Fungi have recently been found to comprise a significant part of the deep biosphere in oceanic sediments and crustal rocks. Fossils occupying fractures and pores in Phanerozoic volcanics indicate that this habitat is at least 400 million years old, but its origin may be considerably older. A 2.4-billion-year-old basalt from the Palaeoproterozoic Ongeluk Formation in South Africa contains filamentous fossils in vesicles and fractures. The filaments form mycelium-like structures growing from a basal film attached to the internal rock surfaces.

The Strategic Plan for Biodiversity, adopted under the auspices of the Convention on Biological Diversity, provides the basis for taking effective action to curb biodiversity loss across the planet by 2020—an urgent imperative. Yet, Antarctica and the Southern Ocean, which encompass 10% of the planet’s surface, are excluded from assessments of progress against the Strategic Plan. The situation is a lost opportunity for biodiversity conservation globally. We provide such an assessment.

The legacy and reach of anthropogenic influence is most clearly evidenced by its impact on the most remote and inaccessible habitats on Earth. Here we identify extraordinary levels of persistent organic pollutants in the endemic amphipod fauna from two of the deepest ocean trenches (>10,000 metres). Contaminant levels were considerably higher than documented for nearby regions of heavy industrialization, indicating bioaccumulation of anthropogenic contamination and inferring that these pollutants are pervasive across the world’s oceans and to full ocean depth.

There has been a progressive deepening of winter convection in the Labrador Sea since 2012, with the individual profile maximum depth exceeding 1800 m since 2014 and reaching 2100 m in 2016. This increase, during repeated positive phases of the winter North Atlantic Oscillation (NAO), resembles that during the formation of the record depth (2500 m) Labrador Sea Water (LSW) class in 1987–1994, attributed to repeated positive NAO forcing having provided critical preconditioning. The 2012–2016 LSW class is one of the deepest and most persistent ever observed (back to 1938).

The ocean is the largest sink for anthropogenic carbon dioxide (CO2), having absorbed roughly 40 per cent of CO2 emissions since the beginning of the industrial era. Recent data show that oceanic CO2 uptake rates have been growing over the past decade, reversing a trend of stagnant or declining carbon uptake during the 1990s. Here we show that ocean circulation variability is the primary driver of these changes in oceanic CO2 uptake over the past several decades.

The ocean's uptake of carbon dioxide increased during the 2000s. Models reveal that this was driven primarily by weak circulation in the upper ocean, solving a mystery of ocean science.

Ocean acidification poses a range of threats to marine invertebrates; however, the emerging and likely widespread effects of rising carbon dioxide (CO2) levels on marine invertebrate behaviour are still little understood. Here, we show that ocean acidification alters and impairs key ecological behaviours of the predatory cone snail Conus marmoreus.

Ongoing ocean acidification is widely reported to reduce the ability of calcifying marine organisms to produce their shells and skeletons. Whereas increased dissolution due to acidification is a largely inorganic process, strong organismal control over biomineralization influences calcification and hence complicates predicting the response of marine calcifyers. Here we show that calcification is driven by rapid transformation of bicarbonate into carbonate inside the cytoplasm, achieved by active outward proton pumping.