Communications Earth & Environment

Bacteria and archaea are currently under-characterised in palaeoecological studies, despite their ubiquity, high diversity and tight integration with the biotic and abiotic environment and human activity. The complexity of their assemblages, and the difficulties in separating living- from paleo-prokaryotes renders analyses challenging. Here we present an ancient prokaryote metagenomic time-series from a sediment core of Lake Constance, a large and deep perialpine lake from temperate Europe, spanning the last 13,500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and estimated the DNA damage of taxa, which displayed a monotonic relationship with time. By constructing co-abundance networks we recognize major microbial assemblages, containing both ancient and living microbes, that show specific dynamics. Short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa that were linked to various freshwater and soil environments persisted through millennia. By extricating various sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing long-term eco-evolutionary outcomes caused by both nature- and humans.

Organic carbon (OC) burial in lakes is an important component of the global carbon cycle, but the source organisms of preserved OC remain poorly resolved. Here we develop the genC pipeline, which combines sedimentary ancient DNA concentrations, read-based taxonomic assignments, and group-specific priors for DNA and cellular carbon content to derive OCDNA-projected, a semi-quantitative proxy for the magnitude and taxonomic composition of preserved sedimentary OC. We apply genC to six high-latitude lake records spanning the last 30,000 years. OCDNA-projected broadly agrees with independent proxies for total organic carbon and aquatic contribution, supporting its reliability. Our results indicate that environmental conditions, especially warming, rather than preservation alone, are the main drivers of preserved OC variation. Terrestrial sources, mainly woody plants, dominate lake sediment OC. Eukaryotic algae as well as aquatic and terrestrial bacteria become more important during the warmer Holocene. These results establish sedaDNA as a taxonomically resolved tool for reconstructing long-term changes in preserved lake-sediment OC.

Timing, duration, and severity of marine heatwaves are changing rapidly in response to anthropogenic climate change, thereby increasing the frequency of coral bleaching events. Mass coral bleaching events occur because of cumulative heat stress, which is commonly quantified through Degree Heating Weeks (DHW). Here we introduce CoralBleachRisk, a daily-resolution global dataset that characterises sea surface temperatures, heat stress anomalies, and the timing, duration, and magnitude of severe coral bleaching conditions from the recent past (1985) to the future (2100) under three contrasting Shared Socioeconomic Pathways. Our projections are downscaled to a 0.5{degrees} resolution (~50km), bias-corrected and validated using remotely sensed data of sea surface temperatures and a global dataset of historical coral bleaching events. An accompanying online software tool allows non-specialist users to access aggregated metrics of coral bleaching risk and generate time series projections of coral vulnerability for Earths coral reefs. More broadly, our dataset enables regional to global comparisons of future trends in severe coral bleaching risk and the identification of potential climate refugia for corals.

Large tropical river dam projects are set to accelerate over the forthcoming decades to satisfy growing demand for energy, irrigation and flood control. When tropical rivers are dammed, the immediate impacts are well studied, but the long-term (decades-centuries) consequences of impoundment remain poorly known. Here, we gather historical and paleoecological data from Gatun Lake, formed by the building of the Gatun Dam (Panama Canal, Panama) over 100 years ago, to reconstruct the limnological evolution of the system in response to individual and linked stressors (river damming, forest flooding, deforestation, invasive species, pollution and hydro-climate). We found that after a century of dam construction parallels associated with the natural hydrological functioning of river floodplains persist. Hence, hydrology remains the most important temporal structural factor positively stimulating primary productivity, deposition of new minerals, and reduction of water transparency during wet periods. During dry periods, clear water and aerobic conditions prevail and nutrients transform into available forms in the detrital-rich reductive sediments. We highlight the importance of climate change as an ultimate rather than proximate anthropogenic factor for sustainable management options of tropical dams.

Kelp forests are one of the earths most productive ecosystems and are at the greatest risk from climate change, yet little is known regarding their future threats and current conservation status. By combining a global remote sensing dataset of floating kelp forests with climate data and projections, we find that exposure to projected marine heatwaves will increase [~]8 times compared to contemporary (2001-2020) exposure for intermediate climate scenarios. While exposure will intensify for all forests, climate refugia emerge for some southern hemisphere kelp forests, which have lower exposure to contemporary and projected marine heatwaves. Under these escalating threats, less than 3% of global kelp forests are currently within highly restrictive marine protected areas, the most effective conservation measure for providing climate resilience. Our findings emphasize the urgent need to increase the global protection of kelp forests and set bolder climate adaptation goals.

Coral reefs are declining worldwide due to anthropogenic-driven environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata, from the Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical, coral holobiont dynamics potentially associated with anthropogenic disturbances.

Rapid coastal development continues to jeopardize the integrity of marine socio-ecological systems. China is now the largest bilateral creditor in the world, committing nearly half a trillion US dollars to overseas development finance since 2008. Meanwhile, there are growing concerns over the impacts of this boom in Chinese development finance on marine systems. Here, we quantify the risks of coastal development projects financed by China to marine biodiversity and coastal Indigenous communities. Ports present the greatest impact risks to marine systems, in terms of both magnitude and area at risk, with power plants, roads, and other facilities presenting relatively high localized risks. Risks are most prominent in Africa and the Caribbean, with coastal Indigenous communities in Western and Central Africa particularly vulnerable to the potential negative impacts of development. All projects present some risk to threatened marine species and potential critical habitats, but few present high risks to nearby marine protected areas. Most projects present additional risks to ecosystems that are already under increasing human pressures, but some are likely to introduce new risks to relatively intact ecosystems. "Bluing" future coastal development projects in Chinas overseas development finance portfolio will require more social and environmental safeguards, higher standards for host-country impact assessments, and greater integration of land-sea risk mitigation and management approaches.

The Arctic is warming rapidly, yet long-term data on how this affects bryophytes, key components of Arctic vegetation, remain limited. Sedimentary ancient DNA (sedaDNA) provides high-resolution taxonomic insights that can reveal vegetational responses to past environmental change, including functional responses via trait associations, but effective genomic tools for bryophyte sedaDNA are lacking. We applied bryophyte-specific primers targeting p6 loop in plastid DNA and compared their performance with bryophyte bycatch from vascular plant-specific primers. Using data from bryophyte-specific primers, we analyzed richness patterns across environmental gradients and assessed their potential for environmental reconstruction. The primers resolved nearly 60% of taxa to species level and over 80% to genus level, recovering 2.63 times more taxa with 1.48 times higher species-level resolution than vascular plant-specific primers. Taxonomic richness increased nonlinearly over time and along precipitation gradients, while exhibiting unimodal relationship with temperature and glacial activity. High-resolution data also enabled trait assignments for most bryophyte taxa, allowing temporal analyses of community development and functional dynamics. Overall, our results demonstrate that bryophyte-specific primers substantially improve bryophyte recovery from sedaDNA and, when combined with trait information, provide a powerful approach for reconstructing past bryophyte ecosystems and investigating functional ecological dynamics under long-term environmental change.

Summary paragraphPlankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the oceans carbon cycle.

The Humboldt upwelling ecosystem has been intensively harvested by people since the early Holocene. Understanding past and present human choices under climatic variability in these productive environments may hold key insights for its future sustainability by unraveling different adaptive pathways. To this end, we studied shellfish exploitation and climate patterns in the Taltal region of the Atacama desert coast (25{whitebullet}S) from the early Holocene until today using a compilation of archaeological, and modern benthic fisheries data together with direct ecological surveys. In addition we obtained satellite sea surface temperature (SST) and published{delta} 18O SST for the study region. The archaeological record and the modern rocky shore assemblage were dominated by herbivorous gastropods -Fissurella spp., Enoplochiton spp., Tegula spp.-and the carnivorous whelk Concholepas concholepas. Functional composition from the early Holocene to the present was remarkably stable. Using SST as a latent variable, we examined changes in functional composition across the Holocene and in a 16-year series of artisanal fisheries landings using bayesian ordination. The analysis identified functional groups characteristic of kelp ecosystems in association with cooler SST conditions during the Holocene and the present. Changes in functional composition during warm and cold periods of the Holocene broadly mirrored effects of interannual SST variability in the modern fisheries. The archaeological record suggests two cross-Holocene transitions social-ecological transitions. The generalized shoreline harvesting strategy that prevailed during the cold early Holocene shifted to a specialized maritime economy towards the warmer mid-Holocene. The maritime technological and cultural adaptions remained, but were part of more diversified lifestyles in the cooler and more variable late Holocene. The latter emerged at the same time as the modern El Nino climate pattern. Our insights from the direct analysis of human choices and SST variability highlight the role of flexibility and agency under a changing environment. The broad range of human decisions in the past, inform current regulatory frameworks for benthic artisanal fisheries. Marine resources and the livelihoods that depend on them are integrated into coupled coastal socioecological systems; their future sustainability hinges on fostering the different dimension of their adaptive capacity.

Marine life contribute to carbon stores helping lock carbon away from the atmosphere. Open-ocean pelagic ecosystems are vastly under-reported in terms of carbon sequestration conservation potential, compared to coastal vegetation blue carbon systems. Here we show that a harvested organism, Antarctic krill, has similar carbon sequestration potential through its sinking faecal pellets as coastal blue carbon stores, namely seagrasses, mangroves and marshes. Building upon recent advances in krill abundance and faecal pellet carbon flux data, and combining these with an ocean circulation model, we show that from Austral spring to early autumn Antarctic krill sequester 20 Mt C into the deep ocean for at least 100 years. This equates to USD$ 4 - 46 billion per spring/summer season depending on the price of carbon. The footprint of remineralised krill pellet carbon has a global extent, with some reaching as far as the North Pacific. The vast area of ocean krill inhabit and their high abundance make their total carbon sequestered each year similar to that from coastal vegetated blue carbon stores. As Antarctic krill are being impacted by rapid polar climate change and they are harvested, both krill populations and their habitat warrant protection to preserve this valuable carbon sink.

The Amazon rainforest, which stores approximately 120 billion tons of carbon and contributes around 16% of global terrestrial photosynthetic productivity, plays a pivotal role in global carbon cycling. Unlike temperate and boreal forests, tropical forests exhibit a bimodal photosynthetic pattern, characterized by distinct peaks in the first and second halves of the year. However, the intra-annual differences in photosynthetic responses to hydrothermal variations between these two periods in the Amazon rainforest remain largely unexplored. Here, utilizing satellite-derived photosynthetic proxies alongside ground-based flux tower observations from 2001 to 2020, we investigated the differences in photosynthetic responses to hydrothermal variations between the first and second halves of the year in the Amazon rainforest. Our observations revealed weaker temperature limitations but stronger precipitation limitations on photosynthesis in the second half of the year compared to the first half. Temperature constraints on photosynthesis have progressively weakened in both periods, while precipitation limitations have intensified, particularly in the latter half. Although the optimal temperature for photosynthesis is higher in the second half of the year, it is reached earlier, resulting in a sharper decline in photosynthetic productivity over the past two decades. Our findings reveal a shift from temperature to precipitation limitation in the Amazon, underscoring intra-annual asymmetry in vulnerability to intensifying heatwaves and droughts and calling for its explicit integration into management strategies and predictive models.

Predicting heterogeneous and non-linear processes remains a fundamental challenge in Earth sciences. Here, we present an artificial intelligence (AI)-guided framework that iteratively combines predictive modeling with targeted field sampling to rapidly improve environmental predictions. We demonstrate our workflow by predicting oxygen consumption, a key process of stream metabolism, across the contiguous United States (CONUS). Our approach consisted of 18 iterative loops of measurements and models, combining distributed participatory field sampling, lab analysis, automated machine learning (ML) predictions, and error and distinctiveness analyses to autonomously guide the next sampling at optimal site locations. Through our approach, we increased the predictive power of sediment oxygen consumption across CONUS by over fifteenfold between the first and last iteration. Relative to our last sampling iteration, our first sampling missed sites with high rates and underestimated median oxygen consumption rates by 68%. In addition to identifying areas of high oxygen consumption rates, iterations enabled refinement of laboratory and data handling methods, and engagement with a broad community of field researchers. We conclude that AI-guided iterative loops between targeted sampling and predictive modeling are a powerful and efficient approach for improving predictions of heterogeneous environmental processes.

Globally, vast amounts of methane are trapped within subseafloor gas hydrates. Recent evidence suggests that climate- and human-induced perturbations can destabilize gas hydrates and trigger methane release, yet the response of deep-sea ecosystems to these changes remains poorly understood. Here we show multi-year in situ monitoring of seabed ecosystem following methane leakage induced by hydrate exploration activities. Within just two years, benthic microbial and eukaryotic diversity in the affected areas declined significantly, while microbial and macrofaunal abundance increased. Integrated geochemical and omics analyses reveal the rapid successional shift of seabed ecosystem to a novel chemosynthetic system. Aerobic methanotrophs (Methyloprofundus) co-established with unexpectedly fast growing anaerobic methanotrophic archaea (ANME-3), accompanied by a rapid recruitment of opportunistic polychaetes that bioirrigated the seabed to >50 cm depths. The active animal-microbe interactions sustained exceptionally high rates of methane oxidation that utilized diverse electron acceptors. We demonstrate that methane hydrate destabilization can trigger rapid collapse of native seabed ecosystem while driving the formation of an effective methane biofilter consuming this potent greenhouse gas much faster than previously estimated. Understanding seabed ecosystem response and feedback is critical for predicting benthic methane cycling under ongoing global change and for developing sustainable strategies for methane hydrate resource management.

The aquifer in subseafloor igneous basement is a massive, continuous microbial substrate, yet sparingly little is known about life in this habitat. The work to date has focused largely on describing microbial diversity in young basement (<10 Ma) at oceanic spreading regions and ridge flanks, where the basaltic crust is still porous and fluid flow through it is active. While the prevailing belief used to be that fluid flow through older parts of the seafloor was non-existent, recent heat flow models predict that fluid moves through subseafloor basement >65 Ma, and that seamounts can act as mid-plate conduits for fluids into and out of the subsurface aquifer in older crustal settings. Here we test the hypothesis that microbial life exists in subseafloor basement >65Ma using samples collected from the Louisville Seamount Chain via seafloor drilling. Cell biomass was heterogeneous in nature and ranged from below detection to [~]104 cells cm-3. Bacterial 16S rRNA genes from core samples and enrichment incubations are dominated by lineages putatively carrying out hydrocarbon oxidation and nitrogen, sulfur and metal redox processes. Samples from two different seamounts were statistically different, indicating some degree of biogeography. Archaea were not detected via quantitative polymerase chain reaction, indicating they are rare in the Louisville subsurface. Taken together, the data indicate that microbial life is indeed present in subseafloor igneous basement >65 Ma, which significantly expands the range of the subseafloor biosphere where microbial life is known to exist. Impact StatementThe aquifer in subseafloor igneous basement is the largest continuous microbial substrate on Earth, but it is difficult to access and therefore understudied. We here collected samples from the Louisville Seamount Chain using seafloor drilling to determine if microbial life exists in the >65 Ma subseafloor basement made at these seamounts. A low biomass environment dominated by Bacteria potentially capable of using the Fe and S inherent in subseafloor basalt was detected, including Bacteria that were revived in enrichment experiments. This discovery expands the range of seafloor where confirmed microbial life exists and indicates the interior of seamounts is habitable.

Benthic ecosystems are shaped by seafloor structure, yet linking geomorphology and biology across environmental gradients remains challenging. Here, we integrate seafloor imagery, multiscale bathymetry, and predictive modelling to quantify benthic biodiversity and its environmental drivers along the Powell Basin flank of the Antarctic Peninsula. Steep geomorphological landforms (terraces and steep slopes) hosted maximal densities and distinct communities, with significant enrichment of corals, sponges, ophiuroids, and sea pens. The marked congruence of slope across bathymetric resolutions enabled regional upscaling, estimating a standing stock of [~]96 billion individuals across 7,400 km{superscript 2} of the basin flank. Decadal oceanographic models indicate that benthic densities peak in cold bottom water below -0.15 {degrees}C. We identified four biodiversity hotspots ([~]33 km2) with slopes >35{degrees} and depths >1,700 m, with up to threefold higher densities. Hotspots align with the pathway of Weddell Sea Deep Water, where thermal decoupling between bottom and overlying waters indicates dynamic hydrography along steep, biodiverse terrain. Furthermore, contrasting sea-ice cover and stratification regimes suggest distinct cryo-pelagic-benthic coupling around hotspots. The concentration of biodiversity through seafloor geomorphology and ocean circulation bridges Antarctic benthic ecology from habitat to biogeography, with implications for monitoring change and guiding conservation in the warming Weddell Sea.

Environmental DNA (eDNA) metabarcoding has the potential to substantially expand our knowledge of global biodiversity beyond that provided by conventional approaches. However, the degree to which eDNA data provides real ecological insight, rather than primarily reflecting environmental factors that affect eDNA shedding and degradation, remains unclear. Additional uncertainties arise in terms of cost-effectiveness and whether the price is worth any extra biodiversity information that is gleaned. Here, we established a high-resolution, bi-weekly eDNA time-series in Germany across aquatic and riparian habitats to quantify seasonal biodiversity dynamics, to relate eDNA to different potential environmental drivers, and to parametrize cost estimates. Over one year, eDNA metabarcoding detected more than 1,000 species across multiple trophic levels and primarily revealed real, taxon-specific seasonal patterns, in addition to some relationships to water temperature, discharge, and conductivity. Compared to historical records dating back to 1891, year-round eDNA monitoring increased reported species numbers by 2.4-fold for invertebrates, 2.2-fold for mammals, 1.7-fold for diatoms, 1.2-fold for fish and lamprey, and 1.03-fold for birds. Cumulative biodiversity estimates increased strongly with sampling frequency, demonstrating the value of eDNA for high-frequency time-series monitoring. Moreover, eDNA monitoring was highly cost-effective, providing more than twice the biodiversity information of many conventional surveys for one-sixth the cost, enabling scalable, high-resolution freshwater biodiversity assessments.

Primary production in the global oceans fuels multiple ecosystem services including fisheries, and the open-ocean biological carbon sink, which support food security and livelihoods1, and the regulation of atmospheric CO2 levels2 respectively. The spatial distributions of these two services are driven by primary production and it is likely that ecosystem disturbance from fishing impacts both the carbon sink and atmospheric CO2. Yet the extent of these impacts from past, present and future fishing is unknown. Here we show that 23% of global export and 40% of fishing effort are concentrated in zones of intensive overlap representing 7% of the global ocean area. This overlap is particularly evident in the Northeast Atlantic and Northwest Pacific. Small pelagic fish dominate catches in these regions and globally, and their exploitation will reduce faecal pellet carbon sinks and may cause tropic cascades affecting plankton communities important in sinking carbon. There is an urgent need to address how fisheries affect carbon cycling, and for policy objectives to include protecting the carbon sink, particularly in areas where fishing intensity and carbon export and storage are high.

MotivationOceanographic connectivity driven by ocean currents is critical in determining the distribution of marine biodiversity. It mediates the genetic and individual exchange between populations, from structuring dispersal barriers that promote long-term isolation to enabling long-distance dispersal that underpins species expansion and resilience against climate change. Despite its significance, comprehensive estimates of oceanographic connectivity on a global scale remain unavailable, while traditional approaches, often simplistic, fail to capture the complexity of oceanographic factors contributing to population connectivity. This gap hinders a deeper understating of species dispersal ecology, survival, and evolution, ultimately precluding the development of effective conservation strategies aimed at preserving marine biodiversity. To address this challenge, we present a comprehensive dataset of connectivity estimates along the worlds coastlines, known for their rich marine biodiversity. These estimates are derived from a biophysical modelling framework that combines high-resolution ocean current data with graph theory to predict multi-generational stepping-stone connectivity. Alongside, we provide coastalNet, an R package designed to streamline access, analysis, and visualization of connectivity estimates. This tool enhances the utility and application of the data, adhering to the FAIR principles of Findability, Accessibility, Interoperability, and Reusability. The dataset and package set a new benchmark for research in oceanographic connectivity, allowing a better exploration of the complex dynamics of coastal marine ecosystems. Main types of variables containedPairwise connectivity estimates (probability and time) between coastal sites. Spatial location and grainGlobal, equal-area hexagons with 8.45 km edge length. Time period and grainDaily, from 2000 to 2020. Major taxa and level of measurementCoastal marine biodiversity. Software formatA package of functions developed for R software.

Uncovering the drivers that shape biodiversity patterns is critical to understand ecological and evolutionary dynamics. Despite evidence that biodiversity composition is influenced by processes at different spatial scales, little is known about the role of fine-scale oceanographic processes on the structure of marine communities. This is particularly important in biodiversity hotspot regions, where small changes in environmental conditions may lead to substantial changes in species composition. We combined ocean modelling and 12S environmental DNA (eDNA) metabarcoding, targeting teleost and elasmobranch species, to explore if oceanographic processes influenced biogeographic patterns around the biodiverse Galapagos Islands. We first detected significant differences in eDNA-measured community structure across the archipelagos diverse seascape. We found no significant relationship between Lagrangian particle tracking metrics and nektonic biodiversity, and thus developed a novel metric to measure the cumulative seawater flow resistance between pairs of geographic sites. This metric explained a significant proportion of variation in eDNA-measured beta dissimilarity between sites, comparable in influence to important abiotic drivers, such as temperature and geographic distance between sites. Cumulatively, our results indicate that marine communities are particularly sensitive to changes in local current systems, and suggest that fine-scale oceanographic processes may have an underappreciated role in structuring marine communities globally.