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Microbial Metabolism Microorganisms can respire sulfur compounds in the absence of oxygen, eventually leading to the production of hydrogen sulfide. This ancient metabolism is common in modern anoxic environments, but the enzymatic pathways aren't yet fully resolved. Through in vivo and in vitro experiments, Santos et al. clarify the enzymology of the sulfate reduction pathway in both bacteria and archaea (see the Perspective by Fritz and Kroneck). Reduction of the sulfite intermediate results in the linkage of two cysteine residues to a third sulfur atom from sulfite, forming a trisulfide product. Because the reduction of sulfite conveys a strong isotopic signature on sulfur in the environment, isotope fractionation models should account for this additional step. Science , this issue p. [1541][1]; see also p. [1476][2] [1]: /lookup/doi/10.1126/science.aad3558 [2]: /lookup/doi/10.1126/science.aad8139

Inorganic Chemistry Making a synthetic analog of plant photosynthesis is a key goal for exploiting solar energy and replacing fossil fuels. Zhang et al. synthesized a manganese-calcium cluster that looks and acts like the oxygen evolution center in photosystem II (see the Perspective by Sun). The mimic structurally resembles the biological complex, with the notable exception of bridging protein ligands and water-binding sites on a dangling Mn atom. Functionally, however, the cluster's metal center readily undergoes four redox transitions, which contribute to splitting water into oxygen. This and other synthetic mimics will pave the way for developing more efficient catalysts for artificial photosynthesis. Science , this issue p. [690][1]; see also p. [635][2] [1]: /lookup/doi/10.1126/science.aaa6550 [2]: /lookup/doi/10.1126/science.aaa9094

Biocatalysis Organic compounds containing silicon are important for a number of applications, from polymers to semiconductors. The catalysts used for creating carbon-silicon bonds, however, often require expensive trace metals or have limited lifetimes. Borrowing from the ability of some metallo

Carbon Footprint![Figure][1] CREDIT: KANEMOTO ET AL. , ENVIRONMENTAL SCIENCE & TECHNOLOGY (1 SEPTEMBER 2016) ©ACS The consumption and production of goods have a much wider impact than simply on the country or region where they are used or made. For example, the carbon footprint of global supply chains varies within and between countries, mostly according to economics and trade. Using spatial modeling, Kanemoto et al. linked carbon emissions maps to industrial activity across 187 countries from 1970 to 2008. The carbon footprints of developed countries such as the United States have become more globally diffuse over that time span, whereas hotspots of carbon footprints in rapidly developing economies such as India and China are located in their expanding urban areas. Environ. Sci. Technol. 10.1021/acs.est.6b03227 (2016). [1]: pending:yes

Biofuels Renewable resources can directly replace fossil fuels for generating electricity, but finding a cleaner replacement for liquid fuels is less clear. Biofuels have shown potential, but the cost of feedstocks, competition with land for food crops, and the overall carbon balance have hindered their progress. Hu et al. integrated two bioreactors to turn syngas—a mixture of CO2, CO, and H2—into lipids that can be used as biodiesel. Although carbon from syngas accounts for just over half of the carbon in the lipids produced, further optimization and recycling of CO2 between bioreactors should improve the net carbon balance of the system. Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.1516867113 (2016).

Enviromental Science Excess nutrients such as nitrogen and phosphorus can negatively affect aquatic ecosystems. Nutrient-rich fertilizer runoff stimulates productivity, which can lead to harmful algal blooms or fish kills. Nolan and Weber show that such pollution has another wide-ranging consequence: increasing the mobility of uranium in groundwater. Geochemical data for two major aquifers in the United States, which in combination provide drinking water to millions and irrigation for one-sixth of U.S. agriculture, show that increased nitrate levels correlate strongly with the presence of uranium. Nitrate can oxidatively dissolve naturally occurring uranium minerals, which in turn can lead to potentially harmful levels of soluble uranium in groundwater, especially in shallow aquifers. Environ. Sci. Technol. Lett. 10.1021/acs.estlett.5b00174(2015).

Microbial Communities Natural microbial communities are frustratingly complex—even with the advent of powerful metagenomic tools. Overlooked abundant organisms often result in an incomplete view of the metabolic processes that affect major geochemical cycles. Hug et al. developed a subsampling metagenomic assembly technique which, when combined with metaproteomics, reveals a preponderance of highly abundant, novel microbial lineages in subsurface sediments at an old uranium mill tailings site. These organisms cycle carbon, nitrogen, and sulfur through unanticipated pathways. For example, despite low ammonium concentrations in the aquifer, the most abundant community member in the sediment is an ammonium-oxidizing archaeon that partially utilizes ammonium produced by nitrate-reducing bacteria. Environ. Microbiol. 17 , 10.1111/1462-2920.12930 (2015).

Nuclear Chemistry Uranium dioxide, the most common form of nuclear fuel, becomes mobile as it oxidizes. Although oxidative corrosion is inherently a surface-mediated process, interstitial oxygen atoms can induce oxidation many atomic layers deeper. By detailing the surface structure and composition of UO2 after exposure to oxygen in air and water, Stubbs et al. show that oxidation does not follow a classical diffusion pattern. Instead, interstitial oxygens preferentially occupy every third atomic layer below the terminal (111) surface. This pattern is a product of the delocalized electronic structure of nonsurface U atoms, which also allows for the coexistence of three U oxidation states. Phys. Rev. Lett. 114 , 246103 (2015).

Mercury Microbiology Genes present in buried lake sediments can help reconstruct how microbial ecosystems responded to past exposure to mercury. When atmospheric mercury transported around the globe is eventually deposited in terrestrial or aquatic environments, microorganisms control its cycling and bioaccumulation. Poulain et al. isolated ancient microbial DNA from sediments in remote subarctic lakes in the Hudson Bay Lowlands of Canada. The distribution of genes coding for mercuric reductase (merA), the primary enzyme involved in mercury detoxification, correlates with historical mercury deposition, including a rapid population shift at the onset of the Industrial Revolution. ISME J. 10.1038/ismej.2015.86 (2015).

Aquatic Microbiology Freshwater lakes are a major contributor of methane to the atmosphere—more so than the world's oceans combined. Some anaerobic microorganisms produce methane in sediments or deep anoxic water, but methane can also be produced biologically in oxic surface water. In the upper layers of methane-supersaturated Lake Matano, Indonesia, Yao et al. find that bacterial methane production is linked to phosphorus availability. Heterotrophic bacteria break down methylphosphonate as a phosphorus source, releasing methane in the process. Methane production decreases in culture when phosphate is added. Models for methane emissions from lakes should therefore incorporate nutrient availability in oxic water columns as another potential factor to help improve global methane predictions. Appl. Environ. Microbiol. 10.1128/AEM.02399-16 (2016).

Bioinorganic Chemistry Nitrogenase enzymes catalyze the biological production of fixed nitrogen. Because this is not enough to sustain modern agriculture, industrial fertilizers containing ammonia are produced via the energy-intensive Haber-Bosch process. Brown et al. developed a way to use nitrogenase enzymes from nitrogen-fixing bacteria to make ammonia in vitro without other biological steps or high-energy inputs. Light-activated CdS nanorods provided electrons to the FeMo nitrogenase enzyme to reduce nitrogen and produce ammonia at rates up to 64% of biological nitrogen fixation. These nanoparticle-protein complexes show the potential for solar-driven ammonia production. Science , this issue p. [448][1] [1]: /lookup/doi/10.1126/science.aaf2091

Biogeochemistry![Figure][1] Lake Powell, seen from Alstrom Point in Arizona, USA. PHOTO: JOHN SHAW/SCIENCE SOURCE Lakes of all sizes are sensitive to local water and pollution management strategies. Excess nutrients in lakes can induce a series of unexpected consequences for water quality or greenhouse gas emissions. Based on previously collected data from over 8000 lakes across six continents, Chen et al. compiled a global estimate of carbon, nitrogen, and phosphorus in lakes. These trace nutrients have intertwined fates in lakes, often related to morphological and climatic factors that change over time. Perturbations of climate or land use by humans will therefore have wide-ranging effects on biogeochemical cycling of nutrients within lakes across the globe. Sci. Rep. 10.1038/srep15043 (2015). [1]: pending:yes

Early Earth Before the rise of oxygen, life on Earth depended on the marine sulfur cycle. The fractionation of different sulfur isotopes provides clues to which biogeochemical cycles were active long ago (see the Perspective by Ueno). Zhelezinskaia et al. found negative isotope anomalies in Archean rocks from Brazil and posit that metabolic fluxes from sulfate-reducing microorganisms influenced the global sulfur cycle, including sulfur in the atmosphere. In contrast, Paris et al. found positive isotope anomalies in Archean sediments from South Africa, implying that the marine sulfate pool was more disconnected from atmospheric sulfur. As an analog for the Archean ocean, Crowe et al. measured sulfur isotope signatures in modern Lake Matano, Indonesia, and suggest that low seawater sulfate concentrations restricted early microbial activity. Science , this issue p. [703][1], p. [742][2], p. [739][3]; see also p. [735][4] [1]: /lookup/doi/10.1126/science.1261676 [2]: /lookup/doi/10.1126/science.1256211 [3]: /lookup/doi/10.1126/science.1258211 [4]: /lookup/doi/10.1126/science.1258966

Metalloproteins Organometallic nickel complexes long synthesized in the laboratory exist naturally in enzymes as well. Desguin et al. determined the structure and metal-binding residues of the Ni-containing active site in bacterial lactate racemase (see the Perspective by Zamble). A dithiodinicotinic acid mononucleotide derivative cofactor binds Ni through sulfur and carbon bonds, resembling synthetic nickel pincer complexes. Genes encoding accessory proteins involved in the synthesis of this cofactor are widely distributed in other bacteria, suggesting its involvement in other enzymes. Science , this issue p. [66][1]; see also p. [35][2] [1]: /lookup/doi/10.1126/science.aab2272 [2]: /lookup/doi/10.1126/science.aac5854

Marine Sulfur Cycle Marine phytoplankton plays a critical role in the global sulfur cycle. Algae, for instance, are the main source of the aromatic compound dimethylsulfide (DMS) released from the oceans into the atmosphere. Alcolombri et al. identified the lyase enzyme responsible for DMS production in the bloom-forming marine phytoplankton Emiliania huxleyi (see the Perspective by Johnston). The presence of this gene in other globally distributed phytoplankton and corals suggests that it may serve as a reliable indicator of DMS production across diverse phyla. Because DMS gets oxidized to sulfur aerosols, which act as cloud condensation nuclei, this enzyme is a key global biogeochemical catalyst. Science , this issue p. [1466][1]; see also p. [1430][2] [1]: /lookup/doi/10.1126/science.aab1586 [2]: /lookup/doi/10.1126/science.aac5661

Biogeochemistry![Figure][1] Soil chlorine inventories depend on the species of trees they host PHOTO: © IMAGEBROKER/ALAMY The density and type of trees in forested ecosystems control the large organic chlorine pool of soils. Chlorine is a trace nutrient for plant growth; however, its distribution is highly variable, even in instances where it was deposited regionally as chloride from the atmosphere. In an experimental forest ecosystem in eastern France, Montelius et al. show that tree species controlled total soil chlorine fluxes over 30 years. Coniferous trees, especially Norway spruce, retained organic chlorine and chloride ions in nearby soil more than deciduous trees. The preferential retention or transformation of certain chlorine compounds beyond microbial processes complicates the terrestrial chlorine cycle. Environ. Sci. Technol. 49 , 4921 (2015). [1]: pending:yes

Freshwater Ecology![Figure][1] Forest-derived leaves and wood support stream functions but are lost with nutrient pollution IMAGE: PHILLIP M. BUMPERS Excess nutrients added to streams result in net carbon loss from aquatic ecosystems. Nitrogen and phosphorus are known to fuel increases in algal carbon. Now, Rosemond et al. show that nutrients stimulate losses of terrestrially derived carbon (e.g., from twigs and leaves). The authors monitored several multiyear experiments on headwater forest streams in the United States. Some of these streams had extra nitrogen and phosphorus added at levels that are now common in many streams and lakes. To successfully manage river ecosystems, we need to take into account nutrient pollution effects on multiple carbon pathways. Science , this issue p. [1142][2] [1]: pending:yes [2]: /lookup/doi/10.1126/science.aaa1958

Environmental Science Treating wastewater removes organic matter that would otherwise harm the environment when released back into waterways. New bioelectrochemical systems provide the added benefit of using this organic matter as a fuel for bacteria to generate hydrogen gas or electricity during

Biochemistry In the mid-20th century, Alfred Redfield posited that the bulk ratio of nitrogen to phosphorus atoms (N:P) in marine microorganisms should maintain a relatively constant value of ∼16. Work since then has shown that the ratio indeed remains relatively constant across many environments

Earth History Oxygen levels in Earth's early atmosphere had an important influence on the evolution of complex life. Planavsky et al. analyzed the isotopic signature of chromium in sedimentary rocks from across the globe—a proxy for past oxygen levels. Oxygen levels in the mid-Proterozoic (1.6

Marine Microbes Nutrients including iron, nitrogen, and phosphorus limit primary productivity in the oceans. Determining how abundant cyanobacteria such as Prochlorococcus adapt to nutrient stress across marine settings requires accurate molecular assays. Saito et al. developed a proteomic and metaproteomic approach capable of targeting specific metabolic biomarkers from mixed communities in seawater (see the Perspective by Moore). Prochlorococcus proteins are indicative of a major limiting nutrient across a wide transect in the Pacific Ocean; however, they also show that the limitation of multiple nutrients at overlapping biomes is an additional source of stress. Science, this issue p. [1173][1]; see also p. [1120][2] [1]: /lookup/doi/10.1126/science.1256450 [2]: /lookup/doi/10.1126/science.1258133

Metalloproteins Microbes require inventive ways to acquire scarce nutrients from the environment. Enzymes that catalyze the acquisition of phosphorus from dissolved organic matter, for example, rely on complex metal cofactors in the active site. Yong et al. determined the crystal structure of the

Nitrogen Cycling Much of the ammonia fertilizer we use ends up in surface or coastal waters as nitrate. This runoff lowers water quality and damages ecosystems. Although microbial nitrogen respiration influences the fate of nitrate, it is unclear which environmental factors exert the most control. Kraft et al. performed multiple long-term incubation studies of microbial communities from marine sediments. The relative supply of nitrate and nitrite, as well as total carbon and nitrogen, provided selective pressures that drove communities toward denitrification or ammonification. The average generation time of the community also strongly influenced which respiration pathway dominated. Science , this issue p. [676][1] [1]: /lookup/doi/10.1126/science.1254070

Subsurface Microbes![Figure][1] The detoxifying bug Shewanella oneidensis (green) growing on crystals of hematite (brown). PHOTO: EMSL/FLICKR In the absence of oxygen, anaerobic bacteria turn to other chemical compounds during respiration. This can be helpful in detoxifying heavy-metal pollution. Flynn et al. (see the Perspective by Friedrich and Finster) found that alkaline conditions prevent a detoxifying bug— Shewanella oneidensis —from using enzymes to reduce rust-like minerals. Instead, the bacteria reduce elemental sulfur compounds, generating hydrogen sulfide that reduces the iron indirectly. This interplay between anoxic biogeochemical cycles may explain why some anaerobic bacteria contain the genetic machinery necessary to reduce multiple compounds besides oxygen. Science , this issue p. [1039][2]; see also p. [974][3] [1]: pending:yes [2]: /lookup/doi/10.1126/science.1252066 [3]: /lookup/doi/10.1126/science.1255442

Subsurface Microbes The sea floor is teeming with microbes, whose sheer numbers produce a major effect on the global biogeochemical cycles of carbon, sulfur, and other important nutrients. Bowles et al. constructed a map showing how deeply sulfates penetrate marine sediments worldwide and how

Geochemistry![Figure][1] CREDIT: J. E. JOHNSON ET AL., PROC. NATL. ACAD. SCI. U.S.A. 110 , 28 (24 JUNE 2013) © 2013 NATIONAL ACADEMY OF SCIENCES The emergence of oxygen-producing photosynthesis had a profound effect on Earth's surface environment. It eventually oxidized the oceans and

Geochemistry The sulfur isotope signatures of sediments and aerosol particles provide a rich record of biological and chemical processes in modern environments and in the geologic record. For example, the ratio of two or more of sulfur's several stable isotopes can indicate whether it was

Geochemistry![Figure][1] CREDIT: YORUNO/WIKIMEDIA COMMONS Not far off the coast of the Mediterranean Sea, meadows of the flowering seagrass Posidonia oceanica , or Neptune grass, cover the seafloor. The vast network of ancient mat deposits in the sediments in and below the root layer

Environmental Science In aquatic or subsurface environments, sulfate-reducing bacteria mediate the transformation of inorganic divalent mercury into highly toxic, bio-available methylmercury (MeHg), but it is unclear how this reaction depends on the phase of the Hg(II). Zhang et al. examined the degree to which sulfate-reducing bacteria methylated three forms of Hg(II), representing different size fractions and different states of aging: dissolved Hg(II) ions, 3- to 4-nm-diameter HgS nanoparticles, and >500-nm HgS particles. The bacteria methylated dissolved Hg(II) fastest, but there were also significant differences between nanoparticles and larger particles of HgS that were attributed to size-dependent crystallinity differences and not simply the amount of reactive surface area. Furthermore, aging HgS nanoparticles—which transformed them into larger HgS particles over time—resulted in less MeHg formation as well, suggesting that methylation is related to the intermediate Hg(II) phases present and the crystal growth kinetics. These observations may help explain the varying production rates of MeHg in the environment. Environ. Sci. Technol. 10.1021/es203181m (2011).

Microbiology For microorganisms in the open ocean, where oligotrophic waters are limited in essential nutrients such as nitrogen, there is a delicate balance between growth and survival. Adapting to maximize the efficiency of biosynthesis may help defray the costs associated with nutrient limitation, but is there also a pressure over time to actually reduce assimilation of such nutrients into biomolecules as a means of minimizing costs? To answer this, Grzymski and Dussaq evaluated several whole-genome sequences and over 20 million protein fragments from databases to look for differences in the use of nitrogen between open-ocean and coastal microbial communities. Indeed, the atomic compositions of amino acids produced by open-ocean microorganisms contain systematically less nitrogen than coastal microbial proteomes to the point that the overall nitrogen requirement is reduced by up to 10% in the open ocean; however, as nitrogen use is minimized, the average mass of amino acids actually increases. Because the effect is pronounced in highly expressed proteins, there must be a fitness trade-off between increased biosynthetic costs of making larger amino acids and minimizing the use of nitrogen. The results show that nutrients are not only important in the life cycle of extant microorganisms, but that their limitation exerts a strong selective pressure on microorganisms over time. ISME J. 10.1038/ismej.2011.72 (2011).

Microbiology When an ecosystem is stressed, do the more tolerant species benefit or do all species decline? In natural microbial communities, examples of both responses occur, but comparisons across field sites and experiments are difficult. In a relatively controlled natural setting, Gough and Stahl studied the stress response to metals in anoxic sediments of a eutrophic lake that are loaded with high but variable levels of metal contaminants from a nearby zinc smelter. By using a broad sequencing technique to identify dominant microbial sequences at the domain level, they found that across a range of metal concentrations, the communities were quite similar, and except in a few instances, the abundance and diversity of bacteria, archaea, and eukaryotes were uncorrelated with metal concentrations. In a notable exception within the archaeal fraction, cold-adapted Crenarchaeota were strongly correlated with high levels of zinc, arsenic, and copper. Although little is known about these freshwater anaerobes—even their metabolic role in the microbial communities is unclear—they appear to have a competitive advantage in their response to metal stress over other archaeal clades, including more common methanogens. ISME J. 4 , 10.1038/ismej.2010.132 (2010).

Biomaterials Methods to synthesize nanomaterials from aqueous metal precursors may one day build on biomineralization mechanisms. Microorganisms often mediate the formation of simple elemental metal or metal-oxide nanoparticulate precipitates at the cell surface. After exposing yeast cells to cerium ions, Jiang et al. instead observed the formation of needle-like cerium(III) phosphate (rather than oxide) nanoparticles on the cell surface, even though no phosphate ions were added to the solution. By controlling the pH during further exposure experiments, the authors concluded that the phosphate originated from inside the cells and was likely released as a toxicity response to high concentrations of cerium at the surface. The experiments showed that the precipitation step was decoupled from metabolic reactions and adsorption of Ce3+ ions onto the cell wall. In addition to providing a basis for understanding nanoparticle synthesis, the results imply that cerium and other potentially harmful rare earth elements that are present in low concentrations in environmental systems may be sequestered at the cell surface of indigenous microorganisms. Chem. Geol. 10.1016/j.chemgeo.2010.07.010 (2010).

Geochemistry![Figure][1] CREDIT: ISTOCK.COM Mercury's toxicity impels wide-ranging study of the binding and redox behavior of the element under varying environmental conditions. Sulfate-reducing bacteria in soils and sediments are known to enhance mercury accumulation in higher species such

Geology![Figure][1] CREDIT: UNIVERSITY OF WASHINGTON Most minerals in Earth's crust are built on a Si–O(2−)–Si framework. Commonly, these minerals contain minor O(−)–O(−) dimers as impurities distributed throughout the bulk of the crystal. When minerals within rocks experience mechanical stress, the weak bonds holding the dimers together are broken, creating a charge imbalance that gives rise to mobile positive holes. These holes travel through stressed mineral grains to other nearby minerals—like current passing through a p-doped semiconductor—until they eventually arrive at the rock's surface. Through a series of electrochemical experiments, Balk et al. demonstrate that such holes at the surface of rocks in simulated seawater rapidly oxidize water to form H2O2. Because crustal rocks are predominately in contact with water and are almost always experiencing some type of stress from processes such as plate tectonics, glacial movement, and lithostatic pressuring, the oxidation of water by stressed minerals might have helped to contribute oxygen to Earth's early atmosphere. Conceivably, H2O2 generated at rock-water interfaces could also have provided evolutionary pressure for local organisms to develop survival mechanisms in highly oxidizing microenvironments. Earth Planet. Sci. Lett. 283 , 87 (2009). [1]: pending:yes

A promising remediation approach to mitigate subsurface uranium contamination is the stimulation of indigenous bacteria to reduce mobile U(VI) to sparingly soluble U(IV). The product of microbial uranium reduction is often reported as the mineral uraninite. Here, we show that the end products of uranium reduction by several environmentally relevant bacteria (Gram-positive and Gram-negative) and their spores include a variety of U(IV) species other than uraninite. U(IV) products were prepared in chemically variable media and characterized using transmission electron microscopy (TEM) and X-ray absorption spectroscopy (XAS) to elucidate the factors favoring/inhibiting uraninite formation and to constrain molecular structure/composition of the non-uraninite reduction products. Molecular complexes of U(IV) were found to be bound to biomass, most likely through P-containing ligands. Minor U(IV)-orthophosphates such as ningyoite [CaU(PO(4))(2)], U(2)O(PO(4))(2), and U(2)(PO(4))(P(3)O(10)) were observed in addition to uraninite. Although factors controlling the predominance of these species are complex, the presence of various solutes was found to generally inhibit uraninite formation. These results suggest a new paradigm for U(IV) in the subsurface, i.e., that non-uraninite U(IV) products may be found more commonly than anticipated. These findings are relevant for bioremediation strategies and underscore the need for characterizing the stability of non-uraninite U(IV) species in natural settings.