Global livestock production represents a primary driver of planetary change, yet its full ecological and public health impacts remain poorly quantified potentially due to a deep-seated data divide. While biodiversity platforms like the Global Biodiversity Information Facility (GBIF) have excelled at aggregating data on wild organisms, crucial data on livestock systems are usually siloed within disparate agricultural and public health sectors. This Forum paper posits that this division is a primary barrier to implementing a true One Health approach, obscuring our understanding of zoonotic diseases and antimicrobial resistance (AMR). We propose a practical solution: a federated data network. This framework leverages modern data science and Application Programming Interfaces (APIs) to link existing databases, rendering large-scale integrated analysis technically feasible. This Forum paper addresses the fragmentation of data regarding livestock's environmental impact. In this Forum paper, I propose a shift from centralised data collection to a federated data network. By utilizing API-based parallel integration and AI-driven harmonisation, I argue that we can achieve real-time, predictive insights while keeping data within its source systems. I argue that historical barriers to integrating heterogeneous data are rapidly diminishing due to advances in AI, which can harmonise formats, extract features and model complex interactions. This enables a system that supports both holistic analysis and targeted filtering, offering a path towards a more comprehensive, evidence-based approach to managing our planet's interconnected agricultural and natural ecosystems.

Riverbed degradation and biodiversity loss downstream of dams are widely recognized; however, the extent to which tributaries with low sand availability can alter these impacts remains unclear. This study investigated longitudinal changes in environmental conditions and benthic macroinvertebrate communities in a dam-regulated river that receives inflow from a sand-poor tributary. Comprehensive surveys of water quality, plankton drift, riverbed substrate, and macroinvertebrates were conducted along the mainstem and the tributary. The results showed that immediately downstream of the dam, macroinvertebrate assemblages were dominated by lentic-associated filter feeders, such as Macrostemum radiatum and Spongillidae, due to increased plankton inputs and coarsened substrates. Downstream, tributary inflow partly altered these dam-associated conditions: dissolved oxygen increased, plankton densities decreased, and riverbed substrate shifted toward finer coarse material, supporting a rise in scraper taxa such as Heptageniidae. In contrast, inorganic case-bearing caddisflies did not respond, consistent with the tributary’s limited supply of coarse sand. The results indicate that even tributaries with low sand resupply may control certain dam-induced environmental changes and contribute to shifts in macroinvertebrate community structure; however, their influence remains constrained for sediment-dependent taxa. Understanding how sediment type shapes tributary effects is essential for managing ecological conditions downstream of dams.

River fragmentation by dams significantly alters downstream biotic communities. Although taxonomic metrics are standard for impact assessments, incorporating functional diversity (FD) indices provides deeper mechanistic insights into ecosystem alterations. Despite most studies focusing on large-scale dams, we here focus on a small-scale dam system with tributary inflow to elucidate how these ubiquitous structures influence downstream ecological organization. We evaluated the impact of Sugo Dam in Hyogo, Japan, on macroinvertebrate communities in winter and summer using taxonomic diversity and FD indices. We found that the dam imposed a persistent environmental filter characterized by substrate coarsening and altered hydraulic conditions, leading to functional homogenization dominated by sessile filter-feeding taxa immediately downstream. With increasing distance from the dam, functional and taxonomic structures exhibited longitudinal functional re-diversification and compositional restructuring. These downstream shifts were associated with attenuation of physical habitat constraints along the main stem, facilitating the occurrence of additional life forms such as grazers and tube-builders and reducing dominance by dam-tolerant taxa. While tributary inflow contributed to localized increases in trait occurrence, functional re-diversification began along the main channel prior to tributary confluence, indicating that longitudinal weakening of physical constraints was the primary driver of community restructuring. Our results demonstrate that integrating functional diversity trajectories with taxonomic patterns improves detection of habitat-mediated ecological reorganization in dam-fragmented rivers, highlighting the importance of substrate heterogeneity and microhabitat complexity in shaping downstream functional structure.

Environmental DNA (eDNA) detection in aquatic systems is influenced by multiple environmental factors that can be broadly classified into physical and biological processes. Physical factors include water flow, turbidity, and ultraviolet radiation, whereas biological factors include microbial activity that promotes DNA degradation. River dynamics, which are often disrupted by flooding and flow events, can affect eDNA detection. The increased flow during floods and sediment drift cause turbidity. The effects of sediment drift on eDNA, including adsorption, degradation, and PCR inhibition, and the effects of flow on eDNA, including dilution, have been previously studied. However, the combined effects of flow and sediments on eDNA detection have not been extensively explored. In the present study, we investigated the influence of flow and sediment on eDNA concentrations in closed-bottle aquariums with zebrafish to distinguish the effects of these physical forces from those of eDNA dilution. Our results revealed that flow affects eDNA concentration not only through dilution, but also through physical destruction, indicating that fast flows can physically degrade eDNA. Additionally, the effects of sediment on eDNA varied with the presence of flow. The eDNA settled in the sediment and could potentially be preserved without flow. However, in the presence of flow, sediment particles caused physical damage to suspended eDNA, thereby accelerating its eDNA degradation. This study represents a first step toward understanding eDNA degradation behavior during floods while considering sediment drift.

Coastal blue-carbon ecosystems, particularly seagrass meadows, play a disproportionate role in global carbon sequestration. However, the spatial distribution of exported particulate organic matter (POM) remains poorly understood at large spatial scales. Satellite remote sensing offers a promising approach for monitoring coastal carbon dynamics, yet most studies have focused on benthic seagrass distribution rather than suspended carbon in the water column. This study evaluated the potential of total suspended matter (TSM) estimated from Global Change Observation Mission-Climate (GCOM-C) observations as a proxy for coastal blue-carbon distribution. Using 250-m gridded data from Sagami Bay and Suruga Bay, Japan, we examined whether TSM reflected POM distribution by testing its relationships with distance from river estuaries and mapped seagrass meadows. TSM showed a significant negative relationship with distance from river estuaries in both bays, consistent with riverine POM inputs. TSM values were also significantly higher within seagrass meadows than in surrounding waters, suggesting that TSM reflects both seagrass-derived organic particles and suspended particles retained within seagrass meadows that may potentially be buried and sequestered. Although TSM integrates both autochthonous and allochthonous material, our results demonstrate that satellite-based TSM provides a feasible, scalable proxy for coastal blue-carbon distribution, supporting future large-scale monitoring and assessment of coastal blue carbon.

Harmful algal blooms (HABs) are an escalating global threat to aquatic ecosystems, reducing biodiversity, degrading water quality, and compromising human health. Climate-driven warming and excessive nutrient inputs are key drivers of HABs in global lakes. However, as nutrient reduction strategies gain traction, the relative contributions of rising water temperatures and nutrient enrichment remain unclear. Here, we compiled a dataset spanning 40 years from 156 lakes worldwide and analyzed the nonlinear response relationship between chlorophyll-a (Chl-a) and water temperature using a combination of empirical mode decomposition (EMD) and a random forest (RF) model. EMD demonstrated strong adaptability in extracting long-term stable signals from non-stationary records, revealing that over 40% of the lakes are eutrophic, with substantial spatial heterogeneity in HAB intensity; mean Chl-a concentrations reached as high as 26 μg L-1 in tropical regions. As warming continues, water temperature emerges as a progressively stronger driver of HABs, surpassing the influences of nutrient availability and stoichiometric balance. Rising water temperatures diminish the reliance of HABs on nutrient availability, while the nitrogen-to-phosphorus ratio consistently explains variation in Chl-a concentrations throughout the warming process. Furthermore, RF-based scenario projections indicate that under current warming and nutrient scenarios, the mean annual Chl-a concentrations of global lakes are projected to rise to 17.7 μg L-1 under RCP 4.5 and 18.4 μg L-1 under RCP 8.5 by the end of the 21st century. These findings highlight the urgent need to incorporate temperature effects into lake HAB management strategies.

Eutrophication-intensified cyanobacterial blooms are increasingly recognized as significant contributors to carbon emissions from shallow lakes, yet the underlying mechanisms remain poorly understood. Here, we combined basin-scale field surveys, satellite-derived floating algae index (FAI), and microcosm incubations to evaluate the effects of cyanobacterial blooms on carbon emissions and sediment carbon loss in seven shallow lakes of the middle and lower Yangtze River Basin. FAI-based analyses showed severe and spatially extensive cyanobacterial blooms, with maximum bloom coverage reaching approximately 68.8% of the lake area in Taihu and nearly complete coverage in Dianshan, while bloom intensity correlated positively with trophic level. Field observations revealed that hypereutrophic lakes with higher total nitrogen (TN), total phosphorus (TP), and organic carbon (OC) concentrations in the overlying water and sediments exhibited strongly elevated CH4 and CO2 fluxes; specifically, CH4 emissions in Taihu (248.6 mu g center dot m(-2)center dot min(-1)) exceeded those in the mesotrophic Lake Caizi (7.1 mu g center dot m(-2)center dot min(-1)) by over an order of magnitude. Furthermore, microcosm experiments demonstrated that cyanobacterial-derived labile carbon enhances the decomposition of macrophyte detritus via co-metabolic-like effect interactions: mixed cyanobacteria-plant treatments resulted in up to approximately 100% and 125% increases in CH4 and CO2 production, respectively, while sediment TOC loss exceeded theoretical expectations. These findings highlight that bloom-driven co-metabolic-like effect is a critical mechanism for amplifying carbon emissions and destabilizing sediment carbon pools in eutrophic lakes, highlighting the necessity of incorporating bloom dynamics and multi-source carbon interactions into regional and global lake carbon budgets.

A long-term study of breeding ecology of gulls has been carried in the area of Lake Chany. Lake Chany is located in the Baraba forest-steppe of the West Siberian Plain, Russia, between the Ob and Irtysh rivers. The Lake is protected by the Ramsar Convention on the Wetlands of International Importance, indicating that the lake is an important site for migrating and breeding birds, including the Common gull Larus canus (Linnaeus, 1758). We provided data on the size and fate of all eggs as well as the size of hatched chicks in Common gull nests from 1993 to 2011. The data can be used to assess how environmental changes caused by human activity, including global warming, affect the reproduction and population dynamics of migratory birds.

Environmental DNA (eDNA) analysis has emerged as a transformative tool for biodiversity assessment and environmental monitoring, offering a non-invasive, cost-effective approach to detecting species and characterizing ecological communities. Despite growing adoption by researchers, regulatory agencies, and industry, the widespread implementation of eDNA methods continues to face challenges, including inconsistent protocols across laboratories and the absence of internationally recognized standards. These barriers have slowed the integration of eDNA into routine monitoring programs and other operational settings, particularly in regulatory contexts. Standardization is widely recognized as an essential prerequisite for building confidence among end users and enabling meaningful comparison of results across studies and jurisdictions. While standards development efforts have begun to emerge at national and regional scales, the lack of international coordination risks producing fragmented or contradictory guidelines that could hinder rather than advance the field. Here, we introduce the International eDNA Standardization Task Force (iESTF; https://iestf.global), an initiative established to facilitate and accelerate the development of inclusive international standards for eDNA-based biodiversity monitoring. The iESTF aims to identify opportunities for new work item proposals within the International Organization for Standardization (ISO) framework, catalog existing standards and best practices, and ensure that standards development is accessible to practitioners in nations historically underrepresented in eDNA research. We outline some key challenges facing eDNA standardization, describe the structure and goals of the iESTF, and present a vision that includes the formation of a truly inclusive international community of practice, the establishment of pipelines for fast-tracking the development of international standards, and support for critical activities such as cross-regional standards testing and validation. The iESTF represents a critical step toward ensuring that eDNA methods achieve their full potential as reliable, globally comparable tools for biodiversity monitoring.

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be “hidden” by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

Aquatic fungi play critical roles in carbon cycling through complex interactions with dissolved organic matter (DOM). However, their community associations with DOM across reservoir ecosystems remain poorly understood. This study investigated the relationships between fungal community structure and chromophoric DOM across Japanese reservoirs based on fungal sequencing and the optical properties of DOM. Fungal α-diversity showed positive correlations with DOM quantitative indicators (absorption coefficients and fluorescence peaks) and quality indicators such as peak M: T (ratio of humic-like to protein-like fluorescence), suggesting that greater DOM quantity and humification were associated with higher fungal α-diversity across reservoirs. Permutational multivariate analysis of variance based on Jaccard dissimilarity revealed that DOM humification indicators were associated with fungal community β-diversity in univariate models; for example, humification degree (peak M: T) explained 2.8

Biological invasion has negative effects on ecological interaction such as competition and predation. The ecological impacts on native communities may also affect two processes that are important in determining community structures, namely, the environmental and spatial processes. Here, we used lake fish species compositions estimated using environmental DNA metabarcoding to investigate the effects of invasive species composition on the native community and on the processes that determine it. The results of PERMANOVA indicated that the native fish assemblage patterns significantly changed along invasive species compositions. Furthermore, it was observed that the diversity of invasive species acted as a potent ecological filter, driving native fish communities towards biological homogenisation. Distance-based Redundancy Analysis revealed that invasive species alter the relationship between ecological communities and their environment. The study suggests invasive species may obscure distinct environmental signals, potentially by having broader environmental tolerances than native species. A comparison of the relative importance of environmental factors and spatial structure in determining species composition between communities, fish species composition in lakes is more strongly influenced by environmental factors than spatial structure, although the predictive power of these factors varies with the presence of invasive species and is most evident in native-only communities. Our results suggest that the need to understand the impacts of invasive species on native species not only through direct effects, but also the complex effects involving the diversity level of invasive species.

Aquatic fungi play an important role in the material cycling, yet the factors structuring the spatial distribution of aquatic fungal communities remain poorly understood. In this study, we investigated fungal community composition across 50 reservoirs in Japan using DNA metabarcoding. Chytridiomycota (chytrids) dominated fungal communities in many reservoirs and constituted a core component of fungal assemblage. Notably, diatom-parasitic taxa were detected in all reservoirs, indicating their ubiquitous occurrence. In contrast, rare and transient components were mainly composed of Dikarya (Ascomycota and Basidiomycota), likely influenced by stochastic processes, such as episodic inputs from terrestrial habitats. Variation partitioning showed that environmental, spatial, and host-related factors each explained only a small proportion of variation in both the total fungal community and chytrids, with spatial effects being slightly stronger for total fungi, whereas environmental and host-related factors contributed relatively more to chytrid communities. Our results indicate reservoir fungal communities are characterized by a ubiquitous chytrid core and substantial unexplained variation reflecting stochastic and within-lake processes.

Despite the popularity of environmental DNA (eDNA) analysis for non-invasive, cost-effective monitoring of aquatic biodiversity, its application for population abundance estimation is in its infancy. One of the uncertainties in eDNA-based abundance estimation surrounds the process of eDNA production: large individuals may produce less eDNA per unit body mass than smaller conspecifics, and there may be an allometric (power-law) relationship between the amount of eDNA released and body mass. Although integrating allometric scaling in eDNA production could refine eDNA-based abundance estimation, this theoretical framework may have a complex relationship with observed eDNA concentrations, especially in natural environments. We conducted a literature search to summarise previous studies that estimated population abundance using a combination of eDNA concentrations and allometric scaling frameworks, and found that allometry improved abundance estimates in only 5 of 12 studies. This did not seem to depend on the type of environment being studied, or the type of eDNA assay that was used. We discuss biological and technical factors that may help to explain the inconsistent allometric relationship between eDNA production and population abundance. We suggest that allometric scaling may be helpful when (i) the target populations exhibit substantial body size variation and (ii) species-specific scaling coefficients are available. However, our review shows that knowledge gaps remain in our understanding of abundance estimates based on eDNA, regardless of whether allometric relationships are factored into analyses.

Marine-derived organic matter forms the foundation of the food web on sandy beaches where primary production is limited. Omnivorous ghost crabs (Ocypode spp.) inhabit sandy beaches and represent highly important consumers within these ecosystems. However, the co-occurrence of numerous ghost crab species indicates potential interspecific differences in resource use. In this study, we investigated the origin of assimilated dietary differences among three sympatric Ocypode species in Japan. To achieve this aim, we measured carbon and nitrogen stable isotope ratios and estimated the contribution of assimilated diet for each species. Carbon and nitrogen stable isotope ratios and Bayesian mixing models indicated that marine-derived resources were the primarily contributor to the assimilated diet of O. ceratophthalma, whereas terrestrial materials substantially contributed to the assimilated diets of O. cordimanus and O. sinensis during sea turtle nesting season (July–October). Conversely, the proportions of terrestrial invertebrates in the assimilated diets of ghost crabs were estimated more during non-nesting season of sea turtle (March–May). Ghost crabs are known as predators of sea turtle eggs, but the estimated assimilated dietary contribution of sea turtle eggs and other potential food resources with similar isotopic signatures was relatively low for all three ghost crab species. This study demonstrates the interspecific differences in the origin of assimilated diet among closely related generalist omnivores in resource-limited environments and the importance of understanding species-specific feeding habits to elucidate flows of organic matter.

We investigated how obligate mutualisms constrain species distributions under climate change, challenging the assumption that biotic interactions are negligible at macro-scales. By integrating host sea anemone distributions into Species Distribution Models for 17 anemonefish species, we found that host availability is a primary determinant of the realised niche, especially for specialists. Under future warming (SSP5-8.5), host immobility creates a biotic constraint, causing fish ranges to lag significantly behind their climatic potential. This mismatch generates over 3.2 million km2 of climatically suitable but ecologically inaccessible ocean. Furthermore, specialist anemonefish species with the narrowest niches face the highest climate velocities while being constrained to the most dispersal-limited hosts. These findings indicate that climate-only assessments underestimate extinction risk. Conservation should shift to a host-first management strategy to prevent the collapse of these mutualisms. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACT Environmental DNA (eDNA) methodology is widely applied in the biomonitoring of organisms, but it requires the target DNA to be detected in a simple, stable, and highly sensitive manner. Detection sensitivity of eDNA measurement becomes particularly critical when monitoring species present at low abundance. In this study, we aimed to improve the detection sensitivity through a method of DNA-extract reconcentration. This approach involves reconcentrating eDNA samples that were originally extracted using the widely adopted DNeasy Blood and Tissue Kit (Qiagen), utilizing the same kit’s reagents, and does not require any additional equipment or reagents. We evaluated the ability of this DNA reconcentration method using field samples including river, lake and costal marine habitats. Evaluation of this DNA reconcentration method showed that when ten conventionally extracted samples were pooled, the DNA concentration increased by approximately sevenfold, as confirmed by DNA quantification and quantitative PCR analyses, demonstrating enhanced detection sensitivity.

Human activities have elevated antibiotic concentrations, such as ciprofloxacin (CIP), in freshwater lakes. While lakes are pivotal to carbon cycling, the effects of increasing antibiotic levels on them remain unclear. Here, we used microcosms with samples from a eutrophic lake, Gehu Lake in China, using six experimental groups (A–F) with initial CIP concentrations of 0, 10, 50, 100, 500, and 1000 µg/L, to assess how CIP influences dissolved organic matter (DOM) transformation during aquatic plant decomposition. Our results showed that increasing CIP concentrations altered plant residue decomposition pathways and microbial-mediated DOM processing by facilitating residue breakdown, transforming DOM into more chemically recalcitrant forms, and suppressing microbial mineralization of DOM. Under high CIP exposure, continuous DOM release was associated with enhanced structural disintegration of plant residues. In the 1000 µg/L treatment, lignin content in residues decreased from 15.52

Marine mammal populations are suspected to have declined over the past century, with the adverse effects of chemical pollutants considered to be one of the major causes. However, field surveys of marine mammal populations are challenging because of technical issues, resulting in limited in situ data and unresolved questions regarding the historical impacts of chemical exposure. Here, we aimed to elucidate the long-term population dynamics of finless porpoise (Neophocaena asiaeorientalis), a sedentary species inhabiting coastal areas. To reconstruct population trends, we analyzed environmental DNA (eDNA) preserved in sediment cores collected from the Beppu Bay, Seto Inland Sea, Japan. eDNA concentrations in the sediment layers were determined using quantitative PCR. Temporal trends showed a distinct increase from the 1940s to the 1950s, followed by rapid decline in the early 1960s and then a recovery around 2000. Further analysis identified a significant negative correlation between the concentrations of sedimentary eDNA (sedDNA) and chemicals such as polychlorinated biphenyls (PCBs) and cadmium. Positive correlations were observed with temperature, prey abundance, and microplastics. Consistent with historical PCB production trends, the PCB concentrations in finless porpoise individuals collected from the Seto Inland Sea during the 1960-1970s were apparently higher than those during the 2000s. These findings suggest that the finless porpoise population in the region experienced a significant decline around 1960 owing to elevated chemical exposure. This study highlights the potential of sedDNA-based approaches to enhance our understanding of anthropogenic disturbances on marine animals over the long term.