Woods Hole Oceanographic Institution

The IntCal09 and Marine09 radiocarbon calibration curves have been revised utilizing newly available and updated data sets from 14 C measurements on tree rings, plant macrofossils, speleothems, corals, and foraminifera. The calibration curves were derived from the data using the random walk model (RWM) used to generate IntCal09 and Marine09, which has been revised to account for additional uncertainties and error structures. The new curves were ratified at the 21st International Radiocarbon conference in July 2012 and are available as Supplemental Material at www.radiocarbon.org. The database can be accessed at http://intcal.qub.ac.uk/intcal13/.

ABSTRACT Radiocarbon ( 14 C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14 C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14 C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14 C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14 C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14 C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.

A complementary DNA for the Aequorea victoria green fluorescent protein (GFP) produces a fluorescent product when expressed in prokaryotic (Escherichia coli) or eukaryotic (Caenorhabditis elegans) cells. Because exogenous substrates and cofactors are not required for this fluorescence, GFP expression can be used to monitor gene expression and protein localization in living organisms.

The IntCal04 and Marine04 radiocarbon calibration curves have been updated from 12 cal kBP (cal kBP is here defined as thousands of calibrated years before AD 1950), and extended to 50 cal kBP, utilizing newly available data sets that meet the IntCal Working Group criteria for pristine corals and other carbonates and for quantification of uncertainty in both the 14 C and calendar timescales as established in 2002. No change was made to the curves from 0–12 cal kBP. The curves were constructed using a Markov chain Monte Carlo (MCMC) implementation of the random walk model used for IntCal04 and Marine04. The new curves were ratified at the 20th International Radiocarbon Conference in June 2009 and are available in the Supplemental Material at www.radiocarbon.org .

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.

The fourth version of the Community Climate System Model (CCSM4) was recently completed and released to the climate community. This paper describes developments to all CCSM components, and documents fully coupled preindustrial control runs compared to the previous version, CCSM3. Using the standard atmosphere and land resolution of 1° results in the sea surface temperature biases in the major upwelling regions being comparable to the 1.4°-resolution CCSM3. Two changes to the deep convection scheme in the atmosphere component result in CCSM4 producing El Niño–Southern Oscillation variability with a much more realistic frequency distribution than in CCSM3, although the amplitude is too large compared to observations. These changes also improve the Madden–Julian oscillation and the frequency distribution of tropical precipitation. A new overflow parameterization in the ocean component leads to an improved simulation of the Gulf Stream path and the North Atlantic Ocean meridional overturning circulation. Changes to the CCSM4 land component lead to a much improved annual cycle of water storage, especially in the tropics. The CCSM4 sea ice component uses much more realistic albedos than CCSM3, and for several reasons the Arctic sea ice concentration is improved in CCSM4. An ensemble of twentieth-century simulations produces a good match to the observed September Arctic sea ice extent from 1979 to 2005. The CCSM4 ensemble mean increase in globally averaged surface temperature between 1850 and 2005 is larger than the observed increase by about 0.4°C. This is consistent with the fact that CCSM4 does not include a representation of the indirect effects of aerosols, although other factors may come into play. The CCSM4 still has significant biases, such as the mean precipitation distribution in the tropical Pacific Ocean, too much low cloud in the Arctic, and the latitudinal distributions of shortwave and longwave cloud forcings.

Abstract Eleven coupled climate–carbon cycle models used a common protocol to study the coupling between climate change and the carbon cycle. The models were forced by historical emissions and the Intergovernmental Panel on Climate Change (IPCC) Special Report on Emissions Scenarios (SRES) A2 anthropogenic emissions of CO2 for the 1850–2100 time period. For each model, two simulations were performed in order to isolate the impact of climate change on the land and ocean carbon cycle, and therefore the climate feedback on the atmospheric CO2 concentration growth rate. There was unanimous agreement among the models that future climate change will reduce the efficiency of the earth system to absorb the anthropogenic carbon perturbation. A larger fraction of anthropogenic CO2 will stay airborne if climate change is accounted for. By the end of the twenty-first century, this additional CO2 varied between 20 and 200 ppm for the two extreme models, the majority of the models lying between 50 and 100 ppm. The higher CO2 levels led to an additional climate warming ranging between 0.1° and 1.5°C. All models simulated a negative sensitivity for both the land and the ocean carbon cycle to future climate. However, there was still a large uncertainty on the magnitude of these sensitivities. Eight models attributed most of the changes to the land, while three attributed it to the ocean. Also, a majority of the models located the reduction of land carbon uptake in the Tropics. However, the attribution of the land sensitivity to changes in net primary productivity versus changes in respiration is still subject to debate; no consensus emerged among the models.

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

We provide here a list of 481 P450 genes and 22 pseudogenes, plus all accession numbers that have been reported as of October 18, 1995. These genes have been described in 85 eukaryote (including vertebrates, invertebrates, fungi, and plants) and 20 prokaryote species. Of 74 gene families so far described, 14 families exist in all mammals examined to date. These 14 families comprise 26 mammalian subfamilies, of which 20 and 15 have been mapped in the human genome and the mouse genome, respectively. Each subfamily usually represents a cluster of tightly linked genes widely scattered throughout the genome, but there are exceptions. Interestingly, the CYP51 family has been found in mammals, filamentous fungi and yeast, and plants-attesting to the fact that this P450 gene family is very ancient. One functional CYP51 gene and two processed pseudogenes, which are the first examples of intronless pseudogenes within the P450 superfamily, have been mapped to three different human chromosomes. This revision supersedes the four previous updates in which a nomenclature system, based on divergent evolution of the superfamily, has been described. For the gene, we recommend that the italicized root symbol "CYP' for human ("Cyp' for mouse and Drosophila), representing "cytochrome P450', be followed by an Arabic number denoting the family, a letter designating the subfamily (when two or more exist), and an Arabic numeral representing the individual gene within the subfamily. A hyphen is no longer recommended in mouse gene nomenclature. "P' ("ps' in mouse and Drosophila) after the gene number denotes a pseudogene; "X' after the gene number means its use has been discontinued. If a gene is the sole member of a family, the subfamily letter and gene number would be helpful but need not be included. The human nomenclature system should be used for all species other than mouse and Drosophila. The cDNAs, mRNAs and enzymes in all species (including mouse) should include all capital letters, and without italics or hyphens. This nomenclature system is similar to that proposed in our previous updates.

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 wide-ranging 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.

Author Posting. © Inter-Research, 2015. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 75 (2015): 129-137, doi:10.3354/ame01753.

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Archaea (archaebacteria) are a phenotypically diverse group of microorganisms that share a common evolutionary history. There are four general phenotypic groups of archaea: the methanogens, the extreme halophiles, the sulfate-reducing archaea, and the extreme thermophiles. In the marine environment, archaeal habitats are generally limited to shallow or deep-sea anaerobic sediments (free-living and endosymbiotic methanogens), hot springs or deep-sea hydrothermal vents (methanogens, sulfate reducers, and extreme thermophiles), and highly saline land-locked seas (halophiles). This report provides evidence for the widespread occurrence of unusual archaea in oxygenated coastal surface waters of North America. Quantitative estimates indicated that up to 2% of the total ribosomal RNA extracted from coastal bacterioplankton assemblages was archaeal. Archaeal small-subunit ribosomal RNA-encoding DNAs (rDNAs) were cloned from mixed bacterioplankton populations collected at geographically distant sampling sites. Phylogenetic and nucleotide signature analyses of these cloned rDNAs revealed the presence of two lineages of archaea, each sharing the diagnostic signatures and structural features previously established for the domain Archaea. Both of these lineages were found in bacterioplankton populations collected off the east and west coasts of North America. The abundance and distribution of these archaea in oxic coastal surface waters suggests that these microorganisms represent undescribed physiological types of archaea, which reside and compete with aerobic, mesophilic eubacteria in marine coastal environments.

In 1996, version 2.5 of the Coupled Ocean–Atmosphere Response Experiment (COARE) bulk algorithm was published, and it has become one of the most frequently used algorithms in the air–sea interaction community. This paper describes steps taken to improve the algorithm in several ways. The number of iterations to solve for stability has been shortened from 20 to 3, and adjustments have been made to the basic profile stability functions. The scalar transfer coefficients have been redefined in terms of the mixing ratio, which is the fundamentally conserved quantity, rather than the measured water vapor mass concentration. Both the velocity and scalar roughness lengths have been changed. For the velocity roughness, the original fixed value of the Charnock parameter has been replaced by one that increases with wind speeds of between 10 and 18 m s−1. The scalar roughness length parameterization has been simplified to fit both an early set of NOAA/Environmental Technology Laboratory (ETL) experiments and the Humidity Exchange Over the Sea (HEXOS) program. These changes slightly increase the fluxes for wind speeds exceeding 10 m s−1. For interested users, two simple parameterizations of the surface gravity wave influence on fluxes have been added (but not evaluated). This new version of the algorithm (COARE 3.0) was based on published results and 2777 1-h covariance flux measurements in the ETL inventory. To test it, 4439 new values from field experiments between 1997 and 1999 were added, which now dominate the database, especially in the wind speed regime beyond 10 m s−1, where the number of observations increased from 67 to about 800. After applying various quality controls, the database was used to evaluate the algorithm in several ways. For an overall mean, the algorithm agrees with the data to within a few percent for stress and latent heat flux. The agreement is also excellent when the bulk and directly measured fluxes are averaged in bins of 10-m neutral wind speed. For a more stringent test, the average 10-m neutral transfer coefficients were computed for stress and moisture in wind speed bins, using different averaging schemes with fairly similar results. The average (mean and median) model results agreed with the measurements to within about 5% for moisture from 0 to 20 m s−1. For stress, the covariance measurements were about 10% higher than the model at wind speeds over 15 m s−1, while inertial-dissipation measurements agreed closely at all wind speeds. The values for stress are between 8% (for inertial dissipation) and 18% (for covariance) higher at 20 m s−1 than two other classic results. Twenty years ago, bulk flux schemes were considered to be uncertain by about 30%; the authors find COARE 3.0 to be accurate within 5% for wind speeds of 0–10 m s−1 and 10% for wind speeds of between 10 and 20 m s−1.

Abstract Matrix population models are discrete‐time structured population models in which individuals are classified into discrete stages (age classes, size classes, developmental stages, spatial locations, etc.).

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called ‘microbial dark matter’. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet. Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla. Currently available genome sequences give us a narrow view of the remarkable diversity of microorganisms because the vast majority of them have never been cultivated in pure culture. Here Tanja Woyke and colleagues use single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats. This information reveals numerous intra- and inter-phylum relationships and a number of unexpected metabolic features. On the basis of the new data the authors propose taxonomic revisions to the archaeal and bacterial domains, including a proposal to reorganizing the Archaea into three superphyla.

Titanium and iron concentration data from the anoxic Cariaco Basin, off the Venezuelan coast, can be used to infer variations in the hydrological cycle over northern South America during the past 14,000 years with subdecadal resolution. Following a dry Younger Dryas, a period of increased precipitation and riverine discharge occurred during the Holocene "thermal maximum." Since approximately 5400 years ago, a trend toward drier conditions is evident from the data, with high-amplitude fluctuations and precipitation minima during the time interval 3800 to 2800 years ago and during the "Little Ice Age." These regional changes in precipitation are best explained by shifts in the mean latitude of the Atlantic Intertropical Convergence Zone (ITCZ), potentially driven by Pacific-based climate variability. The Cariaco Basin record exhibits strong correlations with climate records from distant regions, including the high-latitude Northern Hemisphere, providing evidence for global teleconnections among regional climates.

Abstract The Community Climate System Model version 3 (CCSM3) has recently been developed and released to the climate community. CCSM3 is a coupled climate model with components representing the atmosphere, ocean, sea ice, and land surface connected by a flux coupler. CCSM3 is designed to produce realistic simulations over a wide range of spatial resolutions, enabling inexpensive simulations lasting several millennia or detailed studies of continental-scale dynamics, variability, and climate change. This paper will show results from the configuration used for climate-change simulations with a T85 grid for the atmosphere and land and a grid with approximately 1° resolution for the ocean and sea ice. The new system incorporates several significant improvements in the physical parameterizations. The enhancements in the model physics are designed to reduce or eliminate several systematic biases in the mean climate produced by previous editions of CCSM. These include new treatments of cloud processes, aerosol radiative forcing, land–atmosphere fluxes, ocean mixed layer processes, and sea ice dynamics. There are significant improvements in the sea ice thickness, polar radiation budgets, tropical sea surface temperatures, and cloud radiative effects. CCSM3 can produce stable climate simulations of millennial duration without ad hoc adjustments to the fluxes exchanged among the component models. Nonetheless, there are still systematic biases in the ocean–atmosphere fluxes in coastal regions west of continents, the spectrum of ENSO variability, the spatial distribution of precipitation in the tropical oceans, and continental precipitation and surface air temperatures. Work is under way to extend CCSM to a more accurate and comprehensive model of the earth's climate system.

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.

This paper describes the various physical processes relating near‐surface atmospheric and oceanographic bulk variables; their relationship to the surface fluxes of momentum, sensible heat, and latent heat; and their expression in a bulk flux algorithm. The algorithm follows the standard Monin‐Obukhov similarity approach for near‐surface meteorological measurements but includes separate models for the ocean's cool skin and the diurnal warm layer, which are used to derive true skin temperature from the bulk temperature measured at some depth near the surface. The basic structure is an outgrowth of the Liu‐Katsaros‐Businger [ Liu et al. , 1979] method, with modifications to include a different specification of the roughness/stress relationship, a gustiness velocity to account for the additional flux induced by boundary layer scale variability, and profile functions obeying the convective limit. Additionally, we have considered the contributions of the sensible heat carried by precipitation and the requirement that the net dry mass flux be zero (the so‐called Webb correction [ Webb et al. , 1980]). The algorithm has been tuned to fit measurements made on the R/V Moana Wave in the three different cruise legs made during the Coupled Ocean‐Atmosphere Response Experiment. These measurements yielded 1622 fifty‐min averages of fluxes and bulk variables in the wind speed range from 0.5 to 10 m s −1 . The analysis gives statistically reliable values for the Charnock [1955] constant (α = 0.011) and the gustiness parameter (β = 1.25). An overall mean value for the latent heat flux, neutral bulk‐transfer coefficient was 1.11 × 10 −3 , declining slightly with increasing wind speed. Mean values for the sensible and latent heat fluxes were 9.1 and 103.5 W m −2 ; mean values for the Webb and rain heat fluxes were 2.5 and 4.5 W m −2 . Accounting for all factors, the net surface heat transfer to the ocean was 17.9 ± 10 W m −2 .