Communications Earth & Environment

Identification of early microfossils relies on morphological and chemical criteria assumed to be unique to life, but whether abiotic microstructures can satisfy these criteria has not been rigorously tested. Hydrothermal environments preserve microfossils but are also efficient geochemical reactors for abiotic reactions. Protocells form in hydrothermal conditions and represent a plausible abiotic analogue to early microfossils. Here we show that protocells form from simple organic molecules in low-temperature, alkaline hydrothermal conditions in the presence of silica and produce spheres, filaments, and lenticular structures that strongly resemble the morphology of purported microfossils in Archaean silica cherts. FTIR spectroscopy provides overlapping chemical signatures across protocells, microorganisms, and geologic microstructures. In addition, the FTIR R3/2 ratio, a chemometric index often used to discriminate domains and determine biogenicity, identifies eight different protocell systems as either bacterial, archaeal, or eukaryotic. These data suggest that protocells preserved in ancient hydrothermal deposits can satisfy current biogenicity criteria, undermining the reliability of interpretations of the early fossil record. As life detection is the primary objective for current space exploration endeavours, robust biogenicity protocols that account for abiotic signatures are essential.

Accurate accounting of aquatic methane emissions is critical for climate change mitigation, yet current global budgets overlook a key driver: the elevation-regulated atmospheric pressure. Here, we present the first large-scale investigation of methane ebullition across 164 shallow waters spanning elevations from sea level to 4886 meters. We demonstrate that ebullition rate increases with elevation-over four times higher at >3000 m a.s.l. than at sea level-due to two synergistic, pressure-dependent physical mechanisms: a degas effect (enhanced bubble formation) and a trigger effect (facilitated bubble ascent). Independent theoretical prediction of the combined effects shows near-perfect agreement with the empirical elevation trend, quantitatively confirming that these physical mechanisms are the primary drivers of enhanced ebullition at high elevations. Our findings reveal that mountain aquatic ecosystems represent unaccounted methane hotspots that have been systematically underestimated in global inventories.We therefore call for urgent integration of these ecosystems into IPCC assessments and targeted mountain mitigation and sustainable management strategies.

Commodity maps and the ability to monitor commodity-driven deforestation are essential for sustainability risk assessment and due diligence. Natural rubber (Hevea brasiliensis), used primarily in tyres, remains challenging to map because of its similarity to other tree cover. Integrating optical and radar satellite data, we produced a 10 m map of rubber distribution in Southeast Asia for around 2020 and assessed this map and similar products for deforestation due diligence. In continental Southeast Asia, estimated users accuracy was 0.95 and area-adjusted producers accuracy 0.78. Rubber-associated clearances of natural and semi-natural tree cover during 2011-2016 were estimated at 0.3-0.4 Mha, predominantly associated with industrial-scale plantations and concentrated in Cambodia. Historical clearances were less certain, with plausible bounds of 1.3-3.0 Mha since 1990. Evaluation of rubber and forest maps highlighted persistent limitations, particularly in insular Southeast Asia and smallholder systems. Accounting for these limitations is critical for fair and effective due diligence.

Coral bleaching is among the most infamous climate impacts. Yet the extent of bleaching due to human-caused climate change, as opposed to natural El Nino variability, and the contributions of individual countries and carbon majors (fossil fuel and cement producers) remains unquantified. Here, we leverage coral monitoring globally across 4,479 sites from 1985-2024 to link specific emitters to marine heat stress and bleaching. For events with >10% of corals bleached at a site, we find that 99% (95% CI: 88-100%) were attributable to human-caused climate change. Even during major El Ninos, 97-100% of bleaching events were attributable to human-caused climate change and the extent of damage increases over time from 23% of sites bleached (95% CI: 3-35%) during 1998 to 71% of sites (95% CI: 37-85%) during 2023-2024. Emissions of the United States, the largest historical emitter, contributed to 51% (95% CI: 39-65%) of bleaching events. Emissions linked to Chevron, Saudi Aramco, Gazprom, and ExxonMobil each contributed to 14% (95% CI: 11-19%) of bleaching events -- roughly double the contribution of the 39 countries of the Alliance for Small Island States. It is virtually certain emissions of China, the United States, and Indonesia caused bleaching in their coastal waters. Strong inequalities exist where countries with high socioeconomic dependence on coral reefs experienced 54% of bleaching yet contributed only 5% to bleaching. As global warming rapidly nears levels catastrophic for warm-water corals, our results show the massive contribution from anthropogenic emissions to historical coral beaching and help fill an important evidentiary gap on accountability for non-economic loss and damage from climate change.

The Ocean sustains planetary health through climate regulation, biodiversity, and essential ecosystem services. Plankton underpins these processes by driving primary production, sustaining food webs, and mediating carbon sequestration. Yet the spatial organization of plankton-based ecosystem services remains poorly understood. The High Seas Treaty and the 30% Ocean protection target by 2030 create an urgent need for science-based guidance for global ocean governance. Here, we aim to identify key planktonic areas associated with functional diversity, net primary productivity, and carbon export globally. We used machine learning to integrate omics-derived plankton functions and satellite observations with diversity metric and ecosystem services. Leveraging metagenomic data, we identified molecular functions strongly linked to ecosystem functioning and project their global distributions across seasons. We reveal putative hotspots of functional diversity, net primary productivity, and carbon export. Our analysis pinpoints areas where all three indicators converge synchronously, predominantly along oceanographic structures such as polar fronts and principal current systems. By relying on satellite data as core input, our approach captures the temporal variability of these hotspots, providing a global, dynamic protocol for projections of plankton-based ecosystem services. These findings establish a foundation for developing integrative conservation tools based on ecosystem functioning and inform adaptive management under climate change.

Dissolved organic matter (DOM) is a central component of biogeochemical cycling, but molecular observations generated by ultrahigh-resolution mass spectrometry remain fragmented across studies, limiting quantitative comparisons among ecosystems. Here, we compile and harmonize a global dataset of DOM molecular traits comprising 3,999 samples from 337 studies published between 2005 and 2026. The dataset includes eight intensity-weighted molecular traits: hydrogen-to-carbon (H/C), oxygen-to-carbon (O/C), nitrogen-to-carbon (N/C), and sulfur-to-carbon (S/C) ratios; molecular mass; double-bond equivalents (DBE); modified aromaticity index (AImod); and nominal oxidation state of carbon (NOSC). Samples span aquatic, terrestrial, atmospheric, plant-associated, petroleum-related, and other environments, and are linked, where available, to geographic, physicochemical, nutrient, and climatic metadata. Molecular data were harmonized using common definitions and restricted to negative-mode electrospray-ionization FT-ICR MS to improve cross-study comparability. This resource enables cross-system comparisons of DOM molecular traits and supports analyses of environmental gradients, geographic coverage, and global DOM chemogeography.

Forests are known to burn and desiccate under a changing climate; less appreciated is that they also drown. Across much of the globe, a warming atmosphere is amplifying the length and intensity of both droughts and floods. Whereas massive die-offs from drought and fire are widely studied as consequences of climate change on forests, inundation-induced mortality remains poorly quantified. Using approximately 1 m resolution aerial imagery and deep learning, we tracked over 260 million dead trees across the United States' Great Lakes and ocean coastlines from 2012 to 2023. Within 10 km of the coasts, more than half of mapped mortality was concentrated in just 10% of forests, primarily in high-elevation inland wetlands and low-lying forests prone to inundation. Mortality rates doubled within a decade around expanding freshwater lakes and in inland wetlands experiencing intensifying regional-scale precipitation, while tripling in low-lying coastal forests where salinization compounded inundation in sea-level rise hotspots. Our findings identify rising waters as a widespread, underappreciated driver of forest die-off that can extend far inland, underscoring the need to reassess the impacts of climate change on the functioning, demography, and carbon-methane budgets amongst the world's most carbon-rich forests as seas rise and hydroclimate shifts globally.

Phytoplankton community composition (PCC) impacts global ocean change across scales. Combining the taxonomic resolution of in situ methods with the spatiotemporal coverage of satellite ocean color remains a major challenge. Phytoplankton pigments link PCC to ocean color; past work has demonstrated that 4-6 pigment-based groups can be reconstructed from hyperspectral remote sensing reflectance (Rrs({lambda})). Alternately, metabarcoding approaches reveal thousands of taxa to the species level, but the links between optics and genes are less clear. Here, we compiled a global, coincident dataset of hyperspectral Rrs({lambda}), pigments, and 18S rRNA gene sequences. We used a bio-optical model to produce the relative contributions of 13 eukaryotic phytoplankton classes identified by metabarcoding with high confidence in most cases. Model coefficients were highly spectrally correlated between genes and pigments, revealing the strong PCC signal within Rrs({lambda}). This proof-of-concept study establishes a foundation for detecting eukaryotic PCC beyond pigments in the PACE era.

Marine microbiomes may experience extreme environmental stress during atmospheric transport, yet how near-space conditions reshape natural microbial communities remains poorly understood. Here, we investigated the effects of controlled near-space exposure on a seawater microbiome using high-altitude balloon experiments and 16S rRNA amplicon sequencing. While alpha diversity remained relatively stable across exposure conditions, weighted UniFrac and PERMANOVA analyses revealed reproducible shifts in microbial community composition associated with flight exposure. Taxonomic profiling demonstrated coordinated restructuring across multiple microbial lineages rather than dominance of a single taxon-specific response. Comparable beta-dispersion among groups supported the robustness of these compositional differences. Together, these findings demonstrate that near-space exposure was associated with reproducible restructuring of microbial community composition without substantial loss of overall diversity. Raw sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1479017.

Australias Great Barrier Reef is a biodiversity hotspot critical to ocean health, yet it faces increasing threats from climate change and localised impacts requiring effective conservation and management action. Rezoning of the Great Barrier Reef Marine Park in 2004 expanded No-Take Marine Reserves (NTMRs) to restrict extractive activities like fishing and collecting, creating one of the largest networks of marine reserves globally. Benefits like increased biomass of fisheries-targeted species and improved coral community health metrics have been reported, though the effects of zoning on water chemistry and seawater microbiology remain unexplored. Using data from the Great Barrier Reef Microbial Genomics Database, we investigated the structure of seawater microbiomes on 48 offshore reefs within NTMRs and fished reefs. A supervised classification method (MINT sPLS-DA) identified 350 indicator species that predict zoning with [~]71% accuracy (range 58-85%). Microbial communities broadly reflected reef states, with NTMR zones enriched in streamlined microbial oligotrophs (Pelagibacter and SAR86) correlating with higher cover of hard coral, crustose coralline algae, and herbivore fish abundance under lower nutrient conditions. By contrast, fished reefs harbored opportunists (Flavobacteriales, especially UA16, and Pseudomonadales) associating with elevated nutrients and turf algae cover. Co-occurrence networks revealed stronger competitive interactions in fished reefs, where nutrient-responsive taxa may outcompete other microbes, underscoring the need to investigate how these shifts influence reef nutrient cycling and function. Our findings reveal ecosystem-wide effects of marine zoning beyond fish protection, with distinct seawater microbiomes between fished reefs and NTMRs, which will help build decision tools for more targeted reef health monitoring assessments.

Mineralized dental tissues are formed through biomineralization processes involving the growth and self-organisation of hydroxylapatite (HAP) nanoscale grains. There remain open questions regarding the way elements such as Mg or Na are incorporated in the organic matter between HAP grains or within the grain structure where they influence the nucleation and growth of HAP. Here, mapping the enamel structure and composition of a well-preserved ca. 150-million-year-old Giraffatitan brancai sauropod dinosaur tooth from millimeters down to the near-atomic scale, we reveal the nanoscale accumulation of Mg at HAP grain boundaries, alongside F arising from diagenesis. Within the HAP grains and at HAP grain boundaries organic matter forms clusters that we propose contribute to the fast growth rate of the tooth. Moreover, unexpected Cu3As particles are found across the entire enamel structure. These elements are not in the dentine, that exhibits empty tubules, which suggests that they were integrated during the tooth growth itself. Our multiscale analysis provides new information encouraging to reconsider aspects of the biomineralization and fossilization processes.

Understanding how animals respond to their physical environment requires environmental observations at the scale at which behavioural decisions are made. For soaring birds, the coarse resolution of weather products has long hindered the analysis of their behavioural response to fine-scale atmospheric dynamics, forcing uplift sources to be inferred largely from behaviour itself. Here, we combined high-resolution movement data from 24 golden eagles with the kilometre-scale COSMO weather model. We first classified thermal, orographic, and gravity-wave uplifts using independent atmospheric predictors and then quantified the birds' use of each uplift type and their fine-scale behavioural responses. Eagles relied predominantly on thermals, but opportunistically adjusted their use of uplift sources seasonally. The birds' flight behaviour could not reliably indicate which uplift type was primarily used, and thus suggests that both atmospheric processes and behavioural responses are better described as continua than discrete categories. Finally, we compared vertical wind velocities derived from eagles soaring behaviour with those modelled by the COSMO weather model, showing that most of the thermals exploited by eagles remain unresolved at kilometre-scale model resolution. Our results demonstrate how high-resolution weather models provide new insights into bird movement decisions, while also highlighting the potential of soaring birds as biologically embedded atmospheric sensors that could help closing the resolution gap in atmospheric models.

The Eboliang Hu saline lakes in the hyper-arid Qaidam Basin is a high-altitude, weakly acidic hypersaline system with strong environmental gradients and limited nitrogen availability. To resolve its microbial ecology and evolutionary context, we performed genome-resolved metagenomic sequencing across four distinct habitats, reconstructing 46 medium- to high-quality metagenome-assembled genomes (MAGs) and a comprehensive gene catalog. The community shows pronounced spatial heterogeneity and is dominated by Thermodesulfobacteriota, Pseudomonadota, Bacteroidota, and archaeal lineages. Phylogenomic placement and large-scale sequence comparisons indicate that multiple dominant taxa exhibit affinity to marine- and subsurface-associated reference lineages, consistent with long-term isolation of a marine-derived ecosystem about 10-11 million years ago. Functional reconstruction reveals a distributed metabolic system in which carbon, nitrogen, and sulfur cycling are partitioned across taxa. Notably, hydrogen oxidation and arsenite oxidation are recurrent energy-producing strategies across dominant lineages, indicating redox flexibility under oligotrophic conditions. Comparative genomics further suggests lineage-specific adaptations to osmotic stress, UV exposure, and nutrient limitation. Horizontal gene transfer and phylogenetic incongruence among key metabolic genes indicate that co-evolutionary processes and gene exchange have contributed to functional innovation. These findings provide a framework for understanding microbial persistence and evolution in isolated extreme environments and offer potential analogs for extraterrestrial habitability.

A direct empirical relationship between gross primary productivity (GPP) estimated by the eddy covariance method and satellite vegetation indices (VIs) has been widely observed across diverse ecosystems globally. Building on this observed covariation, VIs are frequently utilized as critical parameters - such as the fraction of absorbed photosynthetically active radiation (fPAR) - within light use efficiency (LUE) and greenness-based models for carbon cycle monitoring. However, actual canopy carbon assimilation is jointly governed by slowly evolving structural parameters and highly dynamic functional traits, such as physiological efficiency. The extent to which the macro-scale VI-GPP covariance is driven by structural scaffolding, and how this structural signal decouples from physiological function under environmental stress, remains to be systematically quantified. Here, we synthesized half-hourly eddy covariance measurements from 328 globally distributed sites and paired them with a rigorously angle-normalized Enhanced Vegetation Index (nadir view and fixed solar zenith angle at 30 degrees, EVI_SZA30). By applying a nonlinear light-response curve model across 54,720 high-frequency temporal windows, we mechanistically disentangled observed actual GPP (GPP_EC) into baseline photosynthetic capacity (P_c) and intrinsic quantum yield (alpha). Our results demonstrate that the macroscopic covariance between EVI_SZA30 and GPP_EC (R^2=0.554) is primarily driven by the index's robust ability to track structural capacity (P_c, R^2=0.538). In contrast, EVI_SZA30 exhibits limited sensitivity to high-frequency variations in functional traits like physiological efficiency (alpha, R^2=0.038). Particularly in water-limited biomes (e.g., open shrublands and woody savannas), intense environmental stress triggers rapid stomatal regulation while the physical canopy structure remains relatively stable. Consequently, the correlation between EVI and P_c becomes notably stronger than its correlation with actual GPP_EC, highlighting a pronounced structural-physiological decoupling. Because discrete overpasses by sun-synchronous polar-orbiting satellites face intrinsic temporal constraints in capturing sub-daily physiological down-regulation (e.g., midday photosynthetic depression), future monitoring paradigms could greatly benefit from the continuous, high-frequency observations provided by next-generation geostationary (GEO) satellites to bridge the gap between structural parameters and transient ecosystem function.

Current planetary protection approaches rely heavily on spore-based tests developed for Mars missions and may not adequately assess contamination risks for icy ocean worlds such as Europa. We developed a genome-based framework combining deep shotgun metagenomics and supervised machine learning to predict survival-relevant microbial traits in ESA JUICE launch-site cleanrooms. From 183 genome bins, 25 representative genomes were analyzed for traits including cryotolerance, desiccation tolerance, salt resilience, anaerobic metabolism, autotrophy, and sporulation. Several skin-associated microbes carried multiple relevant traits, and some appeared actively replicating. A broader meta-analysis of 1,868 genomes showed that trait profiles vary strongly within taxa, demonstrating that taxonomy alone is insufficient for risk assessment. This framework complements current planetary protection assays, helps to predict how microbes would survive in a new biotope, and supports functional, risk-informed contamination monitoring for future space missions.

Tropical forests contain much of Earth's biodiversity, yet community-wide responses to seasonal climate transitions remain poorly resolved. We used weekly airborne environmental DNA sampling, supplemented by spatially intensive dry- and wet-season campaigns, to characterize fungi, plants, arthropods, and vertebrates across the dry-to-wet-season transition in a lowland tropical forest. All four assemblages shifted abruptly and nearly synchronously following rainfall late in the dry season, before the meteorological wet season began. These compositional transitions were largely independent of taxonomic richness and airborne DNA concentrations, indicating coordinated changes in detection patterns rather than simple seasonal gains in richness. Across all samples, we recovered more than 5,400 operational taxonomic units, including 2,148 fungi, 857 plants, 2,157 arthropods, and 239 vertebrates. We also recovered 949 full-length insect DNA barcodes, demonstrating compatibility with standard barcoding approaches and expanding opportunities for species discovery. Because the onset of the meteorological wet season showed no long-term trend at Barro Colorado Island, predicting future phenological and compositional shifts will require greater attention to dry-season rainfall variability and the cues that organisms track during this transition. Airborne environmental DNA offers a scalable, noninvasive framework for monitoring biodiversity and phenology across taxonomic groups.

Mesophotic coral ecosystems are commonly interpreted as thin biological veneers over relict shallow-water reef structures, but their capacity to generate late Holocene carbonate deposits remains poorly quantified. Here we combine diver excavations, rubble-bed thickness surveys, radiocarbon age-depth modelling, sediment grain-size analyses, coral-rubble assemblages, trace-element geochemistry, and modern Alveopora allingi growth measurements from two 40-65 m deep coral-rubble fields in the northern Gulf of Eilat/Aqaba, Red Sea. Rubble deposits are at least 1.0-1.5 m thick and accumulated at mean rates of 2.21 {+/-} 0.52 mm yr-1 at the Dekel site and 1.33 {+/-} 0.13 mm yr-1 at the IUI site, implying persistent carbonate accumulation over centuries to >1 kyr. Age-depth models indicate quasi-continuous deposition despite pronounced faunal changes, including a shift from A. allingi-dominated rubble to upper layers enriched in Euphyllia paradivisa at Dekel. The dominant modern rubble-forming coral, A. allingi, extends at 3.04 {+/-} 0.87 mm yr-1 and has skeletal density of 1.17 {+/-} 0.27 g cm-3. First-order cover-based accretion estimates at present coral cover fall well below the radiocarbon-derived rates, indicating that long-term mesophotic rubble accumulation integrates historical cover, secondary calcification and sediment retention rather than present live coral cover alone. These data demonstrate that mesophotic rubble fields can act as active carbonate factories and palaeoecological archives, challenging the assumption that modern mesophotic habitats are geomorphologically passive.

Airborne environmental DNA can capture biodiversity across the tree of life, but low sample biomass makes rapid, untargeted detection technically challenging. We combined 45-min air collection, nanopore sequencing and real-time taxonomic analysis in a shotgun metagenomic workflow capable of producing results within 3 hours. Across 77 samples from 13 London sites, including a year of weekly sampling at the Natural History Museum Wildlife Garden, we detected 1,916 species spanning bacteria, fungi, plants and animals. Communities varied spatially and seasonally, shifting from plant dominance in spring to ascomycete dominance in summer and basidiomycete dominance in late autumn and winter. Plant read abundance increased with upwind vegetation, linking airborne signals to surrounding habitat. Detection of catalogued garden plants depended on reference availability, dispersal biology, plant size and proximity to the collector. Together, these findings establish airborne shotgun metagenomics as a platform for rapid, repeated and scalable biodiversity assessment across space and time.

Marine diatoms contribute to about 20% of global primary production. We present the first basin-scale, multiyear assessment of diatom communities in the North Pacific, combining taxonomically high-resolution RuBisCO large subunit gene (rbcL) metabarcoding with concurrent environmental measurements. Using a nine-year time series of daily samples resolved at the species level via ~500 bp rbcL fragments, we performed multivariate analyses across biogeographic provinces, identifying significant correlations between community structure and environmental drivers such as temperature and macronutrient availability. We report the prevalence of a previously overlooked centric diatom species in the North Pacific, Eunotogramma lunatum, which appears to be near-dominant even in subarctic high-nitrate, low-chlorophyll waters where pennate diatoms are typically favored. These results demonstrate the power of rbcL for large-scale ocean monitoring and provide a critical baseline for future studies of diatom population dynamics, climate change impacts, and ecosystem resilience in a key marine region.

Environmental molecular monitoring has transformed biodiversity detection, yet most methods capture only species presence through amplified DNA fragments, missing the biological information encoded in native nucleic acids. Here we show that a single shotgun Oxford Nanopore sequencing library from water can be read through several independent biological lenses, and that each class of molecule (environmental RNA, CpG methylation, and bulk DNA) differs in its environmental persistence, which sets the window over which signal can be trusted. Sampling Pacific salmon spawning runs, we simultaneously recovered environmental RNA indicating fresh biological input, CpG methylation profiles reflecting age demographics, and pathogen signatures reflecting health. Environmental RNA tracked spawning phenology, qPCR corroborated the timing of fresh biological input over the weeks sampled, and methylation-based age inference held only while fresh DNA dominated, a condition we term the 'Freshness Gate.' Because environmental water is not a tissue sample, we detect functional transcripts as evidence of biological input but do not infer differential gene expression, and we read methylation state but do not infer biological age outside the Freshness Gate. Variance partitioning is consistent with biological freshness, rather than technical factors such as fragment length or sequencing depth, structuring environmental methylation, though these comparisons did not reach significance at nine time points. Comparable dynamics were observed in Chinook salmon, with timing offsets following their distinct spawning season. By defining when environmental molecules faithfully encode living biology and when degradation decouples signal from current state, our framework sets practical and theoretical boundaries for multi-omic environmental monitoring.