Deep sub-seafloor prokaryotes stimulated at interfaces over geological time

The sub-seafloor biosphere is the largest prokaryotic habitat on Earth but also a habitat with the lowest metabolic rates. Modelled activity rates are very low, indicating that most prokaryotes may be inactive or have extraordinarily slow metabolism. Here we present results from two Pacific Ocean sites, margin and open ocean, both of which have deep, subsurface stimulation of prokaryotic processes associated with geochemical and/or sedimentary interfaces. At 90 m depth in the margin site, stimulation was such that prokaryote numbers were higher (about 13-fold) and activity rates higher than or similar to near-surface values. Analysis of high-molecular-mass DNA confirmed the presence of viable prokaryotes and showed changes in biodiversity with depth that were coupled to geochemistry, including a marked community change at the 90-m interface. At the open ocean site, increases in numbers of prokaryotes at depth were more restricted but also corresponded to increased activity; however, this time they were associated with repeating layers of diatom-rich sediments (about 9 Myr old). These results show that deep sedimentary prokaryotes can have high activity, have changing diversity associated with interfaces and are active over geological timescales.     

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

Two decades of scientific ocean drilling have demonstrated widespread microbial life in deep sub-seafloor sediment, and surprisingly high microbial-cell numbers. Despite the ubiquity of life in the deep biosphere, the large community sizes and the low energy fluxes in this vast buried ecosystem are not yet understood. It is not known whether organisms of the deep biosphere are specifically adapted to extremely low energy fluxes or whether most of the observed cells are in a dormant, spore-like state. Here we apply a new approach--the D:L-amino-acid model--to quantify the distributions and turnover times of living microbial biomass, endospores and microbial necromass, as well as to determine their role in the sub-seafloor carbon budget. The approach combines sensitive analyses of unique bacterial markers (muramic acid and D-amino acids) and the bacterial endospore marker, dipicolinic acid, with racemization dynamics of stereo-isomeric amino acids. Endospores are as abundant as vegetative cells and microbial activity is extremely low, leading to microbial biomass turnover times of hundreds to thousands of years. We infer from model calculations that biomass production is sustained by organic carbon deposited from the surface photosynthetic world millions of years ago and that microbial necromass is recycled over timescales of hundreds of thousands of years.     

Discovering the roles of subsurface microorganisms: Progress and future of deep biosphere investigation

The discovery of the marine “deep biosphere”—microorganisms living deep below the seafloor—is one of the most significant and exciting discoveries since the ocean drilling program began more than 40 years ago. Study of the deep biosphere has become a research frontier and a hot spot both for geological and biological sciences. Here, we introduce the history of the discovery of the deep biosphere, and then we describe the types of environments for life below the seafloor, the energy sources for the living creatures, the diversity of organisms within the deep biosphere, and the new tools and technologies used in this research field. We will highlight several recently completed Integrated Ocean Drilling Program Expeditions, which targeted the subseafloor deep biosphere within the crust and sediments. Finally, future research directions and challenges of deep biosphere investigation towards uncovering the roles of subsurface microorganisms will be briefly addressed.     

Termination of global warmth at the Palaeocene/Eocene boundary through productivity feedback

The onset of the Palaeocene/Eocene thermal maximum (about 55 Myr ago) was marked by global surface temperatures warming by 5-7 degrees C over approximately 30,000 yr (ref. 1), probably because of enhanced mantle outgassing and the pulsed release of approximately 1,500 gigatonnes of methane carbon from decomposing gas-hydrate reservoirs. The aftermath of this rapid, intense and global warming event may be the best example in the geological record of the response of the Earth to high atmospheric carbon dioxide concentrations and high temperatures. This response has been suggested to include an intensified flux of organic carbon from the ocean surface to the deep ocean and its subsequent burial through biogeochemical feedback mechanisms. Here we present firm evidence for this view from two ocean drilling cores, which record the largest accumulation rates of biogenic barium--indicative of export palaeoproductivity--at times of maximum global temperatures and peak excursion values of delta13C. The unusually rapid return of delta13C to values similar to those before the methane release and the apparent coupling of the accumulation rates of biogenic barium to temperature, suggests that the enhanced deposition of organic matter to the deep sea may have efficiently cooled this greenhouse climate by the rapid removal of excess carbon dioxide from the atmosphere.     

Photosynthetic microbial mats in the 3,416-Myr-old ocean

Recent re-evaluations of the geological record of the earliest life on Earth have led to the suggestion that some of the oldest putative microfossils and carbonaceous matter were formed through abiotic hydrothermal processes. Similarly, many early Archaean (more than 3,400-Myr-old) cherts have been reinterpreted as hydrothermal deposits rather than products of normal marine sedimentary processes. Here we present the results of a field, petrographic and geochemical study testing these hypotheses for the 3,416-Myr-old Buck Reef Chert, South Africa. From sedimentary structures and distributions of sand and mud, we infer that deposition occurred in normal open shallow to deep marine environments. The siderite enrichment that we observe in deep-water sediments is consistent with a stratified early ocean. We show that most carbonaceous matter was formed by photosynthetic mats within the euphotic zone and distributed as detrital matter by waves and currents to surrounding environments. We find no evidence that hydrothermal processes had any direct role in the deposition of either the carbonaceous matter or the enclosing sediments. Instead, we conclude that photosynthetic organisms had evolved and were living in a stratified ocean supersaturated in dissolved silica 3,416 Myr ago.     

The timing of the last deglaciation in North Atlantic climate records

To determine the mechanisms governing the last deglaciation and the sequence of events that lead to deglaciation, it is important to obtain a temporal framework that applies to both continental and marine climate records. Radiocarbon dating has been widely used to derive calendar dates for marine sediments, but it rests on the assumption that the 'apparent age' of surface water (the age of surface water relative to the atmosphere) has remained constant over time. Here we present new evidence for variation in the apparent age of surface water (or reservoir age) in the North Atlantic ocean north of 40 degrees N over the past 20,000 years. In two cores we found apparent surface-water ages to be larger than those of today by 1,230 +/- 600 and 1,940 +/- 750 years at the end of the Heinrich 1 surge event (15,000 years BP) and by 820 +/- 430 to 1,010 +/- 340 years at the end of the Younger Dryas cold episode. During the warm B?lling-Aller?d period, between these two periods of large reservoir ages, apparent surface-water ages were comparable to present values. Our results allow us to reconcile the chronologies from ice cores and the North Atlantic marine records over the entire deglaciation period. Moreover, the data imply that marine carbon dates from the North Atlantic north of 40 degrees N will need to be corrected for these highly variable effects.     

Reduced North Atlantic Deep Water flux to the glacial Southern Ocean inferred from neodymium isotope ratios

The global circulation of the oceans and the atmosphere transports heat around the Earth. Broecker and Denton suggested that changes in the global ocean circulation might have triggered or enhanced the glacial-interglacial cycles. But proxy data for past circulation taken from sediment cores in the South Atlantic Ocean have yielded conflicting interpretations of ocean circulation in glacial times--delta13C variations in benthic foraminifera support the idea of a glacial weakening or shutdown of North Atlantic Deep Water production, whereas other proxies, such as Cd/Ca, Ba/Ca and 231Pa/230Th ratios, show little change from the Last Glacial Maximum to the Holocene epoch. Here we report neodymium isotope ratios from the dispersed Fe-Mn oxide component of two southeast Atlantic sediment cores. Both cores show variations that tend towards North Atlantic signatures during the warm marine isotope stages 1 and 3, whereas for the full glacial stages 2 and 4 they are closer to Pacific Ocean signatures. We conclude that the export of North Atlantic Deep Water to the Southern Ocean has resembled present-day conditions during the warm climate intervals, but was reduced during the cold stages. An increase in biological productivity may explain the various proxy data during the times of reduced North Atlantic Deep Water export.     

Decline of surface temperature and salinity in the western tropical Pacific Ocean in the Holocene epoch

In the present-day climate, surface water salinities are low in the western tropical Pacific Ocean and increase towards the eastern part of the basin. The salinity of surface waters in the tropical Pacific Ocean is thought to be controlled by a combination of atmospheric convection, precipitation, evaporation and ocean dynamics, and on interannual timescales significant variability is associated with the El Ni?o/Southern Oscillation cycles. However, little is known about the variability of the coupled ocean-atmosphere system on timescales of centuries to millennia. Here we combine oxygen isotope and Mg/Ca data from foraminifers retrieved from three sediment cores in the western tropical Pacific Ocean to reconstruct Holocene sea surface temperatures and salinities in the region. We find a decrease in sea surface temperatures of approximately 0.5 degrees C over the past 10,000 yr, whereas sea surface salinities decreased by approximately 1.5 practical salinity units. Our data imply either that the Pacific basin as a whole has become progressively less salty or that the present salinity gradient along the Equator has developed relatively recently.     

记录:1 024 AD前后南中国海最强烈的灾难事件

在南海东岛牛塘海鸟粪土沉积层中发现一岩性明显不同于上、下层位的珊瑚砂夹层.通过对沉积柱DY4进行详细的粒度特征、元素地球化学和生物残留分析,结果表明58~69 cm深度的珊瑚砂夹层对应于一次突然的海洋沉积环境事件,很可能与历史时期一次最强台风袭击所导致的冲溢沉积有关.对临近该珊瑚砂夹层的上、下沉积物中(57~58 cm和70~71 cm)多粒陆地植物颖果进行8个样品的AMS14C测年分析,发现上、下两个年龄组非常接近,珊瑚砂夹层沉积大约发生在994~1 075 AD之间,平均中间年龄大约为1 024 AD史前的这次强台风袭击对东岛的生态环境很可能造成了严重的破坏.     

Increased dissolved oxygen in Pacific intermediate waters due to lower rates of carbon oxidation in sediments

Concentrations of dissolved oxygen in the ocean seem to correlate well with climate instabilities over the past 100,000 years. For example, the concentration of dissolved oxygen in Pacific intermediate waters was considerably higher during Pleistocene glacial periods than it is today. This has been inferred from the presence of bioturbated sediments, implying that oxygen levels were sufficient for burrowing organisms to live. Today, basins in the northeastern Pacific Ocean are floored by laminated sediments implying lower oxygen levels, which may be explained by reduced ventilation. Here we report a recent return to bioturbated sediments in the northeastern Pacific Ocean since the late 1970s. From the carbon isotope composition of benthic foraminifers living in the sediment, we infer a twofold decrease in the carbon oxidation rate occurring within sediments, equivalent to an increase in dissolved oxygen concentration of 15-20 micromoles per litre. These changes, at the edges of the Santa Barbara, Santa Monica and Alfonso basins, are coincident with a change in North Pacific climate which has reduced upwelling by 20-30% and increased sea surface temperatures by 1.5-3 degrees C. This suggests that climate effects on surface productivity, reducing the supply organic matter to sediments, may have had a greater effect on benthic oxygen levels than changes in ocean circulation patterns.     

Astronomical pacing of late Palaeocene to early Eocene global warming events

At the boundary between the Palaeocene and Eocene epochs, about 55 million years ago, the Earth experienced a strong global warming event, the Palaeocene-Eocene thermal maximum. The leading hypothesis to explain the extreme greenhouse conditions prevalent during this period is the dissociation of 1,400 to 2,800 gigatonnes of methane from ocean clathrates, resulting in a large negative carbon isotope excursion and severe carbonate dissolution in marine sediments. Possible triggering mechanisms for this event include crossing a threshold temperature as the Earth warmed gradually, comet impact, explosive volcanism or ocean current reorganization and erosion at continental slopes, whereas orbital forcing has been excluded. Here we report a distinct carbonate-poor red clay layer in deep-sea cores from Walvis ridge, which we term the Elmo horizon. Using orbital tuning, we estimate deposition of the Elmo horizon at about 2 million years after the Palaeocene-Eocene thermal maximum. The Elmo horizon has similar geochemical and biotic characteristics as the Palaeocene-Eocene thermal maximum, but of smaller magnitude. It is coincident with carbon isotope depletion events in other ocean basins, suggesting that it represents a second global thermal maximum. We show that both events correspond to maxima in the approximately 405-kyr and approximately 100-kyr eccentricity cycles that post-date prolonged minima in the 2.25-Myr eccentricity cycle, implying that they are indeed astronomically paced.     

Reduced calcification of marine plankton in response to increased atmospheric CO2

The formation of calcareous skeletons by marine planktonic organisms and their subsequent sinking to depth generates a continuous rain of calcium carbonate to the deep ocean and underlying sediments. This is important in regulating marine carbon cycling and ocean-atmosphere CO2 exchange. The present rise in atmospheric CO2 levels causes significant changes in surface ocean pH and carbonate chemistry. Such changes have been shown to slow down calcification in corals and coralline macroalgae, but the majority of marine calcification occurs in planktonic organisms. Here we report reduced calcite production at increased CO2 concentrations in monospecific cultures of two dominant marine calcifying phytoplankton species, the coccolithophorids Emiliania huxleyi and Gephyrocapsa oceanica. This was accompanied by an increased proportion of malformed coccoliths and incomplete coccospheres. Diminished calcification led to a reduction in the ratio of calcite precipitation to organic matter production. Similar results were obtained in incubations of natural plankton assemblages from the north Pacific ocean when exposed to experimentally elevated CO2 levels. We suggest that the progressive increase in atmospheric CO2 concentrations may therefore slow down the production of calcium carbonate in the surface ocean. As the process of calcification releases CO2 to the atmosphere, the response observed here could potentially act as a negative feedback on atmospheric CO2 levels.     

Climate-driven trends in contemporary ocean productivity

Contributing roughly half of the biosphere's net primary production (NPP), photosynthesis by oceanic phytoplankton is a vital link in the cycling of carbon between living and inorganic stocks. Each day, more than a hundred million tons of carbon in the form of CO2 are fixed into organic material by these ubiquitous, microscopic plants of the upper ocean, and each day a similar amount of organic carbon is transferred into marine ecosystems by sinking and grazing. The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron). These growth-limiting factors are in turn regulated by physical processes of ocean circulation, mixed-layer dynamics, upwelling, atmospheric dust deposition, and the solar cycle. Satellite measurements of ocean colour provide a means of quantifying ocean productivity on a global scale and linking its variability to environmental factors. Here we describe global ocean NPP changes detected from space over the past decade. The period is dominated by an initial increase in NPP of 1,930 teragrams of carbon a year (Tg C yr(-1)), followed by a prolonged decrease averaging 190 Tg C yr(-1). These trends are driven by changes occurring in the expansive stratified low-latitude oceans and are tightly coupled to coincident climate variability. This link between the physical environment and ocean biology functions through changes in upper-ocean temperature and stratification, which influence the availability of nutrients for phytoplankton growth. The observed reductions in ocean productivity during the recent post-1999 warming period provide insight on how future climate change can alter marine food webs.     

Southern Ocean dust-climate coupling over the past four million years

Dust has the potential to modify global climate by influencing the radiative balance of the atmosphere and by supplying iron and other essential limiting micronutrients to the ocean. Indeed, dust supply to the Southern Ocean increases during ice ages, and 'iron fertilization' of the subantarctic zone may have contributed up to 40?parts per million by volume (p.p.m.v.) of the decrease (80-100 p.p.m.v.) in atmospheric carbon dioxide observed during late Pleistocene glacial cycles. So far, however, the magnitude of Southern Ocean dust deposition in earlier times and its role in the development and evolution of Pleistocene glacial cycles have remained unclear. Here we report a high-resolution record of dust and iron supply to the Southern Ocean over the past four million years, derived from the analysis of marine sediments from ODP Site 1090, located in the Atlantic sector of the subantarctic zone. The close correspondence of our dust and iron deposition records with Antarctic ice core reconstructions of dust flux covering the past 800,000 years (refs 8, 9) indicates that both of these archives record large-scale deposition changes that should apply to most of the Southern Ocean, validating previous interpretations of the ice core data. The extension of the record beyond the interval covered by the Antarctic ice cores reveals that, in contrast to the relatively gradual intensification of glacial cycles over the past three million years, Southern Ocean dust and iron flux rose sharply at the Mid-Pleistocene climatic transition around 1.25 million years ago. This finding complements previous observations over late Pleistocene glacial cycles, providing new evidence of a tight connection between high dust input to the Southern Ocean and the emergence of the deep glaciations that characterize the past one million years of Earth history.     

Glacial/interglacial variations in atmospheric carbon dioxide

Twenty years ago, measurements on ice cores showed that the concentration of carbon dioxide in the atmosphere was lower during ice ages than it is today. As yet, there is no broadly accepted explanation for this difference. Current investigations focus on the ocean's 'biological pump', the sequestration of carbon in the ocean interior by the rain of organic carbon out of the surface ocean, and its effect on the burial of calcium carbonate in marine sediments. Some researchers surmise that the whole-ocean reservoir of algal nutrients was larger during glacial times, strengthening the biological pump at low latitudes, where these nutrients are currently limiting. Others propose that the biological pump was more efficient during glacial times because of more complete utilization of nutrients at high latitudes, where much of the nutrient supply currently goes unused. We present a version of the latter hypothesis that focuses on the open ocean surrounding Antarctica, involving both the biology and physics of that region.     

Reversal of the net dinitrogen gas flux in coastal marine sediments

The flux of nitrogen from land and atmosphere to estuaries and the coastal ocean has increased substantially in recent decades. The observed increase in nitrogen loading is caused by population growth, urbanization, expanding water and sewer infrastructure, fossil fuel combustion and synthetic fertilizer consumption. Most of the nitrogen is removed by denitrification in the sediments of estuaries and the continental shelf, leading to a reduction in both cultural eutrophication and nitrogen pollution of the open ocean. Nitrogen fixation, however, is thought to be a negligible process in sub-tidal heterotrophic marine systems. Here we report sediment core data from Narragansett Bay, USA, which demonstrate that heterotrophic marine sediments can switch from being a net sink to being a net source of nitrogen. Mesocosm and core incubation experiments, together with a historic data set of mean annual chlorophyll production, support the idea that a climate-induced decrease in primary production has led to a decrease in organic matter deposition to the benthos and the observed reversal of the net sediment nitrogen flux. Our results suggest that some estuaries may no longer remove nitrogen from the water column. Instead, nitrogen could be exported to the continental shelf and the open ocean and could shift the effect of anthropogenic nitrogen loading beyond the immediate coastal zone.     

Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria

Dimethylsulphoniopropionate (DMSP) accounts for up to 10% of carbon fixed by marine phytoplankton in ocean surface waters, producing an estimated 11.7-103?Tmol S per year, most of which is processed by marine bacteria through the demethylation/demethiolation pathway. This pathway releases methanethiol (MeSH) instead of the climatically active gas dimethylsulphide (DMS) and enables marine microorganisms to assimilate the reduced sulphur. Despite recognition of this critical microbial transformation for over two decades, the biochemical pathway and enzymes responsible have remained unidentified. Here we show that three new enzymes related to fatty acid β-oxidation constitute the pathway that assimilates methylmercaptopropionate (MMPA), the first product of DMSP demethylation/demethiolation, and that two previously unknown coenzyme A (CoA) derivatives, 3-methylmercaptopropionyl-CoA (MMPA-CoA) and methylthioacryloyl-CoA (MTA-CoA), are formed as novel intermediates. A member of the marine roseobacters, Ruegeria pomeroyi DSS-3, requires the MMPA-CoA pathway for MMPA assimilation and MeSH production. This pathway and the ability to produce MeSH from MMPA are present in diverse bacteria, and the ubiquitous SAR11 clade bacterium Pelagibacter ubique possesses enzymes for at least the first two steps. Analysis of marine metagenomic data indicates that the pathway is widespread among bacterioplankton in the ocean surface waters, making it one of the most important known routes for acquisition of reduced carbon and sulphur by surface ocean heterotrophs.     

Doubling of marine dinitrogen-fixation rates based on direct measurements

Biological dinitrogen fixation provides the largest input of nitrogen to the oceans, therefore exerting important control on the ocean's nitrogen inventory and primary productivity. Nitrogen-isotope data from ocean sediments suggest that the marine-nitrogen inventory has been balanced for the past 3,000?years (ref. 4). Producing a balanced marine-nitrogen budget based on direct measurements has proved difficult, however, with nitrogen loss exceeding the gain from dinitrogen fixation by approximately 200?Tg?N?yr?1 (refs 5, 6). Here we present data from the Atlantic Ocean and show that the most widely used method of measuring oceanic N2-fixation rates underestimates the contribution of N2-fixing microorganisms (diazotrophs) relative to a newly developed method. Using molecular techniques to quantify the abundance of specific clades of diazotrophs in parallel with rates of 15N2 incorporation into particulate organic matter, we suggest that the difference between N2-fixation rates measured with the established method and those measured with the new method can be related to the composition of the diazotrophic community. Our data show that in areas dominated by Trichodesmium, the established method underestimates N2-fixation rates by an average of 62%. We also find that the newly developed method yields N2-fixation rates more than six times higher than those from the established method when unicellular, symbiotic cyanobacteria and γ-proteobacteria dominate the diazotrophic community. On the basis of average areal rates measured over the Atlantic Ocean, we calculated basin-wide N2-fixation rates of 14?±?1?Tg?N?yr?1 and 24?±1?Tg?N?yr?1 for the established and new methods, respectively. If our findings can be extrapolated to other ocean basins, this suggests that the global marine N2-fixation rate derived from direct measurements may increase from 103?±?8?Tg?N?yr?1 to 177?±?8?Tg?N?yr?1, and that the contribution of N2 fixers other than Trichodesmium is much more significant than was previously thought.     

Widespread iron-rich conditions in the mid-Proterozoic ocean

The chemical composition of the ocean changed markedly with the oxidation of the Earth's surface, and this process has profoundly influenced the evolutionary and ecological history of life. The early Earth was characterized by a reducing ocean-atmosphere system, whereas the Phanerozoic eon (less than 542 million years ago) is known for a stable and oxygenated biosphere conducive to the radiation of animals. The redox characteristics of surface environments during Earth's middle age (1.8-1 billion years ago) are less well known, but it is generally assumed that the mid-Proterozoic was home to a globally sulphidic (euxinic) deep ocean. Here we present iron data from a suite of mid-Proterozoic marine mudstones. Contrary to the popular model, our results indicate that ferruginous (anoxic and Fe(2+)-rich) conditions were both spatially and temporally extensive across diverse palaeogeographic settings in the mid-Proterozoic ocean, inviting new models for the temporal distribution of iron formations and the availability of bioessential trace elements during a critical window for eukaryotic evolution.     

A microbial consortium couples anaerobic methane oxidation to denitrification

Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition. In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.