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Manganese is one of the most abundant elements on Earth. The oxidation of manganese has long been theorized 1 -yet has not been demonstrated 2-4 -to fuel the growth of chemolithoautotrophic microorganisms. Here we refine an enrichment culture that exhibits exponential growth dependent on Mn(II) oxidation to a co-culture of two microbial species. Oxidation required viable bacteria at permissive temperatures, which resulted in the generation of small nodules of manganese oxide with which the cells associated. The majority member of the culture-which we designate 'Candidatus Manganitrophus noduliformans'-is affiliated to the phylum Nitrospirae (also known as Nitrospirota), but is distantly related to known species of Nitrospira and Leptospirillum. We isolated the minority member, a betaproteobacterium that does not oxidize Mn(II) alone, and designate it Ramlibacter lithotrophicus. Stable-isotope probing revealed 13 CO 2 fixation into cellular biomass that was dependent upon Mn(II) oxidation. Transcriptomic analysis revealed candidate pathways for coupling extracellular manganese oxidation to aerobic energy conservation and autotrophic CO 2 fixation. These findings expand the known diversity of inorganic metabolisms that support life, and complete a biogeochemical energy cycle for manganese 5,6 that may interface with other major global elemental cycles.

The cause of changes in atmospheric carbon dioxide (CO 2 ) during the recent ice ages is yet to be fully explained. Most mechanisms for glacial-interglacial CO 2 change have centred on carbon exchange with the deep ocean, owing to its large size and relatively rapid exchange with the atmosphere 1 . The Southern Ocean is thought to have a key role in this exchange, as much of the deep ocean is ventilated to the atmosphere in this region 2 . However, it is difficult to reconstruct changes in deep Southern Ocean carbon storage, so few direct tests of this hypothesis have been carried out. Here we present deep-sea coral boron isotope data that track the pH-and thus the CO 2 chemistry-of the deep Southern Ocean over the past forty thousand years. At sites closest to the Antarctic continental margin, and most influenced by the deep southern waters that form the ocean's lower overturning cell, we find a close relationship between ocean pH and atmospheric CO 2 : during intervals of low CO 2 , ocean pH is low, reflecting enhanced ocean carbon storage; and during intervals of rising CO 2 , ocean pH rises, reflecting loss of carbon from the ocean to the atmosphere. Correspondingly, at shallower sites we find rapid (millennial- to centennial-scale) decreases in pH during abrupt increases in CO 2 , reflecting the rapid transfer of carbon from the deep ocean to the upper ocean and atmosphere. Our findings confirm the importance of the deep Southern Ocean in ice-age CO 2 change, and show that deep-ocean CO 2 release can occur as a dynamic feedback to rapid climate change on centennial timescales.

Earth's mightiest ocean current, the Antarctic Circumpolar Current (ACC), regulates the exchange of heat and carbon between the ocean and the atmosphere, and influences vertical ocean structure, deep-water production and the global distribution of nutrients and chemical tracers. The eastward-flowing ACC occupies a unique circumglobal pathway in the Southern Ocean that was enabled by the tectonic opening of key oceanic gateways during the break-up of Gondwana (for example, by the opening of the Tasmanian Gateway, which connects the Indian and Pacific oceans). Although the ACC is a key component of Earth's present and past climate system, the timing of the appearance of diagnostic features of the ACC (for example, low zonal gradients in water-mass tracer fields) is poorly known and represents a fundamental gap in our understanding of Earth history. Here we show, using geophysically determined positions of continent-ocean boundaries, that the deep Tasmanian Gateway opened 33.5 ± 1.5 million years ago (the errors indicate uncertainty in the boundary positions). Following this opening, sediments from Indian and Pacific cores recorded Pacific-type neodymium isotope ratios, revealing deep westward flow equivalent to the present-day Antarctic Slope Current. We observe onset of the ACC at around 30 million years ago, when Southern Ocean neodymium isotopes record a permanent shift to modern Indian-Atlantic ratios. Our reconstructions of ocean circulation show that massive reorganization and homogenization of Southern Ocean water masses coincided with migration of the northern margin of the Tasmanian Gateway into the mid-latitude westerly wind band, which we reconstruct at 64° S, near to the northern margin. Onset of the ACC about 30 million years ago coincided with major changes in global ocean circulation and probably contributed to the lower atmospheric carbon dioxide levels that appear after this time.

Atmospheric CO2 fluctuations over glacial-interglacial cycles remain a major challenge to our understanding of the carbon cycle and the climate system. Leading hypotheses put forward to explain glacial-interglacial atmospheric CO2 variations invoke changes in deep-ocean carbon storage, probably modulated by processes in the Southern Ocean, where much of the deep ocean is ventilated. A central aspect of such models is that, during deglaciations, an isolated glacial deep-ocean carbon reservoir is reconnected with the atmosphere, driving the atmospheric CO2 rise observed in ice-core records. However, direct documentation of changes in surface ocean carbon content and the associated transfer of carbon to the atmosphere during deglaciations has been hindered by the lack of proxy reconstructions that unambiguously reflect the oceanic carbonate system. Radiocarbon activity tracks changes in ocean ventilation, but not in ocean carbon content, whereas proxies that record increased deglacial upwelling do not constrain the proportion of upwelled carbon that is degassed relative to that which is taken up by the biological pump. Here we apply the boron isotope pH proxy in planktic foraminifera to two sediment cores from the sub-Antarctic Atlantic and the eastern equatorial Pacific as a more direct tracer of oceanic CO2 outgassing. We show that surface waters at both locations, which partly derive from deep water upwelled in the Southern Ocean, became a significant source of carbon to the atmosphere during the last deglaciation, when the concentration of atmospheric CO2 was increasing. This oceanic CO2 outgassing supports the view that the ventilation of a deep-ocean carbon reservoir in the Southern Ocean had a key role in the deglacial CO2 rise, although our results allow for the possibility that processes operating in other regions may also have been important for the glacial-interglacial ocean-atmosphere exchange of carbon.

Global climate and the concentration of atmospheric carbon dioxide (CO2) are correlated over recent glacial cycles. The combination of processes responsible for a rise in atmospheric CO2 at the last glacial termination (23,000 to 9,000 years ago), however, remains uncertain. Establishing the timing and rate of CO2 changes in the past provides critical insight into the mechanisms that influence the carbon cycle and helps put present and future anthropogenic emissions in context. Here we present CO2 and methane (CH4) records of the last deglaciation from a new high-accumulation West Antarctic ice core with unprecedented temporal resolution and precise chronology. We show that although low-frequency CO2 variations parallel changes in Antarctic temperature, abrupt CO2 changes occur that have a clear relationship with abrupt climate changes in the Northern Hemisphere. A significant proportion of the direct radiative forcing associated with the rise in atmospheric CO2 occurred in three sudden steps, each of 10 to 15 parts per million. Every step took place in less than two centuries and was followed by no notable change in atmospheric CO2 for about 1,000 to 1,500 years. Slow, millennial-scale ventilation of Southern Ocean CO2-rich, deep-ocean water masses is thought to have been fundamental to the rise in atmospheric CO2 associated with the glacial termination, given the strong covariance of CO2 levels and Antarctic temperatures. Our data establish a contribution from an abrupt, centennial-scale mode of CO2 variability that is not directly related to Antarctic temperature. We suggest that processes operating on centennial timescales, probably involving the Atlantic meridional overturning circulation, seem to be influencing global carbon-cycle dynamics and are at present not widely considered in Earth system models.

Mass spectrometry with stable isotope labels has been seminal in discovering the dynamic state of living matter, but is limited to bulk tissues or cells. We developed multi-isotope imaging mass spectrometry (MIMS) that allowed us to view and measure stable isotope incorporation with submicrometre resolution. Here we apply MIMS to diverse organisms, including Drosophila, mice and humans. We test the 'immortal strand hypothesis', which predicts that during asymmetric stem cell division chromosomes containing older template DNA are segregated to the daughter destined to remain a stem cell, thus insuring lifetime genetic stability. After labelling mice with (15)N-thymidine from gestation until post-natal week 8, we find no (15)N label retention by dividing small intestinal crypt cells after a four-week chase. In adult mice administered (15)N-thymidine pulse-chase, we find that proliferating crypt cells dilute the (15)N label, consistent with random strand segregation. We demonstrate the broad utility of MIMS with proof-of-principle studies of lipid turnover in Drosophila and translation to the human haematopoietic system. These studies show that MIMS provides high-resolution quantification of stable isotope labels that cannot be obtained using other techniques and that is broadly applicable to biological and medical research.

Geological and geochemical evidence indicates that the Antarctic ice sheet formed during the Eocene-Oligocene transition, 33.5-34.0 million years ago. Modelling studies suggest that such ice-sheet formation might have been triggered when atmospheric carbon dioxide levels (pCO2atm) fell below a critical threshold of approximately 750 p.p.m.v., but the timing and magnitude of pCO2atm relative to the evolution of the ice sheet has remained unclear. Here we use the boron isotope pH proxy on exceptionally well-preserved carbonate microfossils from a recently discovered geological section in Tanzania to estimate pCO2atm before, during and after the climate transition. Our data suggest that are reduction in pCO2atm occurred before the main phase of ice growth,followed by a sharp recovery to pre-transition values and then a more gradual decline. During maximum ice-sheet growth, pCO2atm was between approximately 450 and approximately 1,500 p.p.m.v., with a central estimate of approximately 760 p.p.m.v. The ice cap survived the period of pCO2atm recovery,although possibly with some reduction in its volume, implying (as models predict) a nonlinear response to climate forcing during melting. Overall, our results confirm the central role of declining pCO2atm in the development of the Antarctic ice sheet (in broad agreement with carbon cycle modelling) and help to constrain mechanisms and feedbacks associated with the Earth's biggest climate switch of the past 65 Myr.

Animal-like multicellular fossils appeared towards the end of the Precambrian, followed by a rapid increase in the abundance and diversity of fossils during the Early Cambrian period, an event also known as the 'Cambrian explosion'. Changes in the environmental conditions at the Precambrian/Cambrian transition (about 542 Myr ago) have been suggested as a possible explanation for this event, but are still a matter of debate. Here we report molybdenum isotope signatures of black shales from two stratigraphically correlated sample sets with a depositional age of around 542 Myr. We find a transient molybdenum isotope signal immediately after the Precambrian/Cambrian transition. Using a box model of the oceanic molybdenum cycle, we find that intense upwelling of hydrogen sulphide-rich deep ocean water best explains the observed Early Cambrian molybdenum isotope signal. Our findings suggest that the Early Cambrian animal radiation may have been triggered by a major change in ocean circulation, terminating a long period during which the Proterozoic ocean was stratified, with sulphidic deep water.

The terrestrial sediment record indicates that the Earth's climate varied drastically in the Precambrian era (before 550 million years ago), ranging from surface temperatures similar to or higher than today's to global glaciation events. The most continuous record of sea surface temperatures of that time has been derived from variations in oxygen isotope ratios of cherts (siliceous sediments), but the long-term cooling of the oceans inferred from those data has been questioned because the oxygen isotope signature could have been reset through the exchange with hydrothermal fluids after deposition of the sediments. Here we show that the silicon isotopic composition of cherts more than 550 million years old shows systematic variations with age that support the earlier conclusion of long-term ocean cooling and exclude post-depositional exchange as the main source of the isotopic variations. In agreement with other lines of evidence, a model of the silicon cycle in the Precambrian era shows that the observed silicon isotope variations imply seawater temperature changes from about 70 degrees C 3,500 million years ago to about 20 degrees C 800 million years ago.

Silicon is the second most abundant element on Earth. It is an important nutrient for phytoplankton and is readily absorbed by terrestrial vegetation; it also assists the removal of carbon dioxide from the atmosphere through the weathering of silicates. But the continental cycle of silicon is not well known, and only a few studies have attempted to use silicon stable isotopes (28Si, 29Si and 30Si) to quantify the continental silicon reservoirs. Dissolved silicon in sea and river waters forms a reservoir of mean isotopic value +1.1 per thousand (refs 7, 10). It is enriched in 30Si with respect to the igneous rocks reservoir, which has a mean isotopic value of -0.3 per thousand (refs 4, 9). This enrichment can only be produced by a major fractionation during weathering, and should result in the formation of a continental 30Si-depleted reservoir. Such a reservoir, however, has not been identified to date. Here we analyse silicon isotopes of in situ quartz from a sandstone series in France, using a new-generation secondary ion mass spectrometry apparatus. We show that quartz that precipitates as siliceous cements forms a strongly 30Si-depleted reservoir with isotopic values down to -5.7 per thousand, a more negative value than any previously published for terrestrial samples. Our findings suggest that quartz re-precipitation plays an important role in the biogeochemical cycle of silicon.

Several lines of geological and geochemical evidence indicate that the level of atmospheric oxygen was extremely low before 2.45 billion years (Gyr) ago, and that it had reached considerable levels by 2.22 Gyr ago. Here we present evidence that the rise of atmospheric oxygen had occurred by 2.32 Gyr ago. We found that syngenetic pyrite is present in organic-rich shales of the 2.32-Gyr-old Rooihoogte and Timeball Hill formations, South Africa. The range of the isotopic composition of sulphur in this pyrite is large and shows no evidence of mass-independent fractionation, indicating that atmospheric oxygen was present at significant levels (that is, greater than 10(-5) times that of the present atmospheric level) during the deposition of these units. The presence of rounded pebbles of sideritic iron formation at the base of the Rooihoogte Formation and an extensive and thick ironstone layer consisting of haematitic pisolites and oölites in the upper Timeball Hill Formation indicate that atmospheric oxygen rose significantly, perhaps for the first time, during the deposition of the Rooihoogte and Timeball Hill formations. These units were deposited between what are probably the second and third of the three Palaeoproterozoic glacial events.

The Earth's most severe glaciations are thought to have occurred about 600 million years ago, in the late Neoproterozoic era. A puzzling feature of glacial deposits from this interval is that they are overlain by 1-5-m-thick 'cap carbonates' (particulate deep-water marine carbonate rocks) associated with a prominent negative carbon isotope excursion. Cap carbonates have been controversially ascribed to the aftermath of almost complete shutdown of the ocean ecosystems for millions of years during such ice ages--the 'snowball Earth' hypothesis. Conversely, it has also been suggested that these carbonate rocks were the result of destabilization of methane hydrates during deglaciation and concomitant flooding of continental shelves and interior basins. The most compelling criticism of the latter 'methane hydrate' hypothesis has been the apparent lack of extreme isotopic variation in cap carbonates inferred locally to be associated with methane seeps. Here we report carbon isotopic and petrographic data from a Neoproterozoic postglacial cap carbonate in south China that provide direct evidence for methane-influenced processes during deglaciation. This evidence lends strong support to the hypothesis that methane hydrate destabilization contributed to the enigmatic cap carbonate deposition and strongly negative carbon isotopic anomalies following Neoproterozoic ice ages. This explanation requires less extreme environmental disturbance than that implied by the snowball Earth hypothesis.

Data from the survivors of the atomic bombs serve as the major basis for risk calculations of radiation-induced cancer in humans. A controversy has existed for almost two decades, however, concerning the possibility that neutron doses in Hiroshima may have been much larger than estimated. This controversy was based on measurements of radioisotopes activated by thermal neutrons that suggested much higher fluences at larger distances than expected. For fast neutrons, which contributed almost all the neutron dose, clear measurement validation has so far proved impossible at the large distances (900 to 1,500 m) most relevant to survivor locations. Here, the first results are reported for the detection of 63Ni produced predominantly by fast neutrons (above about 1 MeV) in copper samples from Hiroshima. This breakthrough was made possible by the development of chemical extraction methods and major improvements in the sensitivity of accelerator mass spectrometry for detection of 63Ni atoms (refs 8-11). When results are compared with 63Ni activation predicted by neutron doses for Hiroshima survivors, good agreement is observed at the distances most relevant to survivor data. These findings provide, for the first time, clear measurement validation of the neutron doses to survivors in Hiroshima.

Many independent lines of evidence document a large increase in the Earth's surface oxidation state 2,400 to 2,200 million years ago, and a second biospheric oxygenation 800 to 580 million years ago, just before large animals appear in the fossil record. Such a two-staged oxidation implies a unique ocean chemistry for much of the Proterozoic eon, which would have been neither completely anoxic and iron-rich as hypothesized for Archaean seas, nor fully oxic as supposed for most of the Phanerozoic eon. The redox chemistry of Proterozoic oceans has important implications for evolution, but empirical constraints on competing environmental models are scarce. Here we present an analysis of the iron chemistry of shales deposited in the marine Roper Basin, Australia, between about 1,500 and 1,400 million years ago, which record deep-water anoxia beneath oxidized surface water. The sulphur isotopic compositions of pyrites in the shales show strong variations along a palaeodepth gradient, indicating low sulphate concentrations in mid-Proterozoic oceans. Our data help to integrate a growing body of evidence favouring a long-lived intermediate state of the oceans, generated by the early Proterozoic oxygen revolution and terminated by the environmental transformation late in the Proterozoic eon.

Many amino acids contain an asymmetric centre, occurring as laevorotatory, L, or dextrorotatory, D, compounds. It is generally assumed that abiotic synthesis of amino acids on the early Earth resulted in racemic mixtures (L- and D-enantiomers in equal abundance). But the origin of life required, owing to conformational constraints, the almost exclusive selection of either L- or D-enantiomers, and the question of why living systems on the Earth consist of L-enantiomers rather than D-enantiomers is unresolved. A substantial fraction of the organic compounds on the early Earth may have been derived from comet and meteorite impacts. It has been reported previously that amino acids in the Murchison meteorite exhibit an excess of L-enantiomers, raising the possibility that a similar excess was present in the initial inventory of organic compounds on the Earth. The stable carbon isotope compositions of individual amino acids in Murchison support an extraterrestrial origin -- rather than a terrestrial overprint of biological amino acids-although reservations have persisted. Here we show that individual amino-acid enantiomers from Murchison are enriched in 15N relative to their terrestrial counterparts, so confirming an extraterrestrial source for an L-enantiomer excess in the Solar System that may predate the origin of life on the Earth.

Much effort has been directed to analyses of organic compounds in carbonaceous chondrites because of their implications for organic chemical evolution and the origin of life. We have determined the isotopic composition of hydrogen, nitrogen and carbon in amino acid and monocarboxylic acid extracts from the Murchison meteorite. The unusually high D/H and 15N/14N ratios in the amino acid fraction (delta D = 1,370% after correction for isotope exchange; delta 15N = 90) are uniquely characteristic of known interstellar organic materials. The delta D value of the monocarboxylic acid fraction is lower (377%), but still consistent with an interstellar origin. These results confirm the extraterrestrial origin of both classes of compound, and provide the first evidence suggesting a direct relationship between the massive organo-synthesis occurring in interstellar clouds and the presence of pre-biotic compounds in primitive planetary bodies. The isotope data also bear on the historical problem of distinguishing indigenous material from terrestrial contaminants.

Current theories on the origin of the chemical elements explain the abundance of medium-heavy and heavy nuclides to be due to the capture by pre-existing lighter nuclides of free neutrons on either a slow timescale (s-process) or a rapid timescale (r-process). Experimental evidence in support of these theories comes from the analysis of carbonaceous chondrites. In acid-resistant residues of these meteorites a kind of xenon has been found, the isotopic composition of which matches almost perfectly that predicted for s-process xenon. We report data that allow us, for the first time, to derive with reasonable precision the full isotopic spectrum of s-process krypton as well. We show that this s-Kr in a residue from Murchison meteorite did not originate in one single s-process but rather is a mixture of contributions from stellar environments where the density of free neutrons was not the same. The astrophysical conditions under which this Krypton has been produced were distinct from those that have been invoked to explain the Solar System s-process abundance. Similar to the 13C-rich carbon component in an aliquot of the same residue, the s-process Kr from different astrophysical sites has retained its identity during the accumulation and subsequent history of the meteorite.

Knowledge of the structure of silicate glasses is one key to understanding their chemical and physical properties, as well as those of the high-temperature liquids from which they form. Because first-neighbour ordering into SiO4 tetrahedra is well known, much of the recent discussion about glass structure has concerned intermediate-range order. One of the most fundamental questions that can be posed is the distribution of silicate tetrahedra with n bridging oxygens (shared between two tetrahedra), labelled as 'Qn' (0 less than or equal to n less than or equal to 4). This distribution is probably important in determining the properties of melts and glasses, but considerable controversy exists concerning the identification and quantification of such species. Here I present new evidence from 29Si NMR (nuclear magnetic resonance) spectroscopy that clearly resolves one significant part of this dispute: at least in sodium silicate glasses, a variety of species is present that is greater than that required by composition alone.