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.

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.

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.

Earth's biodiversity is distributed unevenly, typically peaking in warm, vegetated, and stable environments. This has frequently been linked to energy availability, which boosts productivity, bolsters populations, and facilitates coexistence. Here, we examine the relationship between energy and biodiversity across coastal oceans using particulate organic matter biogeochemistry and environmental DNA. We reveal that energy quantity (concentrations of carbon, nitrogen, and hydrolyzable amino acids) and salinity, two variables that co-vary with freshwater inflow, jointly predict species richness at regional and global scales. Biodiversity was lowest at sites and locations with high energy inflow and low salinity, suggesting that environmental filtering associated with the osmotic stress induced by freshwater inflow outweighs raw resource availability in governing species richness. Independent of this gradient, however, energy quality (defined via C:N ratios, {delta}C values, and amino acid profiles) was associated with higher biodiversity. Labile, protein-rich, marine-derived resources supported higher biodiversity across all taxa at the regional scale, and a larger number of planktonic consumer taxa at both regional and global scales. High energy quality sites were also enriched in key planktonic groups such as calanoid and cyclopoid copepods, suggesting that these sites act as hotspots of planktonic biodiversity across coastal seascapes. Our findings suggest that few species can directly harness the plentiful resources provided by terrestrial subsidies in coastal oceans because they arrive in low salinity waters. In turn, high-quality food attracts a diverse range of consumers, which may seed the patchy foraging hotspots that characterize open-water food webs. Altered coastal hydrodynamics and biogeochemistry may therefore affect nearshore biodiversity, food webs, and fisheries.

Long-term microbial population dynamics can reveal how ocean microbiomes respond to environmental variation, but resolving within-species change requires suitable genomic references. We integrated 30 PacBio HiFi long-read metagenome-assembled genomes (MAGs) from the northwestern Mediterranean Sea with monthly Illumina metagenomes from neighboring time series spanning 12 and 7 years. Population differentiation varied widely among genomes and often differed in magnitude between sites, while a subset showed increasing differentiation with temporal distance. Genetic diversity and population structure were frequently seasonal, with populations associated with warm or cold waters and others spanning both thermal regimes. Candidate adaptive genes accounted for 1.6-3.0% of coding sequences, and many were detected in both time series. Their pN/pS trajectories included regular seasonal fluctuations consistent with changing strain or ecotype contributions, alongside irregular temporal patterns. These results show that combining long-read MAG references with dense short-read time series can resolve seasonal population structure, site-specific differentiation, and candidate adaptive variation within marine microbial species, providing a framework for tracking contemporary population-genomic change in the ocean.

The mechanisms by which coarse woody debris (CWD) affects soil microbial diversity across different spatial scales and forest disturbance regimes remain poorly understood. This study investigated the impact of CWD from multiple tree species on forest floor bacterial and fungal communities under varying landscape-scale conditions, specifically comparing old-growth forests situated on Phaozems and Retisols with mass-windthrow areas located on loamy Retisols and sandy Podzols. We analyzed both chemical compound and metagenomic profiles of 63 CWD-associated soil samples collected from the Kaluzhskie Zaseki Nature Reserve (European part of Russia). High-throughput Illumina sequencing of the 16S rRNA gene and the ITS region was used to profile both bacterial and fungal communities, respectively. Scale-dependent diversity patterns and taxonomic accumulation were assessed using GLM, NMDS, dbRDA, and iNEXT frameworks. Our findings revealed a profound spatial decoupling in forest floor microbial communities, where a localized reduction in alpha-diversity under CWD drove a sharp increase in landscape-scale gamma-diversity. While standard soil physicochemical properties rigidly dictated baseline matrix richness, CWD operated as a powerful micro-environmental hotspot overriding these constraints. Deadwood inputs filtered out dominant matrix-associated taxa, creating highly specialized micro-refugia characterized by high compositional dispersion. This niche selection was particularly pronounced beneath Quercus logs on Phaozems and Retisols. Furthermore, post-windthrow microbial responses were heavily filtered by wood traits and baseline soil textures. On loamy Retisols within the windthrow mosaic, this breakaway dynamic was highly taxon-specific: while Acer and Fraxinus CWD triggered partitioned, site-specific hotspot dynamics yielding an exceptionally large pool of unique ASVs for bacteria, the distinct enrichment for fungal communities was primarily driven by Ulmus CWD and log-free windthrow areas. Ultimately, iNEXT accumulation profiles confirmed that deadwood does not merely multiply common soil taxa, but enriches the forest landscape by injecting critical beta-level heterogeneity into the soil matrix. These insights emphasize the role of diverse CWD retention in buffering forest microbiomes against large-scale environmental disturbances across heterogeneous soil landscapes.

Stratified benthic deposits offer crucial modern analogs for Precambrian biogeochemical dynamics, yet whether the vertical organization of deep sedimentary columns reflects depositional history, present-day geochemical conditions, or both remains poorly understood, particularly under extreme oligotrophy. Here, we present a depth-resolved exploratory survey of a continuous 34-cm sediment core partitioned into 11 discrete horizons (L1 to L11) from Poza Roja 2, an alkaline, sub-hypersaline pond in the Cuatro Cienegas Basin, Mexico. Integrating physical stratigraphy, organic carbon and nutrient stoichiometry, and 16S rRNA gene metabarcoding, we evaluated down-core microbial community structure alongside acute phosphorus scarcity. Molar C:Po and N:Po ratios exceeded canonical Redfield proportions (106:16:1) in every layer, by up to 48.5-fold and 87.8-fold, respectively, both peaking in layer L4. Unconstrained ordination (PCoA) and hierarchical clustering grouped the layers into three compositional zones: upper (L2-L4), intermediate (L5-L6), and basal (L8-L11), with L1 and L7 occupying transitional positions. Archaea accounted for 31.0% of prokaryotic reads, ranging from 8.3% (L5) to 43.7% (L9), and were dominated by SM1-50 (Thermoplasmatota) and Halobacteriota. The phototrophic heliobacterium Heliorestis peaked in the intermediate zone (47.6% of bacterial reads in L6). Constrained Redundancy Analysis models lacked statistical significance (P >= 0.12), highlighting the exploratory nature of a single core (n = 11). This pilot characterization provides a baseline for understanding deep biogenic archives under severe nutrient limitation.

Mangrove reforestation is expanding across the Caribbean, but restoration success is still judged almost exclusively by tree survival and canopy cover. Whether the sediment microbiome, which governs carbon burial and nutrient cycling, follows the recovery of the vegetation remains largely unknown. We combined 16S rRNA gene metabarcoding (V4, Illumina MiSeq) with CHNS elemental analysis, pH and salinity measurements to compare sediment prokaryotic communities along 0-100 cm profiles in a reference, a reforested (Rhizophora mangle plantings since 2019) and an altered mangrove within the Las Dunas de Las Calderas Natural Monument, Dominican Republic (39 cores pooled into 28 depth-resolved composite samples). Reference sediments contained 2.5-5.5-fold more organic carbon (median 7.5% vs 3.0% in altered and 1.3% in reforested sediments), had higher C/N ratios and were less alkaline (pH 8.2 vs 8.8). Reference communities were more diverse and even, and differed in composition from both disturbed stands (pairwise PERMANOVA, R^2 ~ 0.09, adjusted P = 0.0015), whereas reforested and altered communities were statistically indistinguishable (R^2 = 0.04, P = 0.25). Disturbed sediments were dominated by Cyanobacteriota (~41-45% of reads), which tracked high pH, whereas reference sediments were enriched in Chloroflexota, Thermodesulfobacteriota and Thermoproteota, lineages linked to anaerobic degradation of complex organic matter and sulfate reduction. Depth structured communities by separating surface from subsurface layers, and sediment organic carbon and nitrogen were the only significant constraints in distance-based redundancy analysis. These results indicate that, within a few years of the first plantings (2019), reforestation had not restored the carbon-rich, anaerobic sediment habitat of the reference forest. We propose sediment organic carbon and microbial community structure as complementary indicators for mangrove restoration monitoring in the Caribbean.

Reforestation is a leading natural climate solution, but bulk soil organic carbon (C) often responds slowly, obscuring early belowground change. We tested whether soil aggregates reveal early structural reorganization that affects C retention pathways at a three-year-old experimental reforestation planting established on former pasture in Oregon, USA. We sampled soils at 0-20 and 20-40 cm beneath incense cedar (Calocedrus decurrens; arbuscular mycorrhizal [AM]), black cottonwood (Populus trichocarpa; AM and ectomycorrhizal [EcM]), ponderosa pine (Pinus ponderosa; EcM), and treeless controls. We measured bulk soil C concentration and C:N, aggregate size distribution and mean weight diameter (MWD), fraction-associated C, and, in a subset of surface aggregate fractions, natural-abundance {delta}13C to evaluate soil C pools, physical structure, C distribution, and C processing. After three years, reforestation did not produce significant differences in bulk soil C between planted trees and treeless controls. In surface soil, MWD averaged 36% higher under incense cedar and 58% higher under black cottonwood than under controls, whereas ponderosa pine remained similar to controls. The clearest treatment differences in C distribution occurred in macroaggregates. Incense cedar and black cottonwood had higher large (>2000 m) macroaggregate-associated C than controls, while black cottonwood combined a greater proportion of large macroaggregates with lower C concentrations, indicating that structural development and C accumulation were partly decoupled. Species patterns were broadly consistent with stronger early aggregate responses under AM-compatible species in former-pasture legacy conditions; by contrast, the EcM-associated ponderosa pine remained closer to treeless controls across multiple aggregate measures. Treatment effects weakened with depth and were limited in microaggregates (250-53 m) and silt-and-clay (<53 m) fractions. Smaller aggregate fractions were progressively enriched in {delta}13C, consistent with greater C processing in protected fractions, but treatment-level isotope differences had not yet emerged. Soil aggregates showed species-associated belowground reorganization, revealing how tree identity and former-pasture legacy may shape early soil C organization before consistent differences emerged in bulk soil C. Aggregate measures can complement bulk soil C measurements in restoration monitoring as early indicators of belowground soil C trajectories shaped by tree species identity and land-use legacy.

Mercury biomagnification in Amazonian rivers is usually assessed through fishes, yet contaminants can also move across riparian food webs through multiple energy pathways. We evaluated how total mercury (THg) is structured across the upper Caqueta River basin, a mining-impacted river floodplain system in the Colombian Amazon. Using stable carbon and nitrogen isotopes, trophic guild classification, biomagnification models, and Bayesian mixing models, we integrated basal resources, macroinvertebrates, fishes, and birds to link mercury exposure with food-web architecture. THg increased with trophic enrichment in fishes, birds, and the combined food web, indicating biomagnification across aquatic and aquatic-associated consumers. Reconstructed pathways showed that phytoplankton and detritus support intermediate fish consumers, which in turn connect basal production to carnivore piscivorous fishes and aquatic predatory birds. Avian results suggest that mercury exposure is not restricted to aquatic predators, as hummingbirds showed unexpectedly elevated THg values that may reflect additional riparian or arthropod-mediated pathways. Overall, mercury transfer in the upper Caqueta emerges from the interaction between trophic position and energy-flow structure, highlighting the need to evaluate contamination magnification through integrated aquatic riparian food webs rather than single consumer groups.

Chemosynthetic symbioses underpin animal life at deep-sea hydrothermal vents, encompassing substantial variabilities in symbiont identity, metabolic capacity, and host dependence. Here, we characterise symbioses in two peltospirid snails from Mid-Atlantic Ridge vents, Peltospira gargantua and P. smaragdina, using 3D anatomical reconstruction, stable isotope analyses, fluorescence in situ hybridization, transmission electron microscopy, and metagenomics. Both species hosted abundant intracellular Campylobacterota within bacteriocytes of a hypertrophied oesophageal gland. Their dominant symbionts belonged to genus Sulfurimonas, but the two hosts were associated with distinct symbiont lineages. Symbiont genomes encoded carbon fixation through the rTCA cycle, sulfide oxidation, and Group I Ni-Fe hydrogenases, indicating combined thiotrophic and hydrogenotrophic capacities. Hydrogenase copy number varied across vent fields from one to three copies. The P. gargantua symbiont from the hydrogen-enriched Hydra vent field carried two divergent copies, including one with a truncated catalytic region, potentially reflecting local adaptation to vent geochemistry. Anatomical and isotopic comparisons further revealed contrasting host dependence, with P. gargantua having a proportionally larger oesophageal gland and ventricle coupled with a reduced radula, as well as a greater nitrogen-isotope enrichment between symbiotic and non-symbiotic tissues. The smaller oesophageal gland and larger feeding apparatus of P. smaragdina point to it being mixotrophic. Previously, all known peltospirid symbioses have partnered with Gammaproteobacteria, and we expand the known diversity of peltospirid symbioses. Our findings underscore how closely related hosts can exhibit different degrees of dependence on symbiosis, and that mixotrophic symbiosis may be prevalent in small vent species previously thought to be non-symbiotic.

Coral reefs support an extraordinary diversity and biomass of fishes. However, whether species coexist through fine-scale niche partitioning, and whether this impacts ecosystem functioning, remain unresolved. We combined DNA metabarcoding and stable isotope analysis to reconstruct a high-resolution food web and quantify the trophic niches of 2,060 reef fishes across 261 species. We observed extreme trophic partitioning: species pairs diverged by a median of 93% (DNA metabarcoding) and 86% (stable isotopes), consistently overlapping far less than expected by chance. Further, communities with greater trophic complementarity supported higher standing-stock biomass, particularly at high species richness. Our results confirm limiting similarity and trophic complementarity as the driving forces of coexistence and ecosystem functioning in the ocean's most diverse ecological community.

Dark waters harbour two-thirds of the ocean's bacterial and archaeal cells, yet the energy sources sustaining microbial life at these depths remain poorly understood. Here we integrate hydrographic profiles with metagenomic analyses and ex situ activity measurements to investigate whether carbon monoxide (CO) and molecular hydrogen (H2) are viable energy sources for epipelagic and mesopelagic microbial populations in the Mariana Trench region. Both gases were detected from 5 to 9,371 m, with concentrations generally higher in the photic zone but anomalously high in several deeper waters. Metagenomic analyses indicate a shift from phototrophic towards lithotrophic energy acquisition with depth. Microbial populations encoding CO dehydrogenases increased from 6.1% at 5 m to 45% at 1,000 m, while those encoding uptake hydrogenases were much less abundant, but increased from 0.34% to 0.63%. Ex situ incubations revealed that in situ cell-specific CO oxidation rates declined with depth, whereas corresponding H2 oxidation rates were significantly higher at 1,000 m than at the surface. At 1,000 m, cell-specific H2 oxidation rates were approximately 4,500-fold higher than those of CO. These contrasting trends suggest that CO oxidation is a widespread auxiliary energy-acquisition strategy, whereas H2 oxidation may sustain hydrogenotrophic growth in dark waters. Together, our results suggest H2 and CO are readily available to pelagic microbial populations and are biologically oxidised in the dark zone, supporting microbial energy acquisition and oceanic biogeochemical cycling.

Plant phenology influences biotic interactions and the cycling of water, carbon, and nutrients, ultimately affecting global climate. Accurately quantifying phenological dynamics is therefore essential for ecological forecasting, yet estimates vary widely depending on data sources, smoothing approaches, and date-extraction techniques. For this reason, the selection of an appropriate processing pipeline requires benchmarking under controlled conditions. In this study, we use a Land Surface Model (LSM) to simulate ecosystem dynamics at four temperate forest sites under five lesser studied climate perturbations. The resulting synthetic dataset allows us to control for environmental conditions while comparing commonly used phenological detection methods (relative thresholds at 10%, 20% and 50%, highest rate of change, detection of inflection points in the curvature angle, detection of recovery and senescence points). Amongst tested methods, we find general agreement in responses to climate alterations, where inflection and low thresholds (10%) methods provide the closest match to the model predicted start of season, with a maximum discrepancy of 4 days. Higher thresholds (20%, 50%) are closer to the model predicted end of season, though discrepancies reach up to 10 days. High thresholds and rate-of-change methods also reliably detect the peak of season. We further show that some methods detect phenological responses missed by temperature-only type growing season, supporting the need for more realistic phenological representations in LSMs. Beyond evaluating extraction methods within a common framework, our study expands on the potential of using LSMs as sandboxes for ecological testing rather than solely predictive tools.

(1) Kelp forests support ecologically, commercially, and culturally important species, yet their benthic communities remain difficult to monitor consistently across space and time. Scientific SCUBA surveys provide valuable observations but can be constrained by safety, bottom time, depth, and the spatial extent that divers can efficiently cover, motivating complementary approaches for collecting standardized benthic imagery. (2) We developed and field-tested a standardized, open-source framework for benthic visual-imaging surveys using a small, modular remotely operated vehicle (ROV). Across four cost-scalable hardware configurations, we integrated navigation sensors, custom BlueOS Extensions, and our surftrak contribution to ArduSub, which enables fixed-altitude flight above the seafloor, and developed two open-source desktop applications that streamline field operations (rov_flight_ops) and imagery processing (rov_imagery_processing). We also evaluated power supplies, benthic lighting, camera settings, field protocols, and telemetry-processing workflows over 303 transects conducted on 64 survey days from 2022 to 2026. (3) The ROV operated across soft-sediment and rocky habitats, currents of 0-3 kt, and underwater visibility of 0-10 m. surftrak held the ROV within 0.2 m of its target altitude for 96% of 21 h of survey transects, producing an approximately 1 m^2 standardized image footprint. Sufficient illumination and optimized camera settings yielded high-resolution imagery in visibility below 2 m, while topside power increased endurance and operational flexibility. Combining Doppler velocity log and underwater acoustic positioning data through the vehicle's extended Kalman filter improved navigation and post hoc transect reconstruction. During 2026 surveys, rov_flight_ops and rov_imagery_processing automated flight logging, log retrieval, fault diagnosis, and the sorting, development, and telemetry annotation of survey imagery. Dense kelp canopies nevertheless constrained vehicle operation, and downward-facing imagery provided limited observations of cryptic or obscured organisms. (4) We provide configuration-specific bills of materials, hardware and wiring documentation, software and firmware inventories, camera settings, open-source field and imagery-processing software, step-by-step field protocols, and pre- and post-dive checklists to support replication and adaptation of the framework. Together, these resources provide a field-tested starting point for expanding standardized benthic imaging while complementing diver surveys across kelp forests and other shallow coastal ecosystems.

Forests regulate climate and sustain biodiversity, but their resilience is increasingly threatened by drought-induced hydraulic failure, when xylem water transport is impaired by embolism. A critical but poorly constrained determinant of this risk largely due to limited observations of deep root water uptake is the amount of root-accessible (sub)soil water storage (SR), which governs land-atmosphere exchanges during prolonged dry periods. While ecohydrological theory has long suggested a balance between soil water storage in the rooting zone, vegetation growth and drought tolerance, this concept has not yet been integrated into predictive models of hydraulic failure. Here we propose a novel, process-based inversion framework that integrates ecohydrological optimality theory with principles of plant hydraulic to infer SR. Using the SurEau plant hydraulic model, we estimate the SR value that balances the costs of soil exploration with the avoidance of drought-induced hydraulic damage. Applied first to a well-instrumented Mediterranean Quercus ilex forest, the inferred SR closely matched independent neutron probe and eddy covariance measurements and accurately reproduced observed drought responses, including leaf water potential and sap flow dynamics. We then scaled the approach across European forests remotely-sensed data, to assess spatially explicit SR estimates and associated hydraulic failure risk. Across more than 20 species and sites, inferred SR and drought stress metrics aligned with field observations and outperformed estimates based on conventional soil databases or remote-sensing-only approaches. By linking plant physiology and ecohydrological theory within a scalable inversion framework, this approach improves predictions of forest drought risk under climate change.

Understanding the consequences of global change for our ecosystems requires reliable, accurate, and scalable tools for detecting ecological change. To this end, recent efforts have focused on scaling up the quantification of demographic processes from individual organisms (the fundamental ecological unit) to the larger spatial scales they inhabit to yield more precise and informative estimations of ecological change, especially in response to disturbance. Here, we describe a transferable workflow that combines robust underwater photogrammetry techniques with machine-learning-assisted image analysis to quantify demographic changes in coral colonies (growth, stasis, partial mortality, and complete mortality) through time on the reef landscape. We then demonstrate several analytical applications of this workflow that can be broadly applied to sessile and/or clonal organisms in other ecosystems. First, we tracked the fates of 3,162 coral colonies through a marine heatwave that caused substantial mortality. Second, our approach enabled detection of size- and taxon-dependent patterns in demographic changes from before to after the heatwave. Finally, for a subset (425) of these colonies, we further demonstrated how our method can be used to track fates across multiple years, including a year of change before and after the heatwave took place, revealing nuanced patterns of survival and mortality, as well as changes in size structure that occurred before and after the disturbance. Our workflow offers an important advance for increasing the accuracy of change detection on coral reefs and other ecosystems by linking demographic changes in individual organisms with spatially extensive image-based surveys through time.