Petabase-scale sequence alignment catalyses viral discovery.

Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by a lack of efficient methods for searching this corpus, which (at the time of writing) exceeds 20 petabases and is growing exponentially1. Here we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) for the hallmark gene RNA-dependent RNA polymerase and identified well over 105 novel RNA viruses, thereby expanding the number of known species by roughly an order of magnitude. We characterized novel viruses related to coronaviruses, hepatitis delta virus and huge phages, respectively, and analysed their environmental reservoirs. To catalyse the ongoing revolution of viral discovery, we established a free and comprehensive database of these data and tools. Expanding the known sequence diversity of viruses can reveal the evolutionary origins of emerging pathogens and improve pathogen surveillance for the anticipation and mitigation of future pandemics.

Footprint evidence of early hominin locomotor diversity at Laetoli, Tanzania.

Bipedal trackways discovered in 1978 at Laetoli site G, Tanzania and dated to 3.66 million years ago are widely accepted as the oldest unequivocal evidence of obligate bipedalism in the human lineage1-3. Another trackway discovered two years earlier at nearby site A was partially excavated and attributed to a hominin, but curious affinities with bears (ursids) marginalized its importance to the paleoanthropological community, and the location of these footprints fell into obscurity3-5. In 2019, we located, excavated and cleaned the site A trackway, producing a digital archive using 3D photogrammetry and laser scanning. Here we compare the footprints at this site with those of American black bears, chimpanzees and humans, and we show that they resemble those of hominins more than ursids. In fact, the narrow step width corroborates the original interpretation of a small, cross-stepping bipedal hominin. However, the inferred foot proportions, gait parameters and 3D morphologies of footprints at site A are readily distinguished from those at site G, indicating that a minimum of two hominin taxa with different feet and gaits coexisted at Laetoli.

Toward defining the Anthropocene onset using a rapid increase in anthropogenic fingerprints in global geological archives.

One of the remaining issues regarding the Anthropocene is the lack of stratigraphic evidence indicating when the cumulative human pressure from the early Holocene began to fundamentally change the Earth system. Herein, we compile anthropogenic fingerprints from various high-precision-dated proxy records for 137 global sites to determine the age of the unprecedented surge in these records over the last 7700 y. The cumulative number of fingerprints revealed an unprecedented surge in diverse anthropogenic fingerprints starting in 1952 ± 3 CE, corresponding to the onset of the Great Acceleration. Notably, the period from 1953 to 1958 CE saw a nearly simultaneous surge in fingerprints across all regions, including Antarctica, the Arctic, East Asia, Europe, North America, and Oceania. This synchronous upsurge reflects the moment when human impacts led to rapid transformations in various natural processes and cycles, with humans becoming a geological force capable of inscribing abundant and diverse anthropogenic fingerprints in global strata. Following this global fingerprint explosion, profound planetary-scale changes, including deviations from the established natural climatic conditions, begin. This unprecedented surge in anthropogenic signals worldwide suggests that human influences started to match many natural forces controlling the processes and cycles and overwhelm some of the functioning of the Earth system around 1952.

Isotopic constraint on the twentieth-century increase in tropospheric ozone.

Tropospheric ozone (O3) is a key component of air pollution and an important anthropogenic greenhouse gas1. During the twentieth century, the proliferation of the internal combustion engine, rapid industrialization and land-use change led to a global-scale increase in O3 concentrations2,3; however, the magnitude of this increase is uncertain. Atmospheric chemistry models typically predict4-7 an increase in the tropospheric O3 burden of between 25 and 50 per cent since 1900, whereas direct measurements made in the late nineteenth century indicate that surface O3 mixing ratios increased by up to 300 per cent8-10 over that time period. However, the accuracy and diagnostic power of these measurements remains controversial2. Here we use a record of the clumped-isotope composition of molecular oxygen (18O18O in O2) trapped in polar firn and ice from 1590 to 2016 AD, as well as atmospheric chemistry model simulations, to constrain changes in tropospheric O3 concentrations. We find that during the second half of the twentieth century, the proportion of 18O18O in O2 decreased by 0.03 ± 0.02 parts per thousand (95 per cent confidence interval) below its 1590-1958 AD mean, which implies that tropospheric O3 increased by less than 40 per cent during that time. These results corroborate model predictions of global-scale increases in surface pollution and vegetative stress caused by increasing anthropogenic emissions of O3 precursors4,5,11. We also estimate that the radiative forcing of tropospheric O3 since 1850 AD is probably less than +0.4 watts per square metre, consistent with results from recent climate modelling studies12.

The marriage between stable isotope ecology and plant metabolomics - new perspectives for metabolic flux analysis and the interpretation of ecological archives.

Even though they share many thematical overlaps, plant metabolomics and stable isotope ecology have been rather separate fields mainly due to different mass spectrometry demands. New high-resolution bioanalytical mass spectrometers are now not only offering high-throughput metabolite identification but are also suitable for compound- and intramolecular position-specific isotope analysis in the natural isotope abundance range. In plant metabolomics, label-free metabolic pathway and metabolic flux analysis might become possible when applying this new technology. This is because changes in the commitment of substrates to particular metabolic pathways and the activation or deactivation of others alter enzyme-specific isotope effects. This leads to differences in intramolecular and compound-specific isotope compositions. In plant isotope ecology, position-specific isotope analysis in plant archives informed by metabolic pathway analysis could be used to reconstruct and separate environmental impacts on complex metabolic processes. A technology-driven linkage between the two disciplines could allow us to extract information on environment-metabolism interaction from plant archives such as tree rings but also within ecosystems. This would contribute to a holistic understanding of how plants react to environmental drivers, thus also providing helpful information on the trajectories of the vegetation under the conditions to come.