A Review of Remote Sensing of Submerged Aquatic Vegetation for Non-Specialists

Resource Characteristics of Common Reed (Phragmites australis) in the Syr Darya Delta, Kazakhstan, by Means of Remote Sensing and Random Forest

Reed beds, often referred to as dense, nearly monotonous extensive stands of common reed (Phragmites australis), are the most productive vegetation form of inland waters in Central Asia and exhibit great potential for biomass production in such a dryland setting. With its vast delta regions, Kazakhstan has the most extensive reed stands globally, providing a valuable case for studying the potential of reed beds for the bioeconomy. However, accurate and up-to-date figures on available reed biomass remain poorly documented due to data inadequacies in national statistics and challenges in measuring and monitoring it over large and remote areas. To address this gap in knowledge, in this study, the biomass resource characteristics of common reed were estimated for one of the significant reed bed areas of Kazakhstan, the Syr Darya Delta, using ground-truth field-sampled data as the dependent variable and high-resolution Sentinel-2 spectral bands and computed spectral indices as independent variables in multiple Random Forest (RF) regression models. An analysis of the spatially detailed yield map obtained for Phragmites australis-dominated wetlands revealed an area of 58,935 ha under dense non-submerged and submerged reed beds (with a standing biomass of >10.5 t ha-1) and an estimated 1,240,789 tons of reed biomass resources within the Syr Darya Delta wetlands. Our findings indicate that submerged dense reed exhibited the highest biomass at 28.21 t ha-1, followed by dense non-submerged reed at 15.24 t ha-1 and open reed at 4.36 t ha-1. The RF regression models demonstrated robust performance during both calibration and validation phases, as evaluated by statistical accuracy metrics using ten-fold cross-validation. Out of the 48 RF models developed, those utilizing the Normalized Difference Vegetation Index (NDVI) and Normalized Difference Water Index (NDWI) as key predictors yielded the best standing reed biomass estimation results, achieving a predictive accuracy of R2 = 0.93, Root Mean Square Error (RMSE) = 2.74 t ha-1 during the calibration, and R2 = 0.83, RMSE = 3.71 t ha-1 in the validation, respectively. This study highlights the considerable biomass potential of reed in the region's wetlands and demonstrates the effectiveness of the RF regression modeling and high-resolution Sentinel-2 data for mapping and quantifying above-ground and above-water biomass of Phragmites australis-dominated wetlands over a large extent. The results provide critical insights for managing and conserving wetland ecosystems and facilitate the sustainable use of Phragmites australis resources in the region.

AqUavplant Dataset: A High-Resolution Aquatic Plant Classification and Segmentation Image Dataset Using UAV

Aquatic vegetation species are declining gradually, posing a threat to the stability of aquatic ecosystems. The decline can be controlled with proper monitoring and mapping of the species for effective conservation and management. The Unmanned Ariel Vehicle (UAV) aka Drone can be deployed to comprehensively capture large area of water bodies for effective mapping and monitoring. This study developed the AqUavplant dataset consisting of 197 high resolution (3840px  × 2160px, 4K) images of 31 aquatic plant species collected from nine different sites in Bangladesh. The DJI Mavic 3 Pro triple-camera professional drone is used with a ground sampling distance (GSD) value of 0.04-0.05 cm/px for optimal image collection without losing detail. The dataset is complemented with binary and multiclass semantic segmentation mask to facilitate ML based model development for automatic plant mapping. The dataset can be used to detect the diversity of indigenous and invasive species, monitor plant growth and diseases, measure the growth ratio to preserve biodiversity, and prevent extinction.

Mapping global lake aquatic vegetation dynamics using 10-m resolution satellite observations

Aquatic vegetation is crucial for improving water quality, supporting fisheries and preserving biodiversity in lakes. Monitoring the spatiotemporal dynamics of aquatic vegetation is indispensable for the assessment and protection of lake ecosystems. Nevertheless, a comprehensive global assessment of lacustrine aquatic vegetation is lacking. This study introduces an automatic identification algorithm (with a total accuracy of 94.4%) for Sentinel-2 MSI, enabling the first-ever global mapping of aquatic vegetation distribution in 1.4 million lakes using 14.8 million images from 2019 to 2022. Results show that aquatic vegetation occurred in 81,116 lakes across six continents over the past four years, covering a cumulative maximum aquatic vegetation area (MVA) of 16,111.8 km2. The global median aquatic vegetation occurrence (VO, in %) is 3.0%, with notable higher values observed in South America (7.4%) and Africa (4.1%) compared with Asia (2.7%) and North America (2.4%). High VO is also observed in lakes near major rivers such as the Yangtze, Ob, and Paraná Rivers. Integrating historical data with our calculated MVA, the aquatic vegetation changes in 170 lakes worldwide were analyzed. It shows that 72.4% (123/170) of lakes experienced a decline in aquatic vegetation from the early 1980s to 2022, encompassing both submerged and overall aquatic vegetation. The most substantial decrease is observed in Asia and Africa. Our findings suggest that, beyond lake algal blooms and temperature, the physical characteristics of the lakes and their surrounding environments could also influence aquatic vegetation distribution. Our research provides valuable information for the conservation and restoration of lacustrine aquatic vegetation.

Bioinspired Control Architecture for Adaptive and Resilient Navigation of Unmanned Underwater Vehicle in Monitoring Missions of Submerged Aquatic Vegetation Meadows

Submerged aquatic vegetation plays a fundamental role as a habitat for the biodiversity of marine species. To carry out the research and monitoring of submerged aquatic vegetation more efficiently and accurately, it is important to use advanced technologies such as underwater robots. However, when conducting underwater missions to capture photographs and videos near submerged aquatic vegetation meadows, algae can become entangled in the propellers and cause vehicle failure. In this context, a neurobiologically inspired control architecture is proposed for the control of unmanned underwater vehicles with redundant thrusters. The proposed control architecture learns to control the underwater robot in a non-stationary environment and combines the associative learning method and vector associative map learning to generate transformations between the spatial and velocity coordinates in the robot actuator. The experimental results obtained show that the proposed control architecture exhibits notable resilience capabilities while maintaining its operation in the face of thruster failures. In the discussion of the results obtained, the importance of the proposed control architecture is highlighted in the context of the monitoring and conservation of underwater vegetation meadows. Its resilience, robustness, and adaptability capabilities make it an effective tool to face challenges and meet mission objectives in such critical environments.

A novel strategy for estimating biomass of submerged aquatic vegetation in lake integrating UAV and Sentinel data

Submerged aquatic vegetation (SAV) plays a fundamental ecological role in mediating carbon cycling within lakes, and its biomass is essential to assess the carbon sequestration potential of lake ecosystems. Remote sensing (RS) offers a powerful tool for large-scale SAV biomass retrieval. Given the underwater location of SAV, the spectral signal in RS data often exhibits weakness, capturing primarily horizontal structure rather than volumetric information crucial for biomass assessment. Fortunately, easily-measured SAV coverage can serve as an intermediary variable for difficultly-quantified SAV biomass inversion. Nevertheless, obtaining enough SAV coverage samples matching satellite image pixels for robust model development remains problematic. To overcome this challenge, we employed a UAV to acquire high-precision data, thereby replacing manual SAV coverage sample collection. In this study, we proposed an innovative strategy integrating unmanned aerial vehicle (UAV) and satellite data to invert large-scale SAV coverage, and subsequently estimate the biomass of the dominant SAV population (Potamogeton pectinatus) in Ulansuhai Lake. Firstly, a coverage-biomass model (R2 = 0.93, RMSE = 0.8 kg/m2) depicting the relationship between SAV coverage and biomass was developed. Secondly, in a designed experimental area, a high-precision multispectral image was captured by a UAV. Based on the Normalized Difference Water Index (NDWI), the UAV-based image was classified into non-vegetated and vegetated areas, thereby generating an SAV distribution map. Leveraging spatial correspondence between satellite pixels and the UAV-based SAV distribution map, the proportion of SAV within each satellite pixel, referred to as SAV coverage, was computed, and a coverage sample set matched with satellite pixels was obtained. Subsequently, based on the sample set, a satellite-scale SAV coverage estimation model (R2 = 0.78, RMSE = 14.05 %) was constructed with features from Sentinel-1 and Sentinel-2 data by XGBoost algorithm. Finally, integrating the coverage-biomass model with the obtained coverage inversion results, fresh biomass of SAV in Ulansuhai Lake was successfully estimated to be approximately 574,600 tons.

Seaweed Growth Monitoring with a Low-Cost Vision-Based System

In this paper, we introduce a method for automated seaweed growth monitoring by combining a low-cost RGB and stereo vision camera. While current vision-based seaweed growth monitoring techniques focus on laboratory measurements or above-ground seaweed, we investigate the feasibility of the underwater imaging of a vertical seaweed farm. We use deep learning-based image segmentation (DeeplabV3+) to determine the size of the seaweed in pixels from recorded RGB images. We convert this pixel size to meters squared by using the distance information from the stereo camera. We demonstrate the performance of our monitoring system using measurements in a seaweed farm in the River Scheldt estuary (in The Netherlands). Notwithstanding the poor visibility of the seaweed in the images, we are able to segment the seaweed with an intersection of the union (IoU) of 0.9, and we reach a repeatability of 6% and a precision of the seaweed size of 18%.

Capturing twenty years of change in ecosystem services provided by coastal Massachusetts habitats

Accounting for ecosystem services across expansive and diverse landscapes presents unique challenges to managers tasked with navigating and synthesizing the social-ecological dynamics of varied stakeholder interests and ecological functions. One approach to this challenge is through expert based matrices that provide valuations for specific service-habitat combinations. In this study, we combine a literature review with local expert input to build an ecosystem service capacity matrix for the Massachusetts Bays National Estuary Partnership (MassBays). We then apply this matrix to a custom conglomerate land cover data set and a habitat connectivity analysis to assess the spatial and temporal dynamics in select ecosystem services of coastal habitats across MassBays from 1996 to 2016. In 1996, saltmarsh was the primary provider of coastal ecosystem services, representing roughly 60% of the total service capacity. More specifically, high elevation saltmarsh was top-ranked, followed by tidal flats, seagrass, low elevation saltmarsh and unclassified saltmarsh. This distribution of service provisioning varied considerably among the five regions of MassBays, reflecting the unique habitat mixes and local expert valuations of each. Although saltmarsh dominated the overall production of services, seagrass and tidal flats drove 97% of the service changes that occurred from one year to the next. From 1996 to 2016, MassBays lost 50% of its seagrass cover and gained 20% more tidal flats, resulting in a 5% overall loss in ecosystem services. Again, this varied among the five regions, with Cape Cod losing as much as 12% of a given service while the Upper North Shore gained 4% in services overall. We bootstrapped the analysis to provide a range of probable outcomes. We also mapped the changes in service production for each of the sixty-eight embayments. This analysis will aid local managers in accounting for ecosystem services as they develop management plans for their represented stakeholders.

Global historical trends and drivers of submerged aquatic vegetation quantities in lakes

Submerged aquatic vegetation (SAV) in lake littoral zones is an inland water wetland type that provides numerous essential ecosystem services, such as supplying food and habitat for fauna, regulating nutrient fluxes, stabilizing sediments, and maintaining a clear water state. However, little is known on how inland SAV quantities are changing globally in response to human activities, where loss threatens the provisioning of these ecosystem services. In this study, we generate a comprehensive global synthesis of trends in SAV quantities using time series (>10 years) in lakes and identify their main drivers. We compiled trends across methods and metrics, integrating both observational and paleolimnological approaches as well as diverse measures of SAV quantities, including areal extent, density, or abundance classes. The compilation revealed that knowledge on SAV is mostly derived from temperate regions, with major gaps in tropical, boreal, and mountainous lake-rich regions. Similar to other wetland types, we found that 41% of SAV times series are largely decreasing mostly due to land use change and resulting eutrophication. SAV is, however, increasing in 28% of cases, primarily since the 1980s. We show that trends and drivers of SAV quantities vary regionally, with increases in Europe explained mainly by management, decreases in Asia due to eutrophication and land use change, and variable trends in North America consistent with invasive species arrival. By providing a quantitative portrait of trends in SAV quantities worldwide, we identify knowledge gaps and future SAV research priorities. By considering the drivers of different trends, we also offer insight to future lake management related to climate, positive restoration actions, and change in community structure on SAV quantities.

Novel approach to large-scale monitoring of submerged aquatic vegetation: A nationwide example from Sweden

According to the EU Habitats directive, the Water Framework Directive, and the Marine Strategy Framework Directive, member states are required to map, monitor, and evaluate changes in quality and areal distribution of different marine habitats and biotopes to protect the marine environment more effectively. Submerged aquatic vegetation (SAV) is a key indicator of the ecological status of coastal ecosystems and is therefore widely used in reporting related to these directives. Environmental monitoring of the areal distribution of SAV is lacking in Sweden due to the challenges of large-scale monitoring using traditional small-scale methods. To address this gap, in 2020, we embarked on a project to combine Copernicus Sentinel-2 satellite imagery, novel machine learning (ML) techniques, and advanced data processing in a cloud-based web application that enables users to create up-to-date SAV classifications. At the same time, the approach was used to derive the first high-resolution SAV map for the entire coastline of Sweden, where an area of 1550 km² was mapped as SAV. Quantitative evaluation of the accuracy of the classification using independent field data from three different regions along the Swedish coast demonstrated relative high accuracy within shallower areas, particularly where water transparency was high (average total accuracy per region 0.60-0.77). However, the classification missed large proportions of vegetation growing in deeper water (on average 31%-50%) and performed poorly in areas with fragmented or mixed vegetation and poor water quality, challenges that should be addressed in the development of the mapping methods towards integration into monitoring frameworks such as the EU directives. In this article, we present the results of the first satellite-derived SAV classification for the entire Swedish coast and show the implementation of a cloud-based SAV mapping application (prototype) developed within the frame of the project. Integr Environ Assess Manag 2022;18:909-920. © 2021 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Submerged aquatic vegetation: Overview of monitoring techniques used for the identification and determination of spatial distribution in European coastal waters

Coastal waters are highly productive and diverse ecosystems, often dominated by marine submerged aquatic vegetation (SAV) and strongly affected by a range of human pressures. Due to their important ecosystem functions, for decades, both researchers and managers have investigated changes in SAV abundance and growth dynamics to understand linkages to human perturbations. In European coastal waters, monitoring of marine SAV communities traditionally combines diver observations and/or video recordings to determine, for example, spatial coverage and species composition. While these techniques provide very useful data, they are rather time consuming, labor-intensive, and limited in their spatial coverage. In this study, we compare traditional and emerging remote sensing technologies used to monitor marine SAV, which include satellite and occupied aircraft operations, aerial drones, and acoustics. We introduce these techniques and identify their main strengths and limitations. Finally, we provide recommendations for researchers and managers to choose the appropriate techniques for future surveys and monitoring programs. Integr Environ Assess Manag 2022;18:892-908. © 2021 SETAC.

Comparing Sentinel-2 and WorldView-3 Imagery for Coastal Bottom Habitat Mapping in Atlantic Canada

Satellite remote sensing is a valuable tool to map and monitor the distribution of marine macrophytes such as seagrass and seaweeds that perform many ecological functions and services in coastal habitats. Various satellites have been used to map the distribution of these coastal bottom habitat-forming species, with each sensor providing unique benefits. In this study, we first explored optimal methods to create bottom habitat maps using WorldView-3 satellite imagery. We secondly compared the WorldView-3 bottom habitat maps to previously produced Sentinel-2 maps in a temperate, optically complex environment in Nova Scotia, Canada to identify the top performing classification and the advantages and disadvantages of each sensor. Sentinel-2 provides a global, freely accessible dataset where four bands are available at a 10-m spatial resolution in the visible and near infrared spectrum. Conversely, WorldView-3 is a commercial satellite where eight bands are available at a 2-m spatial resolution in the visible and near infrared spectrum, but data catalogs are costly and limited in scope. Our optimal WorldView-3 workflow processed images from digital numbers to habitat classification maps, and included a semiautomatic stripe correction. Our comparison of bottom habitat maps explored the impact of improved WorldView-3 spatial resolution in isolation, and the combined advantage of both WorldView’s increased spatial and spectral resolution relative to Sentinel-2. We further explored the effect of tidal height on classification success, and relative changes in water clarity between images collected at different dates. As expected, both sensors are suitable for bottom habitat mapping. The value of WorldView-3 came from both its increased spatial and spectral resolution, particularly for fragmented vegetation, and the value of Sentinel-2 imagery comes from its global dataset that readily allows for large scale habitat mapping. Given the variation in scale, cost and resolution of the two sensors, we provide recommendations on their use for mapping and monitoring marine macrophyte habitat in Atlantic Canada, with potential applications to other coastal areas of the world.

A Simple Cloud-Native Spectral Transformation Method to Disentangle Optically Shallow and Deep Waters in Sentinel-2 Images

This study presents a novel method to identify optically deep water using purely spectral approaches. Optically deep waters, where the seabed is too deep for a bottom reflectance signal to be returned, is uninformative for seabed mapping. Furthermore, owing to the attenuation of light in the water column, submerged vegetation at deeper depths is easily confused with optically deep waters, thereby inducing misclassifications that reduce the accuracy of these seabed maps. While bathymetry data could mask out deeper areas, they are not always available or of sufficient spatial resolution for use. Without bathymetry data and based on the coastal aerosol blue green (1-2-3) bands of the Sentinel-2 imagery, this study investigates the use of band ratios and a false colour HSV transformation of both L1C and L2A images to separate optically deep and shallow waters across varying water quality over four tropical and temperate submerged sites: Tanzania, the Bahamas, the Caspian Sea (Kazakhstan) and the Wadden Sea (Denmark and Germany). Two supervised thresholds based on annotated reference data and an unsupervised Otsu threshold were applied. The band ratio group usually featured the best overall accuracies (OA), F1 scores and Matthews correlation coefficients, although the individual band combination might not perform consistently across different sites. Meanwhile, the saturation and hue band yielded close to best performance for the L1C and L2A images, featuring OA of up to 0.93 and 0.98, respectively, and a more consistent behaviour than the individual band ratios. Nonetheless, all these spectral methods are still susceptible to sunglint, the Sentinel-2 parallax effect, turbidity and water colour. Both supervised approaches performed similarly and were superior to the unsupervised Otsu’s method—the supervised methods featuring OA were usually over 0.70, while the unsupervised OA were usually under 0.80. In the absence of bathymetry data, this method could effectively remove optically deep water pixels in Sentinel-2 imagery and reduce the issue of dark pixel misclassification, thereby improving the benthic mapping of optically shallow waters and their seascapes.

Open-Source Analysis of Submerged Aquatic Vegetation Cover in Complex Waters Using High-Resolution Satellite Remote Sensing: An Adaptable Framework

Despite being recognized as a key component of shallow-water ecosystems, submerged aquatic vegetation (SAV) remains difficult to monitor over large spatial scales. Because of SAV’s structuring capabilities, high-resolution monitoring of submerged landscapes could generate highly valuable ecological data. Until now, high-resolution remote sensing of SAV has been largely limited to applications within costly image analysis software. In this paper, we propose an example of an adaptable open-sourced object-based image analysis (OBIA) workflow to generate SAV cover maps in complex aquatic environments. Using the R software, QGIS and Orfeo Toolbox, we apply radiometric calibration, atmospheric correction, a de-striping correction, and a hierarchical iterative OBIA random forest classification to generate SAV cover maps based on raw DigitalGlobe multispectral imagery. The workflow is applied to images taken over two spatially complex fluvial lakes in Quebec, Canada, using Quickbird-02 and Worldview-03 satellites. Classification performance based on training sets reveals conservative SAV cover estimates with less than 10% error across all classes except for lower SAV growth forms in the most turbid waters. In light of these results, we conclude that it is possible to monitor SAV distribution using high-resolution remote sensing within an open-sourced environment with a flexible and functional workflow.

Multi-Temporal Surface Water Classification for Four Major Rivers from the Peruvian Amazon

We describe a new minimum extent, persistent surface water classification for reaches of four major rivers in the Peruvian Amazon (i.e., Amazon, Napo, Pastaza, Ucayali). These data were generated by the Peruvian Amazon Rural Livelihoods and Poverty (PARLAP) Project which aims to better understand the nexus between livelihoods (e.g., fishing, agriculture, forest use, trade), poverty, and conservation in the Peruvian Amazon over a 35,000 km river network. Previous surface water datasets do not adequately capture the temporal changes in the course of the rivers, nor discriminate between primary main channel and non-main channel (e.g., oxbow lakes) water. We generated the surface water classifications in Google Earth Engine from Landsat TM 5, 7 ETM+, and 8 OLI satellite imagery for time periods from circa 1989, 2000, and 2015 using a hierarchical logical binary classification predominantly based on a modified Normalized Difference Water Index (mNDWI) and shortwave infrared surface reflectance. We included surface reflectance in the blue band and brightness temperature to minimize misclassification. High accuracies were achieved for all time periods (>90%).

Water column compensation workflow for hyperspectral imaging data

Our article describes a data processing workflow for hyperspectral imaging data to compensate for the water column in shallow, clear to moderate optical water types. We provide a MATLAB script that can be readily used to implement the described workflow. We break down each code segment of this script so that it is more approachable for use and modification by end users and data providers. The workflow initially implements the method for water column compensation described in Lyzenga (1978) and Lyzenga (1981), generating depth invariant indices from spectral band pairs. Given the high dimensionality of hyperspectral imaging data, an overwhelming number of depth invariant indices are generated in the workflow. As such, a correlation based feature selection methodology is applied to remove redundant depth invariant indices. In a post-processing step, a principal component transformation is applied, extracting features that account for a substantial amount of the variance from the non-redundant depth invariant indices while reducing dimensionality. To fully showcase the developed methodology and its potential for extracting bottom type information, we provide an example output of the water column compensation workflow using hyperspectral imaging data collected over the coast of Philpott's Island in Long Sault Parkway provincial park, Ontario, Canada.•Workflow calculates depth invariant indices for hyperspectral imaging data to compensate for the water column in shallow, clear to moderate optical water types.•The applied principal component transformation generates features that account for a substantial amount of the variance from the depth invariant indices while reducing dimensionality.•The output (both depth invariant index image and principal component image) allows for the analysis of bottom type in shallow, clear to moderate optical water types.