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Under unfavourable conditions, clonal plants benefit from physiological integration among ramets, sharing resources and information. Clonal integration can buffer against environmental changes and lets the plant clone work as a 'macro' organism. Molecular signals that regulate this phenomenon are completely unknown in marine plants.Here we present a first comprehensive study providing insights into the metabolic role of different types of ramets (i.e. apical vs. vertical) in the foundation species Posidonia oceanica. Plants were exposed to 80% diminishing irradiance level (LL) in a controlled mesocosm system. Subsequent multiscale variations in whole transcriptome expression, global DNA methylation level, photo‐physiology, morphology and fitness‐related traits, were explored at different exposure times. We tested the hypothesis that vertical shoots (the 'vassals') can provide vital resources to apical shoots (the 'kings') under energy shortage, thus safeguarding the whole clone survival.Whole transcriptome analysis of leaves and shoot‐apical meristems (SAMs) emphasized signatures of molecular integration among ramets, which strongly correlated with higher organization‐level responses. In both shoots types, the exposure to LL resulted in a growth slowdown throughout the experiment, which started from immediate signals in SAMs. In apical shoots, this was linked to an acclimative response, where they were suffering a mild stress condition, while in vertical ones it fell in a more severe stress response. Yet, they suffered from sugar starvation and showed a clear cellular stress response in terms of protein refolding and DNA repair mechanisms. Several epigenetic mechanisms modulated the observed gene‐expression patterns and the cross‐talk between DNA methylation and the cellular energetic status appeared to regulate shoot metabolism under LL.Synthesis. Our results demonstrate a high level of specialization of integrated ramets within seagrass clones and a 'division of labour' under adverse conditions. Vertical shoots appear to do 'most of the job' especially in terms of resource providing, whereas activated functions in apical shoots were restricted to few important processes, according to an 'energy‐saving' strategy. The response of vertical shoots could be seen as a 'sacrificing response' allowing the survival of 'the king' that is key for ensuring propagation and population maintenance, and for the colonization of new environments. [ABSTRACT FROM AUTHOR]

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For clonal plants, the role of sexual reproduction in the maintenance of populations can vary widely. Some species are dependent on repeated seedling recruitment. For other species, interactions between adults and seedlings within existing populations can affect seedling survival and limit sexual reproduction in existing populations. Genetic studies of seagrass populations increasingly suggest sexual reproduction is important for the resilience and stability of their populations, but as of yet little observational data support these findings. Because seagrass populations provide important ecosystem services and are threatened with increasing anthropogenic impacts, understanding their reliance on sexual reproduction is evolutionarily and ecologically important.The goals of this study were to determine (a) whether seedlings of a marine angiosperm, Zostera marina, establish and recruit within existing Z. marina meadows and (b) whether interactions between seedlings and surrounding adult shoots influence the survival of established seedlings. To meet these goals, surveys estimated seedling establishment and tracked seedling survival within multiple populations. Manipulative experiments then tested the impact of neighbouring adult shoots on seedling survival and the overall trajectory of experimental plots with and without sexual reproduction.A 3‐year survey identified established seedlings within Z. marina meadows each year. Additionally, concurrent seed addition experiments indicated seed supply could influence seedling establishment rates. A survey tracking the survival of tagged seedlings, as well as the height and density of surrounding adult shoots, showed adult shoots may negatively impact seedling survival. Experiments then demonstrated that seedlings without neighbouring shoots survived longer than those with neighbouring shoots. Lastly, two transplant garden experiments comparing the survival of plots with and without seeds highlighted that seedling recruitment is likely most important to maintain bottom cover where disturbances generate gaps in the adult population.Synthesis. This study demonstrates that seedlings do establish within existing seagrass meadows, and that some survive to recruit into the adult population. Competition with existing vegetation, however, can be a factor compromising seedling survival. Sexual reproduction may thus most likely occur in, and be most important for, clonal plant populations that experience seasonal disturbance. [ABSTRACT FROM AUTHOR]

Halophyte distributions on saltmarshes are strongly related to elevation in the tidal frame. However, collinearity between elevation, the consequent inundation regime, and sediment waterlogging/redox potential obscures the proximate causes of distribution patterns. We sought to distinguish the effects of elevation per se from those of waterlogging by manipulating microtopography.We experimentally manipulated elevation by ±15 cm at locations that spanned the elevation ranges of three saltmarshes recently reactivated by managed coastal realignment. Experimental plots were initially cleared of any vegetation. Elevation and sediment redox potential were determined for each plot. We planted five perennial species (Armeria maritima, Atriplex portulacoides, Limonium vulgare, Plantago maritima and Triglochin maritima) in half of the plots, recording survival over 4 years, and monitored natural colonization of the other plots.Overall, redox potential increased with elevation. Sediments were more oxidizing in raised plots and more reducing in lowered plots. Redox reductions in lowered plots were in line with those that would be predicted from the overall redox/elevation relationship, but increases in raised plots were greater than predicted from elevation alone.Plant colonization and survival was poorer in lowered plots and, for most species, improved in raised plots. This poorer colonization and survival can, in part, be attributed to the concomitant alterations in redox potential and elevation in the tidal frame, but microtopographic manipulation also had substantial independent effects on plant performance, including on the survival of all planted species and the colonization of Puccinellia maritima, Salicornia europaea agg. and Tripolium pannonicum.Synthesis. Microtopography can have effects on sediment chemistry and plant performance similar in magnitude to those of overall tidal elevation. Understanding how its effects modulate the relationship between tidal elevation, redox and other environmental conditions helps clarify the abiotic factors that fundamentally determine halophyte colonization and survival. These results support the use of topographic manipulation to enhance the diversity of created saltmarshes. [ABSTRACT FROM AUTHOR]

Legacy mining facilities pose significant risks to aquatic resources. From March 30th to April 9th, 2021, 814 million liters of phosphate mining wastewater and marine dredge water from the Piney Point facility were released into lower Tampa Bay (Florida, USA). This resulted in an estimated addition of 186 metric tons of total nitrogen, exceeding typical annual external nitrogen load estimates to lower Tampa Bay in a matter of days. An initial phytoplankton bloom (non-harmful diatoms) was first observed in April. Filamentous cyanobacteria blooms (Dapis spp.) peaked in June, followed by a bloom of the red tide organism Karenia brevis. Reported fish kills tracked K. brevis concentrations, prompting cleanup of over 1600 metric tons of dead fish. Seagrasses had minimal changes over the study period. By comparing these results to baseline environmental monitoring data, we demonstrate adverse water quality changes in response to abnormally high and rapidly delivered nitrogen loads. [Display omitted] • 186 metric tons of total nitrogen from wastewater were added to Tampa Bay. • An initial diatom bloom was observed near the release site. • Filamentous cyanobacteria were observed at high biomass. • Karenia brevis (red tide) was at high concentrations, co-occurring with fish kills. • Seagrasses were unimpacted during the six-month study period. [ABSTRACT FROM AUTHOR]

Correction to: I Nature Communications i https://doi.org/10.1038/s41467-022-28194-y, published online 31 January 2022 The original version of this Article contained an error in Fig. The original article can be found online at https://doi.org/10.1038/s41467-022-28194-y. [Extracted from the article]

Tidal creeks play a vital role in influencing geospatial evolution and marsh ecological communities in coastal landscapes. However, evaluating the geospatial characteristics of numerous creeks across a site and understanding their ecological relationships pose significant challenges due to the labor-intensive nature of manual delineation from imagery. Traditional methods rely on manual annotation in GIS interfaces, which is slow and tedious. This study explores the application of Attention-based Dense U-Net (ADU-Net), a deep learning image segmentation model, for automatically classifying creek pixels in high-resolution (0.5 m) orthorectified aerial imagery in coastal Georgia, USA. We observed that ADU-Net achieved an outstanding F1 score of 0.98 in identifying creek pixels, demonstrating its ability in tidal creek mapping. The study highlights the potential of deep learning models for automated tidal creek mapping, opening avenues for future investigations into the role of creeks in marshes' response to environmental changes. [ABSTRACT FROM AUTHOR]

Coastal ecosystems provide critical storm and flood protection but are rapidly degrading worldwide, making their restoration urgent. We evaluated whether successional facilitation, where pioneers facilitate climax species, could be leveraged to accelerate coastal dune revegetation. A survey spanning 270 km of Southeast U.S. coastline revealed that Panicum amarum (bitter panicum) supported higher plant richness than Uniola paniculata (sea oats) and that sea oat cover was 230% greater on mature dunes than disturbed dunes, suggesting bitter panicum functions as a pioneer and sea oats as a climax species. A reciprocal transplant experiment confirmed this interpretation: bitter panicum stem production and height fell by 37% and >20 cm, respectively, when planted proximate to sea oats versus in isolation, whereas sea oats produced 38% more and >12 cm taller stems when planted proximate to bitter panicum versus in isolation. A second experiment evaluating the density‐dependence of this facilitative interaction revealed that sea oats transplanted into low densities of bitter panicum grew >15% taller than isolated and high‐density treatments. However, within 7 months, wave inundation eliminated over 60% of propagules in both experiments. To explore foredune inundation frequency and its implications for dune revegetation, we applied empirical wave runup models at 101 locations throughout Volusia County, Florida. While disturbance frequency varied seasonally and annually, sites with low dune crests and steep beach slopes experienced frequent inundation (>50 events/year). Given the interactions between geomorphology and vegetation success, we present a decision matrix to guide managers in determining optimal revegetation methods tailored to project goals and site conditions. [ABSTRACT FROM AUTHOR]

Ecosystem restoration can increase the health and resilience of nature and humanity. As a result, the international community is championing habitat restoration as a primary solution to address the dual climate and biodiversity crises. Yet most ecosystem restoration efforts to date have underperformed, failed, or been burdened by high costs that prevent upscaling. To become a primary, scalable conservation strategy, restoration efficiency and success must increase dramatically. Here, we outline how integrating ten foundational ecological theories that have not previously received much attention — from hierarchical facilitation to macroecology — into ecosystem restoration planning and management can markedly enhance restoration success. We propose a simple, systematic approach to determining which theories best align with restoration goals and are most likely to bolster their success. Armed with a century of advances in ecological theory, restoration practitioners will be better positioned to more cost-efficiently and effectively rebuild the world's ecosystems and support the resilience of our natural resources. Silliman and colleagues outline how restoration practitioners can leverage insight from ecological theories to increase the scale, success, and resilience of habitat restorations. [ABSTRACT FROM AUTHOR]

• The process-based modeling of SWAT was extended by a machine learning algorithm. • The machine learning algorithm based multi-variable statistical analysis was performed. • Land cover percentage of forest and source areas are the identified variables. • The identified variables affect water quality with a threshold effect. • The thresholds for forest and source areas percentage are 37.47 % and 20.26 % respectively. By integrating soil and water assessment tool (SWAT) modeling and land use and land cover (LULC) based multi-variable statistical analysis, this study aimed to identify driving factors, potential thresholds, and critical source areas (CSAs) to enhance water quality in southern Alabama and northwest Florida's Choctawhatchee Watershed. The results revealed the significance of forest cover and of the lumped developed areas and cultivated crops ("Source Areas") in influencing water quality. The stepwise linear regression analysis based on self-organizing maps (SOMs) showed that a negative correlation between forest percent cover and total nitrogen (TN), organic nitrogen (ORGN), and organic phosphorus (ORGP), highlighting the importance of forests in reducing nutrient loads. Conversely, Source Area percentage was positively correlated with total phosphorus (TP) loads, indicating the influence of human activities on TP levels. The receiver operating characteristic (ROC) curve analysis determined thresholds for forest percentage and Source Area percentage as 37.47 % and 20.26 %, respectively. These thresholds serve as important reference points for identifying CSAs. The CSAs identified based on these thresholds covered a relatively small portion (28 %) but contributed 47 % of TN and 50 % of TP of the whole watershed. The study underscores the importance of considering both physical process-based modeling and multi-variable statistical analysis for a comprehensive understanding of watershed management, i.e., the identification of CSAs and the associated variables and their tipping points to maintain water quality. [Display omitted] [ABSTRACT FROM AUTHOR]

Mangroves provide critical ecosystems services, contributing an estimated 42 billion US dollars to global fisheries, storing 25.5 million tons of carbon per year, and providing flood protection to over 15 million people annually. Yet, they are increasingly threatened by factors ranging from local resource exploitation to global climate change, with an estimated 35% of mangrove forests lost in the past two decades. These threats are difficult to manage due to the intrinsic characteristics of mangrove systems and their provisioning services, and their transboundary and pan-global nature. Due to their unique intertidal ecological niche, mangroves are often treated as a "common pool resource" within national legal frameworks, making them particularly susceptible to exploitation. Moreover, they form ecological connections through numerous biotic and abiotic processes that cross political boundaries. Because of these qualities a cross-scale nested framework of international, regional, and local coordination is necessary to successfully sustain mangrove ecosystems and their valuable services. Although coordination across the geopolitical spectrum is often cited as a need for effective management of common resources such as mangroves, there has been no formal analysis of mangrove multiscale governance. In this paper we address this gap by providing a comprehensive analysis of interactions between and within international, regional, and local mangrove management regimes and examine the challenges and opportunities such multiscale governance frameworks present. We highlight Costa Rica as a case study to demonstrate the universal relevance and potential of multi-scale governance and explore its downscale potential. Using Elinor Ostrom's principles for self-governance of the commons as our touchstone, we identify where improvements to the status quo could be implemented to increase its effectiveness of the current frameworks to meet the ongoing challenge of managing mangrove-derived resources and services in the face of a changing climate and human needs. • Mangroves cover 75% of tropical coastlines and provide numerous ecosystem services. • Importance of mangroves is widely studied, yet they are being lost at an alarming rate. • Vast extent of mangroves and their connections necessitate multiscale management. • This novel analysis assesses management within and across multiple spatial scales. • Identifying connections is needed to guide a multi-scale governance framework. [ABSTRACT FROM AUTHOR]

We present a novel method for detecting red tide (Karenia brevis) blooms off the west coast of Florida, driven by a neural network classifier that combines remote sensing data with spatiotemporally distributed in situ sample data. The network detects blooms over a 1-km grid, using seven ocean color features from the MODIS-Aqua satellite platform (2002-2021) and in situ sample data collected by the Florida Fish and Wildlife Conservation Commission and its partners. Model performance was demonstrably enhanced by two key innovations: depth normalization of satellite features and encoding of an in situ feature. The satellite features were normalized to adjust for depth-dependent bottom reflection effects in shallow coastal waters. The in situ data were used to engineer a feature that contextualizes recent nearby ground truth of K. brevis concentrations through a K-nearest neighbor spatiotemporal proximity weighting scheme. A rigorous experimental comparison revealed that our model outperforms existing remote detection methods presented in the literature and applied in practice. This classifier has strong potential to be operationalized to support more efficient monitoring and mitigation of future blooms, more accurate communication about their spatial extent and distribution, and a deeper scientific understanding of bloom dynamics, transport, drivers, and impacts in the region. This approach also has the potential to be adapted for the detection of other algal blooms in coastal waters. Integr Environ Assess Manag 2024;20:1432-1446. © 2024 SETAC., (© 2024 SETAC.)

Foundation species facilitate communities, modulate energy flow, and define ecosystems, but their ecological roles after death are frequently overlooked. Here, we reveal the widespread importance of their dead structures as unique, interacting components of ecosystems that are vulnerable to global change. Key metabolic activity, mobility, and morphology traits of foundation species either change or persist after death with important consequences for ecosystem functions, biodiversity, and subsidy dynamics. Dead foundation species frequently mediate ecosystem stability, resilience, and transitions, often through feedbacks, and harnessing their structural and trophic roles can improve restoration outcomes. Enhanced recognition of dead foundation species and their incorporation into habitat monitoring, ecological theory, and ecosystem forecasting can help solve the escalating conservation challenges of the Anthropocene., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

The recovery of top predators is thought to have cascading effects on vegetated ecosystems and their geomorphology 1,2 , but the evidence for this remains correlational and intensely debated 3,4 . Here we combine observational and experimental data to reveal that recolonization of sea otters in a US estuary generates a trophic cascade that facilitates coastal wetland plant biomass and suppresses the erosion of marsh edges-a process that otherwise leads to the severe loss of habitats and ecosystem services 5,6 . Monitoring of the Elkhorn Slough estuary over several decades suggested top-down control in the system, because the erosion of salt marsh edges has generally slowed with increasing sea otter abundance, despite the consistently increasing physical stress in the system (that is, nutrient loading, sea-level rise and tidal scour 7-9 ). Predator-exclusion experiments in five marsh creeks revealed that sea otters suppress the abundance of burrowing crabs, a top-down effect that cascades to both increase marsh edge strength and reduce marsh erosion. Multi-creek surveys comparing marsh creeks pre- and post-sea otter colonization confirmed the presence of an interaction between the keystone sea otter, burrowing crabs and marsh creeks, demonstrating the spatial generality of predator control of ecosystem edge processes: densities of burrowing crabs and edge erosion have declined markedly in creeks that have high levels of sea otter recolonization. These results show that trophic downgrading could be a strong but underappreciated contributor to the loss of coastal wetlands, and suggest that restoring top predators can help to re-establish geomorphic stability., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Ecosystem restoration has traditionally focused on re-establishing vegetation and other foundation species at basal trophic levels, with mixed outcomes. Here, we show that threatened shorebirds could be important to restoring coastal wetland multifunctionality. We carried out surveys and manipulative field experiments in a region along the Yellow Sea affected by the invasive cordgrass Spartina alterniflora. We found that planting native plants alone failed to restore wetland multifunctionality in a field restoration experiment. Shorebird exclusion weakened wetland multifunctionality, whereas mimicking higher predation before shorebird population declines by excluding their key prey - crab grazers - enhanced wetland multifunctionality. The mechanism underlying these effects is a simple trophic cascade, whereby shorebirds control crab grazers that otherwise suppress native vegetation recovery and destabilize sediments (via bioturbation). Our findings suggest that harnessing the top-down effects of shorebirds - through habitat conservation, rewilding, or temporary simulation of consumptive or non-consumptive effects - should be explored as a nature-based solution to restoring the multifunctionality of degraded coastal wetlands., (© 2023. The Author(s).)

Transformers are widely used deep learning architectures. Existing transformers are mostly designed for sequences (texts or time series), images or videos, and graphs. This paper proposes a novel transformer model for massive (up to a million) point samples in continuous space. Such data are ubiquitous in environment sciences (e.g., sensor observations), numerical simulations (e.g., particle-laden flow, astrophysics), and location-based services (e.g., POIs and trajectories). However, designing a transformer for massive spatial points is non-trivial due to several challenges, including implicit long-range and multi-scale dependency on irregular points in continuous space, a non-uniform point distribution, the potential high computational costs of calculating all-pair attention across massive points, and the risks of over-confident predictions due to varying point density. To address these challenges, we propose a new hierarchical spatial transformer model, which includes multi-resolution representation learning within a quad-tree hierarchy and efficient spatial attention via coarse approximation. We also design an uncertainty quantification branch to estimate prediction confidence related to input feature noise and point sparsity. We provide a theoretical analysis of computational time complexity and memory costs. Extensive experiments on both real-world and synthetic datasets show that our method outperforms multiple baselines in prediction accuracy and our model can scale up to one million points on one NVIDIA A100 GPU. The code is available at https://github.com/spatialdatasciencegroup/HST.

Ecosystems shaped by habitat-modifying organisms such as reefs, vegetated coastal systems and peatlands, provide valuable ecosystem services, such as carbon storage and coastal protection. However, they are declining worldwide. Ecosystem restoration is a key tool for mitigating these losses but has proven failure-prone, because ecosystem stability often hinges on self-facilitation generated by emergent traits from habitat modifiers. Emergent traits are not expressed by the single individual, but emerge at the level of an aggregation: a minimum patch-size or density-threshold must be exceeded to generate self-facilitation. Self-facilitation has been successfully harnessed for restoration by clumping transplanted organisms, but requires large amounts of often-limiting and costly donor material. Recent advancements highlight that kickstarting self-facilitation by mimicking emergent traits can similarly increase restoration success. Here, we provide a framework for combining expertise from ecologists, engineers and industrial product designers to transition from trial-and-error to emergent trait design-based, cost-efficient approaches to support large-scale restoration., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

The fate of coastal ecosystems depends on their ability to keep pace with sea-level rise-yet projections of accretion widely ignore effects of engineering fauna. Here, we quantify effects of the mussel, Geukensia demissa, on southeastern US saltmarsh accretion. Multi-season and -tidal stage surveys, in combination with field experiments, reveal that deposition is 2.8-10.7-times greater on mussel aggregations than any other marsh location. Our Delft-3D-BIVALVES model further predicts that mussels drive substantial changes to both the magnitude (±<0.1 cm·yr -1 ) and spatial patterning of accretion at marsh domain scales. We explore the validity of model predictions with a multi-year creekshed mussel manipulation of >200,000 mussels and find that this faunal engineer drives far greater changes to relative marsh accretion rates than predicted (±>0.4 cm·yr -1 ). Thus, we highlight an urgent need for empirical, experimental, and modeling work to resolve the importance of faunal engineers in directly and indirectly modifying the persistence of coastal ecosystems globally., (© 2023. The Author(s).)

Habitat heterogeneity is considered a primary causal driver underpinning patterns of diversity, yet the universal role of heterogeneity in structuring biodiversity is unclear due to a lack of coordinated experiments testing its effects across geographic scales and habitat types. Furthermore, key species interactions that can enhance heterogeneity, such as facilitation cascades of foundation species, have been largely overlooked in general biodiversity models. Here, we performed 22 geographically distributed experiments in different ecosystems and biogeographical regions to assess the extent to which variation in biodiversity is explained by three axes of habitat heterogeneity: the amount of habitat, its morphological complexity, and capacity to provide ecological resources (e.g. food) within and between co-occurring foundation species. We show that positive and additive effects across the three axes of heterogeneity are common, providing a compelling mechanistic insight into the universal importance of habitat heterogeneity in promoting biodiversity via cascades of facilitative interactions. Because many aspects of habitat heterogeneity can be controlled through restoration and management interventions, our findings are directly relevant to biodiversity conservation., (© 2022. The Author(s).)

Ecosystems worldwide depend on habitat-forming foundation species that often facilitate themselves with increasing density and patch size, while also engaging in facultative mutualisms. Anthropogenic global change (e.g., climate change, eutrophication, overharvest, land-use change), however, is causing rapid declines of foundation species-structured ecosystems, often typified by sudden collapse. Although disruption of obligate mutualisms involving foundation species is known to precipitate collapse (e.g., coral bleaching), how facultative mutualisms (i.e., context-dependent, nonbinding reciprocal interactions) affect ecosystem resilience is uncertain. Here, we synthesize recent advancements and combine these with model analyses supported by real-world examples, to propose that facultative mutualisms may pose a double-edged sword for foundation species. We suggest that by amplifying self-facilitative feedbacks by foundation species, facultative mutualisms can increase foundation species' resistance to stress from anthropogenic impact. Simultaneously, however, mutualism dependency can generate or exacerbate bistability, implying a potential for sudden collapse when the mutualism's buffering capacity is exceeded, while recovery requires conditions to improve beyond the initial collapse point (hysteresis). Thus, our work emphasizes the importance of acknowledging facultative mutualisms for conservation and restoration of foundation species-structured ecosystems, but highlights the potential risk of relying on mutualisms in the face of global change. We argue that significant caveats remain regarding the determination of these feedbacks, and suggest empirical manipulation across stress gradients as a way forward to identify related nonlinear responses., Competing Interests: The authors declare no conflict of interest., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)