United States Department of Energy

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Abstract Black carbon aerosol plays a unique and important role in Earth's climate system. Black carbon is a type of carbonaceous material with a unique combination of physical properties. This assessment provides an evaluation of black‐carbon climate forcing that is comprehensive in its inclusion of all known and relevant processes and that is quantitative in providing best estimates and uncertainties of the main forcing terms: direct solar absorption; influence on liquid, mixed phase, and ice clouds; and deposition on snow and ice. These effects are calculated with climate models, but when possible, they are evaluated with both microphysical measurements and field observations. Predominant sources are combustion related, namely, fossil fuels for transportation, solid fuels for industrial and residential uses, and open burning of biomass. Total global emissions of black carbon using bottom‐up inventory methods are 7500 Gg yr −1 in the year 2000 with an uncertainty range of 2000 to 29000. However, global atmospheric absorption attributable to black carbon is too low in many models and should be increased by a factor of almost 3. After this scaling, the best estimate for the industrial‐era (1750 to 2005) direct radiative forcing of atmospheric black carbon is +0.71 W m −2 with 90% uncertainty bounds of (+0.08, +1.27) W m −2 . Total direct forcing by all black carbon sources, without subtracting the preindustrial background, is estimated as +0.88 (+0.17, +1.48) W m −2 . Direct radiative forcing alone does not capture important rapid adjustment mechanisms. A framework is described and used for quantifying climate forcings, including rapid adjustments. The best estimate of industrial‐era climate forcing of black carbon through all forcing mechanisms, including clouds and cryosphere forcing, is +1.1 W m −2 with 90% uncertainty bounds of +0.17 to +2.1 W m −2 . Thus, there is a very high probability that black carbon emissions, independent of co‐emitted species, have a positive forcing and warm the climate. We estimate that black carbon, with a total climate forcing of +1.1 W m −2 , is the second most important human emission in terms of its climate forcing in the present‐day atmosphere; only carbon dioxide is estimated to have a greater forcing. Sources that emit black carbon also emit other short‐lived species that may either cool or warm climate. Climate forcings from co‐emitted species are estimated and used in the framework described herein. When the principal effects of short‐lived co‐emissions, including cooling agents such as sulfur dioxide, are included in net forcing, energy‐related sources (fossil fuel and biofuel) have an industrial‐era climate forcing of +0.22 (−0.50 to +1.08) W m −2 during the first year after emission. For a few of these sources, such as diesel engines and possibly residential biofuels, warming is strong enough that eliminating all short‐lived emissions from these sources would reduce net climate forcing (i.e., produce cooling). When open burning emissions, which emit high levels of organic matter, are included in the total, the best estimate of net industrial‐era climate forcing by all short‐lived species from black‐carbon‐rich sources becomes slightly negative (−0.06 W m −2 with 90% uncertainty bounds of −1.45 to +1.29 W m −2 ). The uncertainties in net climate forcing from black‐carbon‐rich sources are substantial, largely due to lack of knowledge about cloud interactions with both black carbon and co‐emitted organic carbon. In prioritizing potential black‐carbon mitigation actions, non‐science factors, such as technical feasibility, costs, policy design, and implementation feasibility play important roles. The major sources of black carbon are presently in different stages with regard to the feasibility for near‐term mitigation. This assessment, by evaluating the large number and complexity of the associated physical and radiative processes in black‐carbon climate forcing, sets a baseline from which to improve future climate forcing estimates.

A biorefinery that supplements its manufacture of low value biofuels with high value biobased chemicals can enable efforts to reduce nonrenewable fuel consumption while simultaneously providing the necessary financial incentive to stimulate expansion of the biorefining industry. However, the choice of appropriate products for addition to the biorefinery's portfolio is challenged by a lack of broad-based conversion technology coupled with a plethora of potential targets. In 2004, the US Department of Energy (DOE) addressed these challenges by describing a selection process for chemical products that combined identification of a small group of compounds derived from biorefinery carbohydrates with the research and technology needs required for their production. The intent of the report was to catalyze research efforts to synthesize multiple members of this group, or, ideally, structures not yet on the list. In the six years since DOE's original report, considerable progress has been made in the use of carbohydrates as starting materials for chemical production. This review presents an updated evaluation of potential target structures using similar selection methodology, and an overview of the technology developments that led to the inclusion of a given compound. The list provides a dynamic guide to technology development that could realize commercial success through the proper integration of biofuels with biobased products.

Carbon capture and storage (CCS) is vital to climate change mitigation, and has application across the economy, in addition to facilitating atmospheric carbon dioxide removal resulting in emissions offsets and net negative emissions. This contribution reviews the state-of-the-art and identifies key challenges which must be overcome in order to pave the way for its large-scale deployment.

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the ∼75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization ∼70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum’s drought tolerance. The Sorghum bicolor genome sequence is published this week. Sorghum is a cereal grown widely as food, animal feed, fibre and fuel. Tolerant to hot, dry conditions, it is a staple for large populations in the West African Sahel region. Comparisons of the genome with those of maize and rice shed light on the evolution of grasses and of C4 photosynthesis, which is particularly efficient at assimilating carbon at high temperatures. In addition, protein coding genes and miRNAs that could contribute to sorghum's drought tolerance may also be found. Sorghum yield improvement has lagged behind that of other crops and the availability of the genome sequence could provide a vital boost to work on its improvement. Sorghum is an African grass that is grown for food, animal feed and fuel. The current paper presents an initial analysis of the ∼730 megabase genome of Sorghum bicolor. Genome analysis and its comparison with maize and rice shed light on grass genome evolution and also provide insights into the evolution of C4 photosynthesis, as well as protein coding genes and miRNAs that might contribute to sorghum's drought tolerance.

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies. The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources. The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat ( Triticum aestivum ) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

The zero-temperature equation of state of metals, in the absence of phase transitions, is shown to be accurately predicted from zero-pressure data. Upon appropriate scaling of experimental pressure-volume data a simple universal relation is found. These results provide further experimental confirmation of the recent observation that the total-binding-energy---versus---separation relations for metals obey a universal scaling relation. Important to our results is a parameter $\ensuremath{\eta}$, which is a measure of the anharmonicity of a crystal. This parameter is shown to be essential in predicting the equation of state. A simple formula is given which predicts the zero-temperature derivative of the bulk modulus with respect to pressure.

Photoelectrochemical water splitting is a promising route for the renewable production of hydrogen fuel. This work presents the results of a technical and economic feasibility analysis conducted for four hypothetical, centralized, large-scale hydrogen production plants based on this technology. The four reactor types considered were a single bed particle suspension system, a dual bed particle suspension system, a fixed panel array, and a tracking concentrator array. The current performance of semiconductor absorbers and electrocatalysts were considered to compute reasonable solar-to-hydrogen conversion efficiencies for each of the four systems. The U.S. Department of Energy H2A model was employed to calculate the levelized cost of hydrogen output at the plant gate at 300 psi for a 10 tonne per day production scale. All capital expenditures and operating costs for the reactors and auxiliaries (compressors, control systems, etc.) were considered. The final cost varied from $1.60–$10.40 per kg H2 with the particle bed systems having lower costs than the panel-based systems. However, safety concerns due to the cogeneration of O2 and H2 in a single bed system and long molecular transport lengths in the dual bed system lead to greater uncertainty in their operation. A sensitivity analysis revealed that improvement in the solar-to-hydrogen efficiency of the panel-based systems could substantially drive down their costs. A key finding is that the production costs are consistent with the Department of Energy's targeted threshold cost of $2.00–$4.00 per kg H2 for dispensed hydrogen, demonstrating that photoelectrochemical water splitting could be a viable route for hydrogen production in the future if material performance targets can be met.

The Human Genome Project has been the first major foray of the biological and medical research communities into “big science.” In this Viewpoint, we present some of our experiences in organizing and managing such a complicated, publicly funded, international effort. We believe that many of the lessons we learned will be applicable to future large-scale projects in biology.

We report the realization of a microstructure which leads to very strong high-temperature flux pinning in ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7}$ crystals. Aligned discontinuous columns of damaged material, about 50 \AA{} in diameter and more than 15 \ensuremath{\mu}m long, are produced by 580-MeV Sn-ion irradiation. The enhancement of flux pinning is largest when the applied magnetic field is aligned with these tracks. At high temperatures and fields the pinning is much greater than that produced by random point defects, and causes a considerable enlargement of the irreversibility region in the H-T plane.

Abstract. This study presents the results of a broad intercomparison of a total of 15 global aerosol models within the AeroCom project. Each model is compared to observations related to desert dust aerosols, their direct radiative effect, and their impact on the biogeochemical cycle, i.e., aerosol optical depth (AOD) and dust deposition. Additional comparisons to Angström exponent (AE), coarse mode AOD and dust surface concentrations are included to extend the assessment of model performance and to identify common biases present in models. These data comprise a benchmark dataset that is proposed for model inspection and future dust model development. There are large differences among the global models that simulate the dust cycle and its impact on climate. In general, models simulate the climatology of vertically integrated parameters (AOD and AE) within a factor of two whereas the total deposition and surface concentration are reproduced within a factor of 10. In addition, smaller mean normalized bias and root mean square errors are obtained for the climatology of AOD and AE than for total deposition and surface concentration. Characteristics of the datasets used and their uncertainties may influence these differences. Large uncertainties still exist with respect to the deposition fluxes in the southern oceans. Further measurements and model studies are necessary to assess the general model performance to reproduce dust deposition in ocean regions sensible to iron contributions. Models overestimate the wet deposition in regions dominated by dry deposition. They generally simulate more realistic surface concentration at stations downwind of the main sources than at remote ones. Most models simulate the gradient in AOD and AE between the different dusty regions. However the seasonality and magnitude of both variables is better simulated at African stations than Middle East ones. The models simulate the offshore transport of West Africa throughout the year but they overestimate the AOD and they transport too fine particles. The models also reproduce the dust transport across the Atlantic in the summer in terms of both AOD and AE but not so well in winter-spring nor the southward displacement of the dust cloud that is responsible of the dust transport into South America. Based on the dependency of AOD on aerosol burden and size distribution we use model bias with respect to AOD and AE to infer the bias of the dust emissions in Africa and the Middle East. According to this analysis we suggest that a range of possible emissions for North Africa is 400 to 2200 Tg yr−1 and in the Middle East 26 to 526 Tg yr−1.

Field-induced strains of 6% are reported in ferromagnetic Ni–Mn–Ga martensites at room temperature. The strains are the result of twin boundary motion driven largely by the Zeeman energy difference across the twin boundary. The strain measured parallel to the applied magnetic field is negative in the sample/field geometry used here. The strain saturates in fields of order 400 kA/m and is blocked by a compressive stress of order 2 MPa applied orthogonal to the magnetic field. The strain versus field curves exhibit appreciable hysteresis associated with the motion of the twin boundaries. A simple model accounts quantitatively for the dependence of strain on magnetic field and external stress using as input parameters only measured quantities.

Mesoporous silica nanoparticles (MSNs) are introduced as chemically and thermally stable nanomaterials with well-defined and controllable morphology and porosity. It is shown that these particles possess external and internal surfaces that can be selectively functionalized with multiple organic and inorganic groups. On the basis of these characteristics, the biocompatibility of silica, and their efficient uptake by mammalian cells, MSNs are proposed as the basis of nanodevices for the controlled release of drugs and genes into living cells.

Francis Martin and colleagues report genome sequences for 18 species of mycorrhizal fungi and a phylogenomic analysis including 32 other fungal genomes. The study identifies cell wall-degradation genes lost in all true ectomycorrhizal species and, using gene expression data, finds candidate genes for the establishment of symbiosis. To elucidate the genetic bases of mycorrhizal lifestyle evolution, we sequenced new fungal genomes, including 13 ectomycorrhizal (ECM), orchid (ORM) and ericoid (ERM) species, and five saprotrophs, which we analyzed along with other fungal genomes. Ectomycorrhizal fungi have a reduced complement of genes encoding plant cell wall–degrading enzymes (PCWDEs), as compared to their ancestral wood decayers. Nevertheless, they have retained a unique array of PCWDEs, thus suggesting that they possess diverse abilities to decompose lignocellulose. Similar functional categories of nonorthologous genes are induced in symbiosis. Of induced genes, 7–38% are orphan genes, including genes that encode secreted effector-like proteins. Convergent evolution of the mycorrhizal habit in fungi occurred via the repeated evolution of a 'symbiosis toolkit', with reduced numbers of PCWDEs and lineage-specific suites of mycorrhiza-induced genes.

As one important component of sulfur cathodes, the carbon host plays a key role in the electrochemical performance of lithium‐sulfur (Li‐S) batteries. In this paper, a mesoporous nitrogen‐doped carbon (MPNC)‐sulfur nanocomposite is reported as a novel cathode for advanced Li‐S batteries. The nitrogen doping in the MPNC material can effectively promote chemical adsorption between sulfur atoms and oxygen functional groups on the carbon, as verified by X‐ray absorption near edge structure spectroscopy, and the mechanism by which nitrogen enables the behavior is further revealed by density functional theory calculations. Based on the advantages of the porous structure and nitrogen doping, the MPNC‐sulfur cathodes show excellent cycling stability (95% retention within 100 cycles) at a high current density of 0.7 mAh cm ‐2 with a high sulfur loading (4.2 mg S cm ‐2 ) and a sulfur content (70 wt%). A high areal capacity (≈3.3 mAh cm ‐2 ) is demonstrated by using the novel cathode, which is crucial for the practical application of Li‐S batteries. It is believed that the important role of nitrogen doping promoted chemical adsorption can be extended for development of other high performance carbon‐sulfur composite cathodes for Li‐S batteries.

The structure of vortices within an infinite stack of thin superconducting layers is considered and examined in detail in the limit of zero interlayer Josephson coupling. The basic building block for the description of three-dimensional (3D) vortex lines is shown to be the 2D pancake vortex, which is a vortex located in only one of the layers; the other layers contain no vortices, but have an important effect in screening the magnetic field generated by currents in the first layer. It is shown that 3D vortex lines can be built up by superposing the contributions of stacks of 2D pancake vortices. Thermal excitation is shown to break up a single 3D vortex line at a temperature corresponding to the Kosterlitz-Thouless temperature of a single superconducting layer. The effect of thermally induced decoupling of the 2D vortex solids in different layers, corresponding to melting only in the direction perpendicular to the layers, is also considered. It is shown that Josephson coupling can be neglected in the high-temperature superconductors only under very stringent conditions. Although these conditions evidently are not met in ${\mathrm{Bi}}_{2}$${\mathrm{Sr}}_{2}$${\mathrm{CaCu}}_{2}$${\mathrm{O}}_{8}$ and ${\mathrm{Tl}}_{2}$${\mathrm{Ba}}_{2}$${\mathrm{Ca}}_{1}$${\mathrm{Cu}}_{2}$${\mathrm{O}}_{8}$, they should be satisfied in superconducting-insulating multilayer systems, such as ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$/${\mathrm{PrBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$.

The potential for removing uranium from contaminated groundwater by stimulating the in situ activity of dissimilatory metal-reducing microorganisms was evaluated in a uranium-contaminated aquifer located in Rifle, Colo. Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells, which was installed upgradient from a series of 15 monitoring wells. U(VI) concentrations decreased in as little as 9 days after acetate injection was initiated, and within 50 days uranium had declined below the prescribed treatment level of 0.18 micro M in some of the monitoring wells. Analysis of 16S ribosomal DNA (rDNA) sequences and phospholipid fatty acid profiles demonstrated that the initial loss of uranium from the groundwater was associated with an enrichment of Geobacter species in the treatment zone. Fe(II) in the groundwater also increased during this period, suggesting that U(VI) reduction was coincident with Fe(III) reduction. As the acetate injection continued over 50 days there was a loss of sulfate from the groundwater and an accumulation of sulfide and the composition of the microbial community changed. Organisms with 16S rDNA sequences most closely related to those of sulfate reducers became predominant, and Geobacter species became a minor component of the community. This apparent switch from Fe(III) reduction to sulfate reduction as the terminal electron accepting process for the oxidation of the injected acetate was associated with an increase in uranium concentration in the groundwater. These results demonstrate that in situ bioremediation of uranium-contaminated groundwater is feasible but suggest that the strategy should be optimized to better maintain long-term activity of Geobacter species.

An intrinsic magnetic tunnel junction An electrical current running through two stacked magnetic layers is larger if their magnetizations point in the same direction than if they point in opposite directions. These so-called magnetic tunnel junctions, used in electronics, must be carefully engineered. Two groups now show that high magnetoresistance intrinsically occurs in samples of the layered material CrI 3 sandwiched between graphite contacts. By varying the number of layers in the samples, Klein et al. and Song et al. found that the electrical current running perpendicular to the layers was largest in high magnetic fields and smallest near zero field. This observation is consistent with adjacent layers naturally having opposite magnetizations, which align parallel to each other in high magnetic fields. Science , this issue p. 1218 , p. 1214

The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus. The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties. Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain. Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes. They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture. The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons. They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups.