fifth Assessment Report.

372 citations


Journal ArticleDOI
TL;DR: The Global Ocean Observing System (GOOS) as discussed by the authors uses a global array of profiling floats to sample the upper 2,000 m of the ocean globally and uniformly in space and time.
Abstract: More than 90% of the heat energy accumulation in the climate system between 1971 and the present has been in the ocean. Thus, the ocean plays a crucial role in determining the climate of the planet. Observing the oceans is problematic even under the most favourable of conditions. Historically, shipboard ocean sampling has left vast expanses, particularly in the Southern Ocean, unobserved for long periods of time. Within the past 15 years, with the advent of the global Argo array of profiling floats, it has become possible to sample the upper 2,000 m of the ocean globally and uniformly in space and time. The primary goal of Argo is to create a systematic global network of profiling floats that can be integrated with other elements of the Global Ocean Observing System. The network provides freely available temperature and salinity data from the upper 2,000 m of the ocean with global coverage. The data are available within 24 hours of collection for use in a broad range of applications that focus on examining climate-relevant variability on seasonal to decadal timescales, multidecadal climate change, improved initialization of coupled ocean–atmosphere climate models and constraining ocean analysis and forecasting systems.

371 citations


Journal ArticleDOI
TL;DR: In regimes with deep surface mixed layers, submesoscale instabilities can cause stratification within days, thereby increasing light exposure for phytoplankton trapped close to the surface, which has implications for interactions within the ecosystem.
Abstract: Life in the ocean relies on the photosynthetic production of phytoplankton, which is influenced by the availability of light and nutrients that are modulated by a host of physical processes. Submesoscale processes are particularly relevant to phytoplankton productivity because the timescales on which they act are similar to those of phytoplankton growth. Their dynamics are associated with strong vorticity and strain rates that occur on lateral scales of 0.1–10 km. They can support vertical velocities as large as 100 m d−1 and play a crucial role in transporting nutrients into the sunlit ocean for phytoplankton production. In regimes with deep surface mixed layers, submesoscale instabilities can cause stratification within days, thereby increasing light exposure for phytoplankton trapped close to the surface. These instabilities help to create and maintain localized environments that favor the growth of phytoplankton, contribute to productivity, and cause enormous heterogeneity in the abundance of phytopla...

370 citations


Journal ArticleDOI
03 Feb 2016-PLOS ONE
TL;DR: The overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability.
Abstract: Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform research and management activities related to understanding and adapting marine fisheries management and conservation to climate change and decadal variability.

361 citations


Journal ArticleDOI
09 Dec 2016-Science
TL;DR: High genetic diversity in killifish seems to allow selection to act on existing variation, driving rapid adaptation to selective forces such as pollution, and the aryl hydrocarbon receptor–based signaling pathway is identified as a shared target of selection.
Abstract: Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediating genes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversity has likely been a crucial substrate for selective sweeps to propel rapid adaptation.

336 citations


Journal ArticleDOI
TL;DR: An overview of different aspects of the HABs phenomena is provided, an important element of the intrinsic links between oceans and human health and wellbeing.
Abstract: Microalgal blooms are a natural part of the seasonal cycle of photosynthetic organisms in marine ecosystems. They are key components of the structure and dynamics of the oceans and thus sustain the benefits that humans obtain from these aquatic environments. However, some microalgal blooms can cause harm to humans and other organisms. These harmful algal blooms (HABs) have direct impacts on human health and negative influences on human wellbeing, mainly through their consequences to coastal ecosystem services (fisheries, tourism and recreation) and other marine organisms and environments. HABs are natural phenomena, but these events can be favoured by anthropogenic pressures in coastal areas. Global warming and associated changes in the oceans could affect HAB occurrences and toxicity as well, although forecasting the possible trends is still speculative and requires intensive multidisciplinary research. At the beginning of the 21st century, with expanding human populations, particularly in coastal and developing countries, mitigating HABs impacts on human health and wellbeing is becoming a more pressing public health need. The available tools to address this global challenge include maintaining intensive, multidisciplinary and collaborative scientific research, and strengthening the coordination with stakeholders, policymakers and the general public. Here we provide an overview of different aspects of the HABs phenomena, an important element of the intrinsic links between oceans and human health and wellbeing.

Journal ArticleDOI
TL;DR: The Arctic Ocean is a fundamental node in the global hydrological cycle and the ocean's thermohaline circulation as discussed by the authors, and its key functions and processes include the delivery of fresh and low-salinity waters to the Arctic Ocean by river inflow, net precipitation, distillation during the freeze/thaw cycle, and Pacific Ocean inflows.
Abstract: The Arctic Ocean is a fundamental node in the global hydrological cycle and the ocean's thermohaline circulation. We here assess the system's key functions and processes: (1) the delivery of fresh and low-salinity waters to the Arctic Ocean by river inflow, net precipitation, distillation during the freeze/thaw cycle, and Pacific Ocean inflows; (2) the disposition (e.g., sources, pathways, and storage) of freshwater components within the Arctic Ocean; and (3) the release and export of freshwater components into the bordering convective domains of the North Atlantic. We then examine physical, chemical, or biological processes which are influenced or constrained by the local quantities and geochemical qualities of freshwater; these include stratification and vertical mixing, ocean heat flux, nutrient supply, primary production, ocean acidification, and biogeochemical cycling. Internal to the Arctic the joint effects of sea ice decline and hydrological cycle intensification have strengthened coupling between the ocean and the atmosphere (e.g., wind and ice drift stresses, solar radiation, and heat and moisture exchange), the bordering drainage basins (e.g., river discharge, sediment transport, and erosion), and terrestrial ecosystems (e.g., Arctic greening, dissolved and particulate carbon loading, and altered phenology of biotic components). External to the Arctic freshwater export acts as both a constraint to and a necessary ingredient for deep convection in the bordering subarctic gyres and thus affects the global thermohaline circulation. Geochemical fingerprints attained within the Arctic Ocean are likewise exported into the neighboring subarctic systems and beyond. Finally, we discuss observed and modeled functions and changes in this system on seasonal, annual, and decadal time scales and discuss mechanisms that link the marine system to atmospheric, terrestrial, and cryospheric systems.

Journal ArticleDOI
29 Jul 2016-Science
TL;DR: Climate and ocean circulation proxies are examined at high resolution in a deep North Atlantic sediment core, suggesting reduced Atlantic overturning circulation during every cool northern stadial, with the greatest reductions during episodic Hudson Strait iceberg discharges, while sharp northern warming followed reinvigorated overturning.
Abstract: The most recent ice age was characterized by rapid and hemispherically asynchronous climate oscillations, whose origin remains unresolved. Variations in oceanic meridional heat transport may contribute to these repeated climate changes, which were most pronounced during marine isotope stage 3, the glacial interval 25 thousand to 60 thousand years ago. We examined climate and ocean circulation proxies throughout this interval at high resolution in a deep North Atlantic sediment core, combining the kinematic tracer protactinium/thorium (Pa/Th) with the deep water-mass tracer, epibenthic δ13C. These indicators suggest reduced Atlantic overturning circulation during every cool northern stadial, with the greatest reductions during episodic Hudson Strait iceberg discharges, while sharp northern warming followed reinvigorated overturning. These results provide direct evidence for the ocean’s persistent, central role in abrupt glacial climate change.

Journal ArticleDOI
01 Jan 2016-Protist
TL;DR: This work proposes a new functional grouping of planktonic protists in an eco-physiological context and incorporates these functional groups within a foodweb structure and shows that there is scope for significant changes in trophic dynamics depending on the protist functional type description.

Journal ArticleDOI
TL;DR: Genetic evidence that some lineages of Bathyarchaeota are acetogens is provided, being capable of homoacetogenesis, a metabolism so far restricted to the domain Bacteria, and a revision of the role of Archaea in the carbon cycle of marine sediments is argued for.
Abstract: Members of the archaeal phylum Bathyarchaeota are widespread and abundant in the energy-deficient marine subsurface sediments. However, their life strategies have remained largely elusive. Here, we provide genetic evidence that some lineages of Bathyarchaeota are acetogens, being capable of homoacetogenesis, a metabolism so far restricted to the domain Bacteria. Metabolic reconstruction based on genomic bins assembled from the metagenome of deep-sea subsurface sediments shows that the metabolism of some lineages of Bathyarchaeota is similar to that of bona fide bacterial homoacetogens, by having pathways for acetogenesis and for the fermentative utilization of a variety of organic substrates. Heterologous expression and activity assay of the acetate kinase gene ack from Bathyarchaeota, demonstrate further the capability of these Bathyarchaeota to grow as acetogens. The presence and expression of bathyarchaeotal genes indicative of active acetogenesis was also confirmed in Peru Margin subsurface sediments where Bathyarchaeota are abundant. The analyses reveal that this ubiquitous and abundant subsurface archaeal group has adopted a versatile life strategy to make a living under energy-limiting conditions. These findings further expand the metabolic potential of Archaea and argue for a revision of the role of Archaea in the carbon cycle of marine sediments.

Journal ArticleDOI
17 Mar 2016-Nature
TL;DR: In this paper, the authors used a manipulation experiment in which sodium hydroxide was added to seawater flowing over a natural coral reef community in situ and showed that when ocean chemistry was restored closer to pre-industrial conditions, net community calcification increased, indicating that ocean acidification may already be impairing coral reef growth.
Abstract: A manipulative experiment in which a reef is alkalinized in situ shows that calcification rates are likely to be lower already than they were in pre-industrial times because of acidification. Ocean acidification is one of several factors projected to threaten coral reef ecosystems, but disentangling its effects from other factors such as temperature is difficult. These authors used a manipulative experiment in which sodium hydroxide was added to seawater flowing over a natural coral reef community in situ. When ocean chemistry was restored closer to pre-industrial conditions, net community calcification increased. This suggests calcification rates are already lower than they were in pre-industrial times because of acidification. Deliberate alkalinization has been proposed as a geoengineering technique to offset ocean acidification, and this work suggests that the method could be effective, but only on a small scale — in protected bays or lagoons, for example. Approximately one-quarter of the anthropogenic carbon dioxide released into the atmosphere each year is absorbed by the global oceans, causing measurable declines in surface ocean pH, carbonate ion concentration ([CO32−]), and saturation state of carbonate minerals (Ω)1. This process, referred to as ocean acidification, represents a major threat to marine ecosystems, in particular marine calcifiers such as oysters, crabs, and corals. Laboratory and field studies2,3 have shown that calcification rates of many organisms decrease with declining pH, [CO32−], and Ω. Coral reefs are widely regarded as one of the most vulnerable marine ecosystems to ocean acidification, in part because the very architecture of the ecosystem is reliant on carbonate-secreting organisms4. Acidification-induced reductions in calcification are projected to shift coral reefs from a state of net accretion to one of net dissolution this century5. While retrospective studies show large-scale declines in coral, and community, calcification over recent decades6,7,8,9,10,11,12, determining the contribution of ocean acidification to these changes is difficult, if not impossible, owing to the confounding effects of other environmental factors such as temperature. Here we quantify the net calcification response of a coral reef flat to alkalinity enrichment, and show that, when ocean chemistry is restored closer to pre-industrial conditions, net community calcification increases. In providing results from the first seawater chemistry manipulation experiment of a natural coral reef community, we provide evidence that net community calcification is depressed compared with values expected for pre-industrial conditions, indicating that ocean acidification may already be impairing coral reef growth.

Journal ArticleDOI
TL;DR: A uniform, systematic, and comprehensive approach to studying sequences is proposed, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies.
Abstract: This review was developed at an investigative workshop, “Analyzing Animal Vocal Communication Sequences” that took place on October 21–23 2013 in Knoxville, Tennessee, sponsored by the National Institute for Mathematical and Biological Synthesis (NIMBioS). NIMBioS is an Institute sponsored by the National Science Foundation, the U.S. Department of Homeland Security, and the U.S. Department of Agriculture through NSF Awards #EF-0832858 and #DBI-1300426, with additional support from The University of Tennessee, Knoxville. In addition to the authors, Vincent Janik participated in the workshop. D.T.B.’s research is currently supported by NSF DEB-1119660. M.A.B.’s research is currently supported by NSF IOS-0842759 and NIH R01DC009582. M.A.R.’s research is supported by ONR N0001411IP20086 and NOPP (ONR/BOEM) N00014-11-1-0697. S.L.DeR.’s research is supported by the U.S. Office of Naval Research. R.F.-i-C.’s research was supported by the grant BASMATI (TIN2011-27479-C04-03) from the Spanish Ministry of Science and Innovation. E.C.G.’s research is currently supported by a National Research Council postdoctoral fellowship. E.E.V.’s research is supported by CONACYT, Mexico, award number I010/214/2012.

Journal ArticleDOI
TL;DR: Questions being addressed using recent methodological and technological developments in analytical chemistry, microbiology, and informatics are considered and how these advances are transforming the authors' understanding of some of the most important reactions of the marine carbon cycle are considered.
Abstract: Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.

Journal ArticleDOI
25 Aug 2016-Nature
TL;DR: The authors used post-ad 1500 palaeoclimate records to show that sustained industrial-era warming of the tropical oceans first developed during the mid-nineteenth century and was nearly synchronous with Northern Hemisphere continental warming.
Abstract: The evolution of industrial-era warming across the continents and oceans provides a context for future climate change and is important for determining climate sensitivity and the processes that control regional warming. Here we use post-ad 1500 palaeoclimate records to show that sustained industrial-era warming of the tropical oceans first developed during the mid-nineteenth century and was nearly synchronous with Northern Hemisphere continental warming. The early onset of sustained, significant warming in palaeoclimate records and model simulations suggests that greenhouse forcing of industrial-era warming commenced as early as the mid-nineteenth century and included an enhanced equatorial ocean response mechanism. The development of Southern Hemisphere warming is delayed in reconstructions, but this apparent delay is not reproduced in climate simulations. Our findings imply that instrumental records are too short to comprehensively assess anthropogenic climate change and that, in some regions, about 180 years of industrial-era warming has already caused surface temperatures to emerge above pre-industrial values, even when taking natural variability into account.

Journal ArticleDOI
TL;DR: This paper used nuclear magnetic resonance spectroscopy to show that polysaccharide esters of three phosphonic acids are important constituents of dissolved organic matter in seawater from the North Pacific.
Abstract: A lot of methane is emitted from oxygenated seawater, where its production should be inhibited. Seawater incubations and organic matter characterizations reveal that bacteria aerobically produce methane from phosphonates in organic matter. Biogenic methane is widely thought to be a product of archaeal methanogenesis, an anaerobic process that is inhibited or outcompeted by the presence of oxygen and sulfate1,2,3. Yet a large fraction of marine methane delivered to the atmosphere is produced in high-sulfate, fully oxygenated surface waters that have methane concentrations above atmospheric equilibrium values, an unexplained phenomenon referred to as the marine methane paradox4,5. Here we use nuclear magnetic resonance spectroscopy to show that polysaccharide esters of three phosphonic acids are important constituents of dissolved organic matter in seawater from the North Pacific. In seawater and pure culture incubations, bacterial degradation of these dissolved organic matter phosphonates in the presence of oxygen releases methane, ethylene and propylene gas. Moreover, we found that in mutants of a methane-producing marine bacterium, Pseudomonas stutzeri, disrupted in the C–P lyase phosphonate degradation pathway, methanogenesis was also disabled, indicating that the C–P lyase pathway can catalyse methane production from marine dissolved organic matter. Finally, the carbon stable isotope ratio of methane emitted during our incubations agrees well with anomalous isotopic characteristics of seawater methane. We estimate that daily cycling of only about 0.25% of the organic matter phosphonate inventory would support the entire atmospheric methane flux at our study site. We conclude that aerobic bacterial degradation of phosphonate esters in dissolved organic matter may explain the marine methane paradox.

Journal ArticleDOI
TL;DR: These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes.
Abstract: Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

Journal ArticleDOI
TL;DR: It is found that violent storms and hurricanes contribute less than 1% to long-term salt marsh erosion rates, and moderate storms with a return period of 2.5 mo are those causing the most salt marsh deterioration.
Abstract: Salt marsh losses have been documented worldwide because of land use change, wave erosion, and sea-level rise. It is still unclear how resistant salt marshes are to extreme storms and whether they can survive multiple events without collapsing. Based on a large dataset of salt marsh lateral erosion rates collected around the world, here, we determine the general response of salt marsh boundaries to wave action under normal and extreme weather conditions. As wave energy increases, salt marsh response to wind waves remains linear, and there is not a critical threshold in wave energy above which salt marsh erosion drastically accelerates. We apply our general formulation for salt marsh erosion to historical wave climates at eight salt marsh locations affected by hurricanes in the United States. Based on the analysis of two decades of data, we find that violent storms and hurricanes contribute less than 1% to long-term salt marsh erosion rates. In contrast, moderate storms with a return period of 2.5 mo are those causing the most salt marsh deterioration. Therefore, salt marshes seem more susceptible to variations in mean wave energy rather than changes in the extremes. The intrinsic resistance of salt marshes to violent storms and their predictable erosion rates during moderate events should be taken into account by coastal managers in restoration projects and risk management plans.

Journal ArticleDOI
TL;DR: In this article, a measurement/ synthesis/modeling framework is proposed to quantify the fates of upper ocean net primary production (NPP) and its impacts on the global carbon cycle based upon the EXPORTS Science Plan.
Abstract: Ocean ecosystems play a critical role in the Earth’s carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean’s interior on time scales of months to millennia. Here we present a measurement / synthesis / modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step towards our understanding of the Earth as an integrated system.

Journal ArticleDOI
Benjamin W. Abbott1, Jeremy B. Jones1, Edward A. G. Schuur2, F. Stuart Chapin1, William B. Bowden3, M. Syndonia Bret-Harte1, Howard E. Epstein4, Mike D. Flannigan5, Tamara K. Harms1, Teresa N. Hollingsworth6, Michelle C. Mack2, A. David McGuire7, Susan M. Natali8, Adrian V. Rocha9, Suzanne E. Tank5, Merritt R. Turetsky10, Jorien E. Vonk11, Kimberly P. Wickland7, George R. Aiken7, Heather D. Alexander12, Rainer M. W. Amon13, Brian W. Benscoter14, Yves Bergeron15, Kevin Bishop16, Olivier Blarquez17, Ben Bond-Lamberty18, Amy L. Breen1, Ishi Buffam19, Yihua Cai20, Christopher Carcaillet21, Sean K. Carey22, Jing M. Chen23, Han Y. H. Chen24, Torben R. Christensen25, Lee W. Cooper26, J. Hans C. Cornelissen11, William J. de Groot27, Thomas H. DeLuca28, Ellen Dorrepaal29, Ned Fetcher30, Jacques C. Finlay31, Bruce C. Forbes, Nancy H. F. French32, Sylvie Gauthier27, Martin P. Girardin27, Scott J. Goetz8, Johann G. Goldammer33, Laura Gough34, Paul Grogan35, Laodong Guo36, Philip E. Higuera37, Larry D. Hinzman1, Feng Sheng Hu38, Gustaf Hugelius39, Elchin Jafarov40, Randi Jandt1, Jill F. Johnstone41, Jan Karlsson29, Eric S. Kasischke, Gerhard Kattner42, Ryan C. Kelly, Frida Keuper43, George W. Kling44, Pirkko Kortelainen45, Jari Kouki46, Peter Kuhry39, Hjalmar Laudon16, Isabelle Laurion15, Robie W. Macdonald47, Paul J. Mann48, Pertti J. Martikainen46, James W. McClelland49, Ulf Molau50, Steven F. Oberbauer14, David Olefeldt5, David Paré27, Marc-André Parisien27, Serge Payette51, Changhui Peng52, Oleg S. Pokrovsky53, Edward B. Rastetter54, Peter A. Raymond55, Martha K. Raynolds1, Guillermo Rein56, James F. Reynolds57, Martin D. Robards, Brendan M. Rogers8, Christina Schaedel2, Kevin Schaefer40, Inger Kappel Schmidt58, Anatoly Shvidenko, Jasper Sky, Robert G. M. Spencer14, Gregory Starr59, Robert G. Striegl7, Roman Teisserenc60, Lars J. Tranvik61, Tarmo Virtanen, Jeffrey M. Welker62, Sergei Zimov63 
University of Alaska Fairbanks1, Northern Arizona University2, University of Vermont3, University of Virginia4, University of Alberta5, United States Department of Agriculture6, United States Geological Survey7, Woods Hole Oceanographic Institution8, University of Notre Dame9, University of Guelph10, VU University Amsterdam11, Mississippi State University12, University of North Texas13, Florida State University14, Université du Québec15, Swedish University of Agricultural Sciences16, McGill University17, United States Department of Energy18, University of Cincinnati19, Xiamen University20, École Normale Supérieure21, McMaster University22, University of Toronto23, Lakehead University24, Aarhus University25, University of Maryland Center for Environmental Science26, Natural Resources Canada27, University of Washington28, Umeå University29, Wilkes University30, University of Minnesota31, Michigan Technological University32, Max Planck Society33, University System of Maryland34, Queen's University35, University of Wisconsin–Milwaukee36, University of Montana System37, University of Illinois at Chicago38, Stockholm University39, University of Colorado Boulder40, University of Saskatchewan41, Alfred Wegener Institute for Polar and Marine Research42, Institut national de la recherche agronomique43, University of Michigan44, Finnish Environment Institute45, University of Eastern Finland46, Fisheries and Oceans Canada47, Northumbria University48, University of Texas at Austin49, University of Gothenburg50, Laval University51, Northwest A&F University52, Tomsk State University53, Marine Biological Laboratory54, Yale University55, Imperial College London56, Duke University57, University of Copenhagen58, University of Alabama59, Centre national de la recherche scientifique60, Uppsala University61, University of Alaska Anchorage62, Russian Academy of Sciences63
TL;DR: As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export as mentioned in this paper, and models predict that some portion of this release w...
Abstract: As the permafrost region warms, its large organic carbon pool will be increasingly vulnerable to decomposition, combustion, and hydrologic export. Models predict that some portion of this release w ...

01 Dec 2016
TL;DR: The findings imply that instrumental records are too short to comprehensively assess anthropogenic climate change and that, in some regions, about 180 years of industrial-era warming has already caused surface temperatures to emerge above pre-industrial values, even when taking natural variability into account.
Abstract: The evolution of industrial-era warming across the continents and oceans provides a context for future climate change and is important for determining climate sensitivity and the processes that control regional warming. Here we use post-ad 1500 palaeoclimate records to show that sustained industrial-era warming of the tropical oceans first developed during the mid-nineteenth century and was nearly synchronous with Northern Hemisphere continental warming. The early onset of sustained, significant warming in palaeoclimate records and model simulations suggests that greenhouse forcing of industrial-era warming commenced as early as the mid-nineteenth century and included an enhanced equatorial ocean response mechanism. The development of Southern Hemisphere warming is delayed in reconstructions, but this apparent delay is not reproduced in climate simulations. Our findings imply that instrumental records are too short to comprehensively assess anthropogenic climate change and that, in some regions, about 180 years of industrial-era warming has already caused surface temperatures to emerge above pre-industrial values, even when taking natural variability into account.

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TL;DR: Ship-based measurements show that vertical diffusivity increases from a minimum in the thermocline to a maximum within the bottom 1,500 m, shifting the physical paradigm of the ocean's overturning circulation.
Abstract: Global ship-based programs, with highly accurate, full water column physical and biogeochemical observations repeated decadally since the 1970s, provide a crucial resource for documenting ocean change. The ocean, a central component of Earth's climate system, is taking up most of Earth's excess anthropogenic heat, with about 19% of this excess in the abyssal ocean beneath 2,000 m, dominated by Southern Ocean warming. The ocean also has taken up about 27% of anthropogenic carbon, resulting in acidification of the upper ocean. Increased stratification has resulted in a decline in oxygen and increase in nutrients in the Northern Hemisphere thermocline and an expansion of tropical oxygen minimum zones. Southern Hemisphere thermocline oxygen increased in the 2000s owing to stronger wind forcing and ventilation. The most recent decade of global hydrography has mapped dissolved organic carbon, a large, bioactive reservoir, for the first time and quantified its contribution to export production (∼20%) and deep-ocean oxygen utilization. Ship-based measurements also show that vertical diffusivity increases from a minimum in the thermocline to a maximum within the bottom 1,500 m, shifting our physical paradigm of the ocean's overturning circulation.

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TL;DR: The COMADRE Animal Matrix Database is introduced, an open‐data online repository, which in its version 1.0 contains data on 345 species world‐wide, from 402 studies with a total of 1625 population projection matrices that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs.
Abstract: 1. The open-data scientific philosophy is being widely adopted and proving to promote considerable progress in ecology and evolution. Open-data global data bases now exist on animal migration, species distribution, conservation status, etc. However, a gap exists for data on population dynamics spanning the rich diversity of the animal kingdom world-wide. This information is fundamental to our understanding of the conditions that have shaped variation in animal life histories and their relationships with the environment, as well as the determinants of invasion and extinction. 2. Matrix population models (MPMs) are among the most widely used demographic tools by animal ecologists. MPMs project population dynamics based on the reproduction, survival and development of individuals in a population over their life cycle. The outputs from MPMs have direct biological interpretations, facilitating comparisons among animal species as different as Caenorhabditis elegans, Loxodonta africana and Homo sapiens. 3. Thousands of animal demographic records exist in the form of MPMs, but they are dispersed throughout the literature, rendering comparative analyses difficult. Here, we introduce the COMADRE Animal Matrix Database, an open-data online repository, which in its version 1.0.0 contains data on 345 species world-wide, from 402 studies with a total of 1625 population projection matrices. COMADRE also contains ancillary information (e.g. ecoregion, taxonomy, biogeography, etc.) that facilitates interpretation of the numerous demographic metrics that can be derived from its MPMs. We provide R code to some of these examples. 4. Synthesis: We introduce the COMADRE Animal Matrix Database, a resource for animal demography. Its open-data nature, together with its ancillary information, will facilitate comparative analysis, as will the growing availability of databases focusing on other aspects of the rich animal diversity, and tools to query and combine them. Through future frequent updates of COMADRE, and its integration with other online resources, we encourage animal ecologists to tackle global ecological and evolutionary questions with unprecedented sample size.

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TL;DR: The strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to physiologically straddle wide-ranging timescales in the alteration of ocean conditions, including the need to adapt to rapidly rising CO2 and also acclimate to environmental heterogeneity in more slowly changing properties such as warming.
Abstract: Organisms are projected to face unprecedented rates of change in future ocean conditions due to anthropogenic climate-change. At present, marine life encounters a wide range of environmental heterogeneity from natural fluctuations to mean climate change. Manipulation studies suggest that biota from more variable marine environments have more phenotypic plasticity to tolerate environmental heterogeneity. Here, we consider current strategies employed by a range of representative organisms across various habitats – from short-lived phytoplankton to long-lived corals – in response to environmental heterogeneity. We then discuss how, if and when organismal responses (acclimate/migrate/adapt) may be altered by shifts in the magnitude of the mean climate-change signal relative to that for natural fluctuations projected for coming decades. The findings from both novel climate-change modelling simulations and prior biological manipulation studies, in which natural fluctuations are superimposed on those of mean change, provide valuable insights into organismal responses to environmental heterogeneity. Manipulations reveal that different experimental outcomes are evident between climate-change treatments which include natural fluctuations vs. those which do not. Modelling simulations project that the magnitude of climate variability, along with mean climate change, will increase in coming decades, and hence environmental heterogeneity will increase, illustrating the need for more realistic biological manipulation experiments that include natural fluctuations. However, simulations also strongly suggest that the timescales over which the mean climate-change signature will become dominant, relative to natural fluctuations, will vary for individual properties, being most rapid for CO2 (~10 years from present day) to 4 decades for nutrients. We conclude that the strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to physiologically straddle wide-ranging timescales in the alteration of ocean conditions, including the need to adapt to rapidly rising CO2 and also acclimate to environmental heterogeneity in more slowly changing properties such as warming.

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TL;DR: It is shown that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean, suggesting that organic ligand composition changes across the surface ocean in response to environmental pressures.
Abstract: Nearly all iron dissolved in the ocean is complexed by strong organic ligands of unknown composition. The effect of ligand composition on microbial iron acquisition is poorly understood, but amendment experiments using model ligands show they can facilitate or impede iron uptake depending on their identity. Here we show that siderophores, organic compounds synthesized by microbes to facilitate iron uptake, are a dynamic component of the marine ligand pool in the eastern tropical Pacific Ocean. Siderophore concentrations in iron-deficient waters averaged 9 pM, up to fivefold higher than in iron-rich coastal and nutrient-depleted oligotrophic waters, and were dominated by amphibactins, amphiphilic siderophores with cell membrane affinity. Phylogenetic analysis of amphibactin biosynthetic genes suggests that the ability to produce amphibactins has transferred horizontally across multiple Gammaproteobacteria, potentially driven by pressures to compete for iron. In coastal and oligotrophic regions of the eastern Pacific Ocean, amphibactins were replaced with lower concentrations (1–2 pM) of hydrophilic ferrioxamine siderophores. Our results suggest that organic ligand composition changes across the surface ocean in response to environmental pressures. Hydrophilic siderophores are predominantly found across regions of the ocean where iron is not expected to be the limiting nutrient for the microbial community at large. However, in regions with intense competition for iron, some microbes optimize iron acquisition by producing siderophores that minimize diffusive losses to the environment. These siderophores affect iron bioavailability and thus may be an important component of the marine iron cycle.

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TL;DR: The extensive influence over the past forty years of Professor Edward D. Goldberg and his call in 1975 for a "Mussel Watch" or bivalve sentinel organism approach to assess geographic status and temporal trends of several chemicals of environmental concern in the coastal ocean are chronicle.