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Microbial Physiology Methane associated with coal beds is an important global resource of natural gas. Much of the methane in coal comes from microbial methanogenesis. Mayumi et al. characterized a strain of Methermicoccus shengliensis that, unexpectedly, is capable of making methane from the dozens of methoxylated aromatic compounds found in a variety of coal types (see the Perspective by Welte). Isotope tracer experiments showed that this organism could also incorporate carbon dioxide into methane. Science , this issue p. [222][1]; see also p. [184][2] [1]: /lookup/doi/10.1126/science.aaf8821 [2]: /lookup/doi/10.1126/science.aai8101

Photosynthesis Some cyanobacteria are able to use the far-red end of the light spectrum by synthesizing chlorophyll f pigments. Introducing the protein responsible for chlorophyll f synthesis into crop plants could potentially expand the range of wavelengths that such plants use during photosynthesis and thereby increase their growth efficiency. Ho et al. identified chlorophyll f synthase (ChlF) in two cyanobacteria that are acclimatized to grow using far-red light. Introducing the ChlF-encoding gene into a model cyanobacterium allowed the organism to synthesize chlorophyll f. Similarities between ChlF and a core protein of photosystem II suggest that they have a close evolutionary relationship, and ChlF may even represent a more primitive photochemical reaction center. Science , this issue p. [886][1] [1]: http://www.sciencemag.org/content/353/6302/886.full

Enzyme Mechanisms Microorganisms are the main drivers of Earth's methane cycle. The enzyme ultimately responsible for biological methane production has an ambiguous mechanism because it involves difficult-to-isolate reaction intermediates. Wongnate et al. used stopped-flow and rapid freeze-quench experiments to trap a methyl radical in the active site of methyl-coenzyme M reductase (see the Perspective by Lawton and Rosenzweig). Spectroscopy demonstrated that cofactor F430 contained Ni(II), consistent with computational results. The final step of methanogenesis thus proceeds through Ni(II)-thiolate and methyl radical intermediates rather than an organometallic methyl-Ni(III) mechanism. Science , this issue p. [953][1];, see also p. [892][2] [1]: /lookup/doi/10.1126/science.aaf0616 [2]: /lookup/doi/10.1126/science.aaf7700

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

Gas Formation Technologies such as hydraulic fracturing, or “fracking,” can now extract natural gas from underground reservoirs. Within the gas, the ratio of certain isotopes holds clues to its origins. Stolper et al. analyzed a wide range of natural gas, including samples from some of the most active fracking sites in the United States. Using a “clumped isotope” technique, the authors could estimate the high temperatures at which methane formed deep underground, as well as the lower temperatures at which ancient microbes produced methane. The approach can help to distinguish the degree of mixing of gas from both sources. Science , this issue p. [1500][1] [1]: /lookup/volpage/344/1500?iss=6191

Vegetative cells of Clostridium acetobutylicum are known to reduce hexavalent uranium (U(VI)). We investigated the ability of spores of this organism to drive the same reaction. We found that spores were able to remove U(VI) from solution when H, was provided as an electron donor and to form a U(IV) precipitate. We tested several environmental conditions and found that spent vegetative cell growth medium was required for the process. Electron microscopy showed the product of reduction to accumulate outside the exosporium. Our results point towards a novel U(VI) reduction mechanism, driven by spores, that is distinct from the thoroughly studied reactions in metal-reducing Proteobacteria. (C) 2010 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Summary The bioremediation of uranium-contaminated sites is designed to stimulate the activity of microorganisms able to catalyze the reduction of soluble U(VI) to the less soluble mineral UO2. U(VI) reduction does not necessarily support growth in previously studied bac- teria, but it typically involves viable vegetative cells and the presence of an appropriate electron donor. We characterized U(VI) reduction by the sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1 grown fermentatively on pyruvate and observed that spores were capable of U(VI) reduction. Hydrogen gas - a product of pyruvate fermentation - rather than pyruvate, served as the electron donor. The presence of spent growth medium was required for the process, suggesting that an unknown factor produced by the cells was necessary for reduction. Ultrafiltration of the spent medium followed by U(VI) reduction assays revealed that the factor's molecular size was below 3 kDa. Pre-reduced spent medium displayed short-term U(VI) reduction activity, suggesting that the missing factor may be an electron shuttle, but neither anthraquinone-2,6-disulfonic acid nor ribofla- vin rescued spore activity in fresh medium. Spores of D. reducens also reduced Fe(III)-citrate under experi- mental conditions similar to those for U(VI) reduction. This is the first report of a bacterium able to reduce metalswhileinasporulatedstateandunderscoresthe novel nature of the mechanism of metal reduction by strain MI-1.

Gas Infrastructure The Aliso Canyon underground gas storage facility outside Los Angeles, CA, houses enormous natural gas reserves. One well at the site experienced a blowout in late October 2015 and began leaking gas until it was sealed in February 2016. Over the course of 13 flights in the region, Conley et al. sampled the air column and determined daily release rates of methane (a powerful greenhouse gas) and ethane throughout the leak. The methane release rates were nearly double that of the entire Los Angeles region combined. Thus, single vulnerabilities can have major implications for state and federal climate policy. Science , this issue p. [1317][1] [1]: /lookup/doi/10.1126/science.aaf2348

Biomineralization![Figure][1] Abalone shells grow from amorphous calcium carbonate precursors CREDIT: P.U.P.A. GILBERT The material inside mollusk shells, nacre, is remarkably tough and also gives the shells their sheen. Nacre is a hybrid of aragonitic calcium carbonate and an organic

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).

Paleobiology Preservation of the tissues of Earth's earliest animals—those that were present before and during the Cambrian explosion—required a lot of luck. According to new isotope data from Conotubus hemiannulatus fossils from Shaanxi Province, China, that luck was a function mostly of microbial activity. Schiffbauer et al. show that decaying carbon-rich animals are preserved typically either by being replaced three-dimensionally by pyrite crystals or compressed as carbonaceous films. Sedimentation rate ultimately controlled whether and for how long animal tissues were exposed to zones of bacterial sulfate reduction or methanogenesis within the sediment and thus their preservational style. Nat. Commun. 10.1038/ncomms6754 (2014).

Trace levels of organic contaminants enter aquatic ecosystems from a variety of sources, including runoff from agricultural lands. When these compounds and their metabolites break down, it is generally assumed that they become inert and pose less ecological risk. Qu et al. tracked the sunlight-mediated transformation of metabolites of trenbolone acetate (TBA)—a common growth-promoting steroid given to beef cattle—across a number of conditions in the laboratory and in the field. When the degradation products were exposed to dark conditions after photodegradation, they surprisingly reverted back to TBA metabolites, including analog steroidal compounds similar to TBA with unknown biological effects. S. Qu, E. P. Kolodziej, S. A. Long, J. B. Gloer, E. V. Patterson, J. Baltrusaitis, G. D. Jones, P. V. Benchetler, E. A. Cole, K. C. Kimbrough, M. D. Tarnoff, D. M. Cwiertny, Product-to-parent reversion of trenbolone: Unrecognized risks for endocrine disruption. Science 342 , 347–351 (2013). [Abstract][Full Text]

Catalysis Microorganisms have evolved sophisticated enzymatic machinery to reduce perchlorate and nitrate ions. Although the energetics of the pathways are different, the heme-containing active sites of the corresponding reductase enzymes are remarkably similar. Ford et al. constructed an inorganic catalyst to mediate these reactions based on these active sites, using a nonheme iron complex. A secondary coordination sphere near the iron center aligned the nitrate or perchlorate oxyanions and formed an iron-oxo complex. Regenerating the catalyst in the presence of protons and electrons released water—a potentially much more sustainable process than reduction strategies that require the use of harsh reagents. Science , this issue p. [741][1] [1]: /lookup/doi/10.1126/science.aah6886

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).

Chemical Biology Chemically modifying proteins after their translation can expand their structural and functional roles (see the Perspective by Hofmann and Bode). Two related methods describe how to exploit free radical chemistry to form carbon-carbon bonds between amino acid residues and a selected functional group. Wright et al. added a wide range of functional groups to proteins containing dehydroalanine precursors, with borohydride mediating the radical chemistry. Yang et al. employed a similar approach, using zinc in combination with copper ions. Together, these results will be useful for introducing functionalities and labels to a wide range of proteins. Science , this issue pp. [597][1] and [623][2]; see also p. [553][3] [1]: http://www.sciencemag.org/content/354/6312/aag1465.full [2]: /lookup/doi/10.1126/science.aah4428 [3]: /lookup/doi/10.1126/science.aai8788

Biomass Processing The lignin found in plants is a desirable renewable feedstock for fuels and other useful compounds. Breaking down such a strong, energy-dense polymer, however, requires pretreatment of plant biomass under harsh conditions. These pretreatment steps often cause side reactions within

Enzymology The last enzymatic step of microbial methanogenesis, and the first step of microbial methane oxidation, relies on the nickel-containing tetrapyrrole coenzyme F430. The successful metabolic engineering of any organism to enzymatically consume methane thus also needs the appropriate machinery to synthesize this compound. Using comparative genomics, Zheng et al. identified several candidate genes responsible for coenzyme F430 biosynthesis. Cloning and expression of all the subsequent proteins in Escherichia coli confirmed the complete in vitro conversion of sirohydrochlorin into mature F430. Science , this issue p. [339][1] [1]: /lookup/doi/10.1126/science.aag2947

Structural Biology![Figure][1] Archaea make methane with a tungsten-containing enzyme. CREDIT: KEVIN SCHAFER/ALAMY STOCK PHOTO The process by which archaea make methane involves a series of reactions and enzymes. First, CO2 and methanofuran (MFR) are reduced to formyl-MFR by an as yet

Bioengineering Contaminating microorganisms can be highly detrimental to the large-scale fermentation of complex low-cost feedstocks, such as sugarcane or dry-milled corn for biofuels or other industrial purposes. The challenge is that foreign organisms have to be inhibited without using antibiotics

Biomineralization Some algae have evolved a remarkable ability to grow ornate crystalline structures called coccoliths. These structures consist of an organic base plate and complex calcium carbonate minerals spreading outward. Gal et al. found that the algae control site-specific mineralization, not by interactions between the base plate and the growing mineral edge, but by directing large amounts of calcium to the base plate. Recognition between two organic constituents determines when and where crystal nucleation will take place. Science , this issue p. [590][1] [1]: /lookup/doi/10.1126/science.aaf7889

Structural Biology Chlorine and other halogens are key constituents of many industrially important compounds. Enzyme-based approaches to transfer halogens to organic compounds are a potentially greener synthetic route, producing less harmful by-products. Mitchell et al. determined a 2.4 A-resolution x-ray crystal structure of a bacterial halogenase protein in a complex with its precursor substrate. The structure reveals how the enzyme chlorinates the substrate through an iron-chlorine intermediate at the active site. A neighboring serine orchestrates ligand dynamics to allow for halogenation instead of hydroxylation. Engineering a related nonhalogenating hydroxylase protein with a serine in the same position makes the enzyme capable of both hydroxylation and halogenation. Nat. Chem. Biol. 10.1038/NCHEMBIO.2112 (2016).

Biofuels The enzymatic conversion of lignocellulose to glucose is a bottleneck in the biological production of ethanol. Inducing the synthesis of active cellulytic enzymes is critical for enhancing the conversion efficiency of a bioreactor. Li et al. developed a method to stimulate the production of high amounts of cellulase in the fungus Trichoderma reesei . The most effective inducer was a sugar mixture synthesized from glucose, which contains sophorose. Batch feeding of the mixture resulted in high cellulase production at levels three to five times higher than previously measured. Adding pretreated corn stover to the reactor resulted in high yields of glucose and of conversion to ethanol. Bioresour. Technol. 216 , 503 (2016).

Toxicology![Figure][1] Ingesting organic compounds can modify the gut microbial communities in zebrafish. PHOTO: KAZAKOV MAKSIM/SHUTTERSTOCK Trace organic compounds can have a range of unintended consequences for environmental ecosystems and exposed animals. The adverse health effects of the antimicrobial compound triclosan and its degradation by-products, for example, have led to bans of its use in some consumer products. Gaulke et al. show how triclosan modifies gut microbial communities after ingestion. In zebrafish fed triclosan-laced diets, gut community composition dramatically shifted over short time intervals. Some community members were highly susceptible to triclosan exposure, whereas others, including members of the genus Pseudomonas and the family Rhodobacteraceae, were more resistant. Overall, triclosan exposure altered ecological dynamics and interaction networks, demonstrating how such trace compounds can have a profound impact on the gut microbiome. PLOS ONE 10.1371/journal.pone.0154632 (2016). [1]: pending:yes

Structural Biology Microorganisms have evolved a number of enzymes to reduce oxygen and prevent oxidative stress. Cytochrome bd oxidases serve this role and also protect pathogenic bacteria from nitric acid; however, this class of enzymes so far has eluded high-resolution crystallography. Safarian et al. were able to resolve the three-dimensional structure of cytochrome bd oxidase from a thermophilic bacterium (see the Perspective by Cook and Poole). The overall structure and triangular arrangement of its heme cofactors bear little structural resemblance to those of other membrane-spanning oxidases, despite serving a similar function. Science , this issue p. [583][1]; see also p. [518][2] [1]: /lookup/doi/10.1126/science.aaf2477 [2]: /lookup/doi/10.1126/science.aaf5514

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

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

Green Chemistry Zeolites can help synthesize cheaper plastic precursors from biologically sourced feedstocks. Producing sustainable plastics must compete with more cost-effective petrochemical-based synthesis routes. Dusselier et al. developed a zeolite-based strategy to catalyze the transformation of microbially produced lactic acid into lactide, a difficult-to-synthesize precursor of biodegradable polylactic acid plastics. The selectivity of nearly 80% is based on active site spatial confinement in the zeolite micropores. This step substantially simplifies current high-cost synthesis routes and generates nearly zero waste using current reactor technologies. Science , this issue p. [78][1] [1]: /lookup/doi/10.1126/science.aaa7169

Photosynthesis Plants rely on large complexes of proteins, chlorophyll, and other cofactors to turn light into chemical energy. Qin et al. present the crystal structures of photosystem I (PSI) and the light-harvesting complex I (LHCI) supercomplex from pea plants (see the Perspective by Croce). The well-resolved structure of the outer antenna complexes and their interaction with the PSI core provide a structural basis for calculating excitation energy transfer efficiency. Moreover, the organization and orientation of chlorophyll and carotenoid cofactors within and between PSI and LHCI hint at energy transfer and photoprotection mechanisms. Science , this issue p. [989][1]; see also p. [970][2] [1]: /lookup/doi/10.1126/science.aab0214 [2]: /lookup/doi/10.1126/science.aab3387

Membrane Science Graphene oxide (GO) surfaces have antibacterial properties, but they are not due to any known specific physical interactions with cells. Because GO is toxic to bacteria, it has been proposed as an antifouling material for membranes during water purification. To test the hypothesis

Subsurface Microbes Retroelements—gene sequences that are introduced into DNA through an RNA intermediate—in subsurface archaea help increase gene and protein diversity. Paul et al. identified an archeal virus from a methane seep in a California borderlands basin that contains a complete and active diversity-generating retroelement (DGR). Furthermore, published metagenomes of two uncultivated nanoarchaea from the marine subsurface contain at least four DGRs, more than any other bacteria or virus known to date. Because anaerobic archaea in the subsurface grow so slowly, and thus have low background genome mutations, DGRs may be a widespread source of genetic diversity in these environments. Nat. Comm. 10.1038/ncomms7585 (2015).

Water Quality Modern wastewater treatment processes still leave behind trace amounts of pharmaceuticals, personal care products, and other potentially harmful or toxic compounds. For example, over 10 metric tons of the antimicrobial compound triclosan are released from wastewater treatment plants into U.S. waterways each year. Hensley et al. detected trace contaminants in the effluent from four U.S. wastewater treatment plants, including triclosan, chlorinated triclosan derivatives, and hydroxylated by-products of polybrominated diphenyl ethers (PBDEs)—recalcitrant compounds used as flame retardants. Chlorinated triclosan derivatives were present at the same low but appreciable levels as PBDE by-products, both of which produce toxic dioxins during photodegradation. Environ. Sci. Water Res. Technol. 10.1039/c4ew00102h (2015).

Geomicrobiology Iron acts as both a source and sink of electrons for microorganisms in the environment. Some anaerobic bacteria use oxidized Fe(III) as an electron acceptor, whereas phototrophic bacteria can use reduced Fe(II) as an electron donor. Byrne et al. show that the iron-bearing mineral magnetite, which contains both Fe(II) and Fe(III), can serve as both an electron acceptor and donor. Cocultures of iron-reducing and iron-oxidizing bacteria exposed to simulated day/night cycles or changes in organic matter altered the ratio of Fe(II) to Fe(III) in magnetite particles. Science , this issue p. [1473][1] [1]: /lookup/doi/10.1126/science.aaa4834

Biofuels To become a widely used source of fuel, widespread industrial production of ethanol using yeast needs to be simple and efficient. However, two conditions ideal for boosting production—tolerance of higher temperatures and high concentrations of ethanol—have been limiting (see the Perspective by Cheng and Kao). Now, Caspeta et al. have used adaptive laboratory evolution to find yeast strains that can tolerate high temperatures and Lam et al. have identified a route to improve yeast's resistance to high concentrations of ethanol. Science , this issue p. [75][1], p. [71][2]; see also p. [35][3] [1]: /lookup/doi/10.1126/science.1258137 [2]: /lookup/doi/10.1126/science.1257859 [3]: /lookup/doi/10.1126/science.1260127

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

Paleontology![Figure][1] CREDIT: GAINES ET AL., PROC. NATL. ACAD. SCI. U.S.A. 109 , 10.1073/PNAS.1111784109 (2012) The Burgess Shale in British Columbia, Canada, is one of the most famous fossil fields in the world, containing remarkably preserved soft-bodied marine life from just after the Cambrian explosion. In most other fossil locations, these soft, fragile tissues usually degrade in sediments soon after they are deposited. By examining the composition of the overlying sediments and measuring the sulfur isotope composition of minerals surrounding the fossils from the Burgess Shale, the Chengjiang in China, and five other Burgess Shale–type deposits, Gaines et al. propose that the unique depositional environment and seawater chemistry composition were the primary factors that facilitated preservation. The seafloor at this time in Earth's history was probably anoxic and also deprived of other oxidants such as sulfate, which inhibited initial bacterial degradation of recently deposited organic remains on the seafloor. Soon after deposition, the fossils were entombed in fine-grained clay sediments and then capped by a thick carbonate cement—a result of increasingly alkaline seawater. The cement further prevented the exchange of oxidants into sediment pore water and allowed the organic matter to remain, eventually transforming into the carbonaceous compressions seen today. Proc. Natl. Acad. Sci. U.S.A. 109 , 10.1073/pnas.1111784109 (2012). [1]: pending:yes

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).

Materials Science Porous networks within coal can determine its value as a fuel; porosity helps define how well certain types of coal burn and whether methane in the pores can be extracted efficiently from coal beds as an additional source of energy. Determining the porosity of complex natural materials such as coal is difficult, because a sample may contain many networks of pores that can be often disconnected from each other and from the surface of samples. Although several techniques for measuring porosity exist, Melnichenko et al. used small-angle neutron scattering to examine the interconnectivity of pores within coal samples as a function of pore size in a noninvasive and quantitative manner. They compared the scattering profiles of a coal sample in a vacuum and the same sample saturated with contrast-matching gases that fill accessible pores and make them invisible to the neutron beam. The analysis confirms that the proportion of isolated and accessible pores varies widely based on coal type, but also shows that pore accessibility varies with gas overpressure. These results may eventually help determine the feasibility of enhanced methane recovery from coal beds by injecting CO2 gas at high pressure. Fuel 90 , 10.1016/j.fuel.2011.06.026 (2011).

Geochemistry![Figure][1] CREDIIT: © FLPA/ALAMY Naturally occurring iron-(hydr)oxide particles have a strong influence over nutrient and contaminant transport in Earth's aqueous surface environments. Most phases have stoichiometrically balanced chemical formulas such as FeOOH and Fe2O3, but ferrihydrite—an abundant yet metastable, poorly crystalline precursor to more thermodynamically stable phases—is not defined by a simple ordering. Furthermore, all natural iron-(hydr)oxides undoubtedly contain numerous internal and adsorbed impurities that have varying effects on reactivity and stability. To understand how these impurities get incorporated into growing particles, Bazilevskaya et al. used a combined experimental and computational approach to track coprecipitation of ferrihydrite with varying amounts of Al3+. When Al3+ was present at low levels, it was incorporated into the ferrihydrite structure; at high Al3+ levels, in contrast, two distinct Al- and Fe-rich phases formed. Computations suggest that when Al-rich ferrihydrite transforms into Al-rich FeOOH over time, Al clusters within the new phase are energetically more favorable than isolated substitutions of Al3+ for Fe3+. In a complementary study, Hansel et al. documented the inhibitory effect of Al-substitution on ferrihydrite transformation. Ferrihydrite was more strongly inhibited from transforming into other, more thermodynamically stable phases when Al was adsorbed on the surface than when it was incorporated into the structure. Geochim. Cosmochim. Acta 75 , 10.1016/j.gca.2011.05.041; 10.1016/j.gca.2011.05.033 (2011). [1]: pending:yes

Geochemistry![Figure][1] CREDIT: THINKSTOCK Vast expansive underground caves start out meagerly as small fractures in carbonate-rich bedrock such as limestones or dolostones. As slightly acidic water, which is undersaturated in carbonate, slowly percolates through the rock, carbonate

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).

Chemistry![Figure][1] CREDIT: [PHOTOS.COM][2] Nanomaterials boast a multitude of current and projected commercial uses that take advantage of their unique and beneficial properties, but the health and environmental risks they present are relatively unknown. Screening and eventual regulation are problematic because even materials of the same chemical composition have such a wide range of morphologies (including size, shape, coating, aggregation state, and crystalline phase variations) that affect their reactivity. In a demonstration of the complexity of such systems, Labille et al. examined the aging of composites of titanium dioxide (TiO2) nanoparticles commonly used in sunscreen and cosmetics. The composites—composed of several nanoparticles surrounded by a thin Al(OH)3 shell and bound in a hydrophobic polymer matrix—dispersed in water over time because of the degradation of the polymer. When aged in the presence of light, the polymer degradation rate increased, possibly due to photocatalysis by TiO2. In either case, once the polymer degraded, the remaining Al(OH)3 shell determined the stability of the composites. Stability was also sensitive to the concentration of natural organic matter; at low levels characteristic of groundwater, the composites aggregated, but higher levels characteristic of surface waters kept the composites suspended. These and similar studies raise the question of whether the nanomaterials studied and characterized in laboratory settings look or behave as they do in the environment. Environ. Pollut. 158 , 10.1016/j.envpol.2010.02.012 (2010). [1]: pending:yes [2]: http://PHOTOS.COM

Evolution The evolution of hard calcified structures such as shells and skeletons gave their bearers a selection advantage over older soft-bodied organisms. Most organisms equipped with such hard structures synthesize enzymes or other biomolecules to serve as sites for controlled crystal growth. The modern sponge Astrosclera willeyana —a living fossil related to some of the most primitive sponges—may form its simple calcite spheres via another mechanism. Within the organic matrix of these spherulites, Jackson et al. found biomarkers exclusive to the biomolecules of bacteria. This finding suggests that A. willeyana degrades the bacteria that enter its much larger cells and then uses the degradation products, rather than its own biomolecules, to nucleate calcite crystals. Bacteria on their own can form large calcified structures such as stromatolites, and did so billions of years ago; however, if sponge-like organisms ∼300 million years ago did not have the full suite of genetic machinery to direct biocalcification themselves, the harvesting of bacteria to jump-start the process would have served as an efficient evolutionary shortcut. The appearance of more sophisticated mineralization pathways, which allowed species related to modern corals to outcompete the ancient sponges that previously dominated ocean reefs, may have occurred much later. Geobiology 8 , 10.1111/j.1472-4669.2010.00236.x (2010).

Microbiology![Figure][1] CREDIT: JUPITERIMAGES Toxicity concerns have largely eliminated chloroform's erstwhile use as an anesthetic, though the compound still plays a role in industrial chemistry. Low levels of chloroform (trichloromethane) inhibit the metabolisms of bacteria responsible for detoxifying many other chlorinated hydrocarbons; therefore, its persistence in the environment not only presents a possible human health risk but also slows down natural remediation processes. Now, however, Grostern et al. have discovered a population of Dehalobacter that can not only tolerate a high level of chloroform but actually grow on it by coupling dechlorination to respiration. Kinetics studies suggest that the bacteria use a reductive dehalogenase enzyme specific to chloroform and the structurally similar trichloroethane. Direct reduction of chloroform coupled to bacterial growth is advantageous for remediation because it is more efficient and does not require the addition of separate growth substrates. Contaminated aquifers—such as the one from which these bacteria were originally isolated—may be fertile grounds for other bacteria with specialized adaptations to tolerate toxins. Environ. Microbiol. 12 , 10.1111/j.1462-2920.2009.02150.x (2010). [1]: pending:yes

Geochemistry![Figure][1] CREDIT: [JUPITERIMAGES.COM][2] High levels of nitrates released from agricultural fertilizers pose a serious threat to groundwater quality. Ameliorating this problem is not easy, but some help may be available from the natural soil bacterial communities that reduce nitrate into inert N2 gas. The rate of this denitrification step typically depends on the nature and concentration of the compounds that feed electrons into the process, providing the bacteria with energy. Most often bacteria use abundant organic matter, but in certain environments the iron(II) in minerals such as pyrite (FeS2) can also be oxidized. By monitoring the groundwater below a stretch of farmland in the Netherlands, Zhang et al. found that pyrite-coupled denitrification was the dominant nitrate-consuming reaction. Due at least in part to this reaction, nitrate levels in the groundwater were lower than levels measured 10 years ago; however, groundwater below a nearby unfertilized forest actually became enriched in nitrate over this same period. The transport of nitrate away from the farmland suggests that despite abundant pyrite remaining in the aquifer, complete denitrification occurs more slowly than nitrate's residence time. Complicating matters is the fact that levels of trace elements associated with pyrite (e.g., As, Zn, Ni) increased below the forest as well, signifying that these bacteria may be mobilizing heavy metals in the subsurface despite their benevolence in removing some of the nitrates. Geochim. Cosmochim. Acta 73 , 6716 (2009). [1]: pending:yes [2]: http://JUPITERIMAGES.COM