Salt Marsh Research Articles

The effect of artificial light at night on settlement patterns of a salt marshes crab

ABSTRACT Quantitative estimation and spatial mapping of aboveground biomass (AGB) for salt marsh vegetation are crucial for modeling biogeochemical cycles and assessing wetland carbon stocks. Remote sensing offers a noninvasive method for monitoring vegetation traits over large areas. However, a single technique often cannot simultaneously capture both spectral information and the vertical structure of vegetation, greatly hindering its capabilities in classifying and estimating AGB of salt marsh vegetation. This work introduces a machine learning and heterogeneous data-based approach for AGB estimation by integrating passive multispectral two-dimensional imagery and active light detection and ranging (LiDAR) three-dimensional point clouds acquired from a drone platform. Vegetation indices along with texture features are extracted from multispectral imagery, whereas intensity values and height attributes are derived from LiDAR data. Four machine learning methods, namely, extreme gradient boosting (XGBoost), random forest (RF), support vector machine (SVM), and light gradient boosting machine (LightGBM), are employed to classify vegetation and estimate AGB through the strategic utilization of a carefully derived multispectral-LiDAR feature set. A comprehensive case study of a coastal salt marsh in Chongming Island, China, reveals that (1) No noticeable discrepancies are found for different machine learning models in AGB estimation, with XGBoost achieving the highest accuracy (R 2 = 0.9207, MAE = 0.2835 kg/m2, RMSE = 0.3229 kg/m2); (2) Feature types and sensors considerably affect AGB estimation accuracy, with height and texture features having greater influence than intensity features and vegetation indices, and LiDAR outperforms multispectral data; and (3) AGB varies remarkably among species and environments, with Spartina alterniflora being more sensitive to changes in soil moisture and nutrients, while Phragmites australis maintains higher AGB even under unfavorable conditions. The proposed approach offers an alternative and effective strategy for AGB estimation and shows strong potential in quantitatively characterizing the ecological processes of salt marsh vegetation.

Predicting climate change impacts on Suaeda japonica distribution in East Asian salt marshes using ensemble modeling.

Rhizosphere properties in salt marshes are shaped by both soil genetic horizons and halophyte species

Shipbreaking-derived metal contamination in coastal wetlands: Risk and source assessment in northern Bay of Bengal, Bangladesh.

Synergistic effects of elevation loss and environmental extremes trigger salt marsh die-off in the Yangtze Estuary

Wetlands, among the most productive ecosystems on Earth, shelter a diversity of species and help maintain ecological balance. However, they are witnessing growing anthropogenic and climatic threats, which underscores the need for regular and long-term monitoring. This study presents a systematic review of 121 peer-reviewed articles published between January 2015 and 30 April 2025 that applied machine learning (ML) and deep learning (DL) for wetland mapping and bird-habitat monitoring. Despite rising interest, applications remain fragmented, especially for avian habitats; only 39 studies considered birds, and fewer explicitly framed wetlands as bird habitats. Following PRISMA 2020 and the SPIDER framework, we compare data sources, classification methods, validation practices, geographic focus, and wetland types. ML is predominant overall, with random forest the most common baseline, while DL (e.g., U-Net and Transformer variants) is underused relative to its broader land cover adoption. Where reported, DL shows a modest but consistent accuracy over ML for complex wetland mapping; this accuracy improves when fusing synthetic aperture radar (SAR) and optical data. Validation still relies mainly on overall accuracy (OA) and Kappa coefficient (κ), with limited class-wise metrics. Salt marshes and mangroves dominate thematically, and China geographically, whereas peatlands, urban marshes, tundra, and many regions (e.g., Africa and South America) remain underrepresented. Multi-source fusion is beneficial yet not routine; The combination of unmanned aerial vehicles (UAVs) and DL is promising for fine-scale avian micro-habitats but constrained by disturbance and labeling costs. We then conclude with actionable recommendations to enable more robust and scalable monitoring. This review can be considered as the first comparative synthesis of ML/DL methods applied to wetland mapping and bird-habitat monitoring, and highlights the need for more diverse, transferable, and ecologically/socially integrated AI applications in wetland and bird-habitat monitoring.

Salinity is a major abiotic stress limiting plant productivity and threatening the integrity of saline ecosystems. The annual halophyte Spergularia marina plays a key ecological role in early successional stages of coastal and inland salt marshes due to its rapid colonization ability, trampling resilience, and tolerance to fluctuating salinity. However, its developmental responses to salinity remain poorly understood. This study evaluated the stage-specific physiological and biochemical responses of S. marina to NaCl stress (0-400 mM), revealing a biphasic tolerance pattern. Germination and early seedling growth were highly sensitive to salinity, while mature plants showed enhanced performance at 100 mM NaCl, including increased biomass, photosynthetic pigment content, osmolyte accumulation, and antioxidant enzyme activity. These adaptive responses minimize oxidative stress, as indicated by lower hydrogen peroxide and malondialdehyde levels. In contrast, concentrations above 150 mM NaCl led to pigment degradation, reduced antioxidant capacity, and growth inhibition. Multivariate analysis confirmed a physiological threshold near 100 mM NaCl (≈ 10 dS·m⁻¹), marking the point of maximal stress resilience. These findings highlight the potential of S. marina for restoring moderately salinized habitats, where its stage-specific plasticity, osmotic adjustment, and redox homeostasis contribute to ecosystem recovery under increasing environmental stress.

Magleholm was excavated in 1978, 1983 and 1984 under direction of E.B. Petersen as part of the Vedbæk project. This paper aims to provide a paleoenvironmental reconstruction of the site, based on analysis of molluscs and botanical macroremains from 16 samples, covering 80 cm of a profile from a trench excavated in 1984. The samples primarily reflect the environment at the time of the Mesolithic Ertebølle culture while few samples in the upper part of the profile reflect the environment during the Early Neolithic Funnel Beaker Culture. The bottom of the profile consists of practically sterile sand. The major part of the profile, consisting of gyttja poor in plant and mollusc taxa, reflects the environment of a brackish lagoon. The uppermost three samples, at least partially corresponding with the Neolithic, show a reduction of the salinity, resulting in a more diverse combination of brackish water and freshwater taxa. Most taxa in the upper samples represent taxa of shallow open water, salt marshes and border zones along freshwater bodies while some plant taxa represent vegetation of dryland terrain. None of the seeds and fruits in the profile were carbonised.

Abstract Calcareous red algae (CRA) are key ecosystem engineers in marine environments, shaping reef architecture and sustaining biodiversity. Through calcification, they produce approximately 1.6 × 10⁹ tonnes of CaCO₃ annually, driving long-term carbon storage and contributing to global carbon cycling at rates comparable to mangroves, salt marshes, and seagrass meadows. This review presents a comprehensive synthesis of current knowledge on calcareous red algae (CRA), including their evolving taxonomic classification based on the morphology, life cycles, reproduction and molecular phylogenetic markers. We also describe the algal habitat and ecosystem dynamics, including responses to abiotic factors, such as light intensity, temperature, and depth (> 270 m). This review elaborates on the cellular and biochemical mechanisms underlying the intricate CRA calcification process and discuss abiotic conditions affecting CRA growth to guide process-centered cultivation optimization. In addition, the impact of climate change on these organisms is explored, highlighting documented reductions in calcification under ocean acidification and warming, and the need for conservation and sustainable cultivation. Despite their ecological importance, exploratory economic potential of CRA remains underreported as compared to seaweed macroalgae. To that end, we provide an outlook on potential economic application in emerging fields, such as construction biotechnology and biomaterials production, linked to biogenic carbon sequestration. This review offers comprehensive and up–to–date information to researchers, industry experts, as well as policy makers, and outlines research priorities requiring interdisciplinary collaboration to fully realize the ecological and biotechnological value of CRA.

Vegetated intertidal ecosystems, such as seagrass meadows, salt marshes, and macroalgal beds, are vital for biodiversity, coastal protection, and climate regulation; however, they remain highly vulnerable to anthropogenic and climate-induced stressors. This study aims to assess interannual changes in intertidal vegetation cover along the Portuguese mainland coast from 2015 to 2024 using Sentinel-2 satellite imagery calibrated with high-resolution multispectral unoccupied aerial vehicle (UAV) data, to determine the most accurate index for mapping intertidal vegetation. Among the 16 indices tested, the Atmospherically Resilient Vegetation Index (ARVI) showed the highest predictive performance. Based on a model relating intertidal vegetation cover to this index, an ARVI value greater than or equal to 0.214 was established to estimate the area covered with intertidal vegetation. Applying this threshold to time-series data revealed considerable spatial and temporal variability in vegetation cover, with estuarine systems such as the Ria de Aveiro and the Ria Formosa showing the greatest extents and marked fluctuations. At the national level, no consistent overall trend was identified for the study period. Despite limitations related to satellite image resolution and single-site validation, the results demonstrate the feasibility and utility of combining UAV data and satellite indices for long-term, large-scale monitoring of intertidal vegetation.

Salt marshes are habitats in the upper coastal intertidal zone between land and open salt-water or brackish water regularly flooded by tides. Consequently, various environmental factors restrict their biodiversity and productivity. They are of concern due to global change as they are highly vulnerable to the predicted sea-level rise. Numerous studies have investigated the fungal assemblages from salt marshes of various biomes worldwide; however, the microfungi diversity from Campos del Tuyú National Park (Argentina) salt marshes has not been previously studied. Therefore, we assessed the fungal assemblages from an alkaline-sodic salt marsh in this reserve. Soil samples were collected from three sites in summer, autumn, winter, and spring during two consecutive years and processed with two culture-dependent methodologies. Soil factors such as ion charge, electrical conductivity, and texture differed between sites. We recovered 87 fungal taxa. No significant differences were observed between seasons. The soil´s richness of active microfungi was low, possibly conditioned by soil texture and organic matter. Our study provides a preliminary basis for future research on the impact of climate change on the ecology of microfungi in an alkaline-sodic marsh of a reserve with biogeographical, environmental, cultural, and historical value.

This article presents the results of studies aimed at identifying the formation features and assessing the drought- and salt-stress-resistant Camphorosma lessingii Litv. specimens. Camphorosma lessingii is a semi-shrub with a height of up to 55 cm from the Chenopodiaceae family. The range covers various areas of the Central Asia and Eastern Europe arid zones, where it grows on sandy, clay, and gravelly soils along the margins of salt marshes, and has a long growing season (240–255 days). Camphorosma lessingii is an ecologically hypergaloxerophyte, characterized by extremely high resistance to environmental conditions of abiotic stress — air and soil drought, heat, and dry weather. It begins to grow in early April, blooms in August, and fruit formation occurs at the end of October. Camphorosma lessingii is characterized by highly competitive resistance in mixed crops with Kochia prostrata and Artemisia lercheana. Camphorosma lessingii is highly nutritious and is well eaten by sheep in summer and autumn. In the fruiting phase, the leaves contain 18.4% crude protein, 10.2% crude fat, and 1.05 fodder units in 1 kg of dry matter, and fruits, re-spectively, 42.6% and 18.0%. Wild populations are characterized by a high degree of biodiversity. We have studied 26 specimens of various ecological and geographical origins. Based on three years of research, spicemens resistant to abiotic environmental factors have been identified, characterized by xerothermal and salt resistance. These spicemens are supposed to be used as a promising source material for breeding programs.

The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.

Soil microbial communities play a pivotal role in salt marsh ecosystem functioning, driving processes such as organic matter decomposition and greenhouse gas cycling. Despite their importance, it remains unclear how climate warming will affect the diversity and activity of salt marsh soil microbial communities, limiting our ability to predict the fate of the vast stores of soil organic carbon in these so-called blue carbon ecosystems. Here, we leveraged the Marsh Ecosystem Response to Increased Temperature (MERIT) experiment to investigate the effects of sustained warming on the structure and function of the putatively active microbial community, as assessed by rRNA transcripts, alongside measurements of exo-enzymatic activities involved in carbon and nitrogen acquisition. Our results reveal that, after 5 years of experimental warming by +1.5°C and +3.0°C, the overall structure of the active microbial community remains remarkably stable, suggesting a high degree of resilience to elevated temperatures in this dynamic environment. However, warming selectively promoted drought-tolerant phyla, particularly Actinobacteriota and Firmicutes, which are known for their ability to degrade complex organic compounds and withstand desiccation. These findings suggest that while the active microbial community is broadly resistant to warming, subtle compositional shifts may enhance decomposition of recalcitrant soil carbon.

Spatial variation of methane emissions and methane-cycling communities in a coastal salt marsh.

Abstract. Salt marshes are blue carbon (C) ecosystems characterized by intense atmospheric CO2 uptake and C sequestration but also by organic and inorganic C exports through the tide. However, uncertainties about the main biotic factors controlling these vertical and horizontal C fluxes imply studying terrestrial and aquatic metabolisms simultaneously at small timescales (diurnal and tidal) to distinguish their contributions to net ecosystem CO2 exchange (NEE). In a temperate salt marsh, four sampling 24 h cycles were performed to measure all water C biogeochemical parameters (including CO2 partial pressures, pCO2), nutrients, and aquatic metabolism simultaneously to NEE from high tide during marsh immersion (imported coastal waters influenced by the continental shelf) to low tide during marsh emersion (exported channel waters influenced by the marsh drainage). At high tide, water CO2 oversaturation (water pCO2 > air pCO2) due to marsh aquatic heterotrophy and CO2-concentrated water inputs from the coastal end-member induced water–air CO2 emissions during marsh immersion. At low tide, water pCO2 in the channel were also mainly controlled by the marsh aquatic metabolism, inducing a water CO2 oversaturation in winter due to dominant heterotrophy and a water CO2 undersaturation in spring and summer due to dominant autotrophy. In winter, the greatest increases in dissolved inorganic carbon (DIC; from 2354 to 3963 µmol kg−1), total alkalinity (TA; from 2508 to 4016 µmol kg−1) and dissolved inorganic nitrogen (DIN; from 27.7 to 68.4 µM) were measured simultaneously during low tide at night, probably due to intense aerobic/anaerobic microbial respiration of organic matter in channel waters and/or sediments resulting in the greatest water pCO2 increase (from 533 to 1461 ppmv). On the contrary, in spring and summer, large water pCO2 decreases (down to 83 ppmv) and dissolved organic carbon (DOC) increases (up to 1040 µM) from high to low tide could be related to intense autochthonous and allochthonous marsh primary production, including benthic microalgae, phytoplankton and macroalgae. This study suggests that the horizontal exchanges of coastal waters with the salt marsh significantly modify water C dynamics and associated water CO2 sink/source state in the channel due to an intense marsh metabolism (production and respiration). At the daily scale, plant and phytoplankton metabolism rates played a major and a minor role, respectively, in the marsh CO2 sink measured by atmospheric eddy covariance at the ecosystem scale (NEE), even during immersion where emerged plants located on the highest marsh levels can maintain a low CO2 uptake, despite aquatic heterotrophy and associated water–air CO2 emissions.

Fungi are key drivers of biogeochemical processes, yet marine fungi remain understudied and under-characterized due to primer biases and database gaps. In this study, we conducted a metabarcoding survey targeting the small and large subunit rRNA genes and the internal transcribed spacer region of fungi (18S, 28S, and ITS2) in the sediment and surface water of salt and brackish marshes in the North Inlet-Winyah Bay estuarine system (Georgetown, South Carolina, USA). The universal 18S/16S primer set (515F-Y and 926R) identified few fungal taxa. The ITS2 primer set (ITS3mix and ITS4) revealed high diversity among Dikarya but failed to capture the full extent of early diverging fungi (EDF). In contrast, the 28S primer set (LR0R and LF402) excelled at identifying EDF lineages, including Chytridiomycota, Mucoromycota, Zoopagomycota, and Blastocladiomycota, many of which dominated the brackish marsh sampling site but were less prevalent in the salt marsh sampling sites. Over half of the fungal OTUs identified by the 28S primer set were from EDF lineages. Copy-normalized 28S qPCR showed that EDF were more abundant in brackish sediments than in the salt marsh. Several putative denitrifying fungi, primarily species from Trichoderma and Purpureocillium, were also detected, suggesting overlooked functional guilds that may contribute to estuarine nitrogen cycling. A FUNGuild analysis found that most lineages were saprotrophic. Overall, our findings show that EDF are key contributors to community differences across salinity gradients and may play more important functional roles in coastal biogeochemistry than is currently understood. The 28S primer set is ideal for marine fungal metabarcoding because it provides comprehensive taxonomic coverage and enables phylogenetic analysis.

Blue carbon storage variability in a hyper-arid evaporitic environment: A comparative study of inland and coastal sabkhas ecosystems

Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.