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Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ~47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 10³ to 6.10 × 10⁵ and 3.28 × 10⁴ to 2.46 × 10⁶ amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ∼40° to 60°C sediment associated with lignite coal beds at ∼1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ∼104 cells cm–3. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.

Proxy reconstructions from marine sediment cores indicate peak temperatures in the first half of the last and current interglacial periods (the thermal maxima of the Holocene epoch, 10,000 to 6,000 years ago, and the last interglacial period, 128,000 to 123,000 years ago) that arguably exceed modern warmth 1 – 3 . By contrast, climate models simulate monotonic warming throughout both periods 4 – 7 . This substantial model–data discrepancy undermines confidence in both proxy reconstructions and climate models, and inhibits a mechanistic understanding of recent climate change. Here we show that previous global reconstructions of temperature in the Holocene 1 – 3 and the last interglacial period 8 reflect the evolution of seasonal, rather than annual, temperatures and we develop a method of transforming them to mean annual temperatures. We further demonstrate that global mean annual sea surface temperatures have been steadily increasing since the start of the Holocene (about 12,000 years ago), first in response to retreating ice sheets (12 to 6.5 thousand years ago), and then as a result of rising greenhouse gas concentrations (0.25 ± 0.21 degrees Celsius over the past 6,500 years or so). However, mean annual temperatures during the last interglacial period were stable and warmer than estimates of temperatures during the Holocene, and we attribute this to the near-constant greenhouse gas levels and the reduced extent of ice sheets. We therefore argue that the climate of the Holocene differed from that of the last interglacial period in two ways: first, larger remnant glacial ice sheets acted to cool the early Holocene, and second, rising greenhouse gas levels in the late Holocene warmed the planet. Furthermore, our reconstructions demonstrate that the modern global temperature has exceeded annual levels over the past 12,000 years and probably approaches the warmth of the last interglacial period (128,000 to 115,000 years ago). Reanalysis of Holocene sea surface temperature records affirms the role of retreating ice and rising greenhouse gases in driving a steady increase in global temperatures over the past 12,000 years.

The origin of eukaryotes remains unclear 1 – 4 . Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea 5 , 6 . Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘ Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea 6 , the isolate has no visible organelle-like structure. Instead, Ca . P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E 3 ) model. Isolation and characterization of an archaeon that is most closely related to eukaryotes reveals insights into how eukaryotes may have evolved from prokaryotes.

The rise of atmospheric oxygen fundamentally changed the chemistry of surficial environments and the nature of Earth’s habitability 1 . Early atmospheric oxygenation occurred over a protracted period of extreme climatic instability marked by multiple global glaciations 2 , 3 , with the initial rise of oxygen concentration to above 10 −5 of the present atmospheric level constrained to about 2.43 billion years ago 4 , 5 . Subsequent fluctuations in atmospheric oxygen levels have, however, been reported to have occurred until about 2.32 billion years ago 4 , which represents the estimated timing of irreversible oxygenation of the atmosphere 6 , 7 . Here we report a high-resolution reconstruction of atmospheric and local oceanic redox conditions across the final two glaciations of the early Palaeoproterozoic era, as documented by marine sediments from the Transvaal Supergroup, South Africa. Using multiple sulfur isotope and iron–sulfur–carbon systematics, we demonstrate continued oscillations in atmospheric oxygen levels after about 2.32 billion years ago that are linked to major perturbations in ocean redox chemistry and climate. Oxygen levels thus fluctuated across the threshold of 10 −5 of the present atmospheric level for about 200 million years, with permanent atmospheric oxygenation finally arriving with the Lomagundi carbon isotope excursion at about 2.22 billion years ago, some 100 million years later than currently estimated. Sulfur isotope and iron–sulfur–carbon systematics on marine sediments indicate that permanent atmospheric oxygenation occurred around 2.22 billion years ago, about 100 million years later than currently estimated.

Mercury is a highly toxic, globally ubiquitous pollutant that can seriously damage human health. Most mercury pollution enters the atmosphere from burning coal and other fossil fuels and from industrial activity, but where does it all go? Zaferani et al. analyzed biogenic siliceous sediments (diatom ooze) from off the coast of Antarctica and found that they contained surprisingly large amounts of mercury. The results suggest that as much as 25% of mercury emissions over the past 150 years could be trapped in sediments like these, revealing the important role that the marine biological pump may play in the global mercury cycle. Science , this issue p. 797 A large fraction of mercury emitted into the environment ends up in biogenic marine sediments. The role of algae for sequestration of atmospheric mercury in the ocean is largely unknown owing to a lack of marine sediment data. We used high-resolution cores from marine Antarctica to estimate Holocene global mercury accumulation in biogenic siliceous sediments (diatom ooze). Diatom ooze exhibits the highest mercury accumulation rates ever reported for the marine environment and provides a large sink of anthropogenic mercury, surpassing existing model estimates by as much as a factor of 7. Anthropogenic pollution of the Southern Ocean began ~150 years ago, and up to 20% of anthropogenic mercury emitted to the atmosphere may have been stored in diatom ooze. These findings reveal the crucial role of diatoms as a fast vector for mercury sequestration and diatom ooze as a large marine mercury sink.

Phosphorus availability in soils is an important parameter influencing primary production in terrestrial ecosystems. Phosphorus limitation exists in many soils since a high proportion of soil phosphorus is stored in unavailable forms for plants, such as bound to iron minerals or stabilized organic matter. This is in spite of soils having a high amount of total soil phosphorus. The feasibility of silicon to mobilize phosphorus from strong binding sites of iron minerals has been shown for marine sediments but is less well studied in soils. Here we tested the effect of silicon on phosphorus mobilization for 143 Artic soils (representing contrasting soil characteristics), which have not been affected by agriculture or other anthropogenic management practices. In agreement with marine studies, silicon availabilities were significantly positive correlated to phosphorus mobilization in these soils. Laboratory experiments confirmed that silicon addition significantly increases phosphorus mobilization, by mobilizing Fe(II)-P phases from mineral surfaces. Silicon addition increased also soil respiration in phosphorus deficient soils. We conclude that silicon is a key component regulating mobilization of phosphorous in Arctic soils, suggesting that this may also be important for sustainable management of phosphorus availability in soils in general.

Declining biodiversity and loss of ecosystem function threatens the ability of habitats to contribute ecosystem services. However, the form of the relationship between biodiversity and ecosystem function (BEF) and how relationships change with environmental change is poorly understood. This limits our ability to predict the consequences of biodiversity loss on ecosystem function, particularly in real-world marine ecosystems that are species rich, and where multiple ecosystem functions are represented by multiple indicators. We investigated spatial variation in BEF relationships across a 300 000 m2 intertidal sandflat by nesting experimental manipulations of sediment pore water nitrogen concentration into sites with contrasting macrobenthic community composition. Our results highlight the significance of many different elements of biodiversity associated with environmental characteristics, community structure, functional diversity, ecological traits or particular species (ecosystem engineers) to important functions of coastal marine sediments (benthic oxygen consumption, ammonium pore water concentrations and flux across the sediment–water interface). Using the BEF relationships developed from our experiment, we demonstrate patchiness across a landscape in functional performance and the potential for changes in the location of functional hot and cold spots with increasing nutrient loading that have important implications for mapping and predicating change in functionality and the concomitant delivery of ecosystem services.

Heatwaves have increased in intensity, duration and frequency over the last decades due to climate change. Intertidal species, living in a highly variable environment, are likely to be exposed to such heatwaves since they can be emerged for more than 6 h during a tidal cycle. Little is known, however, on how temperature affects species traits (e.g. locomotion and behaviour) of slow-moving organisms such as benthic foraminifera (single-celled protists), which abound in marine sediments. Here, we examine how temperature influences motion-behaviour and metabolic traits of the dominant temperate foraminifera Haynesina germanica by exposing individuals to usual (6, 12, 18, 24, 30 °C) and extreme (high; i.e. 32, 34, 36 °C) temperature regimes. Our results show that individuals reduced their activity by up to 80% under high temperature regimes whereas they remained active under the temperatures they usually experience in the field. When exposed to a hyper-thermic stress (i.e. 36 °C), all individuals remained burrowed and the photosynthetic activity of their sequestered chloroplasts significantly decreased. Recovery experiments subsequently revealed that individuals initially exposed to a high thermal regime partially recovered when the hyper-thermic stress ceased. H. germanica contribution to surface sediment reworking substantially diminished from 10 mm 3 indiv −1 day −1 (usual temperature) to 0 mm 3 indiv −1 day −1 when individuals were exposed to high temperature regimes (i.e. above 32 °C). Given their role in sediment reworking and organic matter remineralisation, our results suggest that heatwaves may have profound long-lasting effects on the functioning of intertidal muddy ecosystems and some key biogeochemical cycles.